title: Transcriptomic profiling of lung and kidney tissues in a mouse model of severe pneumonia–associated acute kidney injury (SP-AKI)

city: Nanjing

first: Mengqing

last: Ma

state: Jiangsu

address: 68 Changle Road

institute: Nanjing First Hospital, Nanjing Medical University

summary: Acute kidney injury frequently occurs in patients with severe pneumonia and contributes to poor clinical outcomes. In this study, we established a mouse model of severe pneumonia–associated acute kidney injury (SP-AKI) and performed RNA sequencing to investigate transcriptomic alterations in both lung and kidney tissues. Lung and kidney samples were collected from control mice and SP-AKI mice, followed by high-throughput RNA sequencing. Differential gene expression and pathway analyses were performed to identify molecular mechanisms involved in organ injury and inter-organ communication during SP-AKI. This dataset provides a comprehensive transcriptomic resource for understanding the molecular mechanisms underlying SP-AKI.

overall_design: A mouse model of severe pneumonia–associated acute kidney injury (SP-AKI) was established. Lung and kidney tissues were collected from control mice and SP-AKI mice. Samples were divided into four groups: (1) lung tissues from control mice, (2) lung tissues from SP-AKI mice, (3) kidney tissues from control mice, and (4) kidney tissues from SP-AKI mice. Each group included five independent biological replicates. Total RNA was extracted from each tissue sample and subjected to high-throughput RNA sequencing (RNA-seq) to investigate transcriptomic alterations associated with SP-AKI.

first: Hao

last: Zhang

first: Weijuan

last: Deng

first: Xia

last: Du

first: Mengxing

last: Chen

first: Zhaowei

last: Wang

first: Ting

first: Caimei

first: Xin

last: Wan

first: Changchun

last: Cao


title: Obesity supersizes the immune response to stroke

status: Public on Mar 26 2026

city: Palo Alto

first: Karen

last: Bradshaw

state: CA

address: 1201 Welch Road

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary:
Please cite: Bradshaw K,  Holsten J, Hahn O, Foltz A, Zera KA, Zhu L, Haarslev C, Wyss-Coray T, Peterson TC, Buckwalter M (in press). Obesity supersizes macrophage and neutrophil activation after stroke while lipid droplets play a protective role. Journal of Neuroinflammation.

Obesity is a key risk factor for stroke and by 72 hours after stroke, obese mice have exacerbated stroke sizes, increased neuroinflammation, and motor deficits. To understand how obesity worsens outcomes, we performed single-cell RNA sequencing (scRNASeq) of immune cells in the blood (peripheral blood mononuclear cells, PBMCs) and brain (cortex) 72 hours after stroke or sham surgery in control or diet-induced obese mice. In the blood of obese mice compared to normal diet mice, myeloid cells exhibit the most transcriptional change in both sham and stroke mice. This includes two distinct chemotaxis neutrophil subtypes (enriched with neutrophil chemokine ligand Cxcl2 and receptor Cxcr2, respectively), interferon signaling neutrophils, and two macrophage subtypes enriched in the lipid droplet gene perilipin-2 (Plin2) with and without the foamy macrophage marker Cd36. In the brain, obesity did not induce major transcriptional changes in immune cells in sham mice, but after stroke there were dramatic changes in infiltrating Plin2+ and Plin2- macrophages, interferon-signaling dendritic cells, and 1 chemotaxis neutrophil subtypes. The immune changes induced by stroke in obese mice in brain macrophages and dendritic cells mirrored obesity-induced changes in blood macrophages, including amplification of lipid-related, interferon, and protein degradation genes and downregulation of protein synthesis genes. In neutrophils, obesity amplified interferon and TNF signaling in the blood while in addition enhancing oxidative stress, complement, and a robust pro-thrombotic transcriptional signature in brain neutrophils. Co-expression analysis revealed that Plin2 expression correlates with lipid-related, immune, stress, and coagulation genes, suggesting that lipid droplet accumulation, inflammation, oxidative stress, and coagulation are processes that amplify each other and are attractive candidates for therapies to ameliorate obesity-exacerbated stroke outcomes.

overall_design: Single cell RNA sequencing of the infarct core and surrounding cortex or corresponding region in stroke or sham 24-week old male mice, respectively, fed a 6-week high fat diet or control diet. 10x genomics was used.

first: John

last: Holsten

first: Oliver

last: Hahn

first: Aulden

last: Foltz

first: Kristy

last: Zera

first: Li

last: Zhu

first: Christine

last: Haarslev

first: Tony

last: Wyss-Coray

first: Todd

last: Peterson

first: Marion

last: Buckwalter


title: PWWP-mutants of the transcriptional cofactor JASPer divert promoter and enhancer activities and suppress position effect variegation in Drosophila [Hi-C]

city: Freiburg im Breisgau

first: Derek

last: Atkinson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute for immunobiology and epigenetics

summary: Su(var) genes control heterochromatin establishment and maintenance in Drosophila melanogaster. Through a new Su(var) screen, we identified Su140 and Su113 as very strong Su(var) mutants that are epistatic over Su(var)3-9 in the In(1)wm4h PEV rearrangement. Both Su140 and Su113 encode point mutations in the PWWP domain of the transcriptional cofactor JASPer that has described functions in protecting gene activity in euchromatin. In JasperSu140/Su140 and JasperSu113/Su113 nuclear cycle (NC14) mutant embryos, heterochromatic marks (H3K9me2 and H3K9me3) are reduced, while activating histone modifications (H3K4me1 and H3K27ac) become enriched at heterochromatin. Whereas epitope-tagged wild-type JASPer accumulates over H3K36me3-positive regions in gene bodies, mutant JASPerSu140 is redistributed to cis-regulatory motifs (CRM) in promoters and enhancers. At genes, JASPerSu140 relocates to transcriptional start sites (TSS). Also, one third of developmentally regulated enhancers, including the white enhancer, show enrichment for JASPerSu140 and display elevated levels of eRNA in JasperSu140/Su140 NC14 embryos. In addition, JasperSu140/Su140 mutants induce a partial decompaction of the heterochromatin compartment containing the In(1)wm4h rearrangement and activate satellite repeat expression. Together, these data define Jasper mutants as novel Su(var) genes and highlight the importance of maintaining the balance between euchromatic and heterochromatic domains for controlling position effect variegation.

overall_design: HiC of wm4h and Su140 NC14 embryos, 6 replicates per conditon

first: Francesco

last: Cardamone

first: Yinxiu

last: Zhan

first: Thomas

last: Jenuwein

first: Nicola

last: Iovino


title: PWWP-mutants of the transcriptional cofactor JASPer divert promoter and enhancer activities and suppress position effect variegation in Drosophila [Cut & Tag]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Genome binding/occupancy profiling of selected chromatin marks by high throughput sequencing comparing wildtype and JasperSu140 NC14 (st5) embryos

first: Karolina

last: Barucka


title: Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD-associated kinase LRRK2 between human and mice [multiome mouse]

city: Bethesda

first: Mark

middle: R

last: Cookson

state: MD

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

summary: The genomic locus that encodes the Leucine-rich repeat kinase 2 (LRRK2) gene is highly pleomorphic, being associated with both Parkinson’s disease (PD) and Crohn’s disease (CD). As well as coding variants that are associated with risk of PD and CD and act as gain of function kinase mutations increasing phosphorylation of RAB substrates, non-coding variants in the promoter region of LRRK2 increase expression of the gene, notably in immune cells. If regulation of LRRK2 expression is a causal contributor to age-related diseases, it would therefore be important to understand the mechanism(s) by which LRRK2 is regulated, particularly in the context of inflammation. We were able to show that interferon-ɣ exposure induces robust LRRK2 activation in human iPSC-derived microglia through mechanisms that involve signaling of the Janus-activated Kinase complex to phosphorylate STAT1 which then binds to the LRRK2 promoter and is associated with remodeling of chromatin structure in this genomic locus. Additional regulation includes the stress-induced transcription factor and long non-coding RNA encoded at the same locus, resulting in enhanced LRRK2 mRNA levels. However, we were unable to demonstrate any induction of Lrrk2 mRNA in the mouse brain but could show evidence of the same effect in acutely cultured human brain slices. These divergent results across species are resolved by the demonstration the introduction of a human bacterial artificial chromosome transgene into the mouse genome can then recapitulate sensitivity to interferon-ɣ in microglia. These results demonstrate that there are differences between species in how genes associated with human diseases are regulated and provide important information that should be incorporated in disease modeling.

overall_design: C57Bl/6J WT and LRRK2 knockout micC57Bl/6J WT and LRRK2 knockout mice (3 months old) received bilateral stereotaxic injections of mouse IFN-γ (20 ng/site) or PBS into the striatum and substantia nigra. After 24 hours, the striatum and substantia nigra were dissected, and nuclei were purified using the 10x Genomics Single Cell Nuclei Isolation Kit (PN-1000494) for Single Cell Multiome-seq.e (3 months old) received bilateral stereotaxic injections of mouse IFN-γ (20 ng/site) or PBS into the striatum and substantia nigra. After 24 hours, brains were collected for Single Cell Multiome-seq, western blot, or immunohistochemistry following perfusion and tissue processing.

first: Alexandra

last: Beilina

first: Jae-hyeon

last: Park

first: Natalie

last: Landeck

first: Ruth

last: Chia

first: Jinhui

last: Ding

first: Xylena

last: Reed

first: Hannah

last: Bailey

first: Changyoun

last: Kim

first: Alice

last: Kaganovich

first: Dominic

last: Acri

first: Janet

last: Brooks

first: Kareem

last: Zaghloul

first: Elise

last: Marsan

first: Raphael

middle: J

last: Gibbs

first: Alex

last: DeCasien


title: Culturomics reveals Fusobacterium-Prevotella mutualism as a hallmark of nasopharyngeal tumor microbiota [Bacteria RNA-seq]

city: Guangzhou

first: Liu

state: GuangDong

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

summary: To investigate the functional characteristics of Fusobacterium and Prevotella under monoculture or coculture

sample_organism:
Fusobacterium nucleatum
Prevotella intermedia

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Fusobacterium and Prevotella under monoculture or coculture

first: Ying-Qi

last: Lu

last: Liu


title: Culturomics reveals Fusobacterium-Prevotella mutualism as a hallmark of nasopharyngeal tumor microbiota [Tissue RNA-seq]

summary: To investigate the functional characteristics of nasopharyngeal carcinomas with different intratumoral microbial communities

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NPC tissues with different microbial subtypes.


title: Culturomics reveals Fusobacterium-Prevotella mutualism as a hallmark of nasopharyngeal tumor microbiota

summary: To investigate the functional characteristics of Fusobacterium and Prevotella under monoculture or coculture using single-cell rna sequencing

platform_organism:
Fusobacterium nucleatum
Prevotella intermedia

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for Fusobacterium and Prevotella under monoculture or coculture


title: CCL Signaling Drives T Cell–Macrophage Crosstalk in the Mouse Colon During Chronic Trypanosoma cruzi Infection

city: Silver Spring

first: Erica

last: Silberstein

address: 10903 New Hampshire Ave

department: DETTD

institute: CBER-FDA

summary: Chagas disease, caused by the protozoan Trypanosoma cruzi, is a chronic infection characterized by low levels of parasite persistence in tissues such as the heart, gastrointestinal tract, and skeletal muscle. The mechanisms underlying digestive Chagas disease (DCD), particularly within the colon, remain incompletely defined. To characterize the immune landscape during chronic infection, we used a murine model of DCD and performed single-cell RNA sequencing of colonic lamina propria cells. Immune profiling revealed infiltration of T cells, B cells, and macrophages, with T cells representing the predominant immune population in the chronically infected colon. Computational cell–cell communication analysis predicted activation of chemokine signaling pathways, including the CCL5–CCR5 axis, mediating interactions between CD8+ T cells and macrophages. Processed single-cell gene expression matrices and associated metadata are provided in this submission

overall_design: Colonic lamina propria cells were isolated from C57BL/6 mice chronically infected with the Colombiana strain of Trypanosoma cruzi and from uninfected control mice. Mice were analyzed at 110 days post-infection (n=3 infected, n=3 controls), representing the chronic phase of infection. A total of six biological samples were processed, including three infected and three control mice. Lamina propria cells were isolated by enzymatic digestion of colonic tissue followed by immune cell enrichment. Single-cell gene expression libraries were generated using the BD Rhapsody platform and sequenced on an Illumina NovaSeq 6000 system. Raw sequencing data were processed using the BD Rhapsody analysis pipeline to generate gene-cell count matrices aligned to the mouse reference genome (mm10). Downstream analyses were performed in R (v4.3.3) using Seurat (v4.4) for quality control, normalization, dimensionality reduction, clustering, and cell type annotation. Low-quality cells were excluded based on gene detection thresholds and mitochondrial transcript content. Cell–cell communication analysis was conducted using CellChat (v1). The processed gene expression matrix and cell-type annotation metadata are provided in this submission.

first: Spyros

last: Karaiskos

first: Nikki

last: Tirrell

first: Charles

middle: C

last: Chung

first: Supriya

last: Kumar

first: Jung-Sun

last: Cho

first: Alain

last: Debrabant


title: The cytoskeleton drives abnormal chromatin-lamina interactions in LMNA-deficient cardiomyocytes.

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Spatial organization of chromatin at the nuclear lamina is critical for cellular identity, but mechanisms governing genome-lamina interactions remain unresolved. In particular, it remains unclear if and how mechanical inputs impact genome-lamina interactions. We modeled aspects of laminopathies via siRNA-mediated lamin A/C (LMNA) knockdown to examine how the nuclear lamina and cytoskeleton contribute to loss of lamina-associated domain (LAD) organization. Genomics and imaging analyses reveal spatial positioning of LADs with a specific molecular signature are particularly vulnerable to LMNA reduction. Further, a subset of these LADs retain their lamina-association with either concomitant disruption of the Linker of Nucleoskeleton and Cytoskeleton complex or microtubule depolymerization. Conversely, microtubule stabilization phenocopies spatial positioning changes observed in LMNA-knockdown cells. These data suggest peripheral chromatin organization is regulated by the balance of nuclear lamina and cytoskeletal interactions across the nuclear membrane. In the context of a compromised nuclear lamina, such as LMNA reduction, the cytoskeleton contributes to loss of peripheral chromatin organization.

overall_design:
RNA-seq profiling for human induced pluripotent stem cell-derived cardiomyocytes in siScr control and siLMNA knockdown samples after 48 hours of treatment.
CUT&RUN sequencing for LMNB1 in human induced pluripotent stem cell-derived cardiomyocytes in siScr + mCherry control and siLMNA + mCherry and siLMNA + DNKASH samples after 48 hours of treatment.
CUT&RUN sequencing for LMNB1 in human induced pluripotent stem cell-derived cardiomyocytes in siScr + DNKASH samples after 48 hours of treatment.

first: Kaitlyn

middle: M

last: Shen

first: Rajan

last: Jain


title: Assay for transposase-accessible chromatin using sequencing (ATAC-Seq) of Barley CI 16151 and fast-neutron-derived, immune-compromised mutants infected with the powdery mildew fungus (Blumeria hordei (Bh); isolate 5874)

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

summary: Transcriptional reprogramming is a key component of disease resistance. MLA (mildew locus a), is an immune receptor that interacts with several transcription factors (TFs), and thus, represents a model to explore regulatory architecture during defense. To characterize chromatin accessibility of barley during powdery mildew infection, a series of isogenic mutant genotypes and timepoints were subjected to ATAC sequencing. We designed our study around two diverse genes in host immunity, mildew locus a (Mla6), a nucleotide binding leucine-rich repeat (NLR) immune receptor, and the Blufensin1 (Bln1) basal defense regulator, which influence immunity in a resistance (R)-gene dependent and R-gene independent manner, respectively. In addition to the CI 16151 resistant progenitor (Mla6, Bln1), three mutants were utilized: the susceptible mla6-m18982, the resistant bln1-m19089, and the susceptible double mutant (mla6+bln1)-m19028 (Chapman et al., 2021; Velásquez-Zapata et al., 2024). Four infection timepoints (0, 16, 20, 32 HAI) were taken to sample across key pathogen life cycle events such as appressorial penetration and haustorial development. Validation of the ATAC-Seq dataset was performed using the correlation with gene expression profiles from RNA-Seq data; by checking the presence of epistatic events at the chromatin level, phenomenon that was recently described using RNA-Seq (Velásquez-Zapata et al., 2024).

overall_design: An Assay for Transposase-Accessible Chromatin was coupled with next-generation sequencing to identify chromatin-accessible regions, thereby mapping transcription factor binding sites associated with the immune receptor MLA (mildew locus a). The wild-type progenitor, CI 16151 (Mla6, Bln1) and three fast-neutron derived mutants [m18982 (mla6, Bln1); m19089 (Mla6, bln1); m19028 (mla6, bln1)] were blocked by biological replicate and plant genotype and inoculated with Blumeria hordei (Bh) isolate 5874 (AVRa6). Tissue was collected at four biologically relevant timepoints (0, 16, 20, and 32 HAI). The entire experiment was replicated four times. Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 150 bp reads.

first: Valeria

last: Velasquez-Zapata

first: Gregory

last: Fuerst

middle: P


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (RNA-seq)

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

summary: Loss of DNA methylation is a hallmark of cancer that is proposed to promote carcinogenesis through gene expression alterations, retrotransposon activation and induction of genomic instability. Cancer-associated hypomethylation does not occur across the whole genome but leads to the formation of partially methylated domains (PMDs). However, the mechanisms underpinning PMD formation remain unclear. PMDs replicate late in S-phase leading to the proposal that they become hypomethylated due to incomplete re-methylation by the maintenance methyltransferase DNMT1 during cell division. Here we investigate the role of DNMT1 in the formation of PMDs in cancer by conducting whole genome bisulfite sequencing (WGBS), repli-seq and ChIP-seq on DNMT1 knockout HCT116 colorectal cancer cells (DNMT1 KO cells). We find that DNMT1 loss leads to preferential hypomethylation in late replicating, heterochromatic PMDs marked by the constitutive heterochromatic mark H3K9me3 or the facultative heterochromatic mark H3K27me3. However, we also observe that a subset of H3K9me3-marked PMDs gain methylation in DNMT1 KO cells. We find that, in DNMT1 KO cells, these hypermethylated PMDs remain late replicating but gain DNMT3A localisation. This is accompanied by loss of heterochromatic H3K9me3 and specific gain of euchromatic H3K36me2. Our observations suggest that hypermethylated PMDs lose their heterochromatic state, enabling their methylation by DNMT3A and the establishment of a hypermethylated, non-PMD state, despite their late replication timing. More generally, our findings suggest that the de novo DNMTs play a key role in establishing domain level DNA methylation patterns in cancer cells.

overall_design: This series contains RNA-seq from human cancer cell lines. HCT116 cells and derivatives lacking DNMT1 were grown before RNA was harvested before being quantified by RNA-seq. Includes new samples as well as re-processing of existing GEO samples using the same approach as for the new samples (GSM7818564, GSM7818565, GSM7818566 - all from GSE244518)


title: Cleavage Under Targets & Release Using Nuclease (CUT&RUN) of monosomy 7 compared to normal karyotype control

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale G. Menghini, 9

country: Italy

institute: University of Perugia

summary: Monosomy 7 is one of the most frequent aneuploidies in myeloid malignancies, associated to heterogeneous phenotypes. Its poor prognosis differentiates it from  aberrations leading to partial/complete loss of 7q region.  Underlying pathogenic mechanisms are still undetermined. We performed a comprehensive epi-genomic study of karyotypically isolated monosomy 7 in adult Myelodysplastic Syndromes/Acute Myeloid Leukemias.

overall_design: CUT&RUN was performed in one mon7 case and one nkMN to identify IKZF1 and PAX8 transcription factors binding sites across the genome, starting from 280,000 cells per reaction. The CUT&RUN Assay kit was used following manufacturer’s instruction (Cell Signaling Technology, Danvers, MA, USA), with Ikaros (D6N9Y, 1:100), PAX8 (D2S2I, 1:50), negative control rabbit IgG (DA1E, 1:20), and positive control H3K4me3 (C42D8, 1:50) antibodies (Cell Signaling Technology).

first: Anair

middle: G

last: Lema Fernandez

first: Carlotta

last: Nardelli


title: Transcriptomic profile of Chronic Hepatitis B patients positive for pregenomic RNA.

city: ALEAXNDROUPOLIS

first: AIKATERINI

last: SKEVA

state: EVROS

address: DRAGANA 1

department: MEDICINE

country: Greece

institute: DEMOCRITUS UNIVERSITY OF THRACE

summary: In this cohort, we aimed to study the transcriptomic profile of CHB (Chronic Hepatitis B) HBeAg negative patients treated with Nucleoside Analog (NAs) and examined for the HBV transcriptional maintenance after tested for the pregenomic RNA (pgRNA) index. Twelve HBeAg negative CHB patients, who receive long-term treatment with NAs were included. Plasma samples were quantified by Polymerase Chain Reaction (PCR) for the presence of pgRNA and RNA extraction was performed for  analysing the transcriptomic profile through RNA sequencing.  A total of 18.1% of our sample was positive for HBV pgRNA, delineating a positive correlation with cirrhosis and an apparently negative correlation with therapy duration. HBV pgRNA seems to be a valuable non invasive biomarker, delineating the transcriptional status of the HBV in the liver, even under normal biochemical conditions. The transcriptomic profile of HBV pgRNA positive patients could delineate novel pathways related to cirrhosis and HCC development on CHB patients.

overall_design: RNA sequencing of plasma samples from Chronic Hepatitis B patients detected either positive for the pregenomic RNA index (pgRNA), either negative.

first: Aikaterini

last: Skeva

first: Petros

last: Kolovos

first: Theoxaris

last: Konstantinidis

first: Maria

last: Panopoulou

first: Konstantinos

last: Mimidis


title: STING activation induces cytotoxic and immune responses in meningiomas via inflammatory cell death pathways [scRNA-Seq]

city: Chicago

first: Mark

last: Youngblood

state: IL

address: 676 N. St. Clair Street; Suite 2210

department: Department of Neurological Surgery

institute: Northwestern University

summary: Meningiomas are common tumors of the central nervous system that are typically treated with surgery but lack alternative treatment options. Activation of the stimulator of interferon genes pathway with an agonist such as 8803 can trigger anti-tumor immune responses. Using integrated molecular approaches, here we show this pathway is expressed in both neoplastic and immune populations within meningiomas associated with promoter hypomethylation and increased chromatin accessibility. Treatment of diverse patient meningiomas ex vivo with 8803 induces direct tumor cytotoxicity through pyroptosis and the induction of gasdermin D membrane pore formation. Direct tumor cytotoxicity triggered by 8803 activates macrophages and upregulates matrix metalloproteinase production facilitating degradation of tumor stroma collagen. Treatment of preclinical meningiomas with 8803 induces survival benefits, including in an immune competent orthotopic setting, through remodeling of the tumor microenvironment, immune infiltration, and down regulation of tumor-mediated immune suppression thereby nominating 8803 for treatment consideration in meningiomas.

overall_design: Single cell RNA-seq of whole mouse brains implanted with MGS1 meningioma cells. Each sample was pooled from three mice and either received 8803 or PBS control.

middle: W

first: Shashwat

last: Tripathi

first: Hinda

last: Najem

first: Harrshavasan

last: Congivaram

first: Mateo

last: Gomez

first: Amy

middle: B

last: Heimberger


title: Vitamin D Deficiency Activates Gdnf-Ret-pErk1/2 Signal and induces Kidney Malformations in mice

city: shanghai

first: MINGHUI

last: YU

address: wanyuan road 399

institute: Children’s Hospital of Fudan University

summary: Abstract: Background: Congenital anomalies of the kidney and urinary tract (CAKUT) constitute the most common underlying cause of chronic kidney disease in pediatric populations. Some researchers suggest that adverse maternal factors during pregnancy could may contribute significantly to the pathogenesis of CAKUT. In human populations, maternal hypovitaminosis D is associated with mesoderm-related birth defects such as lower urinary tract malformations and circulatory system abnormalities. Thus, we hypothesized kidney as mesoderm-related organ might be disrupted by maternal vitamin D deficiency, resulting in CAKUT in offspring. Methods: To investigate whether a low-vitamin D level can cause CAKUT, we used vitamin D-free diets to induce maternal vitamin D deficiency mice model. Results: Maternal vitamin D deficiency (VDD) mice models and normal vitamin D status (CON) were successfully established by administering vitamin D-free or vitamin D-sufficient diet for 4 weeks prior to pregnancy. The overall incidence of CAKUT was significantly increased in VDD neonatal mice (19.4% vs. 2.44%; P=0.0006), with a higher incidence of early duplicated budding in E11.5. E11.5 ureteric bud tissue revealed significantly increased activity of Gdnf-Ret-p-Erk1/2 signaling in VDD group. In vivo intervention with the p-Erk1/2 antagonist U0126 in pregnant VDD mice model at E10.5 improved CAKUT occurrence in offspring with p-Erk1/2 expression decreased toward normal levels. Early metanephric ureteric bud H3K4me3 CUT&TAG analysis at E12.5 revealed chromatin activation patterns revealed downregulation of Hnf1β promoter region peaks was accompanied by reduced Hnf1β expression, and Robo2 promoter region peak was upregulated with increased Robo2 expression in VDD group. Conclusions: Maternal vitamin D deficiency in mice significantly increased offspring CAKUT incidence. This phenotype was mediated by enhanced Gdnf-Ret-p-Erk1/2 signaling and reversed by p-Erk1/2 inhibition, with VDD inducing epigenetic remodeling of Hnf1β and Robo2 promoters.

overall_design: H3K4me3 Cut-Tag E12.5 embryonic kidney tissue was extracted and dissociated into a single-cell suspension. After passing the cell counting and viability tests, libraries were constructed using the Vazyme (TD904) kit protocol. The samples were then sent to Novogene for quality control, sequencing, and analysis.

first: Minghui

last: Yu

first: Haixin

last: Ju

first: Ningli

last: Ye

first: Qianfan

last: Miao

first: Chunyan

last: Wang

first: Rufeng

last: Dai

first: Jing

last: Chen

first: Yihui

last: Zhai

first: Lei

last: Sun

first: Xiaohui

last: Wu

first: Hong

last: Xu

first: Qian

last: Shen


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (H3K36me2 native ChIP-seq)

first: Duncan

last: Sproul

overall_design: This series contains H3K36me2 native ChIP-seq from human cancer cell lines. HCT116 cells and derivatives lacking DNMT1 were grown before chromatin was extracted and H3K36me2 levels analysed by native ChIP-seq.


title: RNA Seq of rhabdomyosarcoma cells with sgRNA targeting oncofusion interacting proteins

city: Durham

first: Seth

last: Zimmerman

state: NC

address: 308 Research Dr.

institute: Duke University

summary: We identified the common protein interactome of rhabdomyosarcoma interacting proteins. Here we selected a subset of interactors, targeted them with sgRNA, and performed RNAseq is RH4-flag cells.

overall_design: Cells were transduced in triplicate with each sgRNA, selected for a week and the RNA from resultant cells were sequenced.

first: Christopher

last: Counter


title: Interactome CRISPR screen for rhabdomyosarcoma cells driven by four oncofusions

summary: We identified and interactome for seven diffent rhabdomyosarcoma oncofusions. The proliferative effects of the loss of these proteins was tested by a CRISPR loss of function library screen in four rhabdomyosarcoma cell lines engineered to be driven by 4 different oncofusions.

overall_design: RH4-flag cells expressing a PAX3::FOXO1 targeted shRNA and one of four oncofusions (PAX3::FOXO1, PAX3::NCOA1, PAX3::INO80D, PAX3::MAML3) were transduced with a CRISPR library and CAS9 in triplicate. Initial time points were taken after selection. Final time points were taken after 2 weeks of proliferation.


title: Pathologically Activated Neutrophils Induce Contact-Dependent Suppression of Cytotoxic T Cells

city: Shanghai

first: jiayin

last: Peng

address: Yueyang Road

institute: Center for Excellence in Molecular Cell Science

summary: The immunosuppressive tumor microenvironment remains a major obstacle to successful immunotherapy. Pathologically activated neutrophils, alternatively termed polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs), drive tumor immune evasion principally through induction of CD8+ T cell tolerance. While direct intercellular contact between neutrophils and CD8+ T cells is essential for immunosuppressive activity, the mechanisms mediating this interaction need for deeper understanding. Here, we identify CD300ld, an immune inhibitory receptor on neutrophils, mediates neutrophil-driven contact-dependent suppression of cytotoxic CD8+ T cells via binding to phosphatidylserine (PS). Mice with mutant CD300ld, which lack PS-binding capacity, exhibit reduced immunosuppressive activity, phenocopying CD300ld knockout mice in multiple tumor models. Blockade of the PS-CD300ld interaction by neutralizing antibodies demonstrate therapeutic efficacy against established tumors and synergize with anti-PD-1 therapy. Clinical analyses reveal elevated CD300LD expression inversely associates with intertumoral PShigh CD8+ T cell infiltration and predicts poor responses to checkpoint blockade therapy. Our findings establish CD300ld-PS mediated T cell contact as a critical mechanism of neutrophil-driven immune evasion, revealing a targetable checkpoint pathway to overcome tumor immune resistance and improve immunotherapy outcomes.

overall_design: B16-F10 tumors were dissected from WT or KO mice, and single-cell suspensions were obtained. PShigh and PSlow CD8+ T cells (approximately lowest and highest 1/3 staining, respectively) were enriched using FACS sorting, followed by analysis using scRNA-seq.

first: Chaoxiong

first: Peixuan

last: Zheng

first: Jiayin

first: Yun

last: Zhao


title: Transcription Elongation Factor SPT6 Maintains Epidermal Homeostasis and Suppresses Skin Inflammation in Mice

first: Jingting

last: Li

address: No 1, Zhongshan 2 Road, 12th Floor

department: Institue of Precision Medicine

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

summary: We employed single-cell RNA sequencing (scRNA-seq) using 10x Genomics technology to investigate the impact of Supt6 epidermis-specific knockout on epidermal homeostasis in mice. The histone chaperone SPT6 is a central regulator of genomic stability. Our previous studies have shown that SPT6 promotes epidermal differentiation by regulating transcriptional elongation in human epidermal stem/progenitor cells, but its in vivo role remains unclear. Our research has discovered for the first time that the transcriptional elongation factor SPT6 regulates skin inflammation, hair follicle development, and wound healing, providing a novel therapeutic target for clinical treatment of psoriasis and related skin disorders.

overall_design: single cell RNA-seq of wild-type mice and Supt6 KO mice epidermis, collected on the 5th day after the final tamoxifen injection.

first: Yushuang


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (WGBS)

type: Methylation profiling by high throughput sequencing

overall_design: This series contains WGBS from human cancer cell lines. HCT116 cells and derivatives lacking DNMT1 were grown before genomic DNA was extracted and DNA methylation levels analysed by Whole Genome Bisuflite sequencing (WGBS).


title: Bone marrow derived macrophage response to CSF1R stimulation or starvation after deletion of Ptpn6 or Rraga

city: South San Francisco

first: Xingyue

middle: Monica

last: Ge

address: 1 DNA Way

institute: Genentech

summary: A genome-wide CRISPR screen in primary mouse bone marrow derived macrophages identified Rraga and Ptpn6 as important regulators of cell death upon CSF-1 starvation. To explore how Rraga and Ptpn6 deletion influence cellular state after CSF-1 stimulation or during growth factor starvation, CRISPR-edited BMDMs were harvested at different timepoints after addition of CSF-1, which is required to maintain cellular survival in these cultures. RNA-seq and differential expression analyses were conducted to illuminate differential pro-survival mechanisms in cultures lacking Ptpn6 or Rraga, respectively.

overall_design: To explore Ptpn6 survival mechanisms further, we performed RNA-seq analysis of BMDMs treated with gPtpn6, Rraga, or control guides one week after electroporation of guides. Four wells of each population were harvested at 4 hrs, 24 hrs, or 48 hrs after the time of last CSF-1 supplementation, and purified RNA was used to perform RNA-seq.

first: Julia

middle: A

last: Kuhn

last: Bohlen

first: Brad

last: Friedman


title: Microbiome-produced nicotinic acid controls colon regional identity and injury susceptibility (Bulk-RNAseq)

city: Los Angeles

first: Ophir

last: Klein

state: California

address: 8700 Beverly Blvd

department: Geurin Children's

institute: Cedars Sinai Medical Center

summary: The gut epithelium exhibits regional specialization critical for its function and susceptibility to disease, as gut diseases localize to specific regions of the organ. However, how regionalization is established and its influence on disease susceptibility remain poorly understood. Here, we investigate the role of the gut microbiome—which comprises all microorganisms residing in the gut lumen and is itself regionalized—in regulating regionalization of the colon. We demonstrate that the regional identity of colonocytes is disrupted in mice lacking a microbiome. Mechanistically, we show that the proximal colonic microbiome produces high levels of nicotinic acid, which induces Pparα expression to establish proximal colonocyte identity. Furthermore, we find that microbiome-driven proximal identity confers protection against tissue injury in the mouse. Finally, we show that colon regionalization and the loss of proximal identity during disease are also present in human.

overall_design: We performed bulk-RNAseq on mouse colon organoids treated for two days with Ppara agonist (WY-14643, 100uM) or vehicle (control).

first: Jeremie

last: Rispal

first: Manasa

last: Vegesna

first: Dario

last: Boffelli


title: PWWP-mutants of the transcriptional cofactor JASPer divert promoter and enhancer activities and suppress position effect variegation in Drosophila

first: Derek

last: Atkinson

summary: Su(var) genes control heterochromatin establishment and maintenance in Drosophila melanogaster. Through a new Su(var) screen, we identified Su140 and Su113 as very strong Su(var) mutants that are epistatic over Su(var)3-9 in the In(1)wm4h PEV rearrangement. Both Su140 and Su113 encode point mutations in the PWWP domain of the transcriptional cofactor JASPer that has described functions in protecting gene activity in euchromatin. In JasperSu140/Su140 and JasperSu113/Su113 nuclear cycle (NC14) mutant embryos, heterochromatic marks (H3K9me2 and H3K9me3) are reduced, while activating histone modifications (H3K4me1 and H3K27ac) become enriched at heterochromatin. Whereas wild-type JASPer is enriched over H3K36me3-positive regions in gene bodies, JASPerSu140 is redistributed to regulatory elements in promoters and enhancers. JASPerSu140 directly binds and activates the white gene enhancer in NC14 embryos and JasperSu140/Su140 mutants induce a partial decompaction of the heterochromatin compartment containing the In(1)wm4h rearrangement. In addition, JasperSu140/Su140 and JasperSu113/su113 mutants also display elevated levels for 359bp (satellite) repeat transcripts at later stages of development. Together, these data define Jasper mutants as novel Su(var) genes and highlight the importance of maintaining the balance between euchromatic and heterochromatic domains for controlling position effect variegation.

overall_design: Expression profiling by high throughput sequencing at NC14 (st5) and St7-8 embryos

first: Thomas

last: Jenuwein


title: PWWP-mutants of the transcriptional cofactor JASPer divert promoter and enhancer activities and suppress position effect variegation in Drosophila [ChIP-Seq]

summary: Su(var) genes control heterochromatin establishment and maintenance in Drosophila melanogaster. Through a new Su(var) screen, we identified Su140 and Su113 as very strong Su(var) mutants that are epistatic over Su(var)3-9 in the In(1)wm4h PEV rearrangement. Both Su140 and Su113 encode point mutations in the PWWP domain of the transcriptional cofactor JASPer that has described functions in protecting gene activity in euchromatin. In JasperSu140/Su140 and JasperSu113/Su113 nuclear cycle (NC14) mutant embryos, heterochromatic marks (H3K9me2 and H3K9me3) are reduced, while activating histone modifications (H3K4me1 and H3K27ac) become enriched at heterochromatin. Whereas epitope-tagged wild-type JASPer accumulates over H3K36me3-positive regions in gene bodies, mutant JASPerSu140 is redistributed to cis-regulatory motifs (CRM) in promoters and enhancers. At genes, JASPerSu140 relocates to transcriptional start sites (TSS). Also, one third of developmentally regulated enhancers, including the white enhancer, show enrichment for JASPerSu140 and display elevated levels of eRNA in JasperSu140/Su140 NC14 embryos. In addition, JasperSu140/Su140 mutants induce a partial decompaction of the heterochromatin compartment containing the In(1)wm4h rearrangement and activate satellite repeat expression. Together, these data define Jasper mutants as novel Su(var) genes and highlight the importance of maintaining the balance between euchromatic and heterochromatic domains for controlling position effect variegation.

overall_design: Genome binding/occupancy profiling of JASPER protein by high throughput sequencing comparing Jasper::V5-3xFlag with JasperSu140::V5-3xFlag NC14 (st5) embryos

first: Karolina

last: Barucka


title: Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD-associated kinase LRRK2 between human and mice [snRNA-Seq human]

first: Mark

last: Cookson

summary: The genomic locus that encodes the Leucine-rich repeat kinase 2 (LRRK2) gene is highly pleomorphic, being associated with both Parkinson’s disease (PD) and Crohn’s disease (CD). As well as coding variants that are associated with risk of PD and CD and act as gain of function kinase mutations increasing phosphorylation of RAB substrates, non-coding variants in the promoter region of LRRK2 increase expression of the gene, notably in immune cells. If regulation of LRRK2 expression is a causal contributor to age-related diseases, it would therefore be important to understand the mechanism(s) by which LRRK2 is regulated, particularly in the context of inflammation. We were able to show that interferon-ɣ exposure induces robust LRRK2 activation in human iPSC-derived microglia through mechanisms that involve signaling of the Janus-activated Kinase complex to phosphorylate STAT1 which then binds to the LRRK2 promoter and is associated with remodeling of chromatin structure in this genomic locus. Additional regulation includes the stress-induced transcription factor and long non-coding RNA encoded at the same locus, resulting in enhanced LRRK2 mRNA levels. However, we were unable to demonstrate any induction of Lrrk2 mRNA in the mouse brain but could show evidence of the same effect in acutely cultured human brain slices. These divergent results across species are resolved by the demonstration the introduction of a human bacterial artificial chromosome transgene into the mouse genome can then recapitulate sensitivity to interferon-ɣ in microglia. These results demonstrate that there are differences between species in how genes associated with human diseases are regulated and provide important information that should be incorporated in disease modeling.

overall_design:
Human cortical brain tissue from epilepsy surgery patients (a 27-year-old female, frontal lobe; and a 36-year-old male, anterior temporal cortex) was sectioned into 300 μm slices, halved, and incubated with or without 25 ng/mL IFN-γ in aCSF for 6 hours. Nuclei were isolated (~10,000 per condition) and processed using the 10x Genomics Single Cell 3’ Gene Expression kit, followed by paired-end sequencing on a NovaSeq 6000 and analysis with Cell Ranger (v5.0.1) using intron-inclusive alignment and the GRCh38 reference.

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The raw data being made available for controlled access due to patient privacy concerns
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first: Alexandra

last: Beilina

first: Jae-hyeon

last: Park

first: Natalie

last: Landeck

first: Ruth

last: Chia

first: Jinhui

last: Ding

first: Xylena

last: Reed

first: Hannah

last: Bailey

first: Changyoun

last: Kim

first: Alice

last: Kaganovich

first: Dominic

last: Acri

first: Janet

last: Brooks

first: Kareem

last: Zaghloul

first: Elise

last: Marsan

first: Raphael

last: Gibbs

first: Alex

last: DeCasien


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (histone ChIP-seq)

first: Duncan

last: Sproul

overall_design:
This series contains histone ChIP-seq from human cancer cell lines. HCT116 cells and derivatives lacking DNMT1 were grown before chromatin was extracted and histone modification levels analysed by ChIP-seq.

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The table below lists GEO accessions reused/reanalyzed for this study.
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title: Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD- associated kinase LRRK2 between human and mice [multiome]

first: Mark

last: Cookson

overall_design: Single nuclei were extracted from human iPSC-derived microglia (iMicroglia) generated from LRRK2 WT and knockout (LRRK2 -/-) cell lines (A18945 background). Cells were treated with or without IFN-γ for 24 hours. Joint snRNA-seq and scATAC-seq libraries were prepared using the 10x Genomics platform.


title: Impact of fertility status on epigenetic indicators of future health risk

city: Atlanta

first: Alicia

middle: K

last: Smith

state: GA

address: 101 Woodruff Circle NE

institute: Emory University

type: Methylation profiling by genome tiling array

summary: Infertility affects approximately 10% of women in the United States and is increasingly becoming more common. Recent studies suggest that, in addition to its reproductive consequences, infertility is associated with the development of chronic disease and all-cause mortality. Two examples of this phenomenon that are supported by the literature are risks of cardiovascular disease (CVD) and metabolic syndrome (MetS), both of which are more common in women and have elevated risks after menopause. CVD is the leading cause of death in women, and MetS has a prevalence of approximately 30% and increases risk for mortality. It is likely that there are shared pathways between infertility and CVD and MetS, such as increased inflammation, which may modulate risk for both conditions. Thus evaluating women with infertility for future CVD and MetS provides a unique opportunity for preventative measures and personalized treatments within the context of infertility evaluations. One way to identify women at increased risk for CVD and MetS is through examining differences in DNA methylation. DNA methylation is one mechanism through which gene expression responds to changes in the environment, hormone status, or other physiologic processes. These changes may occur prior to the onset of symptomatic disease and can identify women at increased risk for adverse outcomes. This study will evaluate three DNA methylation-based predictors of long-term health, CVD, and MetS in women with infertility and women without infertility who are undergoing in vitro fertilization. We will also evaluate associations with low ovarian reserve, which is predictive of time to menopause and may also associate with increased risk. First, we will assess an indicator of cellular age acceleration that is predictive of health-span and all-cause mortality. Then, we will leverage combinations of CpG sites to predict a CVD methylation risk score and a separate MetS methylation risk score. We hypothesize that infertility and low ovarian reserve will be associated with increased age acceleration, which would serve as a general marker of future disease and mortality. We hypothesize that the CVD methylation risk score will be associated with infertility and low ovarian reserve due to putative links between infertility and later development of CVD. Finally, we hypothesize that infertility and low ovarian reserve will be associated with increased MetS methylation risk scores as obesity and other MetS risk factors play a role in infertility.

overall_design: Case-control design based on fertility status.  For inclusion into this study, women must be 18 and 50 years of age, planning to have an oocyte retrieval, and able to comprehend written and spoken English. Additionally, women in the infertile group must have a diagnosis of diminished ovarian reserve, ovulatory dysfunction not due to PCOS, recurrent pregnancy loss, endometriosis, or unexplained infertility. Women in the fertile group must be undergoing IVF for male factor infertility, elective preservation, or intent for preimplantation genetic testing (PGT). We will exclude participants with a diagnosis of PCOS due to the likelihood that they already have MetS. We will exclude women who have had a myocardial infarction, stroke, atherosclerosis, diabetes, or cancer. Finally, we will exclude women with uterine and tubal factors as they may be congenital, or induced from surgery, trauma, or infection.

first: Smith

last: Alicia

first: Knight

last: Anna


title: Microbiome-produced nicotinic acid controls colon regional identity and injury susceptibility (Colon and Cecum scRNAseq)

first: Ophir

last: Klein

overall_design: We performed scRNAseq on sorted epithelial cells from the entire mouse colon and cecum of control, antibiotic-treated and germ-free mice.

first: Jeremie

last: Rispal

first: Manasa

last: Vegesna

first: Dario

last: Boffelli


title: Rhabdomyosarcoma transcriptomics upon PAX3-FOXO1 rescue with other fusion proteins

first: Seth

last: Zimmerman

summary: PAX3-FOXO1 is the commonly identified oncofusion gene found in rhabdomyosarcoma. However, other rare fusions are also seen. Here, we have knocked down PAX3-FOXO1 in a fusion-positive RMS cell line (RH4) with shRNA targeting the breakpoint and rescued cell growth with 7 fusions found in this cancer. RNA sequencing was then used to asess how each fusion alters transcription by comparing the RNA sequencing to a PAX3-FOXO1 knock down cell.

overall_design: Samples include RNA from RH4 cells transduced with a doxycycline induced shRNA targeting PAX3-FOXO1 (sh4) and either a vector encoding a control TurboID-NLS or each fusion tagged with the TurboID fused to the C-Terminus. A negative control was also included which consisted of RH4 cell transduced with a scrambled shRNA and TurboID-NLS. All cells were grown in the presense of Doxycycline.  Each sample was generated in technical triplicate


title: Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD- associated kinase LRRK2 between human and mice [ChIP-Seq]

overall_design: ChIP for STAT1 was performed using iPSC-derived microglia treated with either IFN-γ or PBS. STAT1 IP samples included three biological replicates per condition: IFN-γ-treated (STAT1IFN1–3) and PBS-treated (STAT1PBS1–3). Corresponding IgG control IPs (ControlIFN1–3 and ControlPBS1–3) were included for each treatment. Input samples (InputIFN and InputPBS) were collected prior to immunoprecipitation for normalization. Following IP, DNA was purified using spin columns and subjected to high-throughput sequencing.

first: Alexandra

last: Beilina

first: Jae-hyeon

last: Park

first: Natalie

last: Landeck

first: Ruth

last: Chia

first: Jinhui

last: Ding

first: Xylena

last: Reed

first: Hannah

last: Bailey

first: Changyoun

last: Kim

first: Alice

last: Kaganovich


title: A systematic exploration of the intrinsic mechanisms controling axon growth during development

city: Rehovot

first: Oren

last: Schuldiner

address: 234 Herzl Street

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: The ability of neurons to extend axons is governed by tightly regulated genetic programs that vary across developmental stages and cell types. Understanding the molecular features that control axon growth potential is critical for uncovering how neural circuits form, mature, and respond to injury or disease. The Drosophila mushroom body (MB) offers a powerful model to dissect axon growth programs, as lineage-related Kenyon cells (KCs) undergo different developmental events under shared spatiotemporal conditions. During metamorphosis, gamma-KCs undergo axon pruning, followed by developmental regrowth at the same time-frame as alpha-beta-KCs initiate axon outgrowth - thus providing a unique opportunity to compare these distinct growth paradigms. To uncover the underlying genetic programs, we performed RNA-sequencing of alpha-beta- and gamma-KCs during their initial outgrowth and developmental regrowth, respectively, revealing dynamic transcriptional changes and identifying 300 shared genes upregulated during both growth states. A targeted loss-of-function screen revealed genes specifically required for either Alpha-beta initial growth, gamma regrowth, or both. Focusing on one such candidate, pmvk, we found that it plays a crucial role in axon regrowth by acting within the mevalonate pathway. Notably, other enzymes in this pathway were also required, suggesting that the entire metabolic pathway is essential for supporting regrowth. Using mutant analyses and rescue exepriements, we demosntrate that pmvk likely controls axon regrwoth via prenylation of Rheb, an effector of the TOR pathway, which we previously found to be required for regrowth. Our developmental transcriptomic atlas not only advances understanding of intrinsic axon growth programs, but also provides candidate genes and a valuable framework for future studies aimed at enhancing axon regeneration in the adult nervous system

overall_design: Transcriptional profiling of alpha-beta neurons during initial axon outgrowth and gamma neurons during axon regrowth

first: Lora

last: Fahdan

first: Noa

last: Wigoda

first: Hagar

last: Meltzer


title: Integrated Transcriptomic and Proteomic Analysis of the Immune Response in Hyalomma anatolicum to Bacterial Invasion

status: Public on Mar 25 2026

city: Urumqi

first: Ercha

last: Hu

state: Xinjiang

address: East nongda Rd 311，Sayibak district

department: College of Veterinary Medicine

institute: Xinjiang Agricultural University

summary:
Background: Hyalomma anatolicum is a multi-host ectoparasite that carrys and transmits a variety of zoonotic pathogens. Understanding the immune response of ticks to bacterial infections is of research significance for deciphering their immune defense mechanisms and harnessing tick - derived molecules.
Methods: In the current study, transcriptomic and proteomic analyses on H. anatolicum injected with Staphylococcus aureus (SA group), Proteus mirabilis (PM group) or phosphate buffered saline (PBS group) were performed.
Results: In pairwise comparisons among the experimental groups, we identified 9,776 (SA/PBS), 10,230 (PM/PBS), and 1,309 (SA/PM) differentially expressed genes (DEGs), as well as 175 (SA/PBS), 277 (PM/PBS), and 223 (SA/PM) differentially expressed proteins (DEPs), respectively. Subsequent KEGG pathway analysis revealed that these DEGs and DEPs were significantly enriched in a range of pertinent pathways, including the immune system and apoptosis, Toll and IMD signaling pathways, MAPK signaling pathway, and NF - κB signaling pathway. The RT - qPCR detection data exhibited a concordant trend with the RNA - seq data, indicating a substantial alignment in the observed results. Notably, the defensin and lectin gene families emerged as potentially pivotal components within the innate immune defense system of ticks.
Conclusion: Overall, in this study, genes, proteins, and signaling pathways integral to the immune defense of H. anatolicum were identified, offering substantial potential for future research focused on harnessing its intricate immune defense mechanisms for antimicrobial applications.

overall_design: To investigate the gene expression profiles of H. anatolicum in response to bacterial challenges, transcriptome and proteome sequencing were conducted in this study. Specifically, female H. anatolicum ticks, collected from the same breeding experiment two weeks post - molting, were first immersed in sterile phosphate - buffered saline (PBS) solution and gently agitated for 15 s to clean their surfaces for three times. After thorough drying on sterile medical gauze, the ticks were positioned under a dissecting microscope with their ventral side exposed upwards. Each tick was then individually injected with either S. aureus suspended in phosphate-buffered saline (500 nL containing 10⁷ CFU) or P. mirabilis suspended in PBS (500 nL containing 10⁷ CFU), and a small amount of sterile petrolatum was picked up with a sterile needle and quickly applied to seal the wound upon needle withdrawal. This was accomplished through a puncture into their fourth coxal segment using a precision microsyringe (Hamilton Bonaduz, LTD, Switzerland). The control group received an equivalent volume of PBS (500 nL, 10 mM) to allow for comparative analysis of responses during bacterial invasion.

first: Jianlong

last: Li

first: Tingxiang

last: Luo

first: Zhen

last: Ma

first: Depeng

last: Yang

first: Sen

first: Yongchang

first: Bayinchahan

last: Gailike

first: Qingyong

last: Guo

first: Zhengxiang


title: Ex vivo modelling of lung tissue resident antimicrobial responses

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

summary: Tissue resident host responses to microbial infections in the respiratory tract are highly dynamic in space and time and rely on the interaction of a multitude of cell types. To model these multicellular responses reliably in cell culture, we compare here the global transcriptional antimicrobial response to infection with influenza A virus (IAV) in precision cut lung slices (PCLS), volume defined organ discs largely maintaining the cellular composition and 3D architecture of the donor lung. To permit a fair comparison of host responses in an isogenic background we first challenged mice in vivo and murine PCLS (mPCLS) and assess host transcriptomic changes by unbiased RNAseq. While core antiviral responses overlapped substantially, mPCLS lacked certain features—such as type II interferon expression—likely due to the absence of infiltrating immune cells responses. Importantly, when expanding our findings to immune experienced human precision cut lung slices (hPCLS), we find a much broader antiviral response after IAV challenge, including type I, II and III interferons, suggesting the presence of responsive tissue resident lymphocytes. To prove specificity of this response we infected hPCLS with Streptococcus pneumoniae. Ex vivo tissues responded with a distinct proinflammatory gene profile including IL1A, IL1B and IL17 expression. Blocking of IL-1β signaling partially inhibited the proinflammatory response, suggesting cellular crosstalk and a complex and specific antimicrobial reaction in this ex vivo model. In conclusion diversified tissue resident immune cell compartment distinguishes the human ex vivo model, making it an ideal system for microbiological and immunological research.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Lung samples from mouse or human infected in vivo or ex vivo (PCLS model) with Influenza A H1N1 strain were processed to RNA extraction for bulk RNAseq. This allowed us to compare the early host response between the in vivo situation and the ex vivo modelling.

first: Helena

last: Choltus

first: Niccolo

last: Bianchi

first: Nelli

last: Heikkila

first: Fedor

last: Bezrukov

first: Nina

last: Leitner

first: Beryl

last: Mazel-Sanchez

first: Veronique

last: Serre Beinier

first: Wolfram

last: Karenovics

first: Yannick

last: Nissille

first: Benoit

last: Bedat

first: Virginie

last: Prendki

first: Alexander

last: Lobrinus

first: Christiane

last: Eberhardt

first: Simone

last: Beccatini

first: Mirco

last: Schmolke


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (repli-seq)

first: Duncan

last: Sproul

summary: Loss of DNA methylation is a hallmark of cancer that is proposed to promote carcinogenesis through gene expression alterations, retrotransposon activation and induction of genomic instability. Cancer-associated hypomethylation does not occur across the whole genome but leads to the formation of partially methylated domains (PMDs). However, the mechanisms underpinning PMD formation remain unclear. PMDs replicate late in S-phase leading to the proposal that they become hypomethylated due to incomplete re-methylation by the maintenance methyltransferase DNMT1 during cell division. Here we investigate the role of DNMT1 in the formation of PMDs in cancer by conducting whole genome bisulfite sequencing (WGBS), repli-seq and ChIP-seq on DNMT1 knockout HCT116 colorectal cancer cells (DNMT1 KO cells). We find that DNMT1 loss leads to preferential hypomethylation in late replicating, heterochromatic PMDs marked by the constitutive heterochromatic mark H3K9me3 or the facultative heterochromatic mark H3K27me3. However, we also observe that a subset of H3K9me3-marked PMDs gain methylation in DNMT1 KO cells. We find that, in DNMT1 KO cells, these hypermethylated PMDs remain late replicating but gain DNMT3A localisation. This is accompanied by loss of heterochromatic H3K9me3 and specific gain of euchromatic H3K36me2. Our observations suggest that hypermethylated PMDs lose their heterochromatic state, enabling their methylation by DNMT3A and the establishment of a hypermethylated, non-PMD state, despite their late replication timing. More generally, our findings suggest that the de novo DNMTs play a key role in establishing domain level DNA methylation patterns in cancer cells.

overall_design: This series contains repli-seq from human cancer cell lines. HCT116 cells and derivatives lacking DNMT1 were grown before replication timing was profiled using repli-seq.


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A.

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

overall_design: Refer to individual Series


title: RNA-seq analysis of skeletal muscle from control (Cre) and Terf2 knockout (KO) mice in gastrocnemius-plantaris-soleus (GPS) and tibialis anterior (TA)

city: Nice

first: Olivier

last: Croce

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

summary: To investigate the molecular effects of telomere damage in skeletal muscle by Terf2 knockout, we performed bulk RNA sequencing on gastrocnemius-plantaris-soleus (GPS) and tibialis anterior (TA) muscles isolated from Terf2 knockout (KO) and control (Cre) mice. Total RNA was extracted from dissected muscles and used for library preparation followed by paired-end sequencing. Samples include both male and female 8 month old mice. The dataset comprises biological replicates from KO and Cre genotypes for each muscle type. FASTQ files correspond to quality-filtered and trimmed reads used for alignment.

overall_design: Bulk RNA sequencing was performed on skeletal muscle samples collected from Terf2 knockout (KO) and control (Cre) mice. Two muscle types were analyzed: gastrocnemius-plantaris-soleus (GPS) and tibialis anterior (TA). For each animal, RNA was extracted from both muscles and sequenced using paired-end RNA-seq. Biological replicates were included for each genotype and muscle type combination.

first: Maria

middle: S

last: Jacome

first: Eric

last: Gilson


title: High-Resolution Profiling of Osteocyte Transcriptomes via Single-Nucleus RNA Sequencing

city: Indianapolis

first: Gang

last: Peng

state: IN

address: 635 Barnhill Dr

department: Medical & Molecular Genetics

institute: Indiana University

summary: We developed a protocol for snRNA-seq on bone tissue, achieving high-yield recovery of osteocyte nuclei from snap-frozen, marrow-flushed long bones. This approach minimized dissociation bias and enhanced osteocyte representation. We applied this robust method to long bones from young adult male and female mice, generating a high-resolution map of osteocyte gene expression under physiological conditions. Compared to scRNA-seq datasets, where osteocytes represent only 0.18–6.64% of cells, our snRNA-seq approach increased osteocyte capture and transcriptomic fidelity to 18.5%. We identified an osteocyte transcriptomic signature highlighting the top 30 genes, including Sost, which is typically undetected or lowly-expressed in scRNA-seq. Notably, 23 of these genes have not been well-characterized in osteocytes, including Tg, Kcnq5, Rapgef4os1, Cacna1a, Egr3, Dok5, and Lgr6, which may represent novel regulators of osteocyte biology. This study represents the first application of snRNA-seq specifically for osteocyte analysis in bone tissue, providing a valuable resource for investigating osteocyte biology and skeletal disorders.

overall_design: single-nucleus RNA sequencing (snRNA-seq) on snap-frozen, marrow-flushed long bones from young adult male and female mice. Using an optimized protocol designed to minimize dissociation bias and maximize the recovery of osteocyte nuclei, we generated a high-resolution transcriptomic map of osteocyte gene expression under physiological conditions.

first: Yukiko

last: Kitase

first: Jia

last: Ji

first: Lynda

last: Bonewald

first: Matthew

last: Prideaux

first: Hyun Cheol

last: Roh


title: Ectopic MYC Expression Reprograms Epigenetic Landscapes and Transcription Factor Networks to Drive Differentiation Block and Malignant Transformation in AML [RNA-Seq]

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

summary: Overexpression of MYC is a common convergent consequence of genetic driver mutations in acute myeloid leukemia (AML). However, despite extensive research, the mechanisms by which this proto-oncogene promotes leukemogenesis remain incompletely understood. Here, we developed models of deregulated MYC expression in human pluripotent stem cell (hPSC)-derived myelopoiesis. We show that MYC overexpression from the endogenous locus maintaining physiological regulation is insufficient for leukemogenesis. Rather, constitutive MYC overexpression from ectopic alleles is necessary for driving and sustaining leukemia-associated phenotypes. These phenotypes depend on the widespread disruption of epigenetic landscapes imposed by MYC overexpression, which in turn underlies a differentiation arrest and dysregulation of the BACH1 transcription factor network, identified here as a mediator of these changes. Our findings shed new light into the mechanisms underlying MYC-induced malignant transformation and leukemogenesis, suggesting novel therapeutic targets for AML.

overall_design: A total of 22 RNA-Seq libraries from human embryonic stem cell-derived hematopoietic progenitor cells (HPCs) with ectopic MYC expression (+Dox, 10 samples consisting of 2 replicates each for 5 timepoints during HPC culture: days 12, 14, 16, 18 and 20) and control without ectopic MYC expression (-Dox, 12 samples consisting of 2 replicates each for 6 timepoints during HPC culture: days 10, 12, 14, 16, 18 and 20).

first: David

last: Dominguez-Sola

first: Eirini

last: Papapetrou

first: Saul

last: Carcamo


title: Single-nucleus RNA-seq of mouse cortex during mid-gestation pregnancy

city: Ecublens

first: Luca

last: Fusar Bassini

state: Vaud

address: EPFL - SV Building

department: BMI

institute: EPFL

summary: Single-nucleus RNA sequencing (snRNA-seq) was performed on cortical tissue from non-pregnant and pregnant (embryonic day E13.5) female C57BL/6JRj mice (~12 weeks old) to characterize transcriptomic changes in brain cell populations during pregnancy. This dataset accompanies the study "The lipidomic architecture of the mouse brain" (Fusar Bassini et al.), in which MALDI mass spectrometry imaging was used to map 172 lipids across the adult mouse brain. The snRNA-seq data were generated to investigate cell type-specific transcriptomic changes in the cortex of pregnant mice, complementing the spatial lipidomics findings. Nuclei were isolated from microdissected cortex using NP-40 lysis and iodixanol gradient purification, and libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 3' v4 (GEMX) kit. Sequencing was performed on an Element Biosciences AVITI24 system to a depth of ~50,000 reads per nucleus. Between 6,357 and 6,932 nuclei were recovered per sample, with a median of ~3,900-4,500 genes per nucleus.

overall_design: Two biological replicates each of non-pregnant control and pregnant (E13.5) C57BL/6JRj female mice (~12 weeks old) were used. Cortical tissue was microdissected and nuclei were isolated for snRNA-seq using the 10x Genomics Chromium X platform. Libraries were sequenced on an Element Biosciences AVITI24 instrument with paired-end reads (28 bp Read 1, 90 bp Read 2, 10+10 bp dual index). Total sequencing depth was ~1,388 million read pairs across all four libraries.

first: Dogukan

middle: H

last: Ulgen

first: Giovanni

last: D'Angelo

first: Gioele

last: La Manno


title: Ectopic MYC Expression Reprograms Epigenetic Landscapes and Transcription Factor Networks to Drive Differentiation Block and Malignant Transformation in AML [ATAC-seq]

overall_design: A total of 44 ATAC-Seq libraries from human embryonic stem cell-derived hematopoietic progenitor cells (HPCs) with (+Dox) or without (-Dox) ectopic MYC expression.


title: Maternal Microbiome-Derived Propionic Acid: A Key Regulator of Offspring Myelinogenesis Through Histone Lactylation-Mediated cGMP-PKG Activation

city: Xi'an

first: Yuan

last: Zhang

address: No. 620, West Chang'an Avenue, Chang'an District

institute: Shaanxi Normal University

summary: The maternal gut microbiome plays a crucial role in regulating offspring neurodevelopment through microbial metabolite signaling, yet its influence on central nervous system (CNS) myelinogenesis, a pivotal process for neural circuit maturation, remains poorly understood. Here, using antibiotic-induced maternal dysbiosis models, we identify propionic acid (PA), a short-chain fatty acid (SCFA) derived from the maternal microbiome, as a key epigenetic modulator of oligodendrocyte precursor cell (OPC) differentiation. Maternal antibiotic-induced gut dysbiosis led to significant hypomyelination in offspring, an effect that could be rescued by postnatal PA supplementation. PA not only enhanced developmental myelination but also promoted remyelination following lysolecithin-induced demyelination by inducing OPC maturation. Mechanistically, PA induced histone H4K12 lactylation (H4K12la), thereby activating transcription of cGMP-PKG signaling components (e.g., Gna12) and upregulating Sox family transcription factors essential for oligodendrocyte differentiation. These findings establish a propionate-H4K12la-cGMP-PKG axis that links maternal microbial metabolism to offspring myelination, revealing SCFA-driven epigenetic regulation as a promising therapeutic avenue for CNS disorders.

overall_design: Neonatal C57BL/6 mouse brain tissue (postnatal days 0–3, mixed sex) was rapidly dissociated in HBSS. OPCs were isolated using the Neural Tissue Dissociation Kit Ran and CD140a (PDGFRα) MicroBead Kit, seeded into poly-D-lysine–coated 6-well plates, and maintained in DMEM/F12 containing 20 ng/mL PDGF-AA, 2% B27, 20 ng/mL bFGF, 2 mM GlutaMAX, and 1% N2. After 24 h, the proliferation medium was replaced with DMEM/F12 containing 2% B27 and 1% N2, supplemented with either propionic acid (PA, 10 μM) or vehicle to induce differentiation. Two biological replicates were prepared for each condition. After 48 h, cells were trypsinized, and 1 × 10⁵ cells per sample were collected for library construction.

first: Yan

first: Bing

last: Han

first: Xiuqing

last: Li

first: Xing


title: Amniotic fluid cell-free RNA profiling reveals AGMAT as a biomarker for fetal renal abnormalities

city: Hangzhou

first: Xiang

last: Qiu

state: Zhejiang

address: No.1 Xueshi Road, Shangcheng District

institute: Zhejiang University

summary: Background Prenatal renal abnormalities comprise a heterogeneous spectrum of congenital kidney and urinary tract phenotypes detected on fetal ultrasonography and contribute substantially to long-term renal morbidity. Current prenatal assessment relies primarily on ultrasonography and genetic testing. However, approximately 60%-70% of fetuses with congenital anomalies remain without a definitive diagnosis. In fetuses with renal abnormalities, the diagnostic yield is even lower, with only about 13.1% receiving a confirmed molecular diagnosis. These limitations underscore the need for complementary molecular biomarkers to improve etiologic characterization in prenatal diagnosis. Amniotic fluid (AF) cell-free RNA (cfRNA) reflects contemporaneous, organ-specific fetal transcriptional activity and offers a unique opportunity for biomarker discovery in the prenatal evaluation of renal abnormalities. Methods AF cfRNA transcriptomes were profiled in fetuses with apparent ultrasound abnormalities and in propensity score-matched controls. Differential expression and functional enrichment analyses were performed, followed by weighted gene co-expression network analysis (WGCNA) to identify phenotype-associated modules. Candidate genes were prioritized by intersecting differentially expressed genes (DEGs) with the key module, and subsequently refined through feature selection using least absolute shrinkage and selection operator regression, random forest, and support vector machine recursive feature elimination. Functional validation was performed in a CRISPR/Cas9-generated agmat crispant zebrafish model. Results Analysis of 10 case-control pairs after 1:1 propensity score matching identified 546 DEGs, enriched in pathways related to renal epithelial differentiation and tubular function. Integration of WGCNA with differential expression analysis yielded 103 candidate genes, and convergent machine learning (ML) prioritized three core genes: AGMAT, GPX2, and TIMP1. Among these, AGMAT was selected for further investigation based on its kidney-enriched expression profile and limited prior characterization in renal development. In vivo, genetic perturbation of agmat in a zebrafish model recapitulated the RNA profiling results, leading to disrupted renal morphogenesis and significantly reduced early survival. Conclusions By integrating AF cfRNA transcriptomics with ML analyses, we identified AGMAT as a candidate diagnostic biomarker for prenatally detected renal abnormalities. These results position AF cfRNA as a real-time molecular complement to prenatal imaging and genetic testing and provide a framework for etiologic interpretation, risk stratification, and mechanistic interrogation of fetal renal abnormalities.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: RNA-seq profiling of amniotic fluid cell-free RNA from fetuses with renal abnormalities and controls.

first: Jinglan


title: Quantitative transcriptome and proteome maps of classical nonclinical species [b2]

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

institute: Pfizer

summary: The distribution of expression of target genes can provide insights that advance understanding of target availability to aid therapeutic development purposes. The increase of use of biologics and novel modalities, combined with the opportunities of alternative to in vivo experimental methods in safety evaluation of new therapeutics. A detailed understanding of expression levels in target tissues is essential to selecting nonclinical species with the highest translational potential. We quantified the relative RNA and proteinlevels across more than 40 normal tissues and 5 nonclinical species several tissues in human. We identified patterns of cross-species and methodology relationships that can aid in the broader understanding of nonclinical experimental design. We observedexpression profile similarity across tissues that favors species similarity, except for select nervous system and immune tissues. In exploring tissue specificity, we identified ubiquitous transcripts that encode tissue-specific proteins. We also assessed discordance between RNA and protein enrichment and revealed potential sites of synthesis and action of secreted proteins. These data and their relationships are foundational assets in toxicology study design and provide insights into biological regulation in drug discovery.

sample_organism:
Macaca fascicularis
Canis lupus familiaris
Mus musculus
Rattus norvegicus

overall_design: Rna-seq proflining of tissue samples from pre-clinical animals (minipigs, cynomolgus monkeys, beagle dogs, Wistar Han rats, CD1 and C57BL6 mouse) Snap frozen tissue samples were collected from 3 male and 3 female animals (minipig, cynomolgus monkeys and dogs) and for rodents, 5 male and 5 female animals were used for tissue collection.Frozen human tissue samples (3 males and 3 females) were obtained from Pfizer Tissue Bank.  Rodent tissue samples from Rat and Mouse (7 to 9 weeks old, n=5/gender) were pooled & analyzed by gender. Samples (n=3/gender, 6 samples/tissue type/species) from human, cyno, dog, and pigs were pooled by tissue type only.

first: Elias

last: Oziolor

first: Liang

last: Xue

first: Dennis

last: Pelletier

first: Emi

last: Kimoto

first: Joel

middle: D

last: Federspiel

first: Mark

last: Sheehan

first: Seda

last: Arat

first: Leah

last: Newman

first: Sophia

last: Lee

first: Jessie

last: Qian

first: Steven

last: Kumpf

first: Thomas

last: Lanz

first: Mathew

last: Martin

first: Nagappan

last: Mathialagan


title: Quantitative transcriptome and proteome maps of classical nonclinical species [b3]

sample_organism:
Macaca fascicularis
Canis lupus familiaris
Rattus norvegicus


title: SPT6 maintains epidermal homeostasis by inhibiting an NF-κB- positive feedback loop to prevent excessive inflammation

city: Ghuangzhou

first: Yushuang

last: Sun

address: NO.2 Zhongshan Road

department: Institute of Precision Medicine

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: Keratinocytes are increasingly recognized as central regulators of cutaneous immune responses and key contributors to maintaining immune homeostasis. However, whether and how epidermal stem and progenitor cells (EPSCs) actively suppress proinflammatory signaling pathways to prevent excessive inflammation and maintain epidermal immune quiescence remains unclear. Here, we generated a conditional knockout mouse model (K14-CreERT; Supt6fl/fl) to investigate the role of SPT6, a transcription elongation factor, in epidermal and immune homeostasis. Loss of SPT6 in basal keratinocytes led to spontaneous, psoriasis-like skin inflammation, characterized by epidermal hyperplasia, immune cell infiltration, parakeratosis, and hyperkeratosis. SPT6-deficient mice also exhibited significantly delayed wound healing accompanied by impaired Wnt signaling. Moreover, single- cell RNA sequencing revealed distinct keratinocyte subpopulations with inflammatory signatures, elevated NF-κB signaling, and suppressed Wnt signaling. Mechanistically, SPT6 suppresses NF-κB signaling by binding to an enhancer of the RELA gene and preventing its positive transcriptional feedback loop. These findings support a new paradigm in which the default state of the skin may be primed for inflammation, and active suppression by factors such as SPT6 is required to maintain epidermal homeostasis. Taken together, the results of our study reveal a previously unrecognized role for SPT6 as a key regulator of epidermal immune quiescence and tissue integrity.

overall_design: RNA-seq of wild-type mice and Supt6 KO mice, collected on the 10th day after the final tamoxifen injection.

first: Jingting

last: Li


title: Ribosome-associated RNA of cardiac endothelial cells purified from endothelial specific RiboTag mice

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: To assess the expression levels of ribosome-associated RNAs of murine cardiac endothelial cells, hearts were collected from Cdh5-CreERT2;Rpl22tm1.1Psam mice (endothelial specific RiboTag) and ribosomes of endothelial cells containing HA-tagged RPL22 protein were immunoprecipitated. Then, RNA-seq was performed. The mice underwent coronary ligation 7 days before and only the remote healthy area of the heart was analyzed.

overall_design: Three biological replicates for RNA-seq of ribosome-associated RNA of cardiac endothelial cells.

first: Haruya

last: Kawase

last: Offermanns


title: Gene expression profile at single cell level of SARS-CoV-2 mRNA vaccine immunized mouse bone marrow

city: La Jolla

first: Jing

last: Wen

address: 3147 Biomedical Sciences Wy

department: CMM

institute: UCSD

summary: We designed a new SARS-CoV-2 mRNA vaccine G1-C. We immunized mice with 2 doses of GFP, RBD, and G1-C vaccines and then analyzed vaccine-induced immune response in vivo.

overall_design: We immunized mice with 2 doses of GFP, RBD, and G1-C vaccines. 14 days after the booster, we isolated bone marrow cells and performed single-cell RNA sequencing of 9 samples from GFP, RBD and G1-C groups to assess differential gene expression.

first: Jaesu

last: Moon

first: Luca

last: Tucciarone

first: Shania

last: Bu

first: Tariq

last: Rana


title: Epicardial Tcf21 facilitates cardiomyocyte protrusion into the injury area during heart regeneration in zebrafish

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

country: Lithuania

institute: Vilnius University

summary: Unlike mammals, zebrafish (Danio rerio) are able to regenerate their hearts after injury, making them an excellent model organism for studying the molecular mechanisms underlying heart regeneration. Epicardium, the outermost layer of the heart, is an essential player in this process. Injury-induced epicardium activation, characterized by upregulation of embryonic epicardial marker genes including Tcf21 supports cardiac regeneration by providing various cell types and releasing paracrine signals that promote the restoration of damaged tissue. However, the molecular mechanisms involved in this process are insufficiently understood. In this study, we describe a conditional tcf21flox allele and use it to investigate the role of Tcf21 in heart regeneration. By employing 4-hydroxytamoxifen inducible CreERT2 recombinase, we eliminate tcf21 expression in adult fish. Our findings indicate that loss of this transcription factor compromises the migration of dedifferentiated cardiomyocytes into the injury area and impairs heart regeneration. This work provides new insights into the molecular basis of epicardium response to heart injury and its role in guiding heart regeneration.

overall_design: RNA-seq profiling of control and conditional tcf21 knock-out fish ventricles without injury (day 0), 3 days post-cryoinjury (dpci) and 3 days post-sham (dps).

first: Miglė

last: Kalvaitytė-Repečkė

last: Kvederavičiūtė

first: Darius

last: Balciunas


title: Quantitative transcriptome and proteome maps of classical nonclinical species [b1]

first: Darien

last: Capunitan

sample_organism:
Macaca fascicularis
Homo sapiens
Canis lupus familiaris
Sus scrofa
Mus musculus
Rattus norvegicus

first: Elias

last: Oziolor

first: Liang

last: Xue

first: Dennis

last: Pelletier

first: Emi

last: Kimoto

first: Joel

last: Federspiel

first: Mark

last: Sheehan

first: Seda

last: Arat

first: Leah

last: Newman

first: Sophia

last: Lee

first: Jessie

last: Qian

last: Kumpf

last: Lanz


title: Dual RNA-seq analyses provide insights into the biology of the fish pathogen Piscirickettsia salmonis

city: Santiago

first: Veronica

last: Cambiazo

address: Av. El Libano 5524

country: Chile

institute: Instituto de Nutrición y Tecnología de los Alimentos (INTA)

summary: Piscirickettsia salmonis is a facultative intracellular pathogen and the causative agent of piscirickettsiosis, a systemic infection of salmonid fish, with high impact on the salmonid aquaculture in Chile. After invasion, P. salmonis actively replicates in macrophages and monocytes, and its ability to enter and multiply within host cells is essential for pathogenesis. The ability of P. salmonis to subvert the functions of macrophages contributes to bacteria survival and dissemination within the host. Here, we adapted dual RNA-sequencing to define how P. salmonis remodel their gene expression in tandem with that of infected the host cell, a macrophage-like cell line from Salmo salar head kidney, known as SHK1. We found that SHK1 cells increased lysosomal content and activity to defend against invading bacteria, while P. salmonis upregulated gene functions related to virulence, including type IV secretion system (T4SS), iron acquisition, transport and efflux systems.

sample_organism:
Piscirickettsia salmonis
Salmo salar

platform_organism:
Piscirickettsia salmonis
Salmo salar

overall_design: SHK-1 cells infected with P. salmonis CGR02 at day 4 (stationary growth phase), SHK-1 control cells, and P. salmonis CGR02 in exponential phase grown in axenic medium were sequenced using RNA-seq. The transcriptome of SHK-1 infected cells was compared with the SHK-1 control cells, and the intracellular transcriptome of P. salmonis was compared with P. salmonis in exponential phase grown in axenic medium.

first: Pamela

last: Aravena

first: Christian

last: Hodar

first: Daniel

middle: E

last: Palma

first: Javiera

last: Ortiz


title: Study of pan-sRNome and regulatory mechanisms in pseudomonas aeruginosa reveals virulence-related functions of small non-coding RNAs

city: Hongkong

first: Xin

last: Deng

state: 九龍

address: Tat Chee Road, City University of Hong Kong, AC1,B2315

department: BMS

country: Hong Kong

institute: City University of Hong Kong

summary: Small non-coding RNAs (sRNAs) are pivotal regulators of post-transcriptional activities and various cellular processes in bacteria. This study highlighted a framework for understanding novel identified sRNA functions at gene expression and phenotypical levels and provides insights into sRNome assemblies in bacteria.

overall_design: 2 WT RNA-seq for sRNA prediction; 11 sRNA over-expression RNA-seq and 1 WT with EV RNA-seq serving control; additional 2 WT/EV RNA-seq for sRNA expression verification.

first: Tianmin

last: Li

first: Beifang

last: Lu


title: Pharmacological inhibition of GLUT1 alleviates fulminant hepatitis by restraining macrophage-induced inflammatory cascades and restoring metabolic homeostasis

city: Beijing

first: yanlin

last: wang

address: Dongzhimen Hospital

institute: Beijing University of Chinese Medicine

summary: Fulminant hepatitis (FH) is a life-threatening clinical syndrome characterized by massive hepatocyte necrosis and rapid liver failure, with limited therapeutic options beyond transplantation. Although hepatic macrophages are known to drive FH immunopathology, the metabolic mechanisms governing their hyperactivation remain poorly understood. In this study, we investigated the role of glucose transporter 1 (GLUT1)-mediated metabolic reprogramming in the progression of D-gal/LPS-induced FH. GLUT1 is significantly upregulated in hepatic macrophage during acute injury, facilitating a shift toward aerobic glycolysis. This glycolytic surge, regulated via the PI3K/AKT signaling pathway, serves as a fundamental driver for pro-inflammatory M1 macrophage polarization and the subsequent cytokine storm. Notably, pharmacological inhibition of GLUT1 with WZB117 effectively suppressed glycolytic flux, attenuated M1-type activation, and restored lipid metabolic homeostasis, thereby significantly reducing hepatocellular apoptosis and systemic inflammation. Transcriptomic and metabolomic profiling confirmed that GLUT1 inhibition rebalances the immune microenvironment by intercepting the macrophage-mediated inflammatory cascade at its inception. Collectively, these findings identify GLUT1 as a pivotal molecular switch in macrophage-intrinsic metabolic reprogramming and suggest that targeting GLUT1-mediated glycolysis represents a promising therapeutic strategy for the clinical management of fulminant hepatic failure.

overall_design: Analysis of differentially expressed genes in mouse livers subjected to D-gal/LPS-induced acute liver injury and pretreated with GLUT1 inhibitors.

first: Xianqiong

last: Gong

first: Xiaozhen

last: Guo

first: Yanlin

last: Wang

first: Yingying

last: Sun

first: Qiong

first: Youbo

last: Zhang

first: Frank

last: Gonzalez


title: B4GALT1 deficiency attenuates steatohepatitis by regulating the PPARγ/ACSL4 axis

city: Shanghai

first: Youjung

last: Chien

address: 180 Fenglin Road, Shanghai 200032, China.

institute: Zhongshan Hospital, Fudan University

summary: Metabolic dysfunction-associated fatty liver disease (MASLD) can progress to metabolic dysfunction-associated steatohepatitis (MASH) and fibrosis. Previous studies have implicated aberrant glycosylation in MASLD progression. However, the role and underlying molecular mechanisms of B4GALT1 in MASLD progression remain unclear. Our studies demonstrate that B4GALT1 plays a crucial role in MASLD progression by targeting lipid peroxidation in hepatocytes via the PPARγ/ACSL4 axis, thus highlighting a potential therapeutic target for MASLD.

overall_design: Liver RNA-seq profiling of  wildtype and B4galt1 knockout  MASLD mice.


title: MECOM promotes leukemia progression and inhibits mast cell differentiation through functional competition with GATA2 (CordBlood_RNA-seq)

city: Shimotsuke

first: Kohei

last: Iida

state: Tochigi

address: Yakushiji 3311-1

department: Regenerative medicine

country: Japan

institute: Jichi medical university

summary: MECOM is a transcription factor critical for the maintenance of hematopoietic stem cells (HSCs) and the pathogenesis of myeloid leukemia. Germline mutations clustered in the C-terminal zinc finger domain (ZFD) of MECOM are known to cause MECOM-associated syndromes, involving bone marrow failure and skeletal anomalies. However, the molecular consequences of these mutations and the precise downstream mechanisms of MECOM remain elusive. Here, we demonstrate that the C-terminal ZFD serves as the dominant DNA-binding module of MECOM, and that disease-associated mutations abrogate its DNA-binding capacity. Mechanistically, we reveal that MECOM functionally antagonizes GATA2 via C-terminal ZFD-mediated DNA binding and recruitment of the corepressor CtBP. This repression promotes myeloid leukemogenesis while suppressing mast cell differentiation. Furthermore, we generated a knockin mouse model harboring a C-terminal ZFD mutation, which successfully recapitulated the clinical phenotypes of MECOM-associated syndromes, including reduction of HSCs and B cells. Collectively, our findings define C-terminal ZFD mutations as loss-of-function mutations with impaired DNA binding, uncover the MECOM-GATA2 axis as a key regulatory pathway, and provide a valuable mouse model for understanding MECOM-associated syndromes.

overall_design: RNA-seq profiling human CD34+ umbilical cord blood cells transduced with pMYS-IRE-GFP vector, wild-type MECOM, or mutant MECOM (MECOM-R750 or MECOM-DL/AS). GFP+ cells were sorted 48 hours after transduction, and were cultured for 4 days.

first: Tomoya

last: Isobe

first: Shuhei

last: Asada

first: Tomohiro

last: Yabushita

first: Susumu

last: Goyama


title: Affymetrix SNP array data for adult Myelodysplastic Syndromes (MDS)/Acute Myeloid Leukemia (AML) with isolated monosomy 7

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

institute: University of Perugia

summary: Monosomy 7 is one of the most frequent aneuploidies in myeloid malignancies, associated to heterogeneous phenotypes. Its poor prognosis differentiates it from  aberrations leading to partial/complete loss of 7q region.  Underlying pathogenic mechanisms are still undetermined. We performed a comprehensive epi-genomic study of karyotypically isolated monosomy 7 in adult Myelodysplastic Syndromes/Acute Myeloid Leukemias.

overall_design: Copy number analysis of isolated monosomy 7 cases MDS/AML by CytoScan HD Affymetrix platform

first: Valentina

last: Pierini

first: Anair

last: Lema Fernandez

first: Carlotta

last: Nardelli


title: Directed evolution improves the catalytic efficiency of APEX2-mediated proximity-dependent RNA labeling

first: Gang

address: 5th, Yiheyuan Road, Beijing

institute: Peking University

summary: Engineered ascorbate peroxidase APEX2 has seen widely used for spatially restricted profiling of subcellular biomolecules, but its catalytic efficiency toward newly developed probes such as biotin-aniline (Btn-An) remains suboptimal. To overcome this limitation, we performed yeast surface display based directed evolution to enhance APEX2 activity toward Btn-An. The resulting variant, L242FAPEX2, exhibits an approximately two-fold improvement in labeling efficiency, likely through enhanced enzyme-substrate interactions. This increased activity enables rapid and efficient proximity labeling while maintaining spatial specificity. After validating its performance at the ER membrane, we applied L242FAPEX2 to profile the transcriptome proximal to the midbody and identified ANLN as a previously unreported midbody-localized mRNA during telophase. Drug perturbation and reporter assays further revealed that ANLN mRNA targeting to the midbody occurs co-translationally and depends on its nascent N-terminal peptide. Together, this work establishes L242FAPEX2 as an improved and versatile tool for spatially resolved transcriptomics in complex subcellular contexts.

overall_design: APEX2- or APEX2_L242F-mediated RNA labeling libraries were generated from the following six cell lines: (1) APEX2_L242F-ERM (ER membrane); (2) APEX2_L242F-NES (Cytosol); (3) APEX2-ERM (ER membrane); (4) APEX2-NES (Cytosol); (5) BIRC5-APEX2_L242F-EGFP (midbody); (6) KIF23-APEX2_L242F-EGFP (midbody). For each cell line, three or four biological replicates were performed. Total RNAs directly extracted from the cells were set as Input. RNAs labeled by ER membrane- or cytosol-localized APEX2_L242F were set as Enrich. RNAs enriched from negative controls omitting probes were set as Control.

first: Yi

last: Li

first: Peiyuan

last: Meng

first: Peng

last: Zou


title: Multiplex Enhanced Reduced Representation Bisulfite Sequencing (mERRBS) Analysis of adult Myelodysplastic Syndromes (MDS)/Acute Myeloid Leukemia (AML) with isolated monosomy 7 compared to controls

summary: Monosomy 7 is one of the most frequent aneuploidies in myeloid malignancies, associated to heterogeneous phenotypes. Its poor prognosis differentiates it from  aberrations leading to partial/complete loss of 7q region. Underlying pathogenic mechanisms are still undetermined. We performed a comprehensive epi-genomic study of karyotypically isolated monosomy 7 in adult Myelodysplastic Syndromes/Acute Myeloid Leukemias.

overall_design: mERRBS profiles of 3 isolated monosomy 7 cases and 12 controls (6 bone marrow samples from non-neoplastic cytopenias, normal bone marrow morphology and normal karyotype -CTL; 6 MDS and AML with normal karyotype - nkMN)