title: Farrerol reduces fat accumulation induced by citrate in Caenorhabditis elegans via DAF-16 and ameliorates obesity in a high-fat diet mouse model

city: Nanjing City

first: shuting

last: huang

address: No. 109, Longmian Avenue, Jiangning District

institute: Nanjing Medical University

summary: Lipid metabolic homeostasis is fundamental for maintaining normal physiological functions. Abnormal lipid accumulation contributes to the development of various metabolic disorders, including obesity, hepatic steatosis, and type 2 diabetes. Given the high global prevalence of these diseases and the lack of safe and effective therapeutic agents, there is an urgent need to identify novel lipid‑regulating compounds. Farrerol, a major dihydroflavonoid isolated from the medicinal herb Rhododendron dauricum L., has been reported to exert anti‑inflammatory, antioxidant, and pro‑angiogenic activities. However, its specific role in regulating lipid metabolism, the underlying molecular mechanisms, and its efficacy and safety in vitro and in vivo remain unclear. This study aimed to systematically investigate the lipid‑regulatory effects of farrerol, elucidate its potential molecular mechanisms, and validate its anti‑lipidemic activity and safety in cellular and animal models, thereby providing a novel candidate drug and theoretical basis for the clinical treatment of lipid metabolism disorders.

overall_design:
We first evaluated the lipid-lowering effect of farrerol in Caenorhabditis elegans (C. elegans) under physiological and citrate-induced high-fat conditions. Transcriptomic (RNA-seq) analysis and RNA interference (RNAi) screening were performed to identify genes involved in the lipid-regulating effect of farrerol. The role of candidate genes and daf-16 was respectively validated by RNAi knockdown and loss-of-function mutation assays. The lipid-lowering effect of farrerol was further confirmed in HepG2 and 3T3-L1 cells in vitro, and in diet-induced obese (DIO) mice in vivo.

Caenorhabditis elegans is divided into 3 groups: OP for control; HFD for High Fat Diet, and FA for High Fat Diet with farrerol treatment.


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

status: Public on Mar 17 2026

city: Philadelphia

first: Montserrat

last: Anguera

state: PA

address: 3800 Spruce Street, Rosenthal Room 390EB

department: Biomedical Sciences

country: USA

institute: University of Pennsylvania School of Veterinary Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: CUT&RUN analysis for the histone modifications H3K27me3, H2AK119Ub, and H3K27me3 in CD23+ B cells with an in vivo or ex vivo deletion of Xist RNA. in vivo experiments use B cells from female mice with an mb1-cre Xist conditional deletion that were unstimulated or stimulated for 24 hours with CpG (n=3-4 WT control and 3-5 cKO). ex vivo experiments use B cells from female Xist flox/flox mice that were unsitmulated or treated ex vivo with TAT-Cre recombinant protein then stimulated with CpG for 24 hours (n=3 WT and 3 KO).

first: Natalie

middle: E

last: Toothacre

middle: C


title: RNA sequencing of nasal lavage samples from mock- and Streptococcus pneumoniae-infected infant mice

status: Public on Mar 16 2026

city: Manhattan

first: Chaitra

last: Sreenivasaiah

state: NY

address: 227 E 30th St

department: Applied Bioinformatics Laboratory

institute: NYU Langone Health

type: Expression profiling by high throughput sequencing

summary: Nasopharyngeal colonization by Streptococcus pneumoniae (Spn) is common and often asymptomatic, yet prolonged colonization increases the risk of transmission and invasive pneumococcal disease, particularly early in life. Host immune pathways that prevent persistent colonization remain poorly understood. Here, we examined how IL-1R and IL-17RA signaling shape host transcriptional responses during pneumococcal colonization of the upper respiratory tract. Using a mouse model of Spn colonization, we performed bulk RNA-sequencing on nasal lavages from mock-treated and Spn-colonized wild-type, Il1r1-/- and Il17ra-/- mice. In wild-type mice, colonization induced robust upregulation of inflammatory and innate immune gene programs, whereas many of these responses were attenuated in Il1r1-/- and Il17ra-/- mice. Taken together, this analysis demonstrates that IL-1R and IL-17RA signaling are required for full activation of host transcriptional responses that limit persistent Spn colonization.

overall_design: We performed gene expression profiling of nasal lavage samples from mock or Streptococcus pneumoniae-infected WT, Il1r1-/- and Il17ra-/- infant mice, with n=6-7 per group.

first: Teniola

last: Idowu

first: Jeffrey

last: Weiser


title: Müllerian duct maintenance at the cranial region is promoted by Gata2

city: Madison

first: Fei

last: Zhao

state: WI

address: 2015 Linden Drive, Room 4206/4210

department: CBS

institute: School of Veterinary Medicine, University of Wisconsin Madison

summary: The paradigm of sexual differentiation holds that female embryos retain Müllerian ducts (the precursor of female reproductive tract organs) by default in the absence of anti-Müllerian hormone (AMH). Whether Müllerian duct maintenance requires active signaling has remained unclear. Here, we show that deletion of mesenchymal Gata2 induces selective regression of the cranial Müllerian duct (future oviduct). This regression did not result from ectopic AMH signaling but from loss of region-specific NRG1 signaling. In contrast, the caudal Müllerian duct (future uterus) was retained but displayed disrupted epithelial differentiation when Gata2 was deleted in either mesenchymal or epithelial compartments. Our findings reveal a region-specific, GATA2-dependent program that actively maintains the cranial Müllerian duct, reshaping our understanding of female reproductive tract development.

overall_design: Cranial and caudal Mesonephros were collected from control and Gata2 cKO embryos at E16.5 and snap-frozen on dry ice. RNA was extracted using the PicoPure RNA Isolation Kit (Life Technologies, KIT0204) according to the manufacturer’s protocol. Three samples per region per group were sent to Novogene for bulk RNA sequencing.

first: Shuai

last: Jia


title: Single-cell epigenetic landscape, microenvironment interactions, and gene regulatory modules of non-functioning pituitary adenomas (NFPA, bulk methylome)

city: Los Angeles

first: Frederique

last: Ruf-Zamojski

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

type: Methylation profiling by genome tiling array

summary: The epigenetic landscape and tumor microenvironment (TME) interactions of non-functioning pituitary adenomas (NFPAs), benign tumors with high morbidity and recurrence rates, are not well characterized. We completed single-nucleus (sn) multiomics assays on four gonadotrope NFPAs. We identified genes involved in bidirectional tumor-macrophage crosstalk. We uncovered coordinated gene expression and chromatin accessibility programs that distinguished adenoma cells from gonadotropes. Integrated transcriptome-chromatin modeling revealed gene regulatory circuits that showed altered activity in adenoma cells. Our study provides insight into the altered epigenetic gene-control landscape and TME processes of the NFPA tumor phenotype.

overall_design: bulk methylation were profiled individually from four human non-functioning pituitary adenoma tissue samples.

first: Zidong

last: Zhang

first: Yongchao

last: Ge


title: Lineage and Organ Signals Sequentially Build Organ Intrinsic Nervous Systems [Spatial Transcriptomics]

city: New Haven

first: I-Uen

last: Hsu

state: Connecticut

address: 100 College Street

department: Neuroscience

institute: Yale University School of Medicine

summary: Organ intrinsic nervous systems (OINSs) are critical components of the body–brain axis, coordinating visceral organ function with systemic physiological control. Despite their importance, how these distinct neural architectures arise from a common neural crest cell (NCC) origin has remained unclear. Here, we present a systems-level, cross-organ analysis of OINS development, integrating lineage tracing, 3D imaging, single-cell transcriptomics, and genetic perturbations across heart, pancreas, intestine, and lungs. We show that differences in NCC migratory trajectories prefigure the spatial architecture of OINSs, laying the foundation for organ-specific patterning. In contrast, molecular identity emerges largely in response to local environments, indicating that extrinsic cues play a major instructive role. Using in vitro co-cultures, we demonstrate that organ-derived cues reprogram intrinsic neurons toward organ-specific transcriptional profiles and direct neuronal differentiation, with extracellular matrix (ECM) contact identified as a central mediator. In vivo, ECM–integrin signaling supports intrinsic cardiac neuron neurogenesis, while ECM crosslinking stabilizes their stereotyped ganglionic organization. Together, these findings reveal that OINS diversity arises through a dual logic: lineage programs prefigure spatial frameworks, while organ-specific cues instruct final molecular identities and architectural precision. This work establishes a conceptual paradigm for how organs actively build their own nervous systems, illuminating principles that underpin body–brain integration.

overall_design: Hearts from E14.5 Wnt1-Cre;lox-Sun1-GFP mice were acutely dissected and freshly frozen in OCT. Cryosections (10 μm) were cut using a cryostat (Thermo Fisher Scientific) and mounted onto the 10x Visium Spatial Gene Expression Slide. Tissue sections were imaged on a Leica SP8 confocal microscope with a 16× objective to obtain tissue morphology and locate ICNS ganglia. Sequencing libraries were prepared following the manufacturer’s protocol (10x Visium) and sequenced using an Illumina NovaSeq 6000 S4 sequencer at Yale Center for Genomic Analysis.

first: Rui B

last: Chang

first: Le


title: Epigenomic Aberrations in Brains of Humans with Mild Cognitive Impairment and Alzheimer’s Disease [re-analysis]

city: Buffalo

first: Zhen

last: Yan

address: 955 Main St

department: Physiology and Biophysics

institute: University at Buffalo

summary: Epigenetic mechanisms, particularly histone modifications at gene promoters, are crucial for controlling gene transcription. During the progression of neurodegenerative disorders, epigenomic aberrations may contribute to gene dysregulation, leading to manifestation of symptoms. To test this, we employed a multifaceted approach to investigate how the two key histone methylation marks, H3K4me3 (linked to gene activation) and H3K27me3 (linked to gene suppression), are altered in postmortem prefrontal cortex of humans with Mild Cognitive Impairment (MCI) or Alzheimer’s Disease (AD). Compared to controls, MCI and AD exhibited pronounced losses of permissive H3K4me3 peaks at promoters of genes enriched in synaptic plasticity and neurotransmission, and significant gains of H3K4me3 peaks at promoters of genes enriched in transcriptional regulation. AD displayed more substantial H3K4me3 losses on synaptic genes than MCI. Conversely, significant gains of repressive H3K27me3 peaks were observed at synaptic gene promoters in both disease groups, with MCI exhibiting more pronounced H3K27me3 gains on synaptic genes than AD. Weighted Gene Correlation Network Analysis (WGCNA) revealed multiple modules characterizing distinct patterns of gains and losses of H3K4me3 and H3K27me3 during the transition from MCI to AD. Integrative analysis of epigenomic and transcriptomic data indicated that these histone mark alterations were well correlated with the downregulation of synaptic genes and upregulation of transcriptional regulators in AD. This comprehensive profiling uncovers a stage-dependent reorganization of histone modifications at critical gene loci, implicating these events in the molecular cascade of AD pathogenesis. Targeting dysregulated chromatin states may offer novel therapeutic avenues for early intervention of AD.

relation:
Reanalysis of: GSE174885
Reanalysis of: GSE174887
Reanalysis of: GSE174891
Reanalysis of: GSE174897
Reanalysis of: GSE174898
Reanalysis of: GSE174922
Reanalysis of: GSE174946
Reanalysis of: GSE174947
Reanalysis of: GSE174956
Reanalysis of: GSE174968
Reanalysis of: GSE174973
Reanalysis of: GSE174979
Reanalysis of: GSE175016
Reanalysis of: GSE175035
Reanalysis of: GSE175050
Reanalysis of: GSE175088
Reanalysis of: GSE175118
Reanalysis of: GSE175136
Reanalysis of: GSE175180
Reanalysis of: GSE175264
Reanalysis of: GSE175292
Reanalysis of: GSE175301
Reanalysis of: GSE175311
Reanalysis of: GSE175321
Reanalysis of: GSE175330
Reanalysis of: GSE175333
Reanalysis of: GSE175338
Reanalysis of: GSE187069
Reanalysis of: GSE187071
Reanalysis of: GSE187094
Reanalysis of: GSE187117
Reanalysis of: GSE187150
Reanalysis of: GSE187177
Reanalysis of: GSE187182
Reanalysis of: GSE187187
Reanalysis of: GSE187192
Reanalysis of: GSE187211
Reanalysis of: GSE187229
Reanalysis of: GSE187230
Reanalysis of: GSE187248
Reanalysis of: GSE187255
Reanalysis of: GSE187258
Reanalysis of: GSE187399
Reanalysis of: GSE187473
Reanalysis of: GSE187480
Reanalysis of: GSE187527
Reanalysis of: GSE187538
Reanalysis of: GSE187556
Reanalysis of: GSE187649
Reanalysis of: GSE187693
Reanalysis of: GSE187724
Reanalysis of: GSE187736
Reanalysis of: GSE187746
Reanalysis of: GSE187770
Reanalysis of: GSE187834
Reanalysis of: GSE187835
Reanalysis of: GSE187919
Reanalysis of: GSE188003
Reanalysis of: GSE188009
Reanalysis of: GSE188062
Reanalysis of: GSE188103
Reanalysis of: GSE188126
Reanalysis of: GSE188132
Reanalysis of: GSE188135
Reanalysis of: GSE208459
Reanalysis of: GSE208815
Reanalysis of: GSE208830
Reanalysis of: GSE208915
Reanalysis of: GSE209046
Reanalysis of: GSE209052
Reanalysis of: GSE209055
Reanalysis of: GSE209056
Reanalysis of: GSE209146
Reanalysis of: GSE209180
Reanalysis of: GSE209310
Reanalysis of: GSE209327
Reanalysis of: GSE209356
Reanalysis of: GSE209378
Reanalysis of: GSE209382
Reanalysis of: GSE209503
Reanalysis of: GSE209513

overall_design:
Differential and correlation analysis of ChIP-seq data from middle frontal area 46 tissue
Differential binding analysis results with normalized matrix, WGCNA matrix, ranks of differentially bound genes and their module assignment
The 'processed_data_file_list.xlsx' describes the processed data files generated from the re-analyzed samples.
data processing step:
BAM and BED files were used to compare groups (Ctrl, MCI and AD) via DiffBind to generate differentially bound genes (DBGs). Normalized binding scores, with gene isoforms summed, were tranformed and normalized for weighted gene correlation network (WGCNA) analalysis to get module membership. DBG data was combined with WGCNA data to retreive ranks.
genome build/assembly: hg38
processed data files format and content: differential binding data of MCIvCtrl, differential binding data of  ADvCtrl, matrix used for WGCNA, WGCNA module memberships for MCI and AD with ranks.

first: Prachetas

middle: J

last: Patel


title: lncRNA 3222401L13Rik/ENSG00000272070 modulates microglial inflammatory programs in association with PU.1

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Long non-coding RNAs (lncRNAs) are emerging as key regulators of brain function, but their contribution to microglial aging and neurodegenerative disease remains largely unknown. Because only 1.5% of the human genome encodes proteins, whereas the vast majority of transcripts belong to the largely unexplored non-coding RNAome, elucidating the functions of non-coding RNAs provides an unprecedented opportunity to expand the space for therapeutic discovery. We recently identified the glia-enriched lncRNA 3222401L13Rik as upregulated in the aging mouse hippocampus. Here, we investigated its function in microglia and its human homolog ENSG00000272070. We found that 3222401L13Rik is expressed in both astrocytes and microglia and increases with age. Knockdown of 3222401L13Rik in primary microglia led to enhanced expression of pro-inflammatory cytokines, including TNFα, and increased phagocytic activity. RNA-sequencing revealed widespread transcriptional changes enriched for TNF and complement signaling pathways. The human homolog ENSG00000272070 showed conserved functions in iPSC-derived microglia, where its loss similarly promoted inflammatory gene expression and phagocytosis. Mechanistically, 3222401L13Rik interacts with the microglial transcription factor PU.1, and its depletion overlapped with PU.1-driven transcriptional programs. Consistent with these findings, ENSG00000272070 expression was significantly reduced in postmortem Alzheimer’s disease (AD) brains, and AD-associated genes were enriched among 3222401L13Rik-regulated targets. Together, our results identify 3222401L13Rik/ENSG00000272070 as a conserved, aging-associated lncRNA that modulates microglial inflammatory states through interaction with PU.1. This work links glial lncRNA regulation to AD-related neuroinflammation and suggests 3222401L13Rik as a potential molecular target to fine-tune microglial activity in neurodegenerative diseases.

overall_design: RNA-seq profiling from primary microglia treated with either control gapmers or 3222401L13Rik gapmers to knockdown 3222401L13Rik

first: Ranjit

last: Pradhan

first: Lalit

last: Kaurani

first: M Sadman

last: Sakib

first: Dennis

last: Krueger

first: Susanne

last: Burckhardt

first: Anna-Lena

last: Schuetz

first: Deborah

last: Kronenberg-Versteeg

first: Ivana

last: Delalle

first: Farahnaz

last: Sananbenesi

first: André

first: Tonatiuh

last: Pena


title: Lineage and Organ Signals Sequentially Build Organ Intrinsic Nervous Systems [scRNA-seq]

first: I-Uen

overall_design: For single-cell RNA sequencing of organ-intrinsic neuronal cells, the heart, lungs, pancreas and intestines were dissected from Wnt1-Cre;lox-tdTomato, Phox2b-Flpo;frt-tdTomato, or Baf53b-Cre;lox-L10GFP mouse embryos at E12.5, E14.5, E16.5, E18.5 and P56. Fluorescently labelled neuronal cells were enriched by Fluorescence-activated cell sorting (FACS) on a BD FACS Aria cell sorter. For experiments comparing heartnear and heartfar regions, E14.5 atrial regions containing Wnt1-Cre;lox-L10GFP labelled ICNS cells were separated from atrial regions lacking ICNS. Each region was dissociated into single-cell suspensions. For coculture experiments, cardiac atria and intestines were dissected from E13.5 Phox2b-Flpo;frt-tdTomato embryos. FACS-purified enteric neurons were cocultured with non-neuronal cardiac or intestinal cells for 4-5 days before harvesting for single-cell RNA sequencing. Single-cell cDNA libraries were prepared using the Chromium Single Cell 3’ V3 reagent kit and sequenced using an Illumina NovaSeq 6000 sequencer.

last: Zhang


title: Insights into the gene regulation of Listeria monocytogenes incubated on corn salad

city: Hamburg

first: Tim

last: Hoffmann

state: Hamburg

address: Ohnhorststraße 18

institute: Universität Hamburg

summary: Listeria monocytogenes is an important food-borne pathogen which is frequently linked to ready-to-eat vegetables. In this work it was investigated by RNA-seq how the colonization of corn salad leaves and the commonly used packaging material polystyrene impacts on the transcriptome of L. monocytogenes NCTC 10887 at 4 °C and 22 °C. The strongest transcriptional differences occurred on corn salad at 4 °C versus polystyrene at 4 °C, yielding 2,629 differentially expressed genes (91.6% of protein-coding genes), indicating a habitat driven shift under cold-chain conditions. Corn salad promoted regulation of virulence related genes. The prfA gene was upregulated on corn salad compared to polystyrene at both temperatures (log2FC 2.43 at 22 °C and 4.16 at 4 °C), accompanied by increased hly (2.70), inlA (4.46), and inlB (2.10) expression at 4 °C. Stress/proteostasis gene expression was elevated on corn salad, including higher transcripts of clpP (3.34–3.51), clpE (5.58–6.89), and clpB (2.08–3.74), consistent with a stressed yet persistence-prone state on leaf surfaces. This indicates that L. monocytogenes persisting on leafy greens can remain transcriptionally primed for host interaction at 4 °C, implying that refrigeration alone may not mitigate risk on ready-to-eat produce, underlining the importance of pre-harvest hygiene.

overall_design: Prokaryotes RNA-seq Analysis of Listeria monocytogenes NCTC 10887 incubated on corn salad (Valerianella locusta) and polystyrene at 4 °C and 22 °C for 24 h.

first: Hoffmann

last: Tim


title: Targeting RANKL-Independent Osteoclastogenesis Overcomes Denosumab Resistance in ER+ Breast Cancer Bone Metastasis [circRNA-seq]

city: Guangzhou

first: Chang

last: Gong

address: No. 107, Yanjiang West Road, Yuexiu Dist

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: Bone metastasis remains a major cause of morbidity in ER+ breast cancer, with RANKL inhibitor resistance emerging as a critical clinical challenge. Nearly 40% of patients develop progressive skeletal lesions despite denosumab therapy, highlighting an urgent need to identify resistance mechanisms and alternative therapeutic strategies. We identified a RANKL-independent osteoclast activation pathway mediated by the CRKL/circCCDC50/NFATc1 axis. Mechanistically, CRKL promotes EIF4A3-dependent circCCDC50 biogenesis, which is packaged into large oncosomes and transferred to osteoclast precursors. Nuclear circCCDC50 recruits CARM1 to epigenetically activate NFATc1 transcription, establishing a self-reinforcing loop that sustains osteolysis despite RANKL blockade. Pharmacological inhibition of CARM1 (TP-064) effectively suppresses osteoclastogenesis and bone metastasis in denosumab-resistant models. These findings reveal a targetable resistance mechanism and provide a clinically actionable strategy to overcome microenvironment-driven metastasis through dual targeting of tumor and bone niches.

overall_design: circRNA-seq profiling of large oncosomes from primary breast cancer cells derived from a Denosumab-responsive patient (#3) and a non-responsive patient (#5).

first: Qun

last: Lin

first: Jinpeng

last: Luo

first: Zhuxi

last: Duan


title: An atlas of genetic effects on the monocyte methylome across European and African populations

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

institute: Tulane University

type: Methylation profiling by high throughput sequencing

summary: This study investigates the genetic regulation of DNA methylation in purified human monocytes across African American and European American populations. Whole-genome bisulfite sequencing (WGBS) and whole-genome sequencing (WGS) were performed on participants from the Louisiana Osteoporosis Study cohort to characterize methylation quantitative trait loci (meQTLs), heritability patterns, and methylome-wide associations with complex traits. The study provides a comprehensive multi-ancestry monocyte methylome atlas.

overall_design:
Peripheral blood samples were collected from African American and European American adult males. Monocytes were purified using negative selection. DNA methylation was profiled using whole-genome bisulfite sequencing, and genetic variation was assessed using whole-genome sequencing. Cis- and trans-meQTL analyses, methylation heritability estimation, methylation imputation modeling, and methylome-wide association studies were conducted. Processed methylation matrices are provided as chromosome-specific files.

***************************************************************
Based on guidance from the NIH Program Office, arrangements are currently underway to deposit the raw WGBS data (for human/patient samples) in the NIH Aging Research Biobank, an authorized NIH-designated controlled-access repository.
***************************************************************

first: Wanheng

first: Chuan

last: Qiu

first: Xiao

first: Zichen

first: Kuan-Jui

last: Su

first: Zhe

first: Minghui

last: Liu

first: Bingxin

last: Zhao

first: Lang

last: Wu

first: Qing

last: Tian

first: Hui

last: Shen

first: Chong


title: Single-cell RNA analysis of allele-specific MHC expression in peripheral blood mononuclear cells of Mauritian-origin cynomologus and Indian-origin rhesus macaques

first: David

middle: H

last: O'Connor

address: 585 Science Drive

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

summary: We have employed a single-cell sequencing approach using 10X Genomics 5'scRNAseq to study expression of the Major Histocompatibility Complex (MHC) in peripheral blood mononuclear cells (PBMC) from Mauritian-origin cynomolgus and Indian-origin rhesus macaques. The MHC region has undergone a complex series of duplications in macaques relative to humans. Steady-state RNA levels of macaque MHC class I and class II transcripts vary over several orders of magnitude in whole blood and bulk PBMC. This study represents the first 5'scRNAseq analysis to quantify allele-specific levels of MHC transcripts in various PMBC subsets of macaques and provides insights into how they may shape immune responses.

sample_organism:
Macaca fascicularis
Macaca mulatta

platform_organism:
Macaca fascicularis
Macaca mulatta

overall_design: Peripheral blood mononuclear cells (PBMC) from Mauritian-origin cynomolgus and Indian-origin rhesus macaques were isolated from fresh whole blood by Ficoll-Plaque centrifugation and analyzed using 5' scRNA-seq

first: Max

last: Ertl

first: Roger

middle: W

last: Wiseman

first: Anthony

last: Veltri

first: Julie

middle: A

last: Karl

first: Miranda

middle: R

last: Stauss

first: William

middle: K

last: Gardner

first: Nicholas

last: Minor


title: EBV INFECTION OUTCOMES DETERMINED BY MONOCYTE AND TREG-DRIVEN IMMUNE DYNAMICS IN AN EX VIVO PBMC MODEL

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

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

overall_design: Refer to individual Series


title: RNA sequencing analysis of A498 renal cancer cells following knockdown of ELOVL2 and ELOVL5

city: Tsukuba

first: Shotaro

last: Sakka

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary: Long-chain fatty acid elongases ELOVL2 and ELOVL5 are key regulators of polyunsaturated fatty acid metabolism. To investigate transcriptomic changes induced by depletion of these enzymes, RNA sequencing was performed in A498 renal cancer cells following siRNA-mediated knockdown of ELOVL2 and/or ELOVL5. Transcriptomic profiles were compared among control cells, ELOVL2 knockdown cells, ELOVL5 knockdown cells, and double knockdown cells.

overall_design: A498 renal cancer cells were transfected with control siRNA or siRNAs targeting ELOVL2, ELOVL5, or both genes. Three biological replicates were analyzed for each condition, yielding 12 samples in total. Libraries were sequenced on an Illumina NextSeq 500 platform using paired-end 36-base reads.


title: Foxl2 preserves chromatin accessibility at a distal super-enhancer which regulates the Fshb-Kcna4 locus

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: A large “gene desert” located far upstream from Fshb and Kcna4 contains several gonadotrope-specific accessible chromatin sites which were seen in chromatin conformation capture (3C) to make distinct contacts with both genes. Expression of Fshb and Kcna4 was strongly inhibited by JQ-1, which represses super-enhancer activity, and the region displays super-enhancer characteristics. The sites of open chromatin were seen, in chromatin immunoprecipitation (ChIP), to bind Brd4 and Med1, most notably at a site -67 kb from the Fshb gene, as well as binding Ctcf further upstream (-123 kbp), all of which were increased following activin exposure. The locus is transcribed to chromatin-associated lncRNAs whose levels correlate with Fshb and Kcna4 mRNA levels in vivo and in cultured gonadotrope cells, indicating coordinated regulation. CRISPR interference (CRISPRi) confirmed distinct functions for each element and, together with the 3C data, indicate that the -67 kb locus mediates basal and activin-stimulated Fshb expression, while the site at -59 kb contributes to activin-stimulation of both genes. Single-cell multiomics revealed that the -67 kb locus is accessible in pituitary stem cells and throughout gonadotrope differentiation, preceding opening of the Fshb promoter, although it is closed in other differentiated cell types, suggesting a gonadotrope-specific factor that keeps it open at this stage. Foxl2 was found to bind this element, contributes to maintaining its chromatin accessibility, and recruits Supt16h, a component of the Facilitates Active Chromatin Transcription (FACT) histone chaperone complex. These findings define a distal, Foxl2-bound super-enhancer that regulates Fshb transcription and shapes the gonadotrope regulatory landscape.

overall_design: Multiomic analysis of single nuclei from sorted Sox9iresGFP positive pituitary cells from P3 males and females

first: Tal

last: Refael

first: Gil

last: Golan

first: Daniella

last: Darsa

first: Lilach

last: Pnueli

first: Karine

last: Rizzoti

first: Philippa

last: Melamed


title: Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

institute: University Hospital Heidelberg


title: Knockout of kdm4aa Inhibits Early Embryonic Development in Zebrafish via Downregulating cyp26a1

city: shanghai

first: xiaohui

last: chen

address: No.999, Huchenghuan Rd, Nanhui New City, Shanghai, P.R. China

institute: Shanghai Ocean University

summary: Histone lysine demethylase 4A (KDM4A) plays crucial roles in regulating cell proliferation, differentiation, development and tumorigenesis, however its roles in fish are unclear. There are two copies of the kdm4a gene in zebrafish (Danio rerio), namely kdm4aa and kdm4ab. Our previous study showed that knockout of kdm4aa severely disturbs early embryonic development in zebrafish, here we investigated the underlying mechanism. Knockout of kdm4aa in zebrafish resulted in a clearly developmental delay and embryonic lethality, accompanied by increased apoptosis. RT-qPCR and CUT&Tag-qPCR showed kdm4aa knockout downregulated Cytochrome P450 26a1 (cyp26a1), probably through elevated enrichment of H3K9me3 and reduced enrichment of H3K4me3 at promoter region of cyp26a1. Further experiments confirmed that cyp26a1 mRNA partially alleviates stress-induced apoptosis in both WT and kdm4aa knockout embryos, consistent with its known anti-apoptotic function. Our study helps understanding the key functions and mechanisms of kdm4aa in regulating early embryonic development in zebrafish.

overall_design: Phenotypic observations revealed developmental delay and increased apoptosis in kdm4aa knockout embryos. To investigate the underlying mechanism, RNA-seq was conducted to identify downstream targets, leading to the selection of cyp26a1. Subsequently, the epigenetic mechanism was explored using CUT&Tag-qPCR to assess the histone enrichment levels of cyp26a1. Finally, functional validation via mRNA microinjection demonstrated that cyp26a1 alleviates apoptosis in both wild-type and knockout embryos

first: Rui

last: Deng

first: Xinqing

last: Cai

first: Hui

last: Jiang

first: Yuting

last: Luo

first: Weiran

last: Chai

first: Bingshe

last: Han

first: Junfang

last: Zhang


title: Bioinspired, Mitochondria-targeted Single-atom Nanozyme Enhances Bone Regeneration by Reprogramming Stem Cell Energy Metabolism

city: hongkong

first: yuwen

last: wang

address: G10A, G/F, Run Run Shaw Science Building,

department: Biomedical Engineering

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: A bioinspired nanozyme—TPP-DMSN-Fe/Cu—mimics mitochondrial complex IV and targets mitochondria to regulate cellular energy metabolism. This approach markedly boosts bone regeneration in vivo, as demonstrated by enhanced bone volume and mineral density in critical-sized bone defects rat models. The study opens new avenues for mitochondria-targeted therapies in bone repair.

overall_design: Control group; DMSN group; DMSN-Fe/Cu group; TPP-DMSN-Fe/Cu group (all 10ug/ml) treat with C3H/10T1/2 after 7 days osteogenic differentiation.

first: Yuwen

last: Wang

first: Zhong

last: Li


title: ATR and TopBP1 oppose to control dormant origin activity and overall replication dynamics, providing a first defense against replication stress [OK-seq]

city: Paris

first: Chun-Long

last: CHEN

state: Ile-de-France

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Replication stress, a major feature of cancers, and ensuing genomic instability stem from perturbations of replication fork progression. The first line of defense against this stress is the recruitment of extra-origins, called dormant, which assists constitutive origins in completing replication. To determine how the DNA replication checkpoint contributes to this compensation process in human cells, we set a dose-response assay that allows quantification of the compensation efficiencies, enabling accurate comparison of cells depleted of relevant proteins. Results show that ATR activity is essential to dormant origin mobilization. In stark contradiction to what would be expected from its ATR-activating function, TopBP1 represses compensation and acts downstream of ATR. Therefore, our results instead design the TopBP1 function in replisome assembly as key to dormancy. Furthermore, Repli-seq and OK-seq data collectively confirm that ATR inactivation prevents dormant origins from firing under stress. Conversely, constitutive origin activity significantly rises in these conditions, attesting of intrinsic differences between dormant and constitutive origins. Altogether, our results elicit a model positing that TopBP1 specifically locks dormant origins at the pre-initiation stage, an intermediate complex in the replisome assembly process. ATR activation would trigger eviction of TopBP1 from this complex, allowing assembly to proceed and compensation to occur.

overall_design: JEFF (EBV-immortalized human B-lymphoblastoid) cells cultured in RPMI 1640 + 5% FBS. Cells were pulse-labelled with 20 µM EdU for 2 min; 2.5 mM EDTA was added, flasks were rapidly chilled on ice, cells harvested by centrifugation and stored at −80°C. Okazaki-fragment (OK-seq) libraries were prepared as described in [Wu, Y. et al., 2023, https://doi.org/10.1038/s41596-022-00793-5]. Libraries were sequenced on an Illumina NextSeq 500/550 (paired-end, 75 bp). In the study, the two technical replicates were merged for increased depth.

first: Stéphane

last: Koundrioukoff

first: Nathan

last: Alary

first: Su-Jung

last: Kim

first: Collin

last: Thibault

first: Antoine

last: Toffano

first: Rodrigo

last: Melendez-Garcia

first: Xia

last: Wu

first: Yaqun

last: Liu

first: Stefano

last: Gnan

first: Sami

last: El Hilali

first: Olivier

last: Brison

first: Filippo

last: Rosselli

last: Chen

first: Michelle

last: Debatisse


title: Single cell multiomic analysis of the impact of Delta-9-tetrahydrocannabinol on HIV infected CD4 T cells

city: Chapel Hill

first: Manickam

last: Ashokkumar

state: NC

address: 120 Mason Farm Rd

department: Department of Medicine

institute: The University of North Carolina at Chapel Hill

summary: Integrated multiomics (scATACseq and scRNAseq) of PBMCs  from three independent donors with 500nM THC for 6 hrs.

overall_design: Mixture of latently infected CD4 T cells and autologous PBMCs (at a ratio of 1:3) from three independent donors with 500nM THC for 6hrs and processed for scRNA seq using the 10x Genomics 3' v3 platform

first: Edward

last: Browne

first: Alicia

last: Cooper-Volkheimer

first: David

last: Murdoch

last: Margolis


title: Transcriptomic changes in Arabidopsis thaliana (Col-0) upon inhibition of histone deacetylases with valeric acid under normal growth conditions and during heat shock.

city: Warsaw

first: Olaf

last: Geyderowicz

state: Masovian Voivodeship

address: Ilji Miecznikowa 1

department: Faculty of Biology

country: Poland

institute: University of Warsaw

summary: Histone deacetylase (HDA) are highly evolutionarily conserved group of enzymes that regulate chromatin condensation and promote transcription siliencing.  Inhibitors of HDA are extensively studied as potential anti-cancer drugs and their selectivity is in mammalian cells was well determined. In plants, many HDA repress stress responsive genes, thus selective inhibition of  those enzymes is a promising approach to increse plant resistance to abiotic stresses. Here we showed that treatemnt of plants with valeric acid, lately identified human HDA inhibitor, activates many stress-related genes and increases Arabidopsis survival under heat stress.

overall_design: The aim of this experiment was to determine the effect of new histone deacetylase inhibitor- valeric acid- on transcriptomic changes in Arabidopsis under normal growth conditions in a short (after 24 h) and long (after 72 h) term. Additionally, the effect of priming Arabidopsis plants for 3 days before heat shock (HS)(43.5°C; 4h) was assesed by sampling the plants immediately after and 24 h after  the end of the shock.

first: Roksana

last: Iwanicka-Nowicka

first: Marta

last: Gapińska

first: Helena

last: Kossowska

last: Koblowska


title: PPAR-γ Suppresses Macrophage Senescence and Allergic Airway Inflammation through Controlling Lipid Metabolic Pathways

city: Baltimore

first: Peisong

last: Gao

state: MARYLAND

address: 5501 Hopkins Bayview Circle

institute: Johns Hopkins Asthma & Allergy Center

summary:
Background: Cellular senescence has emerged as a key contributor to the pathogenesis of chronic lung diseases. Peroxisome proliferator-activated receptor gamma (PPAR-γ), a nuclear transcription factor, regulates senescence across multiple cell types. However, the role of PPAR-γ in allergic airway inflammation, particularly through regulation of macrophage senescence, remains poorly defined.
Methods: Cellular senescence was evaluated in an allergic asthma mouse model using single-cell RNA sequencing (scRNA-seq). Senescent cells were selectively eliminated with dasatinib and quercetin (D&Q) to assess their contribution to disease pathogenesis. Macrophage-lineage-specific PPAR-γ conditional knockout model (PpargΔCD11c) were generated to define the role of macrophage PPAR-γ in senescence and allergic airway inflammation. PPAR-γ activity was further examined in isolated alveolar macrophages and in vivo using rosiglitazone, including macrophage-targeted delivery via phosphatidylserine-modified liposomes (PSL-ROSI).
Findings: scRNA-seq analysis revealed enhanced senescence signatures in mononuclear phagocytes (MNPs), characterized by increased SenMayo scores and elevated Cdkn2a (p16) expression.  Clearance of senescent cells significantly reduced airway inflammation and Th2 cytokine levels (IL-4, IL-5). Correlation analysis identified PPAR-γ as a key transcriptional regulator inversely associated with cellular senescence. Macrophage-lineage–specific deletion of PPAR-γ (PpargΔCD11c) exacerbated airway inflammation and increased cellular senescence. In vitro, rosiglitazone reduced allergen-induced senescence and suppressed proinflammatory mediators (IL-6, ICAM-1, CCL4, CCL5, TIMP-1, TNF-α) in alveolar macrophages. In vivo, rosiglitazone and inhaled PSL-ROSI attenuated cockroach allergen-induced airway inflammation, with PSL-ROSI effectively bypassing the airway mucus barrier to deliver rosiglitazone to lung macrophages. Integrated chromatin binding and transcriptomic analyses demonstrated that PPAR-γ promotes macrophage lipid metabolic programs (e.g., CD36, Fabp4).
Interpretation: These findings identify macrophage senescence as a pathogenic driver of allergic airway inflammation and establish PPAR-γ as a critical regulator of macrophage senescence and homeostasis, highlighting its potential as a therapeutic target for asthma.

overall_design: mice were sensitized by intra-tracheal (i.t.) inhalation of 20 μg cockroach extract in 50 μL of PBS once on day 1, 3, and 5 and challenged with the same dosage of CRE for 3 successive days (day 11–13). Control mice received the same volume of PBS.

first: Wenjing

last: Gu

first: Rongjun

last: Wan

first: Zhifeng

first: Wenshen

last: Wang

first: Shaobing

last: Xie

first: Chuangli

last: Hao

first: Guangshu

last: Liu

first: Mei


title: Abrogation of SOS mutagenesis by the E. coli OxyR oxidative stress response

first: Damian

last: Gawel

address: Marymoncka 99/103

department: Cell Biology and Immunology

institute: Centre of Postgraduate Medical Education

summary: Most bacteria are capable of living and surviving under a wide range of conditions, including exposures to chemical and physical stressors. A key to survival under adverse conditions is their ability to induce specific stress response systems that mitigate harmful effects. Examples are the well-studied SOS system induced under replication stress caused by DNA damage, and the OxyR response induced by oxidative stress (e.g., hydroxyl radicals). In the present study we have investigated interactions between these two systems under the assumption that harmful conditions may generally induce more than one bacterial response, and in such a case their combined effect might feature additional factors critical for survival. We used Escherichia coli strains that were constitutively induced for the SOS system (using the recA730 allele) in combination with the OxyR oxidative response (using the oxyR2c allele). The main finding was that joint expression of these systems strongly diminished the mutator effect associated with SOS induction. This so-called SOS mutator effect is due to the error-prone DNA polymerase Pol V (product of the umuDC operon, UmuD′2UmuC), which is derepressed upon SOS induction. Gene expression studies revealed an overall reduction of genes of the SOS regulon in the double mutant, with a largest reduction for the genes of the umuDC operon. In parallel, Western blots showed the UmuD and UmuD′ proteins to be severely depleted from extracts of such strains. The data suggest an additional layer of control of SOS mutagenesis under certain stress conditions.

overall_design: RNA-seq profiling in the E. coli MG1655 strain, single mutants OxcRc and RecA730, and double mutant OxcRc+RecA730

first: Adriana

last: Oller

first: Anna

last: Betkowska

first: Marcin

last: Rozwadowski

first: Abdull

last: Massri

first: Roel

middle: M

last: Schaaper


title: Impact of Candida albicans NDT80 and UME6 on biofilm formation and fluconazole susceptibility

city: Athens

first: Katharina

last: Goerlich

state: GA

address: 120E Green St

department: Microbiology

institute: University of Georgia

summary:
The fungus Candida albicans is part of the human microbiome and an opportunistic
pathogen. Virulence traits include its ability to produce biofilm, a surface-associated
growth form that persists on mucosal surfaces and implanted medical devices. C.
albicans clinical isolates vary considerably in ability to produce biofilm and the
constituent filamentous cell types. Here we focus on two transcription factors that
promote filamentation and biofilm formation, Ndt80 and Ume6. We address two
questions. First, how variable is the impact of Ndt80 among C. albicans strains?
Second, what is the genetic interaction between NDT80 and UME6? We find that
Ndt80 is required for filamentation and biofilm formation in five clinical isolates in
addition to the reference strain SC5314, where Ndt80 function has been well
established. RNA-sequencing (RNA-seq) data indicate that UME6 RNA levels are
reduced in an ndt80Δ/Δ mutant, possibly a result of altered RME1 and WOR1
expression, both of which control UME6. Increased expression of UME6 in ndt80Δ/Δ
mutants of three strain backgrounds restores filamentation and biofilm formation, though
RNA-seq assays indicate that it does not suppress the overall ndt80Δ/Δ gene
expression defect. Ndt80 has a second role in promoting tolerance to the antifungal
drug fluconazole, an inhibitor of ergosterol synthesis. Increased expression of UME6 in
ndt80Δ/Δ mutants enhances their susceptibility to fluconazole. Therefore, our results
show an unexpected relationship between Ume6 expression and azole drug sensitivity.
To our knowledge Ume6 has previously been known to function only in filamentation
and biofilm formation.

overall_design: RNA-seq profiling of WT C. albicans cells and their mutant derivatives (ndt80△/△, ndt80△/△UME6OE, and UME6OE). Cells were greown for 4h at 37 degrees in RPMI.

first: Aaron

middle: P

last: Mitchell


title: Catestatin impedes melanoma progression and drug resistance by reprogramming oncogenic signaling pathways

city: San Diego

first: Satadeepa

last: Kal

address: 9500 GILMAN Dr

institute: UCSD

summary: Melanoma remains one of the most aggressive and treatment-resistant cancers, emphasizing the need for novel therapeutics. In our current study we report a peptide-based approach as potential therapeutic. The expression and role of Catestatin(CST), a Chromogranin A(CgA)-derived peptide with immunomodulatory and reparative properties in skin injury led us to examine its connection to melanoma. Advancing melanoma stages showed decreased CST expression. CST administration to patient derived cells and melanoma cell lines A375, B16F10, SKMEL28 revealed increased apoptosis, decreased proliferation and metastatic ability of the melanoma cells without affecting cell viability for normal skin fibroblasts. CST reduced growth kinetics and tumor weight in B16F10 derived in vivo melanoma tumors. Transcriptomic analyses of catestatin treated human cell line and mouse tumor revealed downregulation of hypoxia, collagen remodeling, epithelial to mesenchymal transition pathways (EMT), stress adaptive responses that are accountable for melanoma progression. In Vemurafenib-resistant A375 cells, CST increased apoptosis and repressed multiple resistance associated genes. These results highlight CST as a promising therapeutic candidate capable of opposing melanoma progression and overcoming resistance to current targeted treatments.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq was performed on mouse tumor tissue (C and S groups) and human A375 melanoma cell lines (B, SS, RC, RS groups) with CST-treated and control conditions. Libraries were sequenced on Illumina NovaSeq 6000 (paired-end), and differential expression analyses compared CST-treated versus control within each group.

first: Suborno

last: Jati

first: Sushil

last: Mahata


title: RHOT proteins link mitochondrial motility to cardiomyocyte sarcomere maturation

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: The present study investigates the contribution of embryonic, cardiomyocyte-selective deletion of Rhot1 and Rhot2 to left ventricular mRNA expression at one day and one week of age.

overall_design: RNA-seq profiling of left ventricular tissue from mice with cardiomyocyte-selective deletion of Rhot1 and Rhot2 (DKO) and controls at one day and one week of age

first: Christian

last: Riehle


title: Switchover of electrotrophic and heterotrophic respirations enables the biomonitoring of low concentration of BOD in oxygen-rich environment

city: Tianjin

first: Yilian

last: Han

state: Tianjin

address: 38 Tongyan Road, Haihe Education Park, Jinnan District

institute: Nankai University

summary: Biochemical oxygen demand (BOD) is a key indicator of water quality. However, there is still no technique to directly measure BOD at low concentrations in oxygen-rich environments. Here, we propose a new scheme using  facultative electrotrophs as the sensing element, and confirmed aerobic Acinetobacter venetianus RAG-1 immo_x0002_bilized on electrode was able to measure BOD via the switchover between electrotrophic and heterotrophic respirations. The hybrid binder of Nafion and polytetrafluoroethylene (PTFE) maximized the baseline current (127 ± 2 A/m2) and sensitivity (2.5 ± 0.1 (mA/m2)/(mg/L)). The current decrease and the BOD5 concentration fitted well with a linear model in the case of known contaminants, verified with both lab samples of acetate and glucose (R2 >0.96) and in standard curves of real environmental samples collected from the lake and the effluent of wastewater treatment plant (R2>0.98). Importantly, the biosensor tested actual contaminated water samples with an error of 0.4~10% compared to BOD5 in the case of unknown contaminants. Transcriptomics revealed that reverse oxidative TCA may involve in the electrotrophic respiration of RAG-1 since citrate synthase (gltA) was highly expressed, which was partly downregulated when heterotrophic metabolism was triggered by BOD. This can be returned to electrotroph when BOD was depleted. Our results showed a new way to rapidly measure BOD in oxygen-rich environment, demonstrating the possibility to employ bacteria with two competitive respiration pathways for pollution detection.

sample_organism: Acinetobacter venetianus RAG-1 = CIP 110063

overall_design: RAG-1 samples were collected at four physiological states to investigate transcriptional changes associated with the transition between heterotrophic and electrotrophic respiration during BOD sensing. The four conditions were: (1) HR, heterotrophic respiration, cells cultured in NB medium to logarithmic growth phase; (2) ER, electrotrophic respiration, electrode-associated biofilm at baseline current stabilization prior to BOD testing; (3) DT, during BOD testing, biofilm collected when the current decreased to its minimum value; and (4) AT, after BOD testing, biofilm collected after electrolyte replacement and current re-stabilization.

first: Chengmei

last: Liao

first: Xinyi

last: Meng

first: Qian

last: Zhao

first: Xuejun

last: Yan

first: Lili

last: Tian

first: Ying


title: Targeting RANKL-Independent Osteoclastogenesis Overcomes Denosumab Resistance in ER+ Breast Cancer Bone Metastasis [RNA-seq]

first: Chang

last: Gong

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Bone metastasis remains a major cause of morbidity in ER+ breast cancer, with RANKL inhibitor resistance emerging as a critical clinical challenge. Nearly 40% of patients develop progressive skeletal lesions despite denosumab therapy, highlighting an urgent need to identify resistance mechanisms and alternative therapeutic strategies. We identified a RANKL-independent osteoclast activation pathway mediated by the CRKL/circCCDC50/NFATc1 axis. Mechanistically, CRKL promotes EIF4A3-dependent circCCDC50 biogenesis, which is packaged into large oncosomes and transferred to osteoclast precursors. Nuclear circCCDC50 recruits CARM1 to epigenetically activate NFATc1 transcription, establishing a self-reinforcing loop that sustains osteolysis despite RANKL blockade. Pharmacological inhibition of CARM1 (TP-064) effectively suppresses osteoclastogenesis and bone metastasis in denosumab-resistant models. These findings reveal a targetable resistance mechanism and provide a clinically actionable strategy to overcome microenvironment-driven metastasis through dual targeting of tumor and bone niches.

overall_design: RNA-seq profiling of primary breast cancer cells derived from Denosumab-responsive patients (#1, #2, #3) and Denosumab-non-responsive patients (#4, #5, #6).

first: Qun

last: Lin

first: Jinpeng

last: Luo

first: Zhuxi

last: Duan


title: Phloem proteomics to identify small Open Reading Frame (sORF)-encoded peptides with a putative role in the control of flowering time in Arabidopsis

city: Burjassot, Valencia

first: Irene

last: Moreno Sanguino

address: Cam. del Cementerio, 1

department: Plant Biology

country: Spain

institute: Univeristy of Valencia, Faculty of Pharmacy

summary: Phloem sap proteomic studies have previously revealed that phloem sap composition varies during development and upon floral induction. Specific proteins, lipids, messenger RNAs (mRNAs) and peptides have been shown to accumulate in different developmental stages. Peptides are of special interest since they have the potential to act as regulatory molecules controlling plant responses to environmental changes, such as salinity and water stress, plant-microbe interactions, and developmental changes. In this context, we have characterised Arabidopsis phloem exudates to identify proteins and peptides with potential to control flowering time, acting as signals fine tuning plant development. In this work, we present the proteomic profiles of the phloem sap samples during floral transition along with the identification of interesting proteins and peptides that could have a role in the control of flowering. Among those, we have described the abundance pattern of the sORF1511 peptide in the phloem sap, which varies upon floral induction. We show that sORF1511 overexpression affects bolting time and alters the expression of several genes involved in the control of flowering time.

overall_design: RNA-seq profiling from 12 das seedlings of Col-0 (WT) and the sORF1511-ox line #7 (overexpressor of sORF1511), each condition comprising two biological replicates, with each replicate consisting of five pooled seedlings.

first: Lucía

last: Argente Collàs

first: Göran

last: Samuelsson

first: Gunnar

last: Wingsle

first: Reyes

last: Benlloch


title: Acquisition of luteolytic capacity is accompanied by changes in luteal apoptosis and immune mechanisms

city: University Park

first: Camilla

middle: H. K.

last: Hughes

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

summary: The corpus luteum (CL) produces progesterone to support pregnancy but undergoes luteolysis in response to prostaglandin F2A (PGF2A) when pregnancy is absent. Developing CL resist PGF2A-induced regression. This acquisition of luteolytic capacity (ALC) occurs around day 5 of the estrous cycle in cattle. To understand the mechanisms underlying ALC, we evaluated transcriptomic and proteomic changes in the CL on days 4 and 6 of the estrous cycle. 1190 transcripts were greater on day 4 and 119 were greater on day 6 (Padj < 0.05, log2FC > |1|). In the proteomics dataset, 2 proteins were greater on day 4, with 12 greater on day 6 (Padj < 0.05, log2FC > |1|). Data were integrated with datasets of luteal changes during luteolysis and during early pregnancy, and gene ontology analysis was used to identify candidate pathways regulating luteal PGF2A responsiveness, including apoptosis, cellular stress response, and cytokine signaling. Apoptosis regulators increased on day 6 and increased in response to PGF2A in vivo, indicating a likely role in luteolytic cell death. Changes to regulators of antigen presentation and T cell programming suggested increased T cell activation on day 6. A luteal cell culture experiment revealed that apoptosis pathways were regulated by interferon gamma and immune pathways were regulated by luteinizing hormone in vitro. In summary, integration across datasets from multiple luteal states allowed identification of proposed mediators governing luteal survival and PGF2A response. Apoptosis and immune-related pathways, changes indicating increased activated T cells, may poise the CL to regress in response to PGF2A.

overall_design: Bovine luteal tissue samples were collected on days 4 and 6 of the estrous cycle. Whole tissue samples were snap frozen and used for RNAseq and proteomics.

first: Jillian

last: Hughes-Brown

first: Elizabeth

last: Medich

first: Joy

middle: L

last: Pate


title: Transcriptomic profiling of osteoblasts on hydroxyapatite-coated surfaces reveals enhanced osteogenic and angiogenic processes relevant to accelerated bone healing.

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

institute: Hokkaido University

summary: Hydroxyapatite (HA) coating on orthopedic implants is known to enhance osteogenesis and bone-implant integration. However its molecular basis remains to be investiagated. In this study, we performed transcriptome analysis of osteoblasts on nano-HA-coated surfaces.

overall_design: Human osteoblasts were cultured for 21 days on metal substrates with nano-HA coating or without coating, and comparisons were conducted between day 0 and day 21 within each group.

first: Yuki

last: Ogawa

first: Mohamad

first: Norimasa

last: Iwasaki


title: Rapamycin treatment ameliorates HLA-B27-mediated gut inflammation and alters the microbiome in experimental spondyloarthritis

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Rapamycin treatment reduced stool and colon histological scores in B27-Tg rats compared to vehicle-treated B27-Tg controls. Transcriptome analysis revealed that rapamycin reduced expression of key pro-inflammatory cytokines like Il17a, Il17f, Tnf, Il1a, IL1b, and Il22 in B27-Tg colon tissue compared to vehicle-treated B27-Tg controls. Ex vivo treatment of bulk immune cells isolated from B27-Tg rat colon with rapamycin (25 and 50 nM) reduced expression of Il17a, Il17f, Ifng, and Il22 compared to vehicle-treated cells. Rapamycin treatment decreased the abundance of cecum microbiota associated with inflammation in B27-Tg rats. Rapamycin also altered the gut microbiome in WT rats, without associated changes in the tissue transcriptome.  Our study demonstrates that rapamycin treatment substantially reduces HLA-B27-mediated gut inflammation in experimental SpA. Results from this pre-clinical model suggest further evaluation of rapamycin as a therapeutic strategy in HLA-B27 associated diseases is warranted.

overall_design: HLA-B27/human β2-microglobulin transgenic (B27-Tg) rats with gut inflammation were treated with rapamycin (1.5 mg/kg intraperitoneally, 3 times a week) or vehicle for 5 weeks. Healthy age-matched wild type (WT) rats were treated in parallel. Gut inflammation was evaluated via stool scoring and histological assessment. Transcriptome and microbiome analyses were performed on colon tissue and cecal lumen contents, respectively. Bulk immune cells were isolated from the colonic lamina propria of B27-Tg and WT animals, treated with rapamycin ex vivo, and pro-inflammatory cytokine expression was measured using qPCR.

first: Jinny

last: Van Doorn

first: Francesca

last: LiCausi

first: Kelly

last: Zhou

first: Naga

middle: S

last: Betrapally

first: Eva

last: Gubitz-Hess

first: Antony

last: Cougnoux

first: Stefania

last: Dell’Orso

first: Shamima

last: Islam

first: Robert

last: Colbert

first: Fatemeh

last: Navid


title: Comprehensive single-cell transcriptomic profiling of the scalp from patients with moderate-to-severe alopecia areata

city: New York

first: Emma

last: Guttman-Yassky

state: New York

address: 5 E 98th St

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: Background: Alopecia areata (AA) is an autoimmune hair loss disorder characterized by follicular destruction. While bulk transcriptomic studies have identified contributory inflammatory axes, specific cell pathways remain underexplored. Objective: To characterize the single-cell transcriptomic landscape underpinning AA scalp compared to healthy controls. Methods: We performed single-cell RNA-sequencing on lesional and nonlesional scalp biopsies from 13 patients with moderate-to-severe AA (5 with alopecia totalis/universalis [AT/AU]) and 11 healthy controls. Results: Overall, we profiled 41,067 high-quality cells. Lesional AA samples demonstrated robust Th1 activation and cytotoxicity, with upregulated IFNG, GZMH/K, and XCL1/2. Concurrently, Th2 skewing (IL13, IL13RA1, IL4R) and TNFRSF4/OX40 elevations in lesional CD4+ and regulatory T-cells were also observed. IL15, JAK2/3, and STAT1 levels were increased in distinct lesional dendritic cell subsets, with JAK/STAT genes also upregulated in fibroblasts and keratinocytes. Fibroblasts and smooth muscle cells exhibited enriched pro-inflammatory and pro-fibrotic markers (CXCL9, CCL26, POSTN, COL5A3, COL6A6). Lesional keratinocytes further demonstrated downregulated hair keratins and increased interferon signaling. AA endothelial cells showed increased angiogenic and interferon signatures. Compared to patchy AA and controls, AT/AU demonstrated higher expression of multiple cytotoxic, Th1, Th2, and JAK/STAT markers in immune cells, and proliferative and inflammatory signatures in non-immune cells. Conclusion: This comprehensive high-resolution single-cell map uncovers potential communication networks between immune and non-immune cell populations in AA scalp, possibly disrupting immune privilege at the hair follicle and driving disease progression and/or severity. Clinical Implications: These data provide single-cell-resolution insights into AA pathogenesis and potential molecular targets for precision therapies tailored to AA severity.

overall_design: Lesional and nonlesional skin biopsies were taken from the scalp of 13 patients with moderate-to-severa alopecia areata, as well as biopsies from 11 matching controls. Biopsies were cryopreserved and processed by 10x Genomics. The library was sequenced on the Illumina NovaSeq X platform.

first: Benjamin

middle: D

last: Hu

first: Helen

last: He

first: Swaroop

last: Bose

first: Digpal

last: Gour

first: Monali

last: Nandymazumdar

first: Jerry

first: Anudeep

last: Golla

first: Ester

last: del Duca

first: Jessica

last: Beaziz

first: Gianluca

last: Avallone

first: William

last: Zhao

first: Hailey

last: Pfeifer

first: Madeleine

last: DeGrange

first: Mark

last: Taliercio

first: Anusha

last: Pasumarthi

first: Yeriel

last: Estrada


title: Chromatin-associated RNA in gonadotrope LbetaT2 cells

city: Haifa

first: Philippa

last: Melamed

address: Technion City

country: Israel

institute: Technion-Israel Institute ofTechnology

summary: Cellular fractionation and isolation of cytosolic and chromatin-associated RNA from untreated LβT2 gonadotrope cells was performed according to Conrad and Ørom (10.1007/978-1-4939-4035-6_1).

overall_design: RNA-seq profiling in cytosolic and chromatin-associated fractions of LbetaT2 cells

first: Tal

last: Refael

first: Lilach

last: Pnueli


title: Effect of Myc-activation on transcriptomic profiles of murine pancreatic tumors

city: Houston

first: Fredrik

middle: Ivar

last: Thege

state: Texas

address: 6565 MD Anderson Blvd

department: Translational Molecular Pathology

institute: UT MD Anderson Cancer Center

summary: To investigate the effect of Myc-activation during pancreatic tumorigenesis, we treated CRISPRa-competent PPKS (KRAS(LSL-G12D//wt); TP53(flox/flox); Rosa26(LSL-SAM/wt)) mice with CMV-Cre/U6-sgRNA(MS2) encoding lentivirus carrying Myc-targeted or non-targeted sgRNA. Tumors were harvested at survival endpoint and transcriptomic reprogramming was assessed by RNA-seq

overall_design: 5 PPKS mice were treated with Myc-targeting CMV-Cre/U6-sgRNA(MS2) lentivirus and 5 PPKS mice were treated with non-targeting CMV-Cre/U6-sgRNA(MS2) lentivirus through retrograde ductal injection. Tumors were harvested at survival endpoint and total RNA was extracted. mRNA-sequencing libraries were generated, sequenced and bioinfomatically analyzed.

first: Anirban

last: Maitra

first: Sonja

last: Woermann


title: Effect of Gnmt overexpression on histone methylation abundance in Drosophila melanogaster photoreceptor cells

city: West Lafayette

first: Seth

last: Lammert

state: IN

address: 175 South University Street

department: Biochemistry

institute: Purdue University

summary: In the Drosophila melanogaster eye, the abundance of multiple histone methyl marks decrease in age due to an unknown mechanism. Histone methylation is influenced by the availability of the universal methyl donor S-adenosyl methionine (SAM) and the byproduct of SAM-depednent methylation: S-adenosylhomocysteine (SAH), a potent inhibitor of histone methyltransferases. Glycine-N-methyltransferase (Gnmt) regulates the availability of SAM and SAH by methylating glycine to produce sarcosine. Both Gnmt and SAH are increased in the aging eye, therefore we hypothesize that an increase of Gnmt decreases histone methylation. To test this hypothesis, CUT&RUN was performed on multiple histone methyl marks in photoreceptor nuclei from flies that overexpress Gnmt in the eye versus control.

overall_design: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 200 male flies in triplicate were collected at 10 days post-eclosion (D10) and at Zeitgeber time 12 (ZT12). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw) followed by CUT&RUN (dx.doi.org/10.17504/protocols.io.zcpf2vn). Glycine-N-methyltransferase (Gnmt) was overexpressed in Drosophila eyes using an eye-specific Gal4 driver: LongGMR-Gal4 (derived from Bloomington Drosophila Stock Center 8121) crossed with a line with UAS-Gnmt (https://doi.org/10.1038/ncomms9332). As a negative control, the driver line was outcrossed to w[1118].

first: Lammert

last: Seth

first: Weake

last: Vikki


title: Effect of Sox2-activation on transcriptomic profiles of murine lung tumors

summary: To investigate the effect of Sox2-activation during lung tumorigenesis, we treated CRISPRa competent PPKS (KRAS(LSL-G12D//wt); TP53(flox/flox); Rosa26(LSL-SAM/wt)) mice with CMV-Cre/U6-sgRNA(MS2) encoding lentivirus carrying Sox2-targeted or non-targeted sgRNA. Tumors were harvested at survival endpoint and transcriptomic reprogramming was assessed with RNA-seq.

overall_design: 4 PPKS mice were treated with Sox2-targeting CMV-Cre/U6-sgRNA(MS2) lentivirus and 4 PPKS mice were treated with non-targeting CMV-Cre/U6-sgRNA(MS2) lentivirus through nasal instillation. Tumors were harvested at survival endpoint and total RNA was extracted. mRNA-sequencing libraries were generated, sequenced and bioinfomatically analyzed.


title: MAIT cell enrichment in Lynch syndrome is associated with immune surveillance and colorectal cancer risk

city: Philladephia

first: Hairu

last: Yang

address: Philadelphia, PA 19104

department: Division of Gastroenterology and Hepatology

institute: University of Pennsylvania Perelman School of Medicine

summary: Tissue microenvironment characteristics associated with elevated risk of colorectal cancer (CRC) in Lynch syndrome (LS) are poorly characterized. We applied the multimodal single cell sequencing platform ExCITE-seq to define the colonic cellular composition and transcriptome of LS carriers with and without a history of CRC compared with general population controls. Our analysis revealed widespread remodeling in LS that included striking expansion of epithelial stem and progenitor cells, and loss of fibroblast populations. Although clonally expanded and terminally exhausted CD8 T cells were more prominent in individuals with a history of CRC, LS carriers without CRC displayed enrichment of cytotoxic mucosal-associated invariant T (MAIT) cells associated with CCL20 expression in epithelial progenitors, validated by orthogonal techniques including demonstration of a protective function in a murine model of CRC. These findings highlight cellular features that distinguish LS carriers and suggest a protective role of MAIT cells in human CRC surveillance.

overall_design:
We performed ExCITE-seq on fresh, non-tumor proximal colonic biopsies collected from three age- and sex-matched groups: 10 LS carriers without CRC (LS), 6 LS carriers with a prior history of CRC (disease-free for over two years and not on treatment at the time of collection; LS-CRC), and 8 non-LS controls (undergoing routine screening colonoscopy; CON)

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

first: Ken

last: Cadwell

first: Meenakshi

last: Bewtra

first: Bryson W

last: Katona


title: Transcription regulation in haloalkaliphilic bacterium Spirochaeta africana

city: Turku

first: Georgiy

last: Belogurov

address: Tykistökatu 6

department: Dept. of Life Technologies

country: Finland

institute: University of Turku

summary: The Spirochaetota phylum represents the most basal lineage within the bacterial kingdom Pseudomonadati. These bacteria are distinguished by their long, thin helical shape and a unique flagellum located between the inner and outer membranes. While some spirochetes are pathogenic, causing diseases such as syphilis (Treponema), Lyme disease (Borrelia), and leptospirosis (Leptospira), this study focuses on the non-pathogenic, free-living Spirochaeta africana as a model organism. This approach allows for the investigation of fundamental aspects of gene regulation in spirochetes, free from the genomic reduction often observed in pathogenic spirochetes due to their parasitic lifestyle. We utilized RNA-Seq to assess the in vivo activities of spirochetal promoters and the relative abundance of transcripts encoding components of the spirochetal transcription system. These findings supplement detailed in vitro analyses of spirochetal RNA polymerase and transcription regulators by biochemical and structural methods.

overall_design: RNA prepared from cultures of S. africana in high-salt maltose media.

first: Vilma

last: Trapp

first: Juho

last: Kotikoski


title: ATR and TopBP1 oppose to control dormant origin activity and overall replication dynamics, providing a first defense against replication stress [Repli-Seq]

city: Paris

first: Chun-Long

last: CHEN

address: 26 rue d'Ulm

institute: Institut Curie

summary: Replication stress, a major feature of cancers, and ensuing genomic instability stem from perturbations of replication fork progression. The first line of defense against this stress is the recruitment of extra-origins, called dormant, which assists constitutive origins in completing replication. To determine how the DNA replication checkpoint contributes to this compensation process in human cells, we set a dose-response assay that allows quantification of the compensation efficiencies, enabling accurate comparison of cells depleted of relevant proteins. Results show that ATR activity is essential to dormant origin mobilization. In stark contradiction to what would be expected from its ATR-activating function, TopBP1 represses compensation and acts downstream of ATR. Therefore, our results instead design the TopBP1 function in replisome assembly as key to dormancy. Furthermore, Repli-seq and OK-seq data collectively confirm that ATR inactivation prevents dormant origins from firing under stress. Conversely, constitutive origin activity significantly rises in these conditions, attesting of intrinsic differences between dormant and constitutive origins. Altogether, our results elicit a model positing that TopBP1 specifically locks dormant origins at the pre-initiation stage, an intermediate complex in the replisome assembly process. ATR activation would trigger eviction of TopBP1 from this complex, allowing assembly to proceed and compensation to occur.

overall_design:
Repli-Seq experiments of human lymphoblastoid cells grown in the following conditions: Normal media (1 sample, G1/S1 fraction), 300 nM aphidicolin for 4h (2 samples, G1/S1 fraction), 600 nM aphidicolin for 4h (2 samples, G1/S1 fraction), 100 nM ATRi for 16h (1 sample, 6 fractions; 2 samples, G1/S1 fraction), 100 nM ATRi for 16h and 300 nM aphidicolin for 4h (3 samples, G1/S1 fraction), 100 nM ATRi for 16h and 600 nM aphidicolin for 4h (1 sample, 6 fractions; 2 samples, G1/S1 fraction).
NOTE: The average for untreated cells (NT) is the average of the bigwig deposited here as well as 3 other NT samples available under GEO IDs: GSM3963958, GSM3963964 and GSM5610009.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Stéphane

last: Koundrioukoff

first: Nathan

last: Alary

first: Su-Jung

last: Kim

first: Collin

last: Thibault

first: Antoine

last: Toffano

first: Rodrigo

last: Melendez-Garcia

first: Xia

last: Wu

first: Yaqun

last: Liu

first: Stefano

last: Gnan

first: Sami

last: El Hilali

first: Olivier

last: Brison

first: Filippo

last: Rosselli

last: Chen

first: Michelle

last: Debatisse


title: Unique sequence features define epigenetic longevity of inflammatory memory [scRNA-seq]

first: Luis

middle: F

last: Soto-Ugaldi

state: NY

institute: The Rockefeller University

summary: Many tissues harbor epigenetic memories of inflammation, which heighten sensitivity to diverse future assaults. Whether and how these adaptations are sustained through time and cell division remain poorly understood. Here, we show that epidermal stem cells store functional epigenetic records of a psoriatic skin flare that last a lifetime. Applying deep learning to interrogate these chromatin dynamics, we unearth CpG dinucleotide density as a major driver of memory persistence. Molecularly, while unnecessary for stress-induced chromatin opening, CpG dinucleotides thereafter become essential, reinforcing accessibility across cellular generations through a signature integrating DNA demethylation, methylation-sensitive transcription factors, sequence-intrinsic nucleosome disaffinity and nucleosome-destabilizing histone variant H2A.Z. Thus, inherent CpG enrichment within DNA sequence confers enduring adaptability to environmentally sensitive cis-regulatory elements, with profound consequences to long-term tissue fitness.

overall_design: Epidermal stem cells were collected under four biological conditions—day 30 naïve (D30-Naïve), day 30 post-IMQ inflammation (D30-PIMQ), year-1 naïve (Y1-Control) and year-1 post-IMQ inflammation (Y1-PIMQ)—with two independent replicates per condition. Single-cell libraries were prepared on the 10x Genomics Chromium platform, yielding paired gene-expression (GEX) and hashtag-oligonucleotide (HTO) FASTQ files for each replicate (eight FASTQ files in total).

first: Christopher

last: Cowley

first: Sairaj

last: Sajjath

first: Elaine

last: Fuchs


title: Disruption of the SAGA CORE triggers collateral degradation of KAT2A

city: Vienna

first: Paul

last: Batty

address: Zimmermann Platz 10

country: Austria

institute: CCRI

summary: The SAGA transcriptional co-activator complex regulates gene expression through histone acetylation at promoters, mediated by its histone acetyl transferase, KAT2A. While its structure and function have been extensively investigated, how the stability of individual subunits of SAGA, including KAT2A, is regulated, remains unclear. Here, using a fluorescence-based KAT2A stability reporter, we systematically dissect the molecular dependencies controlling KAT2A protein abundance. We identify the non-enzymatic SAGA CORE module subunits—TADA1, TAF5L, and TAF6L— as necessary for KAT2A stability, with loss of these subunits disrupting the integrity of SAGA, leading to non-chromatin-bound KAT2A that is degraded by the proteasome, consequently leading to reduced H3K9 acetylation. Proteomic profiling reveals progressive loss of CORE and HAT components upon acute disruption of the SAGA CORE, indicating that an intact CORE is required for the stability of numerous components of SAGA. Finally, a focused CRISPR screen of ubiquitin-proteasome system genes identifies the E3 ligase UBR5, a known regulator of orphan protein degradation, and the deubiquitinase OTUD5, as regulators of KAT2A degradation when the SAGA CORE is perturbed. Together, these findings reveal a dependency of KAT2A protein stability on SAGA CORE integrity and define an orphan quality control mechanism targeting unassembled KAT2A, revealing a potential vulnerability in SAGA-driven malignancies.

overall_design: CUT&RUN profiling of KAT2A (WT, KAT2A KO, TAF5L KO) and H3K9ac (WT, KAT2A KO, TAF5L KO, TAF6L KO) in asynchronous HAP1 cells.

first: Hannah

last: Beneder

first: Caroline

last: Schätz

first: Gabriel

last: Onea

first: Maciej

last: Zaczek

first: Ana

last: Kutschat

first: Miriam

last: Abele

first: Sophie

last: Müller

first: Giulio

last: Superti-Furga

first: Georg

last: Winter

first: Davide

last: Seruggia


title: GSK3α functions as a stemness checkpoint across multiple stem cell states

city: Omaha

first: Litao

last: Tao

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

summary: Mouse embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) represent the naïve and primed pluripotent states, respectively, each requiring distinct culture conditions. In this study, we show that BRD0705, a selective GSK3α inhibitor, significantly enhances the self-renewal of both ESCs and EpiSCs. When combined with IWR1, BRD0705 sustains long-term maintenance of ESCs in a naïve state and EpiSCs in a primed state, even preserving their unique identities under long-term co-culture. Single-cell RNA sequencing and histone mark profiling confirm that this regimen maintains distinct gene expression and epigenetic signatures corresponding to each pluripotent state. Importantly, unlike pan-GSK3 inhibitors CHIR-99021 (CHIR), BRD0705 acts independently of β-catenin signaling, unveiling a novel mechanism for supporting pluripotency. Finally, BRD0705/IWR1 also supports the maintenance of the formative pluripotent stem cells and neural stem cells. Collectively, we propose that GSK3α inhibition may preserve diverse stem cell states by insulating stem cells from differentiation cues and promoting their intrinsic self-renewal capacity. We believe our findings lay the foundation for universal stem cell culture methods with significant regenerative medicine applications.

overall_design: Change the β-catenin-/-ESCs culture medium to N2B27 overnight before RNA extraction, then treat with Ctr, BRD0705, or CHIR for 30 minutes respectively. Total RNA was extracted using the GeneJET RNA purification kit. For RNA-seq library preparation, 1 g total RNA was used to prepare the RNA-seq library with the Truseq RNA Library Prep Kit V2 with RiboZero (Illumina).

first: Duo

last: Wang

first: Xiukun

first: Gunag

last: Hu

first: Qi-Long

last: Ying


title: Unique sequence features define epigenetic longevity of inflammatory memory [Bisulfite-Seq]

first: Luis

last: Soto-Ugaldi

overall_design:
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads.

D6: Day 6;  Skin collected 6 days after the final IMQ application (peak inflammation).
D30: Day 30;  30 days post-IMQ, when the tissue has fully resolved and memory is established.
D180: Day 180 (~6 months);  180 days post-IMQ.
Y1: Year 1;  1 year post-IMQ.
Y1.5: Year 1.5;  18 months post-IMQ.
Y2: Year 2;  2 years post-IMQ.
"Naive" samples are age-matched untreated controls harvested at the same time-points; ?PIMQ? samples are from mice that received IMQ and were left untreated for the indicated interval.

first: Christopher

last: Cowley

first: Sairaj

last: Sajjath

first: Elaine


title: Unique sequence features define epigenetic longevity of inflammatory memory [RNA-seq]

overall_design: RNA-seq collected from EpdSCs following 6 hours topical treatment with TPA, one year post-IMQ inflammation together with age-matched control samples. Two replicates per condition/timepoint, with at least two mice pooled per replicate.

last: Fuchs


title: Unique sequence features define epigenetic longevity of inflammatory memory [ATAC-seq]

overall_design: ATAC-seq collected from EpdSCs from Day 180 to 2 years post IMQ inflammation together with control samples. Two replicates per conditoin/timepoint


title: Adipokine Adissp as a potential therapeutic agent for diabetes and cardiometabolic diseases

city: Worcester

first: Marcus

last: Ruscetti

state: MA

address: 364 Plantation Street

department: MCCB

institute: UMass Chan Medical School

summary: Adipokine Adissp simultaneously promotes glucose disposal and energy expenditure in adipose tissue. Treatment with recombinant Adissp (rAdissp) protein normalizes hyperglycemia and provides pleiotropic cardiometabolic benefits in diabetic and obese mice, primarily through its actions in white adipose tissue. RNA-seq analysis of inguinal white fat reveals that rAdissp activates a comprehensive thermogenic program characterized by enhanced mitochondrial metabolism, Ucp1-mediated uncoupling, glycolysis, and fatty acid futile cycling.

overall_design: Diet-induced obese mice were treated with rAdissp daily at 68 nmole/kg for 33 days. Inguinal white fat (iWAT) was collected and analyzed by RNA-seq.

first: Yong-xu

first: Lei

last: Huang

first: Kai


title: Clec3b+ portal fibroblasts as key contributors of periportal fibrosis via the KLF4/periostin axis during cholestatic liver injury

city: Changchun

first: Chenchen

last: Zhao

state: Jilin Province

address: 5333 Xi’an Road

department: College of Veterinary Medicine

institute: Jilin University

summary: Periportal fibrosis is a hallmark of cholestatic liver injury, yet the cellular origins and regulatory mechanisms underlying periportal fibrogenesis remain unclear. This study aims to identify the cellular origins and master regulators of cholestatic periportal fibrosis. Single-cell RNA sequencing was performed on bile duct-ligated (BDL) mouse model. A novel Clec3b-tdTomato lineage-tracing mouse model (Clec3bCreERT2) was generated to track portal fibroblast myofibroblastic activation in both BDL and 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) mouse models. Conditional deletion of Klf4 with Clec3bCreERT2 and adeno-associated virus (AAV6)-mediated KLF4 overexpression were employed to investigate the function of KLF4 in cholestatic liver diseases models. RNA sequencing (RNA-seq) and chromatin immunoprecipitation-sequencing (ChIP-seq) were used to identify KLF4 binding targets. AAV6 carrying short hairpin RNA targeting periostin (POSTN) and neutralizing antibodies were used to gain insight into the underlying mechanisms of POSTN. Single-cell analysis identified MFAP4 as a specific marker of portal fibroblasts and their myofibroblast derivatives during cholestatic liver fibrosis. Cell-fate mapping demonstrated that Clec3b+ portal fibroblasts serve as progenitors of myofibroblasts, and contribute to periportal fibrosis. KLF4 was identified as a pivotal regulator of myofibroblastic activation in portal fibroblasts, with expression inversely correlated with fibrosis severity. Mechanistically, KLF4 represses POSTN expression by binding to its promoter, while POSTN, through interaction with integrin αvβ5, activates fibrogenic signaling in Clec3b+ portal fibroblasts. This study provides new insights into the cellular and molecular mechanisms governing periportal fibrosis in cholestatic liver disease. We identify the Clec3b+ portal fibroblasts as critical contributors to periportal fibrosis and highlight the KLF4/POSTN signaling axis as a key regulatory pathway, offering potential therapeutic approaches for cholestatic liver fibrosis.

overall_design: To investigate the potential mechanisms by which KLF4 influences the transition of Clec3b-tdT⁺ portal fibroblasts into myofibroblasts, Clec3b-tdT⁺ cells were isolated from the livers of normal Clec3bCreERT2;R26tdT mice via fluorescence-activated cell sorting (FACS). These cells were then transduced with either a Klf4-overexpressing lentivirus (Lenti-Klf4) or a control lentivirus (Lenti-Ctrl). Following transduction, total RNA was extracted from the cells under both conditions, and RNA-seq was performed to analyze the gene expression profiles of Clec3b-tdT⁺ cells in response to Klf4 overexpression compared to the control.

first: Lin

last: Lei

first: Wenwen

last: Gao

first: Menglin

last: Liu

first: Guoyue

last: Lv

first: Zhongqi

last: Fan

first: Chantal

last: Housset

first: Fouad

last: Lafdil

first: Axelle

last: Cadoret

first: Sara

last: Lemoinne

first: Yongkang

last: Cheng

first: Jinxia

last: Li

first: Fanrong

last: Kong

first: Xiliang

last: Du

first: Yuxiang

last: Song

first: Guowen

first: Xinwei


title: Cell Death Modalities Modulate Inflammatory and Regenerative Programs in Zebrafish Sensory Organs

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Regeneration is triggered by cells dying due to various types of injuries. However, it remains unclear whether different types of cell death elicit distinct regeneration responses. Here, we systematically profile dynamic transcriptional responses of macrophages and lateral line cells to different cell death modalities during zebrafish sensory hair cell regeneration. We show that chemogenetically induced programmed hair cell death triggers a diminished inflammatory response compared to pharmacologically induced cell lysis, characterized by minimal neutrophil recruitment, distinct transcriptional profiles in phagocytosing macrophages and reduced expression of injury-responsive genes in lateral line cells. Nevertheless, regeneration ultimately converges on a shared set of regeneration-specific genes. Importantly, preventing immune cell recruitment enhances injury-induced support cell proliferation in response to programmed, but not unprogrammed cell death, highlighting cell death-dependent regenerative outcomes following immune cell inhibition. Our findings demonstrate that distinct forms of cell death trigger distinct molecular events, with implications for tailoring regenerative therapies to specific injury contexts.

overall_design: Macrophages and lateral line cells were isolated using FACS sorting and their transcriptomes analyzed using scRNA-seq.

first: Daniela

last: Muench

first: Tatjana

last: Piotrowski


title: In vivo CRISPR activation screening of tumor formation in murine pancreas and lung.

first: Fredrik

last: Thege

summary: We performed in vivo CRISPR activation screening of tumor formation in the pancreas and lung by treating CRISPRa competent PPKS (KRAS(LSL-G12D//wt); TP53(flox/flox); Rosa26(LSL-SAM/wt)) mice with CMV-Cre/U6-sgRNA(MS2) lentivirus containing the Onco1 sgRNA guide library. Tissues were harvested at different timepoints (6 days, 4 weeks, 8 weeks and survival endpoint). HEK293T cell cultures were transduced with the same libraries to generate normalization controls. Library plasmid DNA (pDNA) was sequenced as controls.

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus

overall_design: 24 PPKS mice were treated with the Onco1 library through retrograde ductal injections to the pancreas and 29 mice were treated through nasal instillation. HEK293T cells were transduced with the Onco1 library at an MOI < 0.3. Genomic DNA was extracted from tissues and cell cultures. Sequencing libraries were generated using direct PCR of guide sequence containing region.

first: Anirban

last: Maitra

first: Sonja

last: Woermann


title: Unique sequence features define epigenetic longevity of inflammatory memory [CUT&Run]

first: Luis

last: Soto-Ugaldi

overall_design: CNR-seq was performed from EpdSCs for JUN in mice 1 Year post-IMQ inflammation to gether with never-inflamed mice. CNR-seq was performed from EpdSCs for FOS in mice 1 Year post-IMQ inflammation together with neverinflamed mice when treated with TPA

first: Christopher

last: Cowley

first: Sairaj

last: Sajjath

first: Elaine

last: Fuchs


title: Unique sequence features define epigenetic longevity of inflammatory memory [ChIP-Seq]

overall_design: Mint-ChIP was performed from EpdSCs at Year1 Post IMQ inflammation for H3k4me1 and H3k27ac together with control samples.  Mint-ChIP was also collected from Day 6 IMQ and Day 30 post IMQ for H2A.Z histone variant together with control samples. Two replicates per conditoin/timepoint.


title: Clec3b+ portal fibroblasts as key contributors of periportal fibrosis via the KLF4/periostin axis during cholestatic liver injury [ChIP-Seq]

first: Chenchen

last: Zhao

overall_design: To investigate the potential mechanisms by which KLF4 influences the transition of Clec3b-tdT⁺ portal fibroblasts into myofibroblasts, Clec3b-tdT⁺ cells were isolated from the livers of Clec3bCreERT2;R26tdT mice using fluorescence-activated cell sorting (FACS). ChIP-seq was then performed on these Clec3b-tdT⁺ cells following lentivirus-mediated overexpression of Klf4.

first: Lin

last: Lei

first: Wenwen

last: Gao

first: Menglin

last: Liu

first: Guoyue

last: Lv

first: Zhongqi

last: Fan

first: Chantal

last: Housset

first: Fouad

last: Lafdil

first: Axelle

last: Cadoret

first: Sara

first: Yongkang


title: Widespread non-Mendelian inheritance of DNA methylation patterns in mice [ONT Muscle]

city: Baltimore

first: Adam

last: Davidovich

state: Maryland

address: 855 N. Wolfe Street

institute: Johns Hopkins University

summary: We performed long-read ONT sequencing on two Collaborative Cross mouse strains and their F1 crosses. Allele-specific methylation analyses revealed widespread and diverse patterns of intergenerational epigenetic inheritance. Included among these are a large number of non-Mendelian inheritance patterns, many of which have not previously been observed in naturally occurring mammalian genomes.

overall_design: ONT sequencing was performed on muscle DNA from two Collaborative Cross mouse strains and their F1 crosses.

first: Danila

last: Cuomo

first: Hang

last: Su

first: Sandeep

last: Kambhampati

first: Qingqing

last: Gong

first: Alexandra

last: Naron

first: Rakel

last: Tryggvadottir

first: Leonard

last: McMillan

first: Kasper

last: Hansen

first: David

last: Threadgill

first: Andrew

last: Feinberg


title: Clec3b⁺ fibroblasts are the primary effectors of portal fibrosis following activation via a KLF4/periostin axis

first: Lin

last: Lei

address: 5333 Xi’an Road, Changchun, Jilin, China

department: State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Veterinary Medicine

summary: Portal fibrosis, a determinant of progression in virtually all chronic liver diseases, prototypically develops in biliary diseases. Using single-cell RNA sequencing and genetic cell fate tracing in mouse models, we identified Clec3b⁺ fibroblasts as a distinct subset of portal fibroblasts, which rapidly expand after biliary injury and give rise to the bulk portal myofibroblasts. Mechanistic analyses revealed that Clec3b⁺ portal fibroblasts activation is governed by a Krüppel-like factor 4 (KLF4)/periostin (POSTN) axis, i.e., KLF4 directly binds the Postn promoter and represses its transcription, while POSTN, acting via αvβ5 integrin, drives portal fibroblast activation and portal fibrosis. Our findings identify Clec3b+ portal fibroblasts as the primary effectors of portal fibrosis and demonstrate that the KLF4/POSTN signaling axis regulates their activation, offering potential therapeutic targets for inhibiting fibrosis in biliary diseases.

overall_design:
We conducted a comprehensive scRNA-seq analysis of the bilio-vascular trees from the mice  subjected to bile duct ligation (BDL)-induced cholestasis, and compared the profiles with those of control mice. We identified 15 major hepatic cell clusters comprising myeloid cells, lymphoid cells, endothelial cells, epithelial cells, and mesenchymal cells, and explored the extent of cell diversity within fibrotic mesenchymal cell populations.

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The table below lists GEO accessions reused/reanalyzed for this study.
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last: LEI

first: Chenchen

last: ZHAO

first: Wenwen

last: GAO

first: Guowen

last: LIU

first: Xinwei

last: LI


title: Single-cell epigenetic landscape, microenvironment interactions, and gene regulatory modules of non-functioning pituitary adenomas (non-diseased controls, snMultiome, multiplexed)

city: Los Angeles

first: Frederique

last: Ruf-Zamojski

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: The epigenetic landscape and tumor microenvironment (TME) interactions of non-functioning pituitary adenomas (NFPAs), benign tumors with high morbidity and recurrence rates, are not well characterized. We completed single-nucleus (sn) multiomics assays on four gonadotrope NFPAs. We identified genes involved in bidirectional tumor-macrophage crosstalk. We uncovered coordinated gene expression and chromatin accessibility programs that distinguished adenoma cells from gonadotropes. Integrated transcriptome-chromatin modeling revealed gene regulatory circuits that showed altered activity in adenoma cells. Our study provides insight into the altered epigenetic gene-control landscape and TME processes of the NFPA tumor phenotype.

overall_design: snMultiome: single nuclei were extracted from human control non-diseased human pituitaries samples. Joint snRNA-seq and snATAC-seq libraries were prepared using the 10X Genomics platform. 22 samples were processed as 6 multiplexed runs.

first: Zidong

last: Zhang

first: Wan Sze

last: Cheng

first: Michel

last: Zamojski


title: Single-cell epigenetic landscape, microenvironment interactions, and gene regulatory modules of non-functioning pituitary adenomas (non-diseased controls, snMultiome, single sample)

overall_design: snMultiome: single nuclei were extracted from human control non-diseased human pituitaries samples. Joint snRNA-seq and snATAC-seq libraries were prepared using the 10X Genomics platform. 6 samples were processed as individual runs.


title: Single-cell epigenetic landscape, microenvironment interactions, and gene regulatory modules of non-functioning pituitary adenomas (NFPA)

overall_design: snMultiome: single nuclei were extracted from human non-functioning pituitary adenoma tissue samples. Joint snRNA-seq and snATAC-seq libraries were prepared using the 10X Genomics platform.


title: Single-cell epigenetic landscape, microenvironment interactions, and gene regulatory modules of non-functioning pituitary adenomas (non-diseased controls, bulkRNAseq)

overall_design: Bulk RNA-seq: RNA-seq was performed on the control pituitary tissue per sample for those 22 samples included in the multiplexed snMultiome runs for the purpose of sample deconvolution.

first: German

last: Nudelman