title: A PLURIPOTENT STEM CELL PLATFORM FOR IN VITRO SYSTEMS GENETICS STUDIES OF MOUSE DEVELOPMENT [RNA-seq]

overall_design: We converted embryonic stem cells (ESCs) from the 7 of the 8 Diversity Outbred founder strains (129S1/SvImJ, C57BL/6J, NOD/ShiLtJ, NZO/HiLtJ, CAST/EiJ, PWK/PhJ, WSB/EiJ) to epiblast stem cells (EpiSCs) and collected them for RNA-sequencing at low passage.  We then performed directed differentiation to definitive endoderm (DE) from these cells.  Following 40 hours of differentiation, cells were collected and sorted using magnetic activated cell sorting (MACS) to perform RNA-sequencing on the CXCR4-positive population.


title: Identification of differentially expressed genes involved in the enhancement of thermosensitivity by HIKESHI knockout in human oral squamous cell carcinoma HSC-3 cells

status: Public on Jul 08 2025

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

summary:
HIKESHI has been reported to function as a nuclear carrier protein for Hsp70 under heat-stress conditions. Functional suppression of this protein has also been shown to increase the sensitivity of cancer cells to heat. However, the molecular mechanisms underlying the enhancement of thermosensitivity in HIKESHI-suppressed cells remain unclear.
In this study, we identified differentially expressed genes associated with the enhancement of thermosensitivity resulting from HIKESHI knockout in human oral squamous cell carcinoma HSC-3 cells, using GeneChip® oligonucleotide microarrays.

overall_design: Human oral squamous cell carcinoma HSC-3 cells and HSC-3 HIKESHI-knockout (HIKO) cells (Thermal Med. 2024; 40: 17–29. https://doi.org/10.3191/thermalmed.40.17) were treated with hyperthermia (HT) at 42°C for 90 min, followed by incubation at 37°C for 3 h. As a control, each cell type was cultured at 37°C for 90 min and then incubated at 37°C for 3 h. Total RNA was extracted from the cells, and RNA quality was assessed using the Agilent 4150 TapeStation system. Gene expression analysis was performed using the Affymetrix GeneChip® system with the GeneChip® Human Genome U133 Plus 2.0 Array. Sample preparation for array hybridization was conducted according to the manufacturer’s instructions.


title: TEAD switches interacting partners along neural progenitor lineage progression to execute distinct functions

status: Public on Jul 09 2025

city: Memphis

first: Xinwei

last: Cao

state: TN

address: 62 Danny Thomas Pl

department: Developmental Neurobiology

country: USA

institute: St. Jude Children's Research Hospital

type: Expression profiling by high throughput sequencing

summary: The TEAD family of transcription factors is best known as the DNA-binding factor in the Hippo pathway, where these factors act by interacting with transcriptional coactivators YAP and TAZ (YAP/TAZ). Despite the importance of the Hippo pathway, the in vivo functions of TEAD in mammals have not been well established. By comparing mouse mutants lacking TEAD1 and TEAD2 (TEAD1/2) with those lacking YAP/TAZ, we found that TEAD1/2 have both YAP/TAZ-dependent and YAP/TAZ-independent functions during ventral telencephalon development. TEAD1/2 loss and YAP/TAZ loss similarly disrupt neuroepithelial apical junctions. However, the impacts of their losses on progenitor lineage progression are essentially opposite: YAP/TAZ loss depletes early progenitors and increases later progenitors, consistent with their established function in promoting progenitor self-renewal and proliferation, whereas TEAD1/2 loss expands early progenitors and reduces late progenitors, indicating that TEAD1/2 promote lineage progression. We further show that TEAD1/2 promote neural progenitor lineage progression by at least in part inhibiting Notch signaling and by cooperating with insulinoma-associated 1 (INSM1). Orthologs of TEAD and INSM1 have been shown to cooperatively regulate neuronal cell fate decisions in worms and flies. Our study reveals a remarkable evolutionary conservation of the function of this transcription factor complex during metazoan neural development.

overall_design: The MGEs from wild-type mice at E12.5 and E15.5, as well as Tead1/2 and Yap/Taz knockout mutant mice and appropriate controls at E14.5, were collected for scRNASeq analysis

first: Charles

middle: H

last: Perry

first: Alfonso

last: Lavado

first: Venkata

last: Thulabandu

first: Cody

last: Ramirez

first: Joshua

last: Pare

first: Rajiv

last: Dixit

first: Akhilesh

last: Mishra

first: Jiyuan

last: Yang

first: Jiyang

last: Yu


title: Multimodal antigenic escape to GPRC5D-targeted T-cell engagers in multiple myeloma [scATAC-seq]

status: Public on Jul 05 2025

city: Calgary

first: nizar jacques

last: Bahlis

state: AB

address: 3330 Hospital Dr NW HMRB328

department: Medicine

country: Canada

institute: University of Calgary

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Tumor intrinsic adaptations with emerging resistant clones following T cell targeted immunotherapies pose a major barrier to durable remissions in multiple myeloma (MM). Through integrated genomic, transcriptomic, and epigenomic interrogation of clonal plasma cells, we observed antigenic drift in 68.4% of relapsed cases following anti-GPRC5D T cell engager (TCE) therapy. These escape events were driven by three distinct mutational mechanisms involving i) focal to large biallelic deletions at the GPRC5D gene locus, ii) monoallelic deletion coupled with GPRC5D single nucleotide variants (SNVs) or insertions/deletions (indels) on the remaining allele, as well as iii) epigenetic GPRC5D promoter/enhancer silencing. Beyond biallelic deletions resulting in complete antigenic loss, we demonstrate that GPRC5D SNVs and indels mutate anti-GPRC5D TCE binding epitopes or more commonly affect G-protein couple receptor family conserved motifs critical for protein membrane trafficking resulting in endoplasmic reticulum (ER) GPRC5D trapping. Multiple subclones bearing distinct genomic alterations at GPRC5D locus co-emerged within individual cases, depicting their convergent evolutionary trajectories. Importantly, anti-GPRC5D TCEs with varying epitope specificity, affinity, and valency differentially targeted mutant subclones, underscoring their non-redundant functional roles in overcoming resistance

overall_design: Experiments were conducted on primary patient bone marrow samples, after informed consent, in accordance with the Declaration of Helsinki and following the approval by the Medical Center Institutional Review Board. Sorted CD138+ cells were collected from patients’ bone marrow aspirates pre-and post-treatment with anti-GPRC5D T cell engagers, counted and viably frozen. Frozen cells were then thawed at 37°C, resuspended in RPMI 1640 medium (Gibco) and washed twice by centrifugation at 2000 rpm for 5 min. The desired number of nuclei [2000-8000] was targeted and processed according to the Nuclei Isolation for Single Cell ATAC sequencing (CG000169, 10x Genomics, Pleasanton, CA, USA). Nuclei isolation was performed as indicated in the nuclei isolation protocol for Single Cell ATAC Sequencing (10x Genomics). Based on the starting number of cells and desired final nuclei concentration, primary MM cells were lysed and resuspended in an appropriate volume of chilled Diluted Nuclei Buffer. The resulting nuclei were immediately used to generate scATAC-seq libraries using the Chromium Single Cell ATAC reagent kit (CG000168, 10x Genomics) according to the manufacturer’s protocol.

first: Holly

last: Lee

first: Noémie

last: Leblay

first: Sungwoo

last: Ahn

first: Sacha

last: Benaoudia

first: Elham

last: Hasheminasabgorji

first: Mansour

last: Poorebrahim

first: David

last: Jung

first: Paola

last: Neri

first: Nizar


title: Diverse roles of SERPINE1 in regulating cellular proliferation and invasion

status: Public on Jul 03 2025

city: Tianjin

first: Jing

last: Mo

state: Tianjin

address: 22 Qixiangtai Road, Heping District

department: Pathology

country: China

institute: Tianjin medical university

summary: SERPINE1 is involved in various biological processes, but its roles in promoting or suppressing tumorigenesis remain controversial. To understand the underlying mechanisms, we focused on the effects of SERPINE1 downregulation on cell phenotypes, particularly proliferation and invasion, across three types of tumors. High SERPINE1 levels in breast cancer (BRCA) and low-grade glioma (LGG) were associated with poor prognosis. In contrast, elevated SERPINE1 levels in skin cutaneous melanoma (SKCM) correlated with better outcomes. SERPINE1 knockdown resulted in increased xenograft growth in the melanoma cell line C918. This was characterized by the promotion of the cell cycle through the modulation of minichromosome maintenance protein expression and the activity of p53 and SMAD3. In breast cancer cells (MDA-MB-231) with SERPINE1 knockdown, there was decreased xenograft growth and cell proliferation, attributed to a reduction in the uPAR-mediated ERK/p38 activity ratio. With SERPINE1 knockdown, both C918 and MDA-MB-231 cells demonstrated reduced invasion capabilities, decreased matrix metalloproteinase (MMP) activity, and reduced lung metastasis. In low-grade glioma cells (H4), SERPINE1 knockdown led to decreased cell proliferation due to a reduction in the HSP90-mediated ERK/p38 activity ratio. However, it increased invasion and MMP activity, particularly of MMP-1, regulated by the HSP90-p38 axis. Collectively, our findings reveal that SERPINE1 exerts diverse effects on cell proliferation and invasion through context-dependent mechanisms. These results suggest that targeting SERPINE1 may offer personalized therapeutic strategies to enhance treatment precision and reduce adverse effects.

overall_design: RNA-seq profiling of  MDA-MB-231, H4 and C918 cells and their stably knockdown derivatives (shSE1)

first: Wei

last: Wang

first: Pengfei

last: Zhao

first: Qiang

last: Huang


title: Wnt signaling promotes inflammation and EMT-associated gene expression in mesenchymal TNBC

status: Public on Jul 01 2025

city: Paris

first: Elodie

last: Girard

address: 11-13 rue Pierre et Marie Curie

country: France

institute: Institut Curie

summary: Aberrant activation of the Wnt signaling pathway in triple-negative breast cancer (TNBC) is linked to treatment resistance and recurrence, yet its role in tumoral heterogeneity remains unclear. We developed Wnt reporter cell lines from two mesenchymal TNBC models (MDA-MB-231 and MDA-MB-436) using a Tcf/Lef-eGFP vector and observed intra- and inter-tumoral variation in Wnt activity. Paired Wnt-positive and Wnt-negative TNBC cell lines were established and profiled by RNA-Seq. Integrative analyses revealed that Wnt-positive cells consistently upregulate genes involved in epithelial-to-mesenchymal transition, inflammation (e.g., IL6/JAK/STAT3, TNFα via NF-κB), and extracellular matrix remodeling. A 55-gene Wnt signature common to both nutrient conditions captured these features. Wnt-related gene sets were also enriched in the Mesenchymal-like Immune-Altered subtype of 699 primary TNBC tumors. These findings highlight the role of basal Wnt activity in driving pro-tumorigenic transcriptional programs in TNBC and provide new insight into its contribution to subtype-specific disease features.

overall_design: Two mesenchymal triple-negative breast cancer (TNBC) cell lines, MDA-MB-231 and MDA-MB-436, were stably transfected with the 7TGP Wnt reporter vector, which drives eGFP expression under the control of TCF/LEF-responsive elements. Fluorescence-activated cell sorting (FACS) was used to isolate and expand paired Wnt-positive and Wnt-negative sublines from each model. These reporter-defined cell lines were cultured under two serum conditions: low serum (0.5% FBS) for 3 days and standard serum (10% FBS) for 6 days. Total RNA was extracted from two biological replicates per condition for each cell line for subsequent bulk RNA sequencing.

first: Ramon

last: Garcia-Areas

first: Hamza

last: Lasla

first: Virginie

last: Raynal

first: Amit

last: Kimar Panday

first: Nicolas

last: Servant

first: Pascal

last: Jézéquel

first: Thierry

last: Dubois


title: Identification of the binding DNA of FOXF1 by ChIP in Neuro-2a cells

status: Public on Jun 30 2025

city: Hangzhou

first: Xiang

last: Yuhang

address: Yuhang Tang street

summary: Neuro-2a cells were transfected with pFOXF1 for 42 hours then infected with herpes simple virus1 for 5 hours. Samples infected for 5 hours were sequenced by ChIP for binding DNAs of the FOXF1 in Neuro-2a cells.

overall_design: Input represents unenriched cell samples, and IP represents cell samples after FOXF1 enrichment. We explored the binding pattern of FOXF1 on the viral genome by comparing the differences between the post-IP samples and the Input samples.

first: Dongli

last: Pan

first: Yuhang

last: Xiang


title: Single cell ATAC-seq analysis of H3.3K4M WT and Hom brain samples (10X Genomics Multiome)

status: Public on Jul 14 2025

city: Bethesda

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

summary: Methylation of lysine4 on Histone H3 (H3K4) is require for promoter and enhancer activation at gene loci and presents distinct methylation patterns over developmental gene clusters. Disrupting in the writer, eraser and reader of H3K4 methylation is associated with developmental syndromes. However, less studies focus on the role of H3K4 methylation in development of interneuron and hypothalamus. Here, we explore the role of H3K4 methylation in the medial ganglionic eminence (MGE) derive interneuron and hypothalamus by directly mutating the lysine 4 on H3.3 to the methionine in mice.

overall_design: The Nkx2.1-Cre;H3.3K4M;Sun1-sfGFP mice were generated to harvest all Nkx2.1-lineage GFP+ nuclei via flow cytometry.  Single nuclei from embryonic and adult samples from each genotype were prepared using 10X Genomics Multiome pipeline. Samples: E13.5 MGE and hypothalamus as well as P60 cortex and hypothalamus of H3.3K4M WT and Hom. In addition, one replicate for male and female for each condition.

middle: J


title: Med14 phosphorylation shapes genomic response to GLP-1 agonist [ChIP-seq]

status: Public on Jun 17 2025

city: La Jolla

first: Sam

last: Van de Velde

state: CA

address: 10010 North Torrey Pines Road

department: PBL

institute: Salk Institute

summary: Under feeding conditions, increases in circulating glucose concentrations trigger the release of glucagon-like peptide (GLP-1) from intestinal L cells. GLP-1 promotes insulin secretion and pancreatic beta cell viability in part via triggering of the beta cell GLP-1 receptor and subsequent induction of the cAMP signaling pathway, leading to the protein kinase A (PKA) mediated phosphorylation of CREB and induction of CREB target genes. By contrast with the acute effects of this pathway on immediate early CREB target genes, which attenuate the cAMP-CREB response, sustained exposure of beta cells to GLP-1 agonist (exenatide-4; Ex-4) or adenyl cyclase activator (Forskolin; FSK) stimulates the expression of beta cell specific CREB target genes with delayed kinetics. In a proteomic screen for transcriptional co-regulators that mediate the long-term effects of GLP-1, we identified Med14, a backbone subunit of the Mediator complex. Exposure to either Ex-4 or FSK stimulates Med14 phosphorylation at Ser983, corresponding to a conserved PKA recognition site (RRXS) that is located within an intrinsically disordered region of Med14. Phosphorylation of Med14 is essential for maintenance of enhancers that drive induction of beta cell-specific and diabetes-linked genes.  Mutation of Med14 at Ser983 to alanine decreased beta cell numbers and repressed growth factor signaling in primary mouse islets. Our work reveals how phosphorylation of a general transcription factor in response to GLP-1 analogs triggers a broad genomic response with salutary effects on beta cell function.

overall_design: ChIP-seq of CREB, CRTC2, H3K27Ac, PolIIpS2 and FLAG-Med19 (tagged in the genome) in control and forskolin (FSK) treated INS-1 cells.


title: A developing HPA axis permits neonatal immune sensitivity to common allergens.

city: New York

first: Dr. Shruti

last: Naik

state: NY

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

summary: Atopic and allergic diseases predominantly manifest in early life, a period of profound growth and maturation. Yet, there is a dearth of information on the impact of developmental parameters on the neonatal immune reaction to allergens. Here we demonstrate that common allergens including house dust mite (HDM) elicited potent type 17 inflammatory responses from neonatal but not adult mice. HDM-induced inflammation was abolished in Rorgt-, gd T cell-, or epithelial IL-17RC- deficient animals and surprisingly did not require nociceptors or lymph node engagement. Instead, neonatal CD301b+ type 2 conventional dendritic cells (cDC2s) abundantly engulfed allergen and locally activated gd T cells in the skin. Despite uptaking equivalent antigen to neonates, adult cDC2s did not promiscuously activate in the skin. Mechanistically, this discrepancy was not attributable to cell-intrinsic differences arising from the distinct developmental origins of neonatal and adult cDC2s. Instead, neonatal cDC2 hyperactivation could be traced to a lower systemic glucocorticoid level, a consequence of an immature hypothalamic-pituitary-adrenal (HPA) axis in early life, and could be reversed by cortisol administration at the time of allergen challenge. These findings bring to fore the influence of organismal developmental factors in shaping immune sensitivity to allergens in early life.

overall_design: To unbiasedly investigate the inflammation phenotype in allergens inoculated neonate skin, we performed bulk RNA sequencing with full thickness skin biopsy isolated from PBS control or allergens challenged neonate and adult mice. To study the mechanism how Corticosterone regulate neonate dendrtiic cell allergic response, we sorted dendritic cells from corticosterone or DMSO and HDM or PBS treated neoante skin and applied to bulk RNA sequencing.

first: Yue

last: Xing

first: Jill

last: Wisnewsky

first: Kody

last: Mansfield

first: Aleksandr

last: Prystupa

first: Ikjot

last: Sidhu

first: Shruti


title: Regulation of Epstein–Barr Virus latency by histone variant H2A.Z [RNA-seq]

status: Public on Jul 02 2025

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Chromatin structure plays a central role in the regulation of Epstein-Barr Virus (EBV) latency. The histone variant H2A.Z.1 has been implicated in chromatin structures associated with initiation of transcription and DNA replication. Here, we examined the role of H2AZ.1 in the regulation of EBV chromatin and gene expression during EBV latent infection in two different EBV cancer cell models. We found that H2A.Z.1 is highly enriched with EBNA1 binding sites at oriP and Qp, and to a lesser extent with transcriptionally active CTCF binding sites on the EBV genomes in both Mutu I Burkitt lymphoma (BL) and SNU7-19 EBV-associated gastric carcinoma (EBVaGC) cell lines. RNA-interference depletion of H2A.Z.1 resulted in the reactivation of viral lytic genes (ZTA and EAD) and increases viral DNA copy numbers in both MutuI and SNU719 cells.  H2A.Z depletion also led to a decrease in EBNA1 binding to oriP and Qp, on the viral episome as well as on plasmids independently of other viral genes and genomes. H2A.Z.1 depletion also reduced peaks of H3K27ac and H4K20me3 at regulatory elements in the EBV genome.  In the cellular genome, H2A.Z.1 colocalized with only a subset of EBNA1 binding sites and H2A.Z.1 depletion altered transcription of genes associated with myc targets and mTORC1 signaling.  Taken together, these findings indicate that H2A.Z.1 plays an important regulatory role in the regulation of EBNA1 chromatin binding and function in the EBV episome and host chromosome, as well as the epigenetic programming of the latent episome.

overall_design: SNU-719 cells were treament with siControl and siH2A.Z, after 9 days the celles were recollected and processed to western blot, RNA-seq and ChIP-seq.

first: Leonardo

last: Castro-Muñoz

first: Davide

last: Maestri

first: Leena

last: Yoon

first: Bhanu

middle: C

last: Karisetty

first: Italo

last: Tempera

first: Paul

last: Lieberman


title: mRNA-Engineered CRISPR-Cas Epigenetic Editors Enable Durable and Efficient Gene Silencing in Vivo [WGBS]

status: Public on Jun 20 2025

city: Shenzhen

first: Jian-Kang

last: Zhu

state: Guangdong

address: 1088 Xueyuan Blvd, Nanshan

institute: Southern University of Science and Technology

type: Methylation profiling by high throughput sequencing

summary: Programmable epigenetic editors that achieve long-term gene expression modulation hold immense therapeutic potential. However, the large size of current CRISPR-based epigenome editors has limited their widespread application. This study describes the engineering of compact, mRNA-delivered epigenetic repressors, termed CRISPR OFF-EE, using SpyCas9, intein-based split-SpyCas9 or the smaller SF01 Cas variant, to achieve highly efficient and durable silencing of endogenous genes. We developed "superfolder" V2 mRNA constructs with optimized codon usage, UTRs, and nuclear localization signals, which enhanced mRNA stability, translational output, and LNP packaging. These CRISPR OFF-EE V2 editors demonstrated significantly improved and durable gene silencing across multiple targets in variable cell lines. Remarkably, a single intravenous administration of lipid nanoparticles (LNPs) encapsulating the optimized OFF-EE-V2 mRNA and selected sgRNAs targeting PCSK9 in mice led to an approximately 90% reduction in circulating PCSK9 protein and a 55% reduction in LDL-C levels, with effects persisting for at least 180 days. Whole-genome bisulfite sequencing confirmed the high specificity of these editors, with SF01-based editors exhibiting fewer off-target methylation events than SpCas9-based editors. The platform also demonstrated multiplexing capability and a favorable safety profile with liver-restricted activity. These findings establish a robust foundation for advancing in vivo therapeutics based on precise and durable epigenetic silencing using transiently delivered mRNA editors.

overall_design: Whole-genome bisulfite sequencing of mouse liver tissue and Hepa1-6 hepatocyte lines 180 days after a single LNP delivery of CRISPR OFF-EE mRNA/sgRNA targeting Pcsk9, compared with vehicle controls (n = 3/group).

first: Chao

last: Xu

first: Chen

last: Zeng

first: Mengge

last: Wang

first: Xiaofei

last: Wei

first: Minglei

last: Song

first: Xiaoyi

last: Liu

first: Weiping

first: Qitong

last: Chen

first: Xingkun

last: Ji

first: Pengyu

last: Luo

first: Hanlin

last: Gou

first: Yan

last: Sun

first: Liyong

last: Ma

first: Qianchuan

last: Shi

first: Xiaohua

last: Li

first: Yuxuan

last: lyu

first: Pengpeng


title: [RelA ChIP-seq]: Characterization of transcriptional and chromatin accessibility landscape of human bronchial epithelial cells treated with synergistic immunostimulatory ligands.

status: Public on Jun 15 2025

city: Houston

first: Scott

middle: E

last: Evans

state: TX

address: 6565 MD Anderson Blvd, Unit 1059

department: Pulmonary Medicine

institute: University of Texas MD Anderson Cancer Center

summary: Lower respiratory tract infections remain a leading cause of death worldwide. The increasing prevalence of antibiotic-resistant respiratory pathogens has been a key driver of efforts to develop host-directed therapies that protect patients against pneumonia. Our laboratory has previously reported discovery of an immunostimulatory therapeutic comprised of a synthetic diacetylated lipopeptide, Pam2CSK4 (Pam2), and a class C CpG oligodeoxynucleotide, ODN M362 (ODN). When delivered by inhalation, this dyad protects synergistically against pneumonias caused by Gram-positive and -negative bacteria, seasonal and pandemic viruses, and multiple fungi. Protection is achieved by manipulating the immune defense response from lung epithelial cells. Here, we dissect the lung epithelial transcriptional response to explain the observed synergistic signaling, using RNA-seq and dual transcription factor ChIP-seq. We find cooperation of RelA and cJun following Pam2+ODN treatment that synergistically confers broad inducible resistance against respiratory pathogens. Specifically, transcription factor binding site (TFBS) analysis revealed that cJun occupancy at promoter regions of Pam2+ODN-induced genes facilitated increased RelA occupancy during differential expression, demonstrating cJUN-assisted loading of RelA as a key mechanism of the synergistic signaling events. Increased or decreased RelA occupancy at promoter sites dictated gene up- or down-regulation, respectively, while increased or decreased cJun occupancy at promoter sites directed synergistic or antagonistic gene expression patterns. Together, RelA and cJun work at promoter regions to control directionality and magnitude of gene expression after Pam2+ODN stimulation, rapidly reprograming the lung epithelial transcriptome to combat respiratory infections.

overall_design: RelA TFBS changes of HBEC3-KT cells were profiled after 4-hour treatment with PBS (Control), Pam2 (4 uM), ODN (1 uM) or Pam2+ODN (4+1 uM) using ChIP-seq. Input file of the dual TF ChIP-seq is stored under the [RelA ChIP-seq] GEO Series.

first: Jezreel

last: Pantaleón García


title: [Bulk RNA-seq]: Characterization of transcriptional and chromatin accessibility landscape of human bronchial epithelial cells treated with synergistic immunostimulatory ligands.

overall_design: Gene expression changes of HBEC3-KT cells were profiled after 4-hour treatment with PBS (Control), Pam2 (4 uM), ODN (1 uM) or Pam2+ODN (4+1 uM) using RNA-seq.


title: Transcriptomic response of ethanol extract of Jakyakgamcho-tang (JGT-E) in C2C12 myotube

status: Public on Jun 25 2025

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

summary: Whole transcriptomic analysis in C2C12 myotube cells was conducted, comparing cells treated with a vehicle control to those treated with three different concentrations of JGT-E. All experiments were performed in triplicate.

overall_design: Total whole transcritome profiles treated with vehicle and JGT-E in C2C12 myotubes

first: Aeyung

last: Kim

first: Sang-Min

last: Park


title: Sugarcane streak mosaic virus P1 protein targets the BES1 transcription factor to subvert DAMP-induced immunity in plant

status: Public on Jun 23 2025

city: Yangzhou

first: Zhen

last: He

state: Jiangsu province

address: Wenhui East Road No 4

department: Plant pathology

institute: Yangzhou University

summary: Sugarcane streak mosaic virus (SCSMV) is the most important cause of sugarcane mosaic disease in the main production region. The SCSMV-encoded protein 1 (P1SCSMV) plays a vital role in disease development. However, the molecular mechanisms by which P1SCSMV participates in plant immunity remains unknown. Here, we found that the relative expression levels of P1SCSMV were negatively correlated with the xyloglucan endotransglucosylase/hydrolase gene (XTH) in a linear relationship. P1SCSMV directly interacts with the transcription factor, NbBES1, in vivo and in vitro. P1SCSMV-NbBES1 interaction interferes the binding of NbBES1 to the E-box element on the promoter region of NbXTH1 gene and inhibits the normal transcription of NbXTH1 gene. Furthermore, we found that down-regulation of the NbXTH1 directly resulted in enhanced infection of different plant pathogenic fungi and viruses, disrupted compositions of xyloglucan and xylan in the cell wall, and thinner middle lamellae in cell walls. We found that xyloglucan is a direct trigger of damage-associated molecular pattern- (DAMP) induced plant innate immunity. Moreover, the decrease in xyloglucan content in the cell wall caused by down-regulation of NbXTH1 leads to a reduction in DAMP-triggered immunity. Our study revealed the molecular mechanism of how a plant virus manipulates plant cell wall-mediated plant innate immunity, and identified NbXTH1, a wide-spectrum disease resistance protein for both plant pathogenic fungi and viruses. Our research also provides the basis for the application of the small molecule xyloglucan and the wide-spectrum disease resistance gene, XTH, in wide-spectrum resistance improvement in the future crop molecular breeding.

overall_design: Transcriptome sequencing analysis of healthy sugarcane plants and sugarcane plants infected with SCSMV.

first: Xiaolong

last: Deng

first: Xiaowei

last: Xu

first: Mengyan

last: Tang

first: Yanhong

last: Hua

first: Lang

last: Qin

first: Kun

last: Zhang


title: Elementary 3D organization of active and silenced E. coli genome (MicroC)

status: Public on Jun 24 2025

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

summary: Unraveling how genomes are spatially organized and how their 3D architecture drives cellular functions remains a major challenge in biology. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid. Despite progress in characterizing bacterial 3D genome architecture over recent decades, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods like Hi-C. In this study, we developed an enhanced Micro-C chromosome conformation capture, achieving 10 bp resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the E. coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, play key roles in repressing horizontally transferred genes (HTGs). Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, while removing both H-NS and StpA results in their complete disassembly, increased HTGs transcription, and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.

overall_design: Using the Micro-C technique, we generated contact maps of the E. coli genome at a resolution up to 10 bp. We analyzed wild-type E. coli cells, cells subjected to heat shock, cells treated with different antibiotics and drugs (rifampicin, bleomycin, novobiocin, ciprofloxacin, netropsin), as well as different knockout strains (deltaHNS, deltaStpA, deltaHNSdeltaStpA, deltaFis, deltaMukBEF). We performed gene expression profiling analysis using data obtained from Red-C and RNA-seq. We also performed Hi-C analysis of wild-type E.coli cells.

first: Alexey

last: Gavrilov


title: mRNA-Engineered CRISPR-Cas Epigenetic Editors Enable Durable and Efficient Gene Silencing in Vivo

status: Public on Jun 16 2025

first: Jian-Kang

last: Zhu

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

overall_design: Refer to individual Series


title: mRNA-Engineered CRISPR-Cas Epigenetic Editors Enable Durable and Efficient Gene Silencing in Vivo [RNA-seq]

overall_design: RNA-seq profiling of the same liver and cell-line samples to assess transcriptomic changes caused by long-term Pcsk9 silencing at the 180-day time-point (n = 3/group).

first: Chao

first: Chen

last: Zeng

first: Mengge

last: Wang

first: Xiaofei

last: Wei

first: Minglei

last: Song

first: Xiaoyi

last: Liu

first: Weiping

first: Qitong

last: Chen

first: Xingkun

last: Ji

first: Pengyu

last: Luo

first: Hanlin

last: Gou

first: Yan

last: Sun

first: Liyong

last: Ma

first: Qianchuan

last: Shi

first: Xiaohua

last: Li

first: Yuxuan


title: Cell loss disrupts mechanical homeostasis to drive retinal pigment epithelium ageing-like phenotype in vitro

city: Aachen

first: Jacopo

last: Di Russo

address: Pauwelsstraße 30

country: Germany

institute: Universitätsklinikum Aachen, AöR

summary: Tissue homeostasis emerges from mechanical feedback loops balanced by cell loss and proliferation, a balance that in postmitotic tissues must be maintained without compensatory proliferation. Yet how these tissues preserve mechanical homeostasis and how this challenges function in ageing remains unclear. To establish the relationship between cell density, mechanical homeostasis, and function, we induced age-mimicking cell loss in a postmitotic retinal pigment epithelium (RPE) in vitro. This model recapitulates key structural hallmarks of RPE ageing, including reduced cell height, shortened microvilli and cytoskeletal reorganisation. The density-reduced RPE establishes a new mechanical equilibrium characterised by tissue stiffening and increased junctional contractility. Functionally, these monolayers exhibit impaired phagocytosis of photoreceptor outer segments due to compromised apicolateral plasticity, which is mechanistically linked to the modulation of actin nucleators, Arp2/3 and formins. Altogether, our findings show that a cell loss-induced shift in mechanical homeostasis drives age-related RPE dysfunction, demonstrating that structural remodelling and mechanics alone can compromise tissue function in ageing.

overall_design: RNAseq profiling of 3 weeks mature hiPSCs-derived RPE (iCell-RPE, iRPE) cells 4 days after cell density reduction after on demand apoptosis via FKBP/casp8 activation (AgeD for Apoptosis-genereated Density) and time-matched control hiPSCs-derived RPE cells (Ctrl)

first: Teodora

last: Piskova

first: Aleksandra

middle: N

last: Kozyrina

first: Giedrė

last: Astrauskaitė

first: Mohamed

last: Elsafi Mabrouk

first: Sebastian

last: Schepl

first: Stacy Lok Sze

last: Yam

first: Ragul

last: Ravithas

first: Wolfgang

last: Wagner

first: Massimo

last: Vassalli


title: Elementary 3D organization of active and silenced E. coli genome

first: Ilya

last: Shamovsky


title: Med14 phosphorylation shapes genomic response to GLP-1 agonist [ATAC-seq]

first: Sam

last: Van de Velde

overall_design: ATAC-seq of WT and Med14S983A mutant INS-1 cells treated with Exendin-4 (10nM) or forskolin (FSK; 10 uM) for 1 hour


title: Med14 phosphorylation shapes genomic response to GLP-1 agonist [snRNA-seq]

overall_design: Single nucleus RNA-seq profiling of cultured mouse primary islet tissue (WT and Med14_S983A mutant). Control and 16h exposure to Glp-1 analog Exendin-4 (16h)

first: April

last: Williams

first: Garrett

last: Evensen


title: Combined Flt3L and CD40 agonism restores dendritic cell driven T cell immunity in mouse models and patients with pancreatic cancer [human]

city: St. Louis

first: David

middle: G

last: DeNardo

state: Missouri

address: 425 S Euclid Ave

institute: Washington University

summary: T cell directed immunotherapies have largely failed to demonstrate clinical efficacy in patients with pancreatic ductal adenocarcinoma (PDAC). This broad resistance may result from poor tumor antigenicity and an immunosuppressive tumor microenvironment (TME). We hypothesize that tumor immunity in pancreatic cancer patients is further limited by systemic and tumor-intrinsic suppression of conventional dendritic cells (cDC). Here, we find that low tissue expression of Flt3L may in part underly cDC deficits in PDAC tissues. We show in both autochthonous murine models and samples from a clinical trial, that treatment with systemic Flt3L and CD40 agonists can restore cDC number and function in the PDAC TME. Alone, CD40 agonism failed to fully engage cDC activity; yet when combined with Flt3L, the dual therapy triggered a cDC driven type-I immune response characterized by CD8+ T cell infiltration, interleukin-12 production, and a reciprocal interferon (IFN) response. In mice, type-1 cDCs (cDC1) were directly responsible for the influx of CD8+ T cells, which in-turn supported cDC1 survival via IFN-γ, resulting in a synergistic feed-forward loop. Lastly, while we find that combination Flt3L and CD40 agonism improve tumor immunity, they also increase the number and effector phenotype of FOXP3+ regulatory T cells (Tregs) in a process dependent on type-2 cDCs. Tregs were found to limit therapeutic efficacy by inhibiting mature cDC subsets, and concurrent Treg depletion led to improved tumor control. These data support the continued investigation of combined Flt3L and CD40. agonism, which represent a promising strategy to engage anti-tumor immunity in advanced human malignancies.

overall_design: Consenting patients diagnosed with resectable PDAC at Washington University and Siteman Cancer Center underwent neoadjuvant treatment with CDX-1140 (anti-CD40 IgGs) +/- CDX-301 (Flt3L). Both drugs were provided by Celldex Therapeutics. Patients received either an i.v. injection of CDX1140 (1.5mg/kg) 7-12 days prior to surgery, or 5-subcutaneous doses of CDX-301 (75 mcg/kg/day) followed by CDX1140 on day 8 +/- 1 day, with surgery 7-12 days thereafter.

first: Graham

middle: D

last: Hogg


title: Spatial transcriptomics unveils novel potential disease mechanisms associated with the microenvironment in Multiple Myeloma

status: Public on Jun 09 2025

city: Thuwal

first: Laura

last: Sudupe

address: King Abdullah University of Science and Technology (KAUST)

country: Saudi Arabia

institute: KAUST

summary: Understanding the spatial organization of the bone marrow (BM) microenvironment at single cell resolution and the niche specific transcriptional regulatory programs remains a challenge. Using formalin-fixed paraffin-embedded (FFPE) samples from our recently described MIcγ1 multiple myeloma (MM) mouse model (Larrayoz et al, Nat Med. 2023), we performed spatial transcriptional profiling of healthy and multiple myeloma BM using the Visium Spatial Gene Expression analysis (10x Genomics). A custom data-analysis framework that combines spatial with single-cell transcriptomic profiles allowed us to identify cell type composition and establish specific cell relations within the bone marrow. As a result, we defined the spatial distribution of transcriptionally heterogenous MM plasma cell (MM-PC) groups. Furthermore, we spatially defined transcriptional programs involved in the pathogenesis of MM within the BM microenvironment that were associated with MM-PC density gradient, such as the spatial location of T cells with effector and exhausted phenotypes. Application of spatial transcriptomics to FFPE human BM biopsies with varying degrees of PC infiltration validated findings from our murine model. The application of spatial transcriptomics to fully mineralized tissues provides a comprehensive spatial overview of the BM microenvironment allowing the identification of deregulated mechanism involved in the pathogenesis of diseases such as MM.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: This study includes spatial transcriptomics analysis of bone marrow samples from healthy mice (YFPcγ1 model) and Multiple Myeloma (MM) mice (MIcγ1 model), as well as human bone marrow biopsies from healthy individuals and MM patients. The analysis aims to compare the spatial and transcriptional profiles of healthy and diseased bone marrow, focusing on cell type composition and specific transcriptional programs associated with MM pathogenesis. No external treatments were applied, and samples were processed using 10x Genomics Visium Spatial Gene Expression technology.

first: Emma

last: Muiños-Lopez

first: Ana

middle: R

last: Lopez-Perez

first: Amaia

last: Vilas-Zornoza

first: Sarai

last: Sarvide

first: Purificacion

last: Ripalda-Cemborain

first: Paula

last: Aguirre-Ruiz

first: Patxi

last: San Martin-Uriz

first: Marta

last: Larrayoz

last: Alvarez-Gigl

last: Abengozar

first: Itziar

last: Cenzano

first: Miguel

last: Cócera

first: Javier

last: Ruiz

first: Ignacio

middle: S

last: González

first: Azari

last: Bantan

last: Kurowska

first: Jin

last: Ye

first: Vincenzo

last: Lagani

first: Bruno

last: Paiva

first: Phillip

last: Newton

first: Jesper

last: Tegner

first: Borja

last: Saez

first: Jose

middle: A

last: Martinez-Climent

first: Isabel

last: Calvo

last: Gomez-Cabrero

first: Felipe

last: Prosper


title: Med14 phosphorylation shapes genomic response to GLP-1 agonist [RNA-seq]

first: Sam

last: Van de Velde

overall_design: RNA-seq profiling of INS-1 cells (WT and Med14_S983A mutant) after exposure to Glp-1 analog Exendin-4 or forskolin. Control (no treatment), acute (1h) and sustained (16h) exposure. ERCC spike-in mix was added to each sample for normalization. All samples are in duplicates.

first: Jingting

last: Yu


title: Immunometabolic determinants of long-term response in leukemia patients receiving CD19 CAR T cell therapy

status: Public on Jun 05 2025

city: Duarte

first: WenYong

last: Chen

address: 1500 E. Duarte Road

department: Cancer Biology and Molecular Medicine

institute: City of Hope

summary: Although most patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL) receiving CD19-targeted chimeric antigen receptor (CAR) T cell therapy achieve remission, loss of CAR T cell functionality and subsequent relapse remains an unmet therapeutic need. We applied an integrative approach to study the immunometabolism of pre- and post-infusion CD19-CAR T cells of patients with relapsed/refractory B-ALL. Pre-infusion CAR T cells of long-term responders (LTR) had increased oxidative phosphorylation, fatty acid oxidation, and pentose phosphate pathway activities, higher mitochondrial mass, tighter cristae, and lower mTOR expression compared to products of short-term responders. Post-infusion CAR T cells in bone marrow (BM) of LTR had high immunometabolic plasticity and mTOR-pS6 expression supported by the BM microenvironment. Transient inhibition of mTOR during manufacture induced metabolic reprogramming and enhanced anti-tumor activity of CAR T cells. Our findings provide insight into immunometabolic determinants of long-term response and suggest a therapeutic strategy to improve long-term remission.

overall_design: Generation of CAR T cells with rapamycin. Enriched Tn/mem cells from leukapheresis products were stimulated with GMP Human T-expander CD3/CD28 Dynabeads™ (Dynal Biotech Cat#11141D) at a ratio of 1:3 (T cell:bead) overnight. Activated T cells were subsequently transduced with CD19R(EQ):CD28:ζ/EGFRt clinical construct at MOI=1 in RPMI 1640 containing 10% FBS and 5μg/ml protamine sulfate (Fresenius Kabi, 22905), 50U/mL rhIL-2 (Novartis Pharmaceuticals, NDC0078-0495-61), and 0.5 ng/mL rhIL-15 (CellGenix, 1013-050). Beginning 4 days after bead stimulation, CAR T cells were treated with rapamycin (50 nmol/L) (LC Laboratories, R-5000) or vehicle (DMSO) and refreshed with media containing rapamycin or vehicle every other day. Six days after stimulation, CD3/CD28 Dynabeads™ beads were removed using a DynaMag™-5 Magnet (Invitrogen, 12303D), and cells were maintained at a concentration of 1x106 cells/mL in RPMI 1640/10% FBS, 25U/mL rhIL-2, and 0.25 ng/mL rhIL-15 throughout T cell expansion.

first: Lior

last: Goldberg

first: Min-Hsuan

first: Xiwei

last: Wu

first: Xiuli

last: Wang


title: [cJun ChIP-seq]: Characterization of transcriptional and chromatin accessibility landscape of human bronchial epithelial cells treated with synergistic immunostimulatory ligands.

first: Scott

last: Evans

overall_design: cJun TFBS changes of HBEC3-KT cells were profiled after 4-hour treatment with PBS (Control), Pam2 (4 uM), ODN (1 uM) or Pam2+ODN (4+1 uM) using ChIP-seq. Input file of the dual TF ChIP-seq is stored under the [RelA ChIP-seq] GEO Series.

first: Jezreel

last: Pantaleón García


title: Primary human intestinal organoids recapitulate enteric infection of monkeypox virus and enable scalable drug discovery

city: Chengdu

first: Pengfei

last: Li

address: Chengdu, Sichuan

institute: Sichuan University

summary: Monkeypox virus (MPXV) infection-associated intestinal manifestations including diarrhea and proctitis have been frequently reported during mpox outbreaks. The clade IIb MPXV strain has caused the 2022-2023 global outbreak, whereas the Ia and Ib strains are causing the concurrent outbreaks in Africa. Here, we found clinical evidence that MPXV can directly infect human intestine to induce lesions. Intriguingly, primary organoids cultured from human ileum and rectum support productive infections of MPXV clade IIb, Ia and Ib strains. Upon differentiation, we found that enterocytes and goblet cells but not enteroendocrine cells are capable of supporting viral replication. Given that primary intestinal organoids can be rapidly expanded in large scale, we were able to screen a broad-spectrum antiviral drug library. We identified 12 leading candidates of safe-in-human agents including clinically used drugs such as clofarabine. We extensively validated the anti-MPXV activity of clofarabine in human intestinal and skin organoids, and consistently demonstrated the potent antiviral activity against clade Ia, Ib and IIb strains. These findings are important for better understanding the clinical manifestations of mpox. Primary intestinal organoids-based infection models and the established antiviral drug discovery pipeline bear major implications in responding to the current mpox global health emergency, and sustaining epidemic poxvirus preparedness.

overall_design: RNA-seq profiling of healthy control of human intestinal organoids, Monkeypox virus infected intestinal organoids harvested at 1, 24, 48 and 96 hours respectively, and intestinal organoids infected with Monkeypox virus treated with 1uM clofarabine for 96 hours.


title: A Single-Cell Atlas of DNA Methylation in Autism Spectrum Disorder Reveals Distinct Regulatory and Aging Signatures

city: Los Angeles

first: Nasser

last: Elhajjaoui

address: 695 Charles E Young Dr S

department: Human Genetics

institute: University of California, Los Angeles

summary: Autism spectrum disorder (ASD) is a prevalent and heterogeneous condition that profoundly impacts health and behavior. Analysis of gene expression in the cortex broadly implicates decreased synaptic functioning in excitatory neurons and increased reactivity in glia in ASD; however, whether these phenotypes are reflected in epigenetic signatures is unknown. Here, we report on the first single-cell analysis of DNA methylation (DNAm) in ASD. We profile DNAm from over 60,000 nuclei derived from 49 donors and interpret our findings with gene expression from the same nuclei using snmCT-seq.

overall_design:
Single-nucleus joint profiling of postmortem cortical brain samples isolated from the prefrontal cortex (PFC; Brodmann area 9, BA9) of 26 autistic male donors and 23 non-autistic male  controls. 1 low RIN donor (5302) was excluded from RNA analysis.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
The raw data (controlled-access, fastq files) is going to be submitted and available through NeMO.
***************************************************************

first: Katherine

middle: W

last: Eyring

first: Cuining

last: Liu

first: Kevin

last: Abuhanna

first: Yi

last: Zhang

first: Zachary

last: von Behren

first: Eleazar

last: Eskin

first: Daniel

last: Geschwind

first: Chongyuan

last: Luo

first: Min

last: Tsai


title: A developing HPA axis permits neonatal immune sensitivity to common allergens

first: Dr. Shruti

last: Naik

overall_design: To unbiasedly investigate the inflammation phenotype in allergens inoculated neonate skin, we performed bulk RNA sequencing with full thickness skin biopsy isolated from PBS control or allergens challenged neonate and adult mice. To study the mechanism how Corticosterone regulate neonate dendrtiic cell allergic response, we sorted dendritic cells from corticosterone or DMSO and HDM or PBS treated neoante skin and applied to bulk RNA sequencing.

first: Yue

last: Xing

first: Jill

last: Wisnewsky

first: Kody

last: Mansfield

first: Ikjot

last: Sidhu

first: Aleksandr

last: Prystupa

first: Shruti


title: Single-Cell and Spatial Multi-Omics Reveal Mechanical Stress Driving Heterogeneous Xylem Development in Populus [LCM Spatial RNA-seq]

city: Taipei

first: Ying-Chung Jimmy

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Life Science

country: Taiwan

institute: National Taiwan University

summary: Xylem, the predominant tissue for structural support, forms tension wood with G-layer-rich fibers under mechanical stress. Despite being recognized over a century ago, three key biological questions remained unclear: (1) Are fibers in normal and tension wood distinct cells due to morphological differences? (2) Do tension wood fibers arise from different lineages? (3) What are the key genes regulating tension wood formation? We conducted single-cell RNA-seq on normal, tension and opposite xylem. Fibers in normal and tension wood belong to the same cell type and lineage. Differential developmental speed and cell-type ratio in tension and opposite xylem were further validated by spatial transcriptomics and metabolomics. Phosphoproteomics uncovered mechanical sensing mechanisms conserved between stems and roots across angiosperms. We identified a group of genes involved in the cell fate transition in tension wood. The knowledge on the heterogeneity of cell development offers insights for optimizing biomass production and bioenergy yield.

overall_design: Illumina RNA sequencing of normal and tension stem differentiating xylem (SDX) in P. trichocarpa

first: Jo-Wei Allison

last: Hsieh

first: Pin-Chien

last: Liou

first: Chia-Chang

first: Xiufang

last: Dai

first: Chen-Wei

last: Hu

first: I-Fan

last: Wang

first: Jr-Fong

last: Dang

first: Yi-Chi

last: Ho

first: Kai-Wen

last: Cheng

first: Wenjing

last: Xu

first: Shang-Che

last: Kuo

first: Chung-Ting

last: Kao

first: Dian-Xuan

last: Yang

first: Ray

first: Ke

last: Xiao

first: Jeng-Shane

first: Cheng-Chih

last: Hsu

first: Chuan-Chih

first: Te-Lun

last: Mai

first: Yuxiang

first: Mei-Chun

last: Tseng

first: Wei

last: Li

first: Ying-Lan

last: Chen


title: Uncovering the novel signaling components in warm temperature mediated regulation of transcriptome in Arabidopsis thaliana

status: Public on Jun 03 2025

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: Transcriptome analysis suggests that lrb123 and pif3 mutants have similar gene expression profiles with pif4 mutants, suggesting that LRBs and PIF3 have overlapping functions with PIF4. Further analysis revealed that most of the genes induced by PIF4 in a temperature-dependent manner are strongly downregulated. These genes belong to the Auxin/BR growth hormone pathways, wherein genes involved in auxin/BR biosynthesis and signalling are severely perturbed in response to 27°C compared to 22°C. These results indicate that LRBs and PIF3-mediated induction of PIF4 target genes in response to warm temperature is likely through PIF4. Moreover, our data also demonstrate that both LRBs and PIF3 inhibit the expression of light-responsive genes in response to warmth, further highlighting the role of LRBs and PIF3 in promoting thermomorphogenesis, is by directly promoting growth-responsive genes, and second by inhibiting light signalling genes. Together, we conclude that LRBs and PIF3 are novel components of the thermosensory pathway and are essential to promote themomorhogensis, likely by enhancing the PIF4 activity and down gene expression.

overall_design: To understand the mechanism of regulation of thermomorphogenesis by LRB E3 ubiquitin ligases and PIF3 transcription factor, whole transcriptome (RNA-seq) analysis of lrb123 and pif3 were performed in comparison to the wild-type (Col-0) under normal and warm temperature conditions. Also, we compared their gene expression profiles with the pif4-101 mutant to know the extent of overlapping function in regulating temperature-mediated transcriptome.

first: Gangappa

last: Sreeramaiah

first: Singhal

last: Chirag

first: Das

last: Sreya

first: Rajkumar

last: Mohan

first: Jain

last: Mukesh


title: ACOD1 regulates microglial arginine metabolism and inflammatory responses

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

summary: Itaconate is produced by inflammatory macrophages and negatively feedbacks on inflammation. It is synthesized by aconitate decarboxylase 1 (ACOD1) from cis-aconitate, a metabolite of the tricarboxylic acid cycle. Here, we studied the role of ACOD1 in the inflammatory response of microglia, the resident macrophage-like cells of the brain. Similarly to macrophages, ACOD1 deficient microglia displayed a stronger inflammatory response to lipopolysaccharide (LPS) compared to their wild type counterparts. ACOD1 deficiency reprogramed arginine metabolism by enhancing argininosuccinate synthesis in the expense of polyamine synthesis in an ACLY-dependent manner. These findings provide new insights in the immunometabolic role of ACOD1 in inflammatory microglia.

overall_design:
LPS versus PBS (in-vitro): Primary murine microglia were treated with 100 ng/ml LPS or carrier (PBS) for 4 h. Transcriptional changes were analyzed by bulk RNAseq.
LPS versus PBS (in-vivo): C57BL/6J mice were treated interaperitoneally with 3 mg/kg LPS or PBS and 4 h later whole brain  microglia (CD45intermCD11b+Ly6G-) were FACS sorted and analyzed by bulk RNAseq.
Acod1-/- versus Wt: Acod1-/- and Wt mice were treated interaperitoneally with 3 mg/kg LPS or PBS and 16 h later whole brain  microglia (CD45intermCD11b+Ly6G-) were FACS sorted and analyzed by bulk RNAseq.

first: V

middle: I

first: A

last: Sinha


title: [scRNA-seq]: Inhaled PRR Agonists Reprogram Lung Epithelial Cells to Prevent Type 2 Allergic Inflammation

first: Scott

last: Evans

summary: The increasing prevalence of chronic allergic lung diseases demands development of new preventative strategies. We previously demonstrated that therapeutic inhalation of the synergistic agents ODN M362, a TLR9 ligand, and Pam2CSK4, a TLR2/6 ligand (collectively, “Pam2ODN”) protects mice against both infectious challenges and allergic lung disease models, including allergic inflammation caused by mouse house dust mite (HDM) extract. By preventing sensitization, Pam2ODN reduces HDM-induced eosinophilic and lymphocytic inflammation. How Pam2ODN affects the interactions of lung epithelial cells, dendritic cells, and T cells to prevent lung eosinophilic inflammation has not been established. In the present study, we show that a single inhaled dose of Pam2ODN prior to HDM sensitization reduces Th2 polarization of airway CD4+ T cells without affecting the immune responses of Th1 or Treg cells. Furthermore, Pam2ODN pre-treatment inhibits recruitment of lung monocyte-derived dendritic cells (moDCs) and conventional type 2 migratory dendritic cells (DC2s) while preventing HDM-induced decrease of conventional type 1 migratory dendritic cells (DC1s). Bulk RNA-seq of whole lung homogenates reveals that Pam2ODN pretreatment restricts the expression of HDM sensitization-induced proinflammatory transcripts. This tolerogenic effect is also reflected at the single-cell level in lung epithelial cells where many proinflammatory transcripts, pathways and chromatin accessibility are inhibited. These results indicate that Pam2ODN reprograms lung epithelial cells to attenuate allergen-induced lung proallergic DC cytokines while maintaining the population of protective DC1s, which prevents lung injury and Th2 polarization. Collectively, our findings suggest that the development of Th2-induced chronic allergic lung diseases may be mitigated by lung epithelium-targeted immunomodulatory strategies.

overall_design: A single aerosol treatment of PBS or Pam2ODN was administered 7-days before intratracheal sensitization of naïve Balb/c mice with 100 µg HDM. Whole lungs were harvested 12 hours after the HDM administration. Lungs were enzymatically digested, and single cell suspensions prepared for flow cytometry sorting of lung immune cells (CD45+) and epithelial cell populations, followed by subsequent single-cell RNA sequencing analysis.

first: Mbaya

last: Ntita

first: Richa

last: Nayak

first: Celine Shuet Lin

last: Kong


title: [RNA-seq]: Inhaled PRR Agonists Reprogram Lung Epithelial Cells to Prevent Type 2 Allergic Inflammation

summary: The increasing prevalence of chronic allergic lung diseases demands development of new preventative strategies. We previously demonstrated that therapeutic inhalation of the synergistic agents ODN M362, a TLR9 ligand, and Pam2CSK4, a TLR2/6 ligand (collectively, “Pam2ODN”) protects mice against both infectious challenges and allergic lung disease models, including allergic inflammation caused by mouse house dust mite (HDM) extract. By preventing sensitization, Pam2ODN reduces HDM-induced eosinophilic and lymphocytic inflammation. How Pam2ODN affects the interactions of lung epithelial cells, dendritic cells, and T cells to prevent lung eosinophilic inflammation has not been established. In the present study, we show that a single inhaled dose of Pam2ODN prior to HDM sensitization reduces Th2 polarization of airway CD4+ T cells without affecting the immune responses of Th1 or Treg cells. Furthermore, Pam2ODN pre-treatment inhibits recruitment of lung monocyte-derived dendritic cells (moDCs) and conventional type 2 migratory dendritic cells (DC2s) while preventing HDM-induced decrease of conventional type 1 migratory dendritic cells (DC1s). Bulk RNA-seq of whole lung homogenates reveals that Pam2ODN pretreatment restricts the expression of HDM sensitization-induced proinflammatory transcripts. This tolerogenic effect is also reflected at the single-cell level in lung epithelial cells where many proinflammatory transcripts, pathways and chromatin accessibility are inhibited. These results indicate that Pam2ODN reprograms lung epithelial cells to attenuate allergen-induced lung proallergic DC cytokines while maintaining the population of protective cDC1s, which prevents lung injury and Th2 polarization. Collectively, our findings suggest that the development of Th2-induced chronic allergic lung diseases may be mitigated by lung epithelium-targeted immunomodulatory strategies.

overall_design: A single aerosol treatment of PBS or Pam2ODN was administered 7-days before intratracheal sensitization of naïve Balb/c mice with 100 µg HDM. After euthanasia, the thoracic cavity was dissected, lungs were removed and RNA was isolated from whole lungs using Qiagen RNeasy mini kits (Qiagen, CA, USA) according to the manufacturers' instructions, then submitted for RNA sequencing.


title: Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates

status: Public on May 31 2025

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

country: United Kingdom

institute: The Babraham Institute

overall_design: Refer to individual Series


title: Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations

status: Public on Jun 10 2025

city: Charlottesville

first: Luke

last: Dillard

state: VA

institute: UVA

summary: Genome-wide association studies (GWASs) have identified many sources of genetic variation associated with bone mineral density (BMD), a clinical predictor of fracture risk and osteoporosis. Aside from the identification of causal genes, other difficult challenges to informing GWAS include characterizing the roles of predicted causal genes in disease and providing additional functional context, such as the cell type predictions or biological pathways in which causal genes operate. Leveraging single-cell transcriptomics (scRNA-seq) can assist in informing BMD GWAS by linking disease-associated variants to genes and providing a cell type context for which these causal genes drive disease. Here, we use large-scale scRNA-seq data from bone marrow–derived stromal cells cultured under osteogenic conditions (BMSC-OBs) from Diversity Outbred (DO) mice to generate cell type-specific networks and contextualize BMD GWAS-implicated genes. Using trajectories inferred from the scRNA-seq data, we identify networks enriched with genes that exhibit the most dynamic changes in expression across trajectories. We discover 21 network driver genes, which are likely to be causal for human BMD GWAS associations that colocalize with expression/splicing quantitative trait loci (eQTL/sQTL). These driver genes, including Fgfrl1 and Tpx2, along with their associated networks, are predicted to be novel regulators of BMD via their roles in the differentiation of mesenchymal lineage cells. In this work, we showcase the use of single-cell transcriptomics from mouse bone-relevant cells to inform human BMD GWAS and prioritize genetic targets with potential causal roles in the development of osteoporosis.

overall_design: scRNA-seq on bone marrow-derived stromal cells cultured under osteogenic condition (BMSC-OBs) from Diversity Outbred (DO) mice. Each sample pool (e.g., sample pool 1) contains 4 to 5 mice, which are listed in the 'mouse_id' column. Each sample pool (e.g., sample pool 1) was split across two runs (i.e., HGYVNCCX2 or HHFFMCCX2).

first: Gina

middle: M

last: Calabrese

first: Larry

last: Mesner

first: Charles

last: Farber


title: Transcriptomic profiling of lesional and healthy skin in pemphigus patients reveals IL-17–driven immune response

status: Public on Jun 11 2025

city: Berlin

first: Alberto

last: Mesas-Fernández

state: Berlin

address: Luisenstraße 2

department: Dermatology

institute: Charité - Universitätsmedizin Berlin

summary: Pemphigus is a rare autoimmune blistering skin disease characterized by autoantibodies against desmoglein 1 and/or 3. To better understand the immunopathology of pemphigus, we performed RNA sequencing of lesional skin biopsies from pemphigus patients (n=6) and compared them to skin biopsies from healthy controls (n=6). Our data reveal an IL-17/IL-21–dominated transcriptional signature, with upregulation of inflammatory cytokines, chemokines, and tissue remodeling genes. These findings support the hypothesis that pemphigus pathogenesis is driven by a TH17/TFH17-type immune response and offer insights into potential therapeutic targets.

overall_design: Skin punch biopsies were obtained from six patients with clinically active pemphigus (lesional skin) and six age- and sex-matched healthy individuals (control skin). Total RNA was isolated and quality-controlled using Nanodrop, Qubit, and Bioanalyzer. RNA-seq libraries were prepared and sequenced using the Illumina NextSeq 500 platform (single-end, 75 bp). Raw reads were aligned to the GRCh37 reference genome using STAR, and gene-level expression quantification was performed with Subread.

first: Julia

last: Holstein

first: Farzan

last: Solimani

first: Kamran

last: Ghoreschi


title: [scATAC-seq]: Inhaled PRR Agonists Reprogram Lung Epithelial Cells to Prevent Type 2 Allergic Inflammation

overall_design: A single aerosol treatment of PBS or Pam2ODN was administered 7-days before intratracheal sensitization of naïve Balb/c mice with 100 µg HDM. Whole lungs were harvested 12 hours after the HDM administration. Lungs were enzymatically digested, and single cell suspensions prepared for flow cytometry sorting of lung immune cells (CD45+) and epithelial cell populations, followed by subsequent single-cell ATAC sequencing analysis.

first: Dalia

last: Hassan


title: Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs

first: juan

middle: li

last: chen

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

summary: Cells are the functional intermediaries linking genotypes to phenotypes. However, the systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation of complex phenotypes are still understudied in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell atlas of adult pigs that encompasses 229,268 high-quality nuclei from 19 tissues. We further deconvolute bulk RNA-seq samples from 17 matching tissues in the PigGTEx project, dissecting thousands of genetic variants with cell-type interaction effects on gene expression (ieQTL) . Additionally, We colocalize ieQTL with variants associated with 268 complex traits.

overall_design: Expression profiling by high throughput sequencing

first: Guoqiang

last: Yi


title: A cost-effective and flexible workflow for high-resolution spatial transcriptomics in fixed tissue

status: Public on May 26 2025

city: qingdao

first: Xue

last: Dong

address: 238 songling road

institute: Ocean University of China

summary: The spatial heterogeneity of gene expression has driven the development of diverse spatial transcriptomics technologies. Here, we introduce photocleavage and ligation sequencing (PCL-seq), a spatial indexing method based on a light-controlled DNA labeling strategy applied to tissue sections. PCL-seq employs photocleavable oligonucleotides and sequence adapters to construct transcriptional profiles of specific regions of interest (ROIs), designated via microscopically controlled photo-illumination. In frozen mouse embryos, PCL-seq generates spatially aligned gene expression matrices and achieves high-quality data outputs, detecting approximately 170,000 unique molecular identifiers (UMIs) and 8,600 genes (irradiation diameter=100 µm). Moreover, PCL-seq is compatible with formalin-fixed and paraffin-embedded (FFPE) tissues, successfully identifying thousands of differentially enriched transcripts in the digits and vertebrae of FFPE mouse embryo sections. Additionally, PCL-seq achieves subcellular resolution, as demonstrated by differential expression profiling between nuclear and cytoplasmic compartments. These features establish PCL-seq as an accessible and versatile workflow for spatial transcriptomic analyses in both frozen and FFPE tissues at subcellular resolution.

overall_design: We designed a series of experiments to evaluate the performance of our newly developed sequencing method, PCL-seq. This method utilizes a photocleavable (PC) linker as a photosensitive compound, enabling precise photolytic cleavage and ligation of target regions within tissue sections. To verify the ability of PCL-seq to specifically amplify cDNA molecules from illuminated regions, we performed an experiment using co-cultured cells. In this setup, one cell type served as a non-illuminated background, while a small portion of the other cell type was selectively illuminated at varying ratios. The specificity of PCL-seq was assessed by comparing the differential genic reads between the two cell types through sequencing.Furthermore, we evaluated the data quality of PCL-seq on both cryo-preserved and FFPE (formalin-fixed paraffin-embedded) tissue sections, examining its ability to maintain spatial localization of gene expression. To test whether PCL-seq can achieve subcellular resolution, we irradiated the nuclear and cytoplasmic regions of HeLa cells separately and analyzed the resulting data. These experiments allowed us to systematically characterize the precision, spatial resolution, and versatility of PCL-seq under diverse experimental conditions.

first: Mengzhu

last: Hu

first: Xiaonan

last: Cui

first: Wenjian

last: Zhou


title: An alternative transcription factor isoform controls AML chemoresistance [LongRead_mRNA]

status: Public on May 29 2025

city: Farmington

first: Harshpreet

last: Chandok

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

summary: Aberrant splicing is a hallmark of many cancers, including Acute Myeloid Leukemia (AML), but its role in post-treatment relapse remains poorly understood. Here, we analyzed the alternative splicing landscape of 19 AML patients during chemotherapy treatment. We found an upregulation of the long isoform of the transcription factor RUNX1 (also known as RUNX1C) in relapsed cohorts, which conferred chemotherapy resistance. Notably, these patients showed elevanted intragenic DNA methylation at the RUNX1 proximal promoter, thereby activating RUNX1C transcript through its alternative distal promoter. Mechanistically the N-terminus region of RUNX1C is required to promote chemoresistance by regulating a distinct RUNX1 transciptional program. Among these target genes, B-cell translocation gene 2 (BTG2) mediates a quiescent-like phenotype by deadenylating ribosomal RNAs to reduce global protein synthesis. Lastly, we harnessed orthogonal RNA-targeting strategies to target RUNX1C isoform, which led to augmented chemotherapy efficacy. Collectively, our finidngs delineate a transcriptional circuity orchestrated by a transcription factor isoform that underpins chemotherapy responsiveness and a potential therapeutic strategy to mitigate disease recurrence.

overall_design: To determine the role of BTG2 on mRNA stability, MOLM13 cells were transcuded with a cDNA to overexpress BTG2 or with an empty vector control, and mRNA was isolated for long-read sequencing.

first: Cuijuan

last: Han

first: Eric

last: Wang


title: GCN5-mediated histone H3 Acetylation Orchestrates Gene Expression and Plant Development via H2A.Z [RNA-seq]

status: Public on May 24 2025

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

summary: H2A.Z is a conserved histone variant that plays essential roles in various DNA-templated processes across eukaryotes. H2A.Z and histone post-translational modifications (PTMs) exert a bidirectional and context-dependent influence on each other. Nevertheless, the functions of the interplay between PTMs and H2A.Z level and the underlying molecular mechanism remain poorly understood. Here, we found that the loss of the histone acetyltransferase GCN5 impedes the overexpression of BSU1 typically observed in nrp1-1 nrp2-2, accompanied by changes in H3 acetylation and H2A.Z levels. Interestingly, the increment in H2A.Z levels typical of nrp1-1 nrp2-2 mutant alleviates the morphological and molecular phenotypes of gcn5. Conversely, H2A.Z-depleted mutants aggravate the phenotype of gcn5. In the gcn5 mutant, the H2A.Z level is globally reduced in the gene bodies, and this reduction is dependent on the histone chaperones NRP1 and NRP2. Additionally, the reduction of H3 acetylation levels caused by GCN5 depletion can be recovered in the nrp1-1 nrp2-2 mutant background, likely due to the over-accumulation of H2A.Z. In conclusion, our genetic, molecular, and genomic findings demonstrate that GCN5-mediated H3 acetylation promotes H2A.Z deposition, H2A.Z over-accumulation recovers the loss of GCN5-mediated H3 acetylation, and this interplay is crucial for regulating gene expression and plant development.

overall_design: RNA-Seq profiling of wildtype Columbia-0, along with gcn5-7, nrp1-1 nrp2-2 and gcn5-7 nrp1-1 nrp2-2 mutants at 12 days after germination (12DAG) seedlings.

first: Israel

last: Ausin

first: Yafei

first: Yingpei

last: Su

first: Qin

first: Weiye

last: Qian

first: Min

last: Liu

first: Chao

last: Xu

first: Junjie


title: The dynamic change of microRNA expression profile in endometrium and peripheral blood during the peri-implantation window

status: Public on May 22 2025

city: Zhubei City, Hsinchu County

first: An

last: Hsu

address: 7F-6, No. 66, Shengyi 5th Road

institute: INTI Labs

type: Non-coding RNA profiling by high throughput sequencing

summary: Previous studies have shown that microRNAs (miRNAs) play a crucial role in human embryo implantation by regulating the expression of genes involved in the process. While dynamic changes in plasma miRNA during the peri-implantation period have been established, systematic and comprehensive studies on miRNA expression changes in both endometrial tissue and blood during this period are lacking. A total of 62 subjects, including 62 endometrial tissue samples and 62 paired peripheral blood samples, were collected from participants undergoing hormone treatment cycles between day P+3 to P+7. Next-generation sequencing (NGS) assay was used to profile miRNA expression levels, and the results were annotated using miRBase. To identify the dynamic differentially expressed (DE) miRNAs between day P+3 to P+7, we compared the following group pairs: P+3 and P+4, P+4 and P+5, P+5 and P+6, and P+6 and P+7. We then perform functional miRNA-target interaction (MTI) and pathway enrichment analyses to understand the biological functions of dynamic DE miRNAs. We identified 76 and 48 dynamic DE miRNAs in endometrial tissue and peripheral blood samples, respectively. Functional MTI and pathway enrichment analyses revealed that these DE miRNAs influence numerous biological pathways and functions related to implantation, such as cell senescence, cell growth, apoptosis, focal adhesion, autophagy, platelet activation and signaling. Although only 10 DE miRNAs overlapped between endometrial tissue and peripheral blood, 7 of these showed consistent dynamic expression changes. Further analysis revealed a high similarity in the biological pathways and functions involving the target genes of DE miRNAs in both endometrial tissue and peripheral blood. 76 and 48 dynamic DE miRNAs were identified in endometrial tissue and peripheral blood samples, respectively. These miRNAs influence numerous biological pathways and functions related to implantation.

overall_design: miRNA-seq profiling of 62 endometrial tissue samples and 62 peripheral blood samples at day P+3 to P+7 after progesterone treatment

first: Chun-I

last: Lee

first: Eric Pok

last: Yang

first: Tsung-Hsien

first: Maw-Sheng


title: Synaptic and Intrinsic Plasticity Mediated by CCK-type Signaling Coordinates Behavioral Changes During Motivational State Shifts

status: Public on May 17 2025

city: Nanjing

first: Guo

last: Zhang

address: Xianlin street 163

institute: Nanjing University

summary: Transitions from hunger to satiety involve multiple behavioral changes, including modulation and inhibition of feeding behavior. Cholecystokinin (CCK), a key satiety peptide in mammals, plays a critical role in these processes, though whether and how CCK might induce satiety via synaptic and intrinsic plasticity remain unclear. Here, we demonstrate that CCK acts as a classical brain-gut peptide in a protostome, mollusk Aplysia. CCK neurons, located in the gut, project centrally to release CCK at the site of the feeding pattern generator. In vivo, CCK reduced food intake, while in vitro, it shifted motor patterns towards egestion and inhibited feeding programs. Mechanistically, CCK primarily modulated the excitability of the egestive-promoting B20 interneuron and suppressed synaptic inputs to protraction motoneurons, thereby altering program type and inhibiting feeding program generation. These findings highlight the importance of both synaptic and intrinsic plasticity in specific circuit elements for implementing motivational shifts induced by satiety peptides.

overall_design: Smart single-cell sequencing of Aplysia B20 neuron and B34 neuron

first: Xue-Ying

last: Ding

first: Elena

middle: V

last: Romanova

first: Cui-Ping

first: Michael

last: Barry

first: Alisha

last: Doda

first: Qian-Xue

last: Chen

first: Carrie

last: Reaver

first: Qing-Chun

last: Jin

first: Stanislav

last: Rubakhin

first: Fan

last: Li

first: Yu-Fei

first: Yan-Sheng

last: Kan

first: Yu-Ling

first: Shi-Qi

last: Guo

first: Ying-Yu

last: Xue

first: Yu-Shuo

last: Mei

first: Ping

last: Fu

first: Ju-Ping

first: Rui-Ting

last: Mao

first: Cheng-Yi

first: Yan-Chu-Fei

first: Yi-Long

first: Jian-Hui

last: Chang

first: Shao-Qian

last: Wu

first: Hui-Ying

first: Wei-Jia

first: Zhen

first: Hai-Bo

first: Quan

last: Yu

first: James

last: Checco

first: Jonathan

last: Sweedler

first: Elizabeth

last: Cropper

first: Jian

last: Jing


title: Developmental Timing Establishes Hematopoietic Stem and Progenitor Cell Lineage Bias

status: Public on May 12 2025

city: Bronx

first: Teresa

last: Bowman

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Embryonic development is a critical time window for the establishment of the hematopoietic and immune systems. During embryogenesis, hematopoietic stem and progenitor cells (HSPCs) that possess divergent differentiation preferences arise and sustain lifelong hematopoiesis. How the pace and differentiation repertoire of native hematopoiesis is set in development and how it evolves as the organism grows is incompletely elucidated. Here, we use temporal lineage tracing of the emerging hematopoietic system during zebrafish development coupled with single cell RNA sequencing to define the origins of larval and adult hematopoietic cells. In both larvae and adult tissues, HSPCs arising earlier during embryogenesis show a predilection for lymphoid lineage production while those arising later are skewed towards erythroid. Moreover, early arising HSPCs are the main contributors to adult tissue resident lymphocytes. Mechanistically, early and late arising HSPCs show divergent transcriptional signatures and differential sensitivities to the levels of the transcription factor Runx1. Additionally, we identified that young larvae possess a more heterogeneous set of lymphoid cells than previously recognized including diverse T-lymphocytes and Innate Lymphoid-like Cells (ILCs). We demonstrated that these newly described larval ILC-like cells reside in lymphoid and mucosal organs and are responsive to viral mimic immune stimulation, indicating their relevance in early vertebrate life. The work provides new fundamental knowledge on how the heterogeneous HSPC pool establishes early immune hierarchies during embryogenesis and its persistence in adulthood.

overall_design:
For lineage tracing in larvae, HSPCs were labled with mCherry at 3 timepoints in development: either at 1, 2, or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish larvae using FACS at one-day-post labelling, 6 dpf, and 10 dpf.                 For rag1/R848 experiment, mCherry cells derived from early-HSPCs (1dpf) were isolated at 8 dpf from slc24a5 crispant controls, rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.
For lineage tracing to adult tissues, the embryonic HSPCs were labeled at 1 or 3 dpf, corresponding to early or late tracing, respectively. The heritable mCherry label was followed into adult tissues at 4 months of age. We compared the contributions of early versus late HSPCs to tissue-resident immune cells in adulthood. The tissues examined were kidney marrow, thymus, intestine, and the tesselated lymphoid network (TLN). Immune cells were analysed using single cell RNA sequencing.

first: Anastasia

last: Nizhnik

first: Bianca

last: Ulloa

first: Kevyn

last: Jackson

first: Deyou

last: Zheng


title: Contrasting functions of CD73 and adenosine in CD8+ T cell exhaustion

status: Public on May 30 2025

city: SANTIAGO

first: Alvaro

last: Lladser

state: Región Metropolitana

address: Avenida del Valle Norte 725

country: Chile

institute: Fundacion Ciencia & Vida

summary: T cell exhaustion is a state of functional decline in T cells, driven by chronic antigen exposure and inhibitory signals within the tumor microenvironment. Exhausted CD8+ T cells (Tex) derive from precursor exhausted T cells (Tpex), a self-renewing population responsible for the proliferative burst observed in anti-PD-1 therapies. Exhausted cells are exposed to adenosine in the tumor, yet the role of the CD73/adenosine axis and Tpex/Tex differentiation remains unclear. Using an in vitro model for CD8+ T cell exhaustion, we found that CD73 expression increased during Tpex formation and that its expression is negatively correlated with Tex generation. CD73-deficient (CD73KO) CD8⁺ T cells showed impaired activation and reduced progression to Tex. Moreover, we demonstrated that CD73 promotes transcriptional expression of the adenosine receptor A2A (A2AR) and the differentiation into IFNγ/TNFα-producing Tex cells. RNAseq analysis of exhausted CD73KO CD8+ T cells showed a more stem-like transcriptomic profile and enrichment in genes associated with the immune response than their WT counterpart. In vivo, co-transfer of naïve CD73 KO and WT tumor antigen-specific CD8⁺ T cells into tumor-bearing mice showed increased Tpex frequency and numbers among CD73KO cells in tumors. Conversely, in vitro exhaustion in the presence of A2AR agonists decreased Tex frequency and activation/exhaustion markers, while increasing CD73 and CD62L, markers associated with stemness. Supporting this, A2AR blockade with SYN115 in tumor-bearing mice reduced Tpex markers and increased Tex differentiation. Altogether, our data suggest CD73 promotes Tpex-to-Tex differentiation, whereas adenosine-A2AR signaling supports Tpex maintenance in the tumor microenvironment.

overall_design: RNA-seq profiling of wild-type and CD73 KO OT-I cells after 5 days of stimulation with the SIINFEKL peptide (10 ng/mL) in the presence of IL-7 (5 ng/mL) and IL-15 (5 ng/mL) to induce in vitro exhaustion. Live in vitro-exhausted OT-I cells were sorted before RNA extraction.

first: Juan

last: Saavedra-Almarza

first: Solange

last: Gouët

first: Felipe

last: Malgue

first: Catalina

last: Bascuñan

first: Camilo

last: Villaman

first: Moira

last: García-Gómez

first: Andrés

last: Hernández-Oliveras

first: Javiera

last: Reyes-Alvarez

first: José

last: Corrales-Bermúdez

first: Joaquín

last: De la Rosa

first: Alberto

last: Martin

first: Álvaro

first: Mario

last: Rosemblatt

first: María Rosa

last: Bono

first: Daniela

last: Sauma


title: Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice

status: Public on May 10 2025

city: Stockholm

first: Masomeh

last: Askari

address: Svante Arrhenius väg 20C

country: Sweden

institute: Stockholm University

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


title: Hierarchical ZIF-8@Au cluster Nanocarriers for In Situ CAR-M programming and Immunotherapy in Prostate Cancer

city: nanjing

first: zichen

last: liang

state: jiangsu

address: Xianlin campus, Nanjing University, Qixia District

institute: nanjing university

summary: Here, we have successfully constructed a novel nano-delivery system based on the Zeolitic Imidazolate Framework-8 (ZIF-8), which revealed high CAR gene encapsulation efficiency, reduced non-specific hepatic accumulation, targeted delivery of tumor-associated macrophages (TAM) and efficient intracellular gene transfection efficiency enable the in-situ construction of CAR-M cells. Meanwhile, the co-delivery of the IFN-γ and CAR genes not only maintains the specific killing and phagocytic activity of CAR-M against tumor cells but also activates the adaptive immunity, inducing excellent anti-tumor efficacy in a prostate cancer mouse model. In summary, this strategy provides a novel approach for the systematic in vivo editing of CAR-M.

overall_design: The obtained bone marrow-derived macrophages were transfected with PCI plasmid and PC plasmid via our nanocarriers, respectively, and then incubated with the cell incubator at 37 ° C for 48h and then collect these cells. There were two parallel experimental groups in each group.The RNA was extracted by Trizol method, and the library was constructed using Fast Rna-Seq Lib Prep Kit V2 (Cat.No.RK20306). Transcriptome related data of these macrophages were generated by deep sequencing, in triplicate, using Illumina NovaSeq X Plus. RNA samples were subjected to rigorous quality control through an Agilent 2100 bioanalyzer. PCI plasmid structure include PSMA-CAR-IFN-γ, while PCI plasmid structure just include PSMA-CAR. PSMA is the abbreviation of prostate cancer-specific antigen, CAR is the abbreviation of chimeric antigen receptor, IFN-γ is the abbreviation of interferon-γ.

first: Zichen

last: Liang

first: Rui

last: Wang

first: Yiyang

first: Qing

first: Yihan

last: Chen

first: Zehui

last: Zhang

first: Mengyuan

last: He

first: Jiajie

last: Yang

first: Luchen

last: Sun

first: Hongqian

last: Guo

first: Pingping

last: Shen

first: Nanfei


title: Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [BiSulfite-seq]

first: Laura

last: Biggins

summary: Recent breakthroughs in single-cell genomics allow probing molecular states of cells with unprecedented detail along the sequence of the DNA. Biological function relies, however, on emergent processes in the three-dimensional space of the nucleus, such as droplet formation through phase separation. Here, we use single-cell multi-omics sequencing to develop a theoretical framework to rigorously map epigenome profiling along the DNA sequence onto a description of the emergent spatial dynamics in the nucleus. Drawing on scNMT-seq multi-omics sequencing in vitro and in vivo we exemplify our approach in the context of exit from pluripotency and global de novo methylation of the genome. We show how DNA methylation patterns of the embryonic genome are established through the interplay between spatially correlated DNA methylation and topological changes to the DNA. This feedback leads to the predicted formation of 30-40nm sized condensates of methylated DNA and determines genome-scale DNA methylation rates. We verify these findings with orthogonal single cell multi-omics data that combine the methylome with HiC measurements. Notably, this scale of chromatin organization has recently been described by super-resolution microscopy. Using this framework, we identify local methylation correlations in gene bodies that precede transcriptional changes at the exit from pluripotency. Our work provides a general framework of how mechanistic insights into emergent processes underlying   cell fate decisions can be gained by the combination of single-cell multi-omics and methods from theoretical physics that have not been applied in the context of genomics before.

overall_design: E14 mESC were cultured in 2i+LIF media. For induction for 2i-relase experiment, the cell been rinsed with PBS before the culture media was changed to serum + LIF medium. 0h, 24h, and 48h after induction of 2i-release single cells were distracted and sc-NMT sequencing was performed.

first: Fabrizio

last: Olmeda

first: Tim

last: Lohoff

first: Stephen

last: Clark

last: Benson

first: Felix

last: Krueger

first: Wolf

last: Reik

first: Steffen

last: Rulands


title: Macrophages expressing Macrophage Receptor with Collagen Structure Attenuate Liver Fibrosis Through a Tissue Restoration Phenotype [macrophage_liverFibrosis_scRNA-seq]

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Liver macrophages are central in maintaining hepatic homeostasis and mediating immune responses during liver injury, including fibrosis. Macrophages may have proinflammatory or anti-inflammatory properties, but which properties influence fibrosis remains unclear. To explore the role of macrophages in liver fibrosis, we performed single-cell RNA sequencing in a mouse model of liver injury and found that macrophage diversity was increased. A subset of macrophages expressing high levels of Marco gene was the most significantly upregulated after injury but was spatially segregated to non-fibrotic areas. The macrophage receptor with collagenous structure (MARCO) protein is a scavenger receptor expressed by specific subsets of macrophages, and its role in liver fibrosis is unclear. In vitro induction of Marco in bone marrow-derived macrophages decreased proinflammatory gene expression, increased anti-inflammatory and antifibrotic gene expression, and enhanced phagocytosis, indicating a restorative phenotype. Adoptive transfer of MARCO-positive macrophages in a mouse model of liver fibrosis reduced the expression of extracellular matrix (ECM)-associated genes in hepatic stellate cells (HSCs) and reduced collagen deposition, which did not occur with the transfer of MARCO-negative macrophages. Therefore, MARCO-positive macrophages have a tissue restorative role in the liver and attenuate fibrogenesis through interaction with HSCs, thereby providing a novel therapeutic pathway for liver fibrosis.

overall_design:
Isolated primary cells from mice livers that underwent 6 weeks of Carbon tetrachloride administration to induce fibrosis were subjected to Single Cell RNA sequencing.

C57B6 mice underwent 6 weeks of Carbon tetrachloride administration to induce liver fibrosis. Intrahepatic leukocytes were isolated from perfused livers and subjected to scRNAseq via the 10X Genomics GEM-X FLEX assay.

first: Sofia

last: Jerez

first: Shawna

last: Cooper

first: Usman

last: Yaqoob

first: Bushra

last: Arif

first: Maleeha

middle: F

last: Kalaiger

first: Abid

last: Anwar

first: Mandy

last: Wong

first: Nidhi

last: Jalan-Sakrikar

first: Ying

last: Li

first: Moira

middle: B

last: Hilscher

first: Enis

last: Kostallari

first: Sheng

last: Cao

first: Vijay

last: Shah


title: Inflammation drives TGFβ1 activation via the αvβ6 integrin-mechanotransduction pathway in human skin

status: Public on May 28 2025

city: geneva

middle: Henning

last: Boehncke

address: Rue Michel servet 1

country: Switzerland

institute: Univeristy of Geneva

summary: Transforming growth factor β (TGFβ) is a critical regulator of skin homeostasis and is implicated in skin inflammation, including psoriasis. We investigated the molecular mechanisms of TGFβ1 regulation during cutaneous inflammation using reconstructed human epidermis. We report a mechanosensitive positive feedback loop, that occurs downstream of inflammatory stimuli and involves TGFβ-mediated activation of mechanotransduction pathways, further promoting αvβ6 integrin-dependent TGFβ1 activation in keratinocytes.

overall_design: N/TERT-1 keratinocytes were cultured to create 3D reconstituted human epidermis model (10 days at the air-liquid interphase), and then stimulated with 10ng/ml TGFβ1 for 3 days.

first: Xuewei

last: Jiang

first: Sihem

last: Sellami

first: Jérémy

last: Kessler

first: Michael

last: Bachmann

first: Fanny

last: Noulet

first: Barbara

last: Russo

first: Nicolo

middle: C

last: Brembilla

first: Guerkan

last: Kaya

first: Andrei

last: Ivanov

first: Bernhard

last: Wehrle-Haller

first: Wolf-Henning

first: Maria

last: Shutova


title: Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq]

first: Laura

last: Biggins

first: Fabrizio

last: Olmeda

first: Tim

last: Lohoff

first: Stephen

middle: J

last: Clark

last: Benson

first: Felix

last: Krueger

first: Wolf

last: Reik

first: Steffen

last: Rulands


title: Glomerular Transcriptome from Experimental Nephrotic Syndrome Model and Treatment with PPARgamma Agonists [ADR]

status: Public on Jun 02 2025

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

summary: Nephropathy was induced with puromycin amino-nucleoside (PAN) in Wistar rats and treated with daily treatments of Pioglitazone (Pio) and GQ-16. Nephropathy was induced in a separate group of rats with Adriamycin (ADR) in Wistar rats. Total glomerular RNA was isolated, and mRNA libraries were generated and subjected to sequencing using NovaSeq6000 SP. Injury with PAN and ADR resulted in differential expression of genes (DEGs). Many of the PAN-induced DEGs were restored with Pio and GQ16 treatments.

overall_design: 1 group with 4 replicates sequenced over 2 lanes

first: Shipra

last: Agrawal

last: Webb

first: Claire

last: Bryant


title: Identification of key genes associated with circadian rhythm as potential diagnostic biomarkers for cytomegalovirus infection in very low birth weight infants

status: Public on May 14 2025

city: Xuzhou

first: qianqian

last: Li

address: No.46 Heping Road

institute: Xuzhou maternal and child Health care hospital

summary: After HCMV infection, most individuals have no obvious symptoms. However, HCMV infection in very low birth weight infants can cause liver function damage, thrombocytopenia, hearing damage, cholestasis and so on. Cytomegalovirus is generally thought to lurk and activate in monocytes. In this study, we performed transcriptomic analysis of RNA-seq on peripheral blood mononuclear cells of very low birth weight infants infected with HCMV, bringing new insights into a comprehensive understanding of the immune mechanisms involved during their infection.

overall_design: In order to detect CMV infection, urine CMV-DNA-PCR was routinely performed on very low birth weight infants (birth weight < 1500g) during hospitalization. In order to explore the transcriptome changes after HCMV infection in very low birth weight infants, we randomly selected 3 patients with persistent urine CMV-DNA-PCR negative as the control group, and 3 patients with urine CMV-DNA-PCR positive as the HCMV infection group. Blood samples were collected between 9 am and 10 am, and peripheral blood monocytes were extracted and sent for RNA-seq. Enrichment analysis was performed using transcript results.

first: Qianqian

first: Junmei

last: Yan


title: Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [CUT&RUN]

first: Masomeh

last: Askari

summary: Meiotic prophase I characterized by homologous recombination and synapsis is an intricate step for spermatogenesis. This process entails extensive changes to chromatin and transcription. Recent studies have revealed that prior to prophase I, accessible chromatin bound by paused Pol II at meiotic gene promoters is essential for their timely activation during later stages of prophase I. However, the factor responsible for promoting accessible chromatin at meiotic gene promoters before entry into prophase I is unknown. Here, we discovered that NFYA expressed in pre-meiotic germ cells promotes accessible chromatin at meiotic gene promoters. Concordantly, conditional germline deletion of Nfya in male mice blocks meiotic entry. Functionally, our spatial and single-cell ATAC-seq data revealed that loss of NFYA in pre-meiotic cells disrupts accessible chromatin at meiotic gene promoters. Our study identifies a pioneer role for NFYA in facilitating permissive chromatin at meiotic gene promoters before meiosis, thereby controlling the timely activation of meiotic genetic program during later meiosis.

overall_design: CUT&RUN was performed to profile [H3K4me3 and  NFYA] binding sites in FACS-sorted cells from adult testis.

first: Martin

last: Säflund

first: Atiyeh

last: Eghbali

first: Mukhtar

last: Mohammed Abdi

first: Ann-Kristin Iréne

last: Östlund Farrants

first: Tianxiong

last: Yu

first: Deniz

last: Özata


title: Macrophages expressing Macrophage Receptor with Collagen Structure Attenuate Liver Fibrosis Through a Tissue Restoration Phenotype [macrophage_liverFibrosis_GeoMx_spatial-seq]

first: William

last: Sherman

overall_design: Isolated regions of interest via IF with differential MARCO expression for macrophage populations from mice livers that underwent 6 weeks of Carbon tetrachloride administration to induce fibrosis were subjected to spatial transcriptomic sequencing using NanoString GeoMx.

first: Sofia

last: Jerez

first: Shawna

last: Cooper

first: Usman

last: Yaqoob

first: Bushra

last: Arif

first: Maleeha

last: Kalaiger

first: Abid

last: Anwar

first: Mandy

last: Wong

first: Nidhi

last: Jalan-Sakrikar

first: Ying

first: Moira

last: Hilscher

first: Enis

last: Kostallari

first: Sheng

last: Cao

first: Vijay

last: Shah


title: Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [ATAC-seq]

first: Masomeh

last: Askari

overall_design: Chromatin accessibility was assessed by performing ATAC-seq on fluorescence-activated cell-sorted (FACS) populations derived from adult testis samples

first: Martin

last: Säflund

first: Atiyeh

last: Eghbali

first: Mukhtar

last: Mohammed Abdi

first: Ann-Kristin Iréne

first: Deniz M.