title: Non-canonical roles of Keap1/Nrf2 in regulating quiescence and early activation in adult muscle stem cells [RNA-Seq]

status: Public on Sep 28 2025

city: Hong Kong

first: Lifang

last: HAN

address: 6202D, Clear Water Bay

department: LIFS

institute: HKUST

summary: Adult muscle satellite cells (MuSCs) are mostly quiescent in uninjured muscles under normal homeostasis. Although several mechanisms underlying quiescence maintenance are known, our understanding of the process remains incomplete. Here, we show that Keap1 regulates MuSC quiescence maintenance by promoting Nrf2 protein degradation. Inducible deletion of Keap1 activates MuSCs to different extent in a sex-specific manner via differential Nrf2 protein levels: in Keap1-null MuSCs from male mice, Nrf2 protein is at an intermediate level due to the action of a GSK3beta-dependent Nrf2 degradation system, which promotes mutant MuSCs to enter a GAlert-like state; in Keap1-null MuSCs from female mice, the loss of Keap1 together with estrogen-mediated GSK3beta inactivation renders Nrf2 at its highest level, which induces the expression of multiple metabolic genes resulting in metabolic reprogramming, spontaneous activation and gradual depletion of MuSCs. Consistently, interference of selected Nrf2-regulated metabolic genes impairs early activation of MuSCs. Thus, Keap1/Nrf2 regulates quiescence maintenance and early activation of MuSCs independently of its canonical roles in the antioxidant response.

overall_design: To understand why Keap1/Nrf2 signaling regulate MuSC maintenance and activation in a gender-dependent manner, we freshly isolated MuSCs from Keap1 Hetz and KO female and male mice.

last: Han

first: Zhenguo

last: Wu


title: OSR1 and SIX2 Drive Divergent Transcriptional Programs in Human Kidney Cells: Implications for Regeneration and Tumorigenesis\

status: Public on Sep 26 2025

city: TEL AVIV

first: Naomi

last: Pode-Shakked

address: Weizmann St 6

department: Pediatric Nephrology

country: Israel

institute: Tel Aviv Souraski Medical Center

type: Expression profiling by high throughput sequencing

summary: During human nephrogenesis, nephron progenitor cells generate approximately one million nephrons. We investigated the effects of ectopic expression of OSR1 and SIX2, both individually and in combination, in adult human kidney cells. OSR1 and SIX2 induced distinct reprogramming programs with differential functional outcomes. SIX2 overexpression maintained epithelial morphology while significantly enhancing proliferation and clonogenic efficiency. Transcriptionally, SIX2 established epithelialization and cell cycle networks, downregulating proximal tubule markers, while upregulating distal nephron markers and proliferation genes. In vivo, SIX2-expressing cells formed organized tubular structures with distinct luminal architecture. In contrast, OSR1 overexpression induced morphological changes and activated developmental morphogenetic pathways but did not enhance proliferation and showed minimal tubulogenic capacity. RNA sequencing analysis revealed coordinated changes in nephron segment-specific markers and activation of distinct transcriptional programs.\

overall_design:
Expression profiling by high-throughput RNA sequencing. Adult human kidney epithelial cells (hKEpCs) were transduced with lentiviral vectors encoding SIX2, OSR1, OSR1+SIX2, or mCherry control. Three biological replicates per condition (except Double condition with 2 replicates). RNA extracted using RNeasy Mini Kit, libraries prepared with TruSeq Stranded mRNA Library Prep Kit, sequenced on Illumina NovaSeq 6000 (paired-end 150bp, >30M reads/sample). Differential expression analyzed with DESeq2.\

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first: Osnat

last: Cohen-Zontag

first: Dorit

last: Omer

first: Orit

last: Harari-Steinberg

first: Einav

last: Vax

first: Oren

last: Pleniceanu

first: Benjamin

last: Dekel


title: A sperm-enriched 5’fragment of tRNA-Valine regulates preimplantation embryonic transcriptome and development

status: Public on Sep 30 2025

city: Santa Cruz

first: Upasna

last: Sharma

state: California

address: 1156 High St

department: MCD Biology

country: USA

institute: UCSC

summary: Sperm small RNAs have been implicated in intergenerational epigenetic inheritance of paternal environmental effects; however, their biogenesis and functions remain poorly understood. We previously identified a 5’ fragment of tRNA-Valine-CAC-2 (tRFValCAC) as one of the most abundant tRNA fragments in mature mouse sperm. We previously reported that tRFValCAC is specifically enriched in sperm during post-testicular maturation in the epididymis, and extracellular vesicles secreted by the epididymis epithelial cells can deliver tRFValCAC to sperm. Here, we investigated the mechanistic basis of tRFValCAC delivery from epididymis to sperm and its functions during early embryonic development. We show that tRFValCAC interacts with an RNA binding protein, heterogeneous nuclear ribonucleoprotein A/B (hnRNPAB), in the epididymis and that hnRNPAB regulates the levels of tRFValCAC in the vesicles secreted by epididymis epithelial cells. Inhibition of tRFValCAC in preimplantation embryos altered the transcript abundance of genes involved in RNA splicing and mRNA processing. Importantly, tRFValCAC-inhibited embryos showed altered mRNA splicing, including alternative splicing of various splicing factors and genes important for proper preimplantation embryonic development. Moreover, our data suggest that tRFValCAC regulates its target genes via interaction with RNA-binding proteins. Finally, we find that inhibition of tRFValCAC in zygotes delayed preimplantation embryonic development. Together, our results reveal a potential function of a sperm-enriched tRF in regulating alternating splicing and preimplantation embryonic development and shed light on the mechanism of sperm small RNA-mediated epigenetic inheritance.

overall_design: We examined the regulatory roles of tRFValCAC in early preimplantation embryos by inhibiting tRFValCAC using an antisense locked-nucleic acid (LNA) containing oligo targeting tRFValCAC (Val_LNA). Embryos were microinjected with either H3.3-GFP mRNA with LNA-containing scramble oligo (Ctrl_LNA) (control group) or H3.3-GFP mRNA plus tRFValCAC antisense LNA oligo (Val_LNA) (experimental group). GFP-positive embryos were cultured until the late 2-cell stage for mRNA-seq (28 hours post-IVF).

first: Simeiyun

last: Liu

first: Andrew

middle: D

last: Holmes

first: Sol

last: Katzman


title: Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma

status: Public on Sep 29 2025

city: Camperdown

first: George

middle: Louis

last: Joun

state: NSW

address: John Hopkins Drive

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Non-canonical roles of Keap1/Nrf2 in regulating quiescence and early activation in adult muscle stem cells

country: China


title: MeRIP-seq and RNA-seq Reveals RNA m6A Methylation Patterns and Gene Expression Profile of Arabidopsis Plants in Response to CMV Infection

city: Shenzhen

first: yujing

last: lin

address: No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen City, Guangdong Province

institute: Southern University of Science and Technology

type: Methylation profiling by high throughput sequencing

summary: We reported that m6A plays a positive role in plant defense against virus pathogen Cucumber mosaic virus (CMV). CMV genomic RNAs can be m6A modified during plant infection, leading to reduced stability of viral RNAs. Dysfunctions of m6A writers and some readers led to increased susceptibility to CMV. Intriguingly, the increased susceptibility was only observed in the absence of 2b protein encoded by CMV. Our data demonstrated that CMV-2b can inhibit the deposition of m6A at viral RNAs through interfering with the assembly of m6A catalytic complexes. Expression of 2b protein can also antagonize plant m6A deposition. Moreover, CMV-2b was also found to interact with m6A reader proteins to disrupt its recognition of m6A-marked viral RNAs. Our findings unraveled an antagonistic mechanism of m6A-mediated plant antiviral defense.

overall_design: The Arabidopsis Col-0 plants were inoculated by wild-type cucumber mosaic virus (CMV) and the mutated virus deficient in 2b protein (CMVΔ2b). At 14 days post infection, CMV and CMVΔ2b-infected plants as well as uninfected mock plants were subjected to MeRIP-seq and RNA-seq analysis.

first: Jiahui

first: Yujing

last: Lin

first: Chengguo

last: Duan


title: Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma [ChIP-seq]

summary: Chemotherapy often kills a large fraction of cancer cells but leaves behind a small population of drug-tolerant persister cells. These persister cells survive drug treatments through reversible, non-genetic mechanisms and cause tumour recurrence upon cessation of therapy. Here, we report a drug tolerance mechanism regulated by the germ-cell-specific H3K4 methyltransferase PRDM9. Through histone proteomic, transcriptomic, lipidomic, and ChIP-sequencing studies combined with CRISPR knockout and phenotypic drug screens, we identified that chemotherapy-induced PRDM9 upregulation promotes metabolic rewiring in glioblastoma stem cells, leading to chemotherapy tolerance. Mechanistically, PRDM9-dependent H3K4me3 at cholesterol biosynthesis genes enhances cholesterol biosynthesis, which persister cells rely on to maintain homeostasis under chemotherapy-induced oxidative stress and lipid peroxidation. PRDM9 inhibition, combined with chemotherapy, resulted in strong anti-cancer efficacy in preclinical glioblastoma models, significantly enhancing the magnitude and duration of the antitumor response by eliminating persisters. These findings reveal a previously unknown role of PRDM9 in promoting metabolic reprogramming that enables the survival of drug-tolerant persister cells.

overall_design: PRDM9 Knock-out RKI1 glioblastoma stem cell line was treated with +/- 10µM CMPD1 for 72 hours. The KO cell line was compared to Non-Targetted Control (NTC) RKI1 glioblastoma stem cell line, also treated with +/- 10µM CMPD1 for 72 hours, of the same transduction batch and passage number within each biological replicate. There are two biological repeats. We excluded RKI1 n=2 NTC UT (Sample013) from downstream analysis due to suspected sample degradation in the H3K4me3 ChIP sample.

first: Lenka

last: Munoz


title: Biomimetic fractal topography enhances podocyte maturation in vitro

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

country: Canada

institute: University of Toronto

summary: Cells and tissues in their native environment are organized into intricate fractal structures, which are rarely recapitulated in their culture in vitro. The extent to which fractal patterns that resemble complex topography in vivo influence cell maturation, and the cellular responses to such shape stimulation remain inadequately elucidated. Yet, the application of fractal cues (topographical stimulation via self-similar patterns) as an external input may offer a much-needed solution to the challenge of improving the differentiated cell phenotype in vitro. Here, we established fractality in the kidney glomerulus and podocytes, branching highly differentiated kidney cells within the glomerulus. Biomimetic fractal patterns derived from glomerular histology were used to generate topographical (2.5-D) substrates for cell culture. Podocytes grown on fractal topography expressed higher levels of functional markers and exhibited enhanced cell polarity. To track morphological complexities of differentiated podocytes, we employed a fluorescent labelling assay where labelled individual cells are tracked within otherwise optically silent confluent cell monolayer to reveal single-cell borders. RNAseq analysis suggested enhanced ECM deposition and remodeling in podocytes grown on fractal substrates versus flat surfaces, and enhanced maturation accompanied by stress in podocytes grown on fractal versus non-fractal topography. The incorporation of fractal topography into standard tissue culture well plates as demonstrated here may serve as a user-friendly bioengineered platform for high-fidelity cell culture.

overall_design: RNA-seq profiling of E11 murine porodyctes cultured on polydimethylsiloxane (PDMS) substrates with No Topography (NT), Round Topography (RT), and High Fractal (HF) topography where NT and RT serve as non-fractal non-topographic control and non-fractal topographic control groups, respectively, and HF refers to a biomimetic high fractal topographic group derived from healthy histological glomerular tracing

first: Chuan

first: Praful

last: Aggarwal

first: Karl

middle: T

last: Wagner

first: Shira

middle: S

last: Landau

first: Teng

last: Cui

first: Xin

last: Song

first: Laleh

last: Shamaei

first: Naimeh

last: Rafatian

first: Yimu

last: Zhao

first: Sonia

last: Rodriguez-Ramirez

first: Keith

last: Morton

first: Elizabeth

last: Virlee

first: Chen Yu

last: Li

first: Dawn

last: Bannerman

first: Simon

last: Pascual-Gil

first: Sargol

last: Okhovatian

first: Anastasia

first: Sergi

last: Clotet-Freixas

first: Teodor

last: Veres

first: Mohtada

last: Sadrzadeh

first: Tobin

last: Filleter

first: Ulrich

last: Broeckel

first: Ana

last: Konvalinka


title: RNA-seq analysis of the impact of intermediate passaging on cell fate determination of mesendoderm progenitors

city: Macau

first: Guokai

last: Chen

address: University of Macau Avenida da Universidade Taipa, Macau, China

institute: University of Macau

summary: To investigate the impact of intermediate passaging on cell fate determination, cells were passaged during mesendoderm differentiation, and samples collected at different time points were subjected to bulk RNA-seq. We report here that intermediate passaging alters cell fate and directs mesendodermal progenitors toward cardiac cell fate.

overall_design: Bulk RNA-seq on samples collected on Day 0,1,2,3,5,7,10 of differentiation, comparing non-passaged cells differentiated in the presence and absence of WNT inhibitor versus cells that differentiated following intermediate passaging.

first: Weiwei

last: LIU

first: Chuyu

first: Ningyi

last: SHAO

last: CHEN


title: Single-cell RNA sequencing of lung tissues from non-irradiated wild-type, irradiated conditional knockout with drug treatment, and irradiated wild-type mice

city: Seoul

first: Yoon-Jin

last: Lee

address: Nowon GU

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences

summary: This dataset provides scRNA-seq profiles of lung tissues from three experimental groups: non-irradiated wild-type controls, irradiated conditional knockout mice treated with drug, and irradiated wild-type mice. The data enable analysis of radiation-induced lung injury, gene expression reprogramming, and the modulatory role of both conditional gene deletion and pharmacological intervention.

overall_design: Lung tissues were collected from three groups of mice: 1.Non-irradiated wild-type mice (control) : NoIR2 2.Irradiated conditional knockout mice treated with drug : KO 3.Irradiated wild-type mice : WT

first: Jeeyong

first: Jae-Kyung

last: Nam


title: Translatome of Dorsal Striatum Parvalbumin interneurons revisited: insights across diverse experimental paradigms [RiboTag]

status: Public on Sep 25 2025

city: Bellaterra (Cerdanyola del Vallès)

first: Laura

last: Cutando Ruiz

state: Barcelona

address: Facultat de Medicina, M1/125, Av. de Can Domènech Campus de la UAB · 08193 Bellaterra

department: Department of Cellular Biology, Physiology and Immunology - Institute of Neurosciences

country: Spain

institute: Universitat Autònoma de Barcelona

summary: Parvalbumin (PV) interneurons in the dorsal striatum (DS) are fast-spiking GABAergic cells critical for feedforward inhibition and synaptic integration within basal ganglia circuits. Despite their well-characterized electrophysiological roles, their molecular identity remains incompletely defined. Using the Ribotag approach in Pvalb-Cre mice, we profiled the translatome of DS PV interneurons and identified over 2,700 transcripts significantly enriched (fold-change > 1.5) in this population. Our data validate established PV markers and reveal a distinct molecular signature of DS PV neurons compared to PV interneurons from the nucleus accumbens. Gene ontology analyses highlight prominent expression of genes related to extracellular matrix components, cell adhesion molecules, synaptic organization, ion channels, and neurotransmitter receptors, particularly those mediating glutamatergic and GABAergic signaling. Notably, perineuronal net markers were robustly expressed in DS PV interneurons and confirmed by immunofluorescence. Transcriptomic analysis of DS PV neurons following repeated d-amphetamine exposure identified Gm20683 as the only differentially expressed transcript between treated groups. Furthermore, RNAseq analysis of mice subjected to an operant behavior paradigm with two types of food reward (high-palatable diet or standard chow) identified over 1,000 and 100 genes enriched in DS PV neurons from standard and high-palatable masters, respectively. These findings provide a comprehensive molecular profile of DS PV interneurons, distinguishing them from other striatal PV populations, and reveal specific gene expression changes associated with psychostimulant exposure and reward-driven behaviors. Our findings deepen insight into the molecular mechanisms of PV interneuron activity in striatal circuits and their potential roles in neuropsychiatric, motor and reward-related disorders.

overall_design: Whole striata were extracted from adult Pvalb-Ribotag mice, as previously described (Puighermanal et al., 2020). Striatal tissue from two to three mice was pooled to generate a single sample for polyribosome immunoprecipitation and subsequent RNAseq. Punches containing striata of Pvalb-Cre:RiboTag mice were homogenized and incubated with anti-hemagglutin (HA) antibodies and protein A/G magnetic beads to isolate the polysome-associated mRNAS in PV neurons.

first: Emmanuel

last: Valjent

last: Cutando


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues [ChIP-Seq]

city: La Jolla

first: Julie

middle: A

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: Plant Molecular and Cellular Biology

institute: Salk Institute for Biological Studies

summary: DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to anther or ovule tissues. We designate these factors as REM INSTRUCT METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. Furthermore, we demonstrate that mis-expression of RIM12 is sufficient to initiate siRNA production at ovule targets in anthers. These findings reveal a critical role for genetic information in targeting DNA methylation in reproductive tissues, expanding our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

overall_design: 14 ChIP-seq libraries were sequenced.

first: Guanghui

last: Xu

first: Yuhan

last: Martins

first: En

last: Li

first: Fuxi

last: Wang

first: Tulio

last: Magana

first: Junlin

last: Ruan


title: Non-canonical roles of Keap1/Nrf2 in regulating quiescence and early activation in adult muscle stem cells [ChIP-Seq]

first: Lifang

last: HAN

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Nrf2 in freshly isolated Keap1-null and Nrf2-null muscle satellite cells

last: Han

first: Zhenguo

last: Wu


title: Regional Conservation and Transcriptional Regulation of  Tumor-Associated Genes by macroH2A1 Deposition in  Mammalian Cells

city: Minhang

first: deng

last: yongzhuo

state: Shanghai

address: DongchuanoRoad N0.800

institute: Shanghai Jiao Tong University

summary: Histone variant macroH2A1 has been widely recognized as a suppressor of gene expression. Recently, a cell cycle dependent deposition of macroH2A1 is discovered in mouse cells, but whether this process exists in human chromatin is unclear, which might be crutial for related diseases, particularly cancer. In this study, we firstly demonstrate that dynamic macroH2A1 domains occurs in both normal and cancerous human cells. Our findings provide new epigenetic insights into the role of macroH2A1 in malignant proliferation, offering a novel perspective for furture cancer research.

overall_design: native Chromatin immunoprecipitation and DNA-sequencing (nChIP-seq) for histone variants macroH2A1 in ARPE-19 cells and HeLa cells in G1/S phase and metaphase

first: Yongzhuo

last: Deng

first: Zeqian

first: Xinhui

first: Le

last: Zhang

first: Zhifeng

last: Shao

first: Bishan

last: Ye


title: Translatome of Dorsal Striatum Parvalbumin interneurons revisited: insights across diverse experimental paradigms [RNA-Seq]

first: Laura

last: Cutando Ruiz

first: Emmanuel

last: Valjent


title: The impact of hsa_circ_0001910 on downstream gene expression changes in breast cancer cells

city: Shijiazhuang

first: Fei

last: Liu

state: China

address: No. 12 Jiankang Road

institute: The Fourth Hospital of Hebei Medical University Cancer Institute

summary: To investigate the impact of hsa_circ_0001910 on downstream genes in breast cancer cells, we knocked down the expression of hsa_circ_0001910 in MDA-MB-231 cells and observed the changes in downstream gene expression.

overall_design: MDA-MB-231 cells were transfected with hsa_circ_0001910 siRNA and siNC. Three independent experiments were performed.

first: Yang

last: Sang


title: Single cell analysis of the impact of intermediate passaging on cell fate determination of mesendoderm progenitors

first: Guokai

last: Chen

summary: To investigate the impact of intermediate passaging on cell fate determination, cells were passaged during mesendoderm differentiation, and samples collected at different time points were subjected to single cell RNA sequencing. We report here that intermediate passaging alters cell fate and directs mesendodermal progenitors toward cardiac cell fate.

overall_design: Single cell RNA sequencing on samples collected on Day 2, 3 and 10 of differentiation, comparing passaged and non-passaged cells in the presence and absence of WNT inhibitor.

first: Weiwei

last: LIU

first: Chuyu

first: Ningyi

last: SHAO

last: CHEN


title: Transient RORβ Knockdown by Cell-penetrating siRNA Alleviates Retinal Degeneration Caused by Proteotoxicity

city: Ulsan

first: Hyo Kyung

last: Lee

address: UNIST-gil 50

department: Biomedical engineering

institute: UNIST

summary: Retinitis pigmentosa (RP) is characterized by rod photoreceptor degeneration-driven apoptosis, which secondarily triggers cone photoreceptor loss and eventual blindness. Preserving rod function remains a primary therapeutic objective. Inspired by prior studies demonstrating that neural retina leucine zipper (Nrl) knockdown conferred resistance to rod mutations and induced in vivo rod-to-cone conversion with therapeutic effects in inherited retinal degeneration (IRD) models, we hypothesized that knockdown of retinoid-related orphan receptor beta (RORβ), an upstream regulator of Nrl, could yield similar or superior outcomes. To test this, we developed a cell-penetrating asymmetric siRNA (cp-asiRNA) targeting RORβ (cp-asiRORB), designed to overcome conventional siRNA limitations, including inefficient cellular delivery, off-target effects, and immune activation. Intravitreal administration of cp-asiRORB in RhoP23H mice—an autosomal dominant RP model harboring the P23H rhodopsin mutation—successfully reduced RORβ expression in rod photoreceptors. Contrary to our initial expectation of observing an in vivo reprogramming effect, RORβ knockdown did not seem to induce rod-to-cone conversion. Instead, transient RORβ suppression effectively mitigated apoptosis by enhancing proteostasis, leading to improved rod survival, reduced degeneration, and preserved visual function.  Furthermore, single-cell RNA sequencing of retinas treated with cp-asiRORB in RhoP23H mice revealed significant upregulation of proteasomal subunits in RORβ-reduced rod photoreceptors. Consistent with these findings, in HEK293T cells under proteotoxic stress, RORβ knockdown reduced apoptosis, improved cell viability, and diminished aggresome formation. These results demonstrate that transient RORβ suppression alleviates RP progression by augmenting proteasomal activity to resolve proteotoxicity, offering a novel therapeutic avenue for RP patients.

overall_design: All animal experiments were performed in accordance with the guidelines approved by the Institutional Animal Care and Use Committee (IACUC) of Konkuk University (Approval No. KU24219). The mice were housed under a 12-hour light/dark cycle at a temperature of 22 ± 2°C and humidity of 50 ± 10%, with free access to food and water. Two- and eight-week-old C57BL/6J mice were obtained from DBL (Incheon, Korea), while RhoP23H mice and rd10 mice were purchased from Jackson Laboratory (Bar Harbor, Maine, USA) and bred under Specific Pathogen-Free (SPF) conditions at the Konkuk University Laboratory Animal Research Center. Genotyping was performed using PCR with specific primers (primer sequences in Supplementary Table S1). Experiments involving RhoP23H mice utilized heterozygous animals, while those involving rd10 mice used homozygous animals. All experimental groups were randomly assigned. Two-week-old RhoP23H and rd10 mice were carefully administered an intravitreal injection of cp-asiRORβ (1 μg/μL), followed by analysis three weeks later. The same procedure was performed on two- and eight-week-old C57BL/6J mice.

first: Chanok

last: Son

first: Hyoik

last: Jang

first: Chul-Woo

last: Park

first: Dong Ki

first: Semin

first: Hyewon

last: Chung


title: Time-course Transcriptomics Reveals Impact of Treponema pallidum on Microvascular Endothelial Cell Function and Phenotype

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

institute: Simon Fraser University

summary: Syphilis, caused by Treponema pallidum subsp. pallidum, is an urgent global public health threat. Syphilis vaccine development has been impeded by limited understanding of the molecular mechanisms that enable T. pallidum to establish and maintain infection. The vascular endothelium is critical for T. pallidum attachment, dissemination, and host immune response initiation; however, the molecular details of T. pallidum-endothelial interactions are incompletely understood. To enhance understanding, we performed time-course transcriptomic profiling on T. pallidum-exposed brain microvascular endothelial cells. These analyses showed T. pallidum exposure alters pathways related to extracellular matrix, growth factors, integrins, and Rho GTPases. The induced transcriptional response was consistent with endothelial to mesenchymal transition, a key process involved in fetal development and vascular dysfunction. This study provides a comprehensive understanding of the molecular response of endothelial cells to T. pallidum and identifies the host pathways that may cause syphilis disease symptoms, information that could aid syphilis vaccine design.

overall_design: This project aimed to investigate the temporal transcriptomic response of hCMEC/d3 human brain microvascular endothelial cells to T. pallidum. To complete this aim we exposed hCMEC/d3 cells to Treponema pallidum subsp. pallidum at a multiplicity of infection of 30, or a background control lacking the pathogen, and measured the endothelial transcriptional response at 45-minutes, 4-, 12-, and 24-hours post-exposure.

first: Sean

last: Waugh

first: Mara

middle: C

last: Goodyear

first: Alloysius

last: Gomez

first: Akash

last: Ranasinghe

first: Karen

middle: V

last: Lithgow

first: Robert

middle: E

last: Hancock

first: Amy

middle: H

first: Caroline

last: Cameron


title: RNA-seq analysis of the impact of intermediate passaging on cell fate determination of mesendoderm progenitors [Day 12 & 16]

first: Guokai

last: Chen

overall_design: Bulk RNA-seq on samples were collected on Day 12 and Day 16 of differentiation, comparing non-passaged cells differentiated in the presence and absence of WNT inhibitor versus cells that differentiated following intermediate passaging.

first: Weiwei

last: Liu

first: Chuyu

first: Ningyi

last: Shao


title: WT1-Expressing Mesenchymal Cells Promote Pancreatic Cancer Growth

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

summary: Here, we sought to understand the functional role of WT1-Expressing cells in pancreatic ductal adenocarcinoma.

overall_design: Normal Pancreata were collected from 2 adult male mice (7 months old) and processed for sequencing. For sequencing of untreated orthotopic tumors, 2 adult female mice (6 months old) received orthotopic injections of 50,000 7940b cells (C57Bl6J strain, Ptf1acre/+;KrasLSLG12D/+;p53flox/+) into the pancreas. Orthotopic tumors grew for 3 weeks before the tumors were dissected for sequencing. For sequencing of diptheria toxin treated tumors, 3 adult male R26tdTomato/DTR mice and 2 adult male WT1-CreERT2/+; R26tdTomato/DTR mice were implanted orthotopically with 50,000 7940b cells. Four days following orthotopic injection, mice recieved 5 daily doses of oral gavage tamoxifen (4mg/daily) and were maintained on tamoxifen chow for the remaining duration of the experiment. The day after the final dose of oral gavage tamoxifen, mice recieved intraperitoneal injections of diptheria toxin every 4-7 days (25ug/kg) until mice were euthanized and tumors dissected for sequencing (3 weeks after orthotopic implantation).

first: Allison

last: Bischoff

first: Yaqing

last: Zhang


title: Human B cells induced by primary SARS-CoV-2 infection

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E 69th St

department: Pediatrics

institute: Weill Cornell Medicine

summary: This study was designed to capture the single cell transcriptome and BCR sequence of B cells that were bait sorted using oligo-tagged viral antigens.

overall_design: Human B cells (viable/CD19+/antigen-PE+ or viable/CD19+/antigen-APC+) were bait sorted after initial magnetic enrichment and used in downstream sequencing.

first: Siriruk

last: Changrob

first: Lei

last: Li

first: Chloe

last: Troxell


title: Protective effect of Golden Bifid treatment on slow transit constipation rat

city: Fuzhou

first: Aling

last: Shen

state: Fujian

address: 1 Qiuyang road, Minhou Shangjie

institute: Fujian university of Traditional Chinese Medicine

summary: The goal of this study is to compare the differently expressed genes in colon tissue of Control and loperamide (LOP) induced slow transit constipation (STC) rat model with or without Golden Bifid (Jin Shuang Qi, JSQ) or positive control group (Prukapril Succinate Tablet, PST) treatment. The loperamide induced STC rat model were randomly divided into 3 groups: LOP, LOP + JSQ and LOP + PST groups (n=6 for each group). Control rats (n=6) were set as control. The STC rat model was induced by administering loperamide intraperitoneally at a dose of 3 mg/kg body weight twice daily for 21 days in all groups except the Control group. On the 8th day, the LOP + JSQ group was intragastrically with 0.540 g/kg/d 1 h after each loperamide administration for 14 days. The LOP + PST group was given prucalopride succinate tablets at a dose of 0.18 mg/kg/d by oral gavage 1 h after each loperamide administration for 14 days. Then the colon tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with colonic rats in 4 groups: Control, LOP, LOP + JSQ and LOP + PST treated (n=6 for each group) to identify the differently expressed genes and related pathway.

first: Liya

first: Ying

last: Cheng


title: Engineered 3D Immuno-Glial-Neurovascular Human miBrain Model

status: Public on Sep 24 2025

city: Cambridge

first: Benjamin

last: James

state: MA

address: 32 Vassar St

institute: Massachusetts Institute of Technology

summary: Patient- specific, human-based cellular models integrating a biomimetic blood–brain barrier, immune, and myelinated neuron components are critically needed to enable accelerated, translationally relevant discovery of neurological disease mechanisms and interventions. To construct a human cell-based model that includes these features and all six major brain cell types needed to mimic disease and dissect pathological mechanisms, we have constructed, characterized, and utilized a multicellular integrated brain (miBrain) immuno-glial-neurovascular model by engineering a brain-inspired 3D hydrogel and identifying conditions to coculture these six brain cell types, all differentiated from patient induced pluripotent stem cells. miBrains recapitulate in vivo–like hallmarks inclusive of neuronal activity, functional connectivity, barrier function, myelin-producing oligodendrocyte engagement with neurons, multicellular interactions, and transcriptomic profiles. We implemented the model to study Alzheimer’s Disease pathologies associated with APOE4 genetic risk. APOE4 miBrains differentially exhibit amyloid aggregation, tau phosphorylation, and astrocytic glial fibrillary acidic protein. Unlike the coemergent fate specification of glia and neurons in other organoid approaches, miBrains integrate independently differentiated cell types, a feature we harnessed to identify that APOE4 in astrocytes promotes neuronal tau pathogenesis and dysregulation through crosstalk with microglia.

overall_design: This study profiled RNA expression from multiple cell types isolated from human iPSC-derived ‘miBrains’ and matched monocultures. Neurons, astrocytes, oligodendroglia, and microglia were differentiated from the same iPSC batches, cultured in miBrains for two weeks (plus an additional 4 days for iMG), and isolated by FACS based on fluorescent reporters or CD45 expression. Parallel monocultures of each cell type were maintained under matched conditions. Triplicate biological replicates were collected per condition. The design enables comparison of gene expression between organoid-incorporated versus monoculture conditions across multiple neural cell types

first: Alice

last: E. Stanton

first: Adele

last: Bubnys

first: Emre

last: Agbas

first: Dong

last: Park

first: Alan

last: Jiang

first: Rebecca

last: Pinals

first: Liwang

first: Nhat

last: Truong

first: Anjanet

last: Loon

first: Colin

last: Staab

first: Oyku

last: Cerit

first: Hsin-Lan

last: Wen

first: David

last: Mankis

first: Margaret

last: Bisher

first: Abigail

middle: K

last: Lytton-Jean

first: Manolis

last: Kellis

first: Joel

middle: W

last: Blanchard

first: Robert

last: Langer

first: Li-Huei

last: Tsai


title: Single-Cell RNA Sequencing Reveals Cellular Heterogeneity and Reparative Mechanisms in Cystic Change of Osteonecrosis of the Femoral Head

city: Guangzhou

first: Xiaoqiang

last: YANG

address: 12,Jichang Road

institute: Guangzhou University of Chinese Medicine

summary:
Aims:
Steroid-induced osteonecrosis of the femoral head (SIONFH) is a debilitating condition often accompanied by cystic change in the affected bone. Previous studies and our clinical observation have suggested the potential for tissue repair within the cystic change, but the underlying cellular mechanisms remain unclear. This study aims to investigate the heterogeneity of cells in the cystic change region, focusing on chondrocytes and endothelial cells, using single-cell RNA sequencing (scRNA-seq) and subsequent histological validation.
Method:
Cystic change tissues were obtained from patients undergoing total hip arthroplasty. Single-cell RNA sequencing was performed to identify distinct cell populations, particularly chondrocytes and endothelial cells. Alcian blue staining was employed to detect chondrocytes, while immunohistochemistry (IHC) was used to verify the presence of repair-associated chondrocytes. Additionally, HE staining was performed to further analyze tissue architecture like blood vessels.
Results:
ScRNA-seq analysis identified two major cell types in the cystic change region: endothelial cells involved in angiogenesis and chondrocytes, which included subpopulations associated with cartilage repair. Alcian blue staining showed strong cartilage matrix staining within the cystic change. Immunohistochemistry further validated the expression of repair-associated markers in the chondrocyte population, suggesting active cartilage repair. Cellular communication analysis revealed intercellular interactions between reparative chondrocyte via matrix proteins (FN1, COL1A1) and integrin receptors on angiogenic endothelial cell, suggesting their potential collaboration in the repair process.
Conclusion:
This study highlights the positive effects of cystic change region of SIONFH in the process of repair based on clinical observations and single-cell RNA sequencing technology. The presence of functionally distinct cell populations, including angiogenic endothelial cells and repair-associated chondrocytes, within cystic change region of SIONFH. The findings suggest a biological basis for repair in the cystic change tissue, providing insights that may inform future therapeutic strategies targeting bone and cartilage regeneration in osteonecrosis.

overall_design: Single-cell sequencing analysis was conducted from four cystic change samples from SIONFH patients.


title: Chemotherapy-driven de novo Wnt pathway activation dictates a dynamic shift to a drug-tolerant state in breast cancer cells

city: Leuven

first: Frederic

last: Lluis

state: Leuven

address: Herestraat 49

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

summary: Triple-negative breast cancer (TNBC) initially exhibits a robust response to chemotherapy; however paradoxically, the treatment enriches a population of drug-tolerant persister (DTP) cells, which are known to drive therapy resistance. Therefore, it is crucial to, foremost, identify and subsequently target the signaling pathways implicated in therapy-induced drug resistance and the emergence of DTP cells.  In this study, by combining the use of human TNBC cell lines, 3D patient-derived organoid models, and in vivo xenograft models, we identified activation of the Wnt/β-catenin signaling pathway as a common mechanism underlying early DTP cell(s) enrichment in response to different chemotherapeutic agents. Live-cell imaging using Wnt-reporter TNBC cell lines validated diverse patterns of Wnt-transcriptional enrichment, encompassing both intrinsic selection and acquired de novo activation in response to chemotherapy treatment. Purification of differential Wnt-transcriptional populations revealed that post-treatment WntLow cells succumb to apoptosis, while, in contrast, chemotherapy-treated Wnt-active (WntHigh) cells adopt stem cell-like traits, exhibit reduced proliferation, and are, in turn, refractory to treatment. The transition to a post-treatment WntHigh state is orchestrated by increased expression of Wnt ligands, R-spondins, and factors facilitating Wnt ligand secretion, such as PORCN. Consequently, genetic or concomitant - but not sequential - pharmacological inhibition of Wnt ligand secretion alongside chemotherapy prevents treatment-induced WntHigh enrichment and sensitizes TNBC tumors to chemotherapy. Taken together, these observations provide a strong rationale for testing dual treatment comprising chemotherapy and Wnt ligand secretion inhibitors in clinical trials, extending to all TNBC patients.

overall_design: MDA-MB-231 TNBC cell line treated with different chemotherapeutic agents (Docetaxel and Carboplatin) for 72 hours.

first: Youssef

last: El Laithy

middle: L

last: Vinas


title: Role for NF-kB in herpes encephalitis pathology in mice genocopying an inborn error of IRF3-IFN immunity

city: Aarhus

first: Soren

last: Paludan

address: CF Møllers Alle 6, Building 1115

department: Biomedicine

country: Denmark

institute: Aarhus university

summary: Herpes simplex encephalitis (HSE) is a devastating disease with high mortality and serious sequelae. Genetic defects in the interferon (IFN-I) pathway predispose individuals to HSE, but underlying mechanisms remain unclear. Using transgenic mice with the IRF3 R278Q mutation, orthologue to HSE-associated IRF3 R285Q, and iPSC-derived CNS cells from a pediatric patient carrying the variant, we investigated mechanisms in HSE. IRF3 R278Q transgenic mice exhibited aggravated HSV-1 brain disease and elevated CNS viral loads. Accordingly, microglia from the IRF3 R278Q mice showed reduced HSV-1-induced IFN-I expression. Surprisingly, unaltered Ifnb levels along with elevated levels of inflammatory cytokines were detected in infected transgenic mouse brains, correlating with higher viral load. This was successfully modelled in patient microglia. Multiomics-based immune profiling revealed an inflammatory monocyte population in the infected IRF3 R278Q mouse brain, which was enriched for NF-κB activation. NF-κB inhibition improved disease outcomes, surpassing the effect of acyclovir. These findings suggest that IFN-I defects lead to elevated levels of HSV-1 replication in the brain, which subsequently enables NF-κB-driven immunopathology, offering insights with therapeutic potential.

overall_design: Brain stems from IRF3 full knockout mice, transgenic mice homozygous for an IRF3 R278Q aminoacid substitution and WT mice were harvested on day 5 post ocular HSV-1 infection. Two to three brain stems were pooled per sample. Single-cell suspensions were used to generate barcoded single-cell RNA-seq libraries according to the manufacturer’s protocol. Library quality control was performed, and sequencing was carried out on a high-throughput sequencer.


title: RNA sequencing analysis of 5- and 7-day old salivary gland organoids

status: Public on Sep 23 2025

city: Groningen

first: Davide

last: Cinat

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

summary: The specific effects of different radiation types, such as photons and protons, on normal stem cell activity and tissue regeneration remain poorly understood. In our previous work, we characterized salivary gland organoids at 2 days post-irradiation (corresponding to 7-day-old organoids) using single-cell RNA sequencing. To compare the cellular composition of 5-day-old organoids (day of irradiation) with that of 7-day-old organoids, we performed bulk RNA sequencing and applied the deconvolution tool CIBERSORTx, using the 7-day single-cell dataset as a reference. This analysis confirmed that the cell populations in 5- and 7-day-old salivary gland organoids were comparable.

overall_design: Organoids derived from 3 different mice were were collected at day 5 and day 7 and processed for RNA-seq analysis.

first: Rob

middle: P

last: Coppes

first: Lara

last: Barazzuol


title: Effect of NEK7 hepatocyte knock-out on gene expression in the mice livers.

city: Nanjing

first: Zhenzhen

last: Sun

address: Guangzhou Road#72

institute: Children’s Hospital of Nanjing Medical University

summary: To investigate the genes and pathways affected by depletion of hepatocyte NEK7 in the mice livers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver tissue from the NEK7 hepatocyte knock-out mice (Homo_1, Homo_2, Homo_3) and wild type mice (Ctrl_1, Ctrl_2, Ctrl_3).

first: Zhanjun

last: Jia


title: ZDHHC13 Modulates Tumor Microenvironment Interactions to Suppress Melanoma Metastasis [scRNA-Seq]

city: Cleveland

first: Shuyang

last: Chen

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: This dataset supports a study investigating the role of ZDHHC13 in melanoma development. Using bulk RNA sequencing and 10x Genomics single-cell RNA sequencing, we analyzed how ZDHHC13 influences tumor progression and the tumor microenvironment. These data provide insights into the transcriptomic changes associated with ZDHHC13 activity in melanoma and serve as a resource for understanding gene expression dynamics in both tumor cells and surrounding immune components.

overall_design: For single-cell RNA sequencing, ZDHHC13-overexpressing or control B16F10 cells were subcutaneously inoculated into immunocompetent C57BL/6 mice. Tumors were harvested at defined time points, dissociated into single-cell suspensions, and processed using the 10x Genomics platform. This design allowed us to examine both tumor-intrinsic and tumor microenvironment responses to ZDHHC13 expression at single-cell resolution.

first: Hongjin

last: Li


title: Comparative bulk RNAseq between EpH4 WT and Cldn-null cells

city: Kyoto

first: Kazuto

last: Tsukita

state: Kyoto

address: 54 Shogoin-Kawaharacho

country: Japan

institute: Kyoto university

summary: The claudin (CLDN) family, comprising 27 members, includes crucial cell–cell adhesion molecules that form tight junctions (TJs), essential for paracellular barrier and channel functions. The functional diversity among CLDNs may lead to diversity of TJs, contributing to various biological systems and pathological processes. To characterize the functional diversity of CLDNs, we developed a first-ever complete Cldn-null EpH4 epithelial cell line. This cell line was used for the expression of single Cldn family members, uncovering their specific intrinsic properties. Unlike the conventional binary classification of CLDNs as either paracellular barrier or channel forming, we discovered a novel classification axis where CLDNs form TJs autonomously or non-autonomously, exhibiting extensive variation in ion conductivity and selectivity, leading to an innovative classification. This classification offers a fundamental framework for understanding the mechanisms underlying TJ diversity in vivo, and provides a basis for the development of therapies targeting the epithelial barrier.

overall_design: To investigate the overall gene expression profiling, we conducted a comparative bulk RNAseq analysis between EpH4 WT and Cldn-null cells.

first: Hiroka

last: Kashihara

first: Hiroo

last: Tanaka

first: Atsushi

last: Tamura

first: Sachiko


title: ZDHHC13 Modulates Tumor Microenvironment Interactions to Suppress Melanoma Metastasis [RNA-Seq]

overall_design: For bulk RNA sequencing, we engineered B16F10 murine melanoma cells to stably overexpress ZDHHC13 using a lentiviral vector. RNA was extracted from both ZDHHC13-overexpressing and control (empty vector) B16F10 cells for transcriptomic profiling to assess the direct effects of ZDHHC13 on tumor cell gene expression.


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues [methylC-seq]

first: Julie

last: Law

summary: DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to anther or ovule tissues. We designate these factors as REM INSTRUCT METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. Furthermore, we demonstrate that mis-expression of RIM12 is sufficient to initiate siRNA production at ovule targets in anthers. These findings reveal a critical role for genetic information in targeting DNA methylation in reproductive tissues, expanding our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

overall_design: 30 methylC-seq libraries were sequenced.

first: Guanghui

last: Xu

first: Yuhan

first: Laura

last: Martins

first: En

first: Fuxi

last: Wang

first: Tulio

last: Magana

first: Junlin

last: Ruan


title: KANSL3 directs transcriptional programs essential for hepatic metabolism and differentiation [RNA-seq]

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Understanding the molecular mechanisms governing liver homeostasis and disease progression is essential for advancing therapeutic strategies for chronic liver diseases and hepatocellular carcinoma, with emerging evidence highlighting the pivotal role of epigenetic regulation in these progressive types of diseases. Here, we show that hepatic deletion of the epigenetic regulator KANSL3 initiates a series of pathological changes leading to early-onset chronic liver disease. The absence of KANSL3 leads to biliary hyperplasia and early hepatic fibrosis. We identify KANSL3 as a master regulator of core hepatocyte gene expression through its regulation of histone acetylation, which significantly alters transcriptional networks in the liver. Single-cell RNA sequencing (scRNA-seq) analysis of Kansl3 liver knockout (LKO) animals reveals a marked shift in liver cellular composition following Kansl3 depletion. We show that the hepatic epithelial cells of Kansl3 LKO mice and Kansl3-depleted ductal organoids exhibit impaired differentiation into mature hepatocytes, uncovering the importance of KANSL3 in hepatic cell fate decisions. Ultimately, chronic loss of KANSL3 induces significant changes in the liver microenvironment, promoting a premalignant state characterized by an immunosuppressive environment linked to hepatocellular carcinoma (HCC) progression. These results highlight KANSL3 as a crucial regulator of liver homeostasis and a promising target for drug discovery.

overall_design: Liver RNA-seq: Comparison of total RNA expression in whole liver tissue isolated from 3-week-old (P21) control liver and Kansl3 LKO mice. Organoid RNA-seq: Time-course mRNA expression analysis of ductal organoids generated from neonatal livers undergoing hepatocyte differentiation in vitro. Comparison of control (iWT) and Kansl3-iKO organoids, depletion of Kansl3 was induced by 4OHT treatment at day 3 for 48hrs. Hepa16 RNA-Seq: mRNA expression analysis in Hepa 1-6 HA-dTAG-KANSL3 cells upon degradation of KANSL3. Hepa 1-6 HA-dTAG-KANSL3 cells were treated for 24hrs with either dTAG-NEG control compound or dTAG13 to rapidly degrade KANSL3. 72hrs prior to the treatment cells were induced with the lentiviral pCHDblast MCSNard empty vector (EV) and selected with Blasticidine.

first: Meike

last: Wiese

first: Eray

last: Akbas

first: TzsHong

last: Tsang

first: Yidan

first: Kerstin

last: Ganter


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues [mRNA-seq]

city: La Jolla

address: 10010 North Torrey Pines Rd

institute: Salk Institute for Biological Studies

overall_design: 24 mRNA-seq libraries were sequenced.

last: Chen


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues [small RNA-seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: 148 smRNA-seq libraries were sequenced.

last: Li


title: Maternal Cholesterol Deficiency Predisposes Congenital Heart Defect Risk

status: Public on Sep 22 2025

first: Jimiao

last: Gao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

summary: The relationship between maternal cholesterol deficiency and the risk of congenital heart defects (CHD) in offspring is not fully understood. In a birth cohort study of 5,041 family trios, we found that low maternal cholesterol levels were significantly associated with an increased risk of CHD, with relative risk (RR) of 1.52 in the second trimester and 1.73 in the third trimester. To further investigate this link, we treated pregnant mice with cholesterol-lowering agents, namely ezetimibe or atorvastatin. Both treatments led to a significant increase in the incidence of CHD in their offspring. To identify a pathogenic variant that could provide genetic evidence linking cholesterol synthesis to CHD occurrence and serve as a target for constructing genetic mouse models, we performed whole-genome sequencing (WGS) on 103 CHD cases from the birth cohort. We identified a recurrent functional variant in the CYP51A1 gene (c.1147A>G, p.Ile383Val). We then developed a CYP51A1I383V knock-in mouse model. This variant disrupted cholesterol synthesis, resulting in CHD through impaired hedgehog (Hh) signaling. Most intriguingly, maternal dietary intervention to increase cholesterol intake effectively reduced the risk of CHD in CYP51A1I383V mutant offspring. Our study suggests that low maternal cholesterol during pregnancy increases the risk of CHD in offspring by inhibiting Hh signaling, and that maternal cholesterol supplementation during pregnancy may reduce the occurrence of CHD.

overall_design: Single cell RNA sequencing of mice E10.5 hearts from wild-type and Cyp51 I383V mutant.


title: Rare non-canonical megakaryocyte progenitors increase in number and gain enhanced function with age

city: Santa Cruz

first: Paloma

last: Medina

address: 1156 High St.

institute: University of California Santa Cruz

overall_design: CITEseq via the 10X Genomics platform was performed simultaneously with our previously published scRNAseq data of young and aged FlkSwitch mice. Briefly, cKit-enriched BM was sorted into CD150+ and CD150- fractions and incubated with CITEseq antibodies (BioLegend) per manufacturer’s instructions. All other steps as described in Poscablo et al., 2024. Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) reagents and protocols utilized as specified. Sequencing depth of 5,000 read pairs per cell was performed.  Cells expressing fewer than 200 genes were excluded from the analysis. Cells were further filtered based on surface protein marker expression; specifically, double-negative cells for CD117 ADT and Kit RNA were excluded, removing 13 cells from the dataset. To normalize the CITE-seq data, we implemented a centered log-ratio (CLR) transformation for each cell. For each cell's antibody-derived tag (ADT) count vector, we first computed the natural logarithm of the counts, offset by one, for all non-zero elements. The sum of these log-transformed values was then divided by the total number of features, and the exponential of this mean was used to normalize the original counts. Finally, a log transformation was applied to the resulting normalized values to stabilize variance across features.

first: Bryce

last: Manso

first: Camilla

last: Forsberg


title: Single cell sequencing analysis of control, photon- and proton- irradiated salivary gland organoids at day 7 and control salivary gland organoids at day 11

first: Davide

last: Cinat

summary: The specific impact of different radiation types, such as photons and protons, and their effects on normal stem cell activity and tissue regeneration are unknown. In this study, we used a scRNA-seq approach to characterize our mouse salivary gland organoid model at day 7 and 11 and assess the effects of photon and proton irradiation on salivary gland stem/progenitor cells at day 7.

overall_design: Mouse salivary gland organoids derived from 4 different animals were irradiated at day 5 with either 7 Gy photons or 7 Gy protons (plateau). Non-irradiated (control), photon- and proton-irradiated organoids were collected at day 7 (2 days after irradiation) and pooled before the sequencing run. After trypsinization, propidium iodide (PI) was used to isolate live cells (PI negative) by flowrescence-activated cell sorting (FACS). Cells were then analysed using scRNA-seq. Fresh isolated submandibular salivary gland tissue was also included in the analysis together with non-irradiated 11-day old salivary gland organoids. 11-day salivary gland organoids were run separately.

first: Rob

last: Coppes

first: Lara

last: Barazzuol


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues [WGS]

first: Julie

last: Law

summary: DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to male or female reproductive tissues. We designate these factors as REM INSTRUCT METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. These findings not only reveal RIMs as the first sex-specific RdDM proteins but also establish a critical role for genetic information in targeting DNA methylation. This novel mode of targeting expands our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

overall_design: 6 whole genome sequencing libraries were sequenced.

first: Guanghui

last: Xu


title: Methylome of grape berry reveal tissue specific features associated with metabolic processes [RNA-seq]

status: Public on Sep 21 2025

city: Shenzhen

first: Yu

last: Ma

address: 1088 Xueyuan Bivd, Nanshan District

institute: Southern University of Science and Technology

summary: DNA methylation is a conserved epigenetic mark that is involved in many biological processes including the ripening process of various crop species bearing fleshy fruit, such as tomato, strawberry, and orange. The dynamics and importance of DNA methylation during grapefruit ripening, has however not yet been characterized. In this study, we observed an increase in DNA methylation level during grape berry ripening. The application of a DNA methylation inhibitor delayed ripening, consistent with an important role for DNA methylation in grape berries.  In addition, we characterized the methylomes of the flesh and the skin the two main tissues of grape berry pericarp, as they present very distinct metabolic features. Results indicate that grape berry skin has a lower DNA methylation level than the flesh. Whereas in both tissues ripening is associated with an increase in DNA methylation, methylation patterns are clearly distinct between these two tissues as are the metabolic and transcriptomic profiles. Results indicated that the DNA methylation changes are associated with tissue specific metabolic modifications that occur during ripening, and involved in the synthesis of secondary metabolites.

overall_design: mRNA sequencing (mRNA-Seq) data of grape fruit pulp and berry extracted in F+6W and V+3W

first: P

last: Gallusci

first: Zhaobo

last: Lang


title: A genome-wide survey reveals a diverse array of enhancers coordinate the Drosophila innate immune response

city: Boston

first: Zeba

last: Wunderlich

state: Massachusetts

address: 610 Commonwealth Ave

department: Biology

institute: Boston University

summary: To defend against microbes, animals regulate a complex immune response. The Drosophila innate immune system deploys a large transcriptional induction of signaling proteins, anti-microbial effectors, and other critical immune factors. This transcriptional response is encoded in enhancers, cis-regulatory sequences that modulate gene expression by binding transcription factors (TFs). While enhancers and transcription factor binding sites (TFBS) have been identified for several immune responsive genes in Drosophila, most enhancers that regulate immune-induced genes are unknown. By identifying enhancers, we can understand how their composition controls expression and contributes to infection outcome. We employed STARR-seq (Self Transcribing Active Regulatory-Region sequencing) in a hemocyte-like cell line to identify immune-specific enhancers across the D. melanogaster genome and performed ATAC-seq in hemocytes extracted from adult flies to assess the chromatin state of these enhancers before and after immune stimulus. We identified thousands of enhancers responsive to IMD stimulation, one of the two primary immune signaling pathways in Drosophila. As expected, immune enhancers are enriched for motifs of Relish, an NF-κB factor, and Kay/Jra, a bZip heterodimer pair, involved in the Imd and JNK pathways respectively, compared to enhancers active in unstimulated cells. However, when grouping enhancers by their target gene’s expression timing or functional role or by the enhancers’ chromatin accessibility pre- or post-stimulus, different groups of TFBS motifs are enriched, suggesting distinct regulatory logic for different parts of the immune response. Identification and characterization of the diverse array of enhancers that regulate the innate immune response expands our understanding of how animals fight infections.

overall_design:
RNA-seq of S2* cells with three Treatments: Control, 20E and IMD stimulation. IMD stimulation includes 20E treatment and heat killed Serratia marcescens (HKSM).
STARR-seq in S2* cells transfected with a genome wide library of from iso-1 flies in the pSTARR-seq plasmid
ATAC-seq on hemocytes extracted from Oregon R adult files 24 hours after injection with heat killed Serratia marcescens (Imd stimulation) .

first: Lianne

middle: B

last: Cohen

first: Tamara

last: Hadzic

first: Caitlin

last: Sauer

first: Julia

middle: R

last: Gibbs


title: KANSL3 directs transcriptional programs essential for hepatic metabolism and differentiation [scRNA-seq]

first: Asifa

last: Akhtar

summary: Understanding the molecular mechanisms governing liver homeostasis and disease progression is crucial for developing new therapeutic strategies for chronic liver diseases and liver cancer, with emerging evidence underscoring the key role of epigenetic regulation. Here, we show that hepatic deletion of the epigenetic regulator KANSL3, a component of the NSL complex, causes early-onset chronic liver disease, distinct from metabolic dysfunction-associated steatohepatitis (MASH). Loss of KANSL3 leads to biliary hyperplasia and early hepatic fibrosis, indicating its vital role in liver structure and function. KANSL3 acts as a master regulator of hepatocyte gene expression through histone acetylation, impacting global liver transcriptional networks. scRNA-seq analysis uncovers that KANSL3 deletion disrupts hepatocyte differentiation in vivo and in hepatic organoids. Ultimately, chronic KANSL3 loss alters the liver microenvironment and promotes an immunosuppressive premalignant state linked to hepatocellular carcinoma (HCC).

overall_design: Comparison of liver cells isolated from control mice or mice with liver-specific knockout of Kansl3 of two diferent ages. Neonatal experiment: Control (n=3) and Kansl3 LKO (n=3) neonatal (P7) livers were isolated. One piece of the liver was used for BEC isolation and the other for hepatocyte isolation. For BEC isolation single cell suspensions were prepared by 0.25mg/ml collagenase (Sigma C2674) digest at 37°C for 1 hr. For the BECs population Zombie NIR (Biolegend, 423105) negative (live cells), CD45/CD31/CD11b- and EpCAM+ cells were sorted. For the hepatic stellate cell (HSC) enriched population Zombie NIR (Biolegend, 423105) negative (live cells), CD45/CD31/CD11b/EpCAM- cells were sorted. For hepatocyte isolation, single cell suspensions were prepared  by 0.8mg/ml collagenase (Sigma C2674) and 50 U/μl) DNase I (Applichem) in DMEM) digest at 37°C for 30 min. For the hepatocyte enriched population Zombie NIR negative, large cells were sorted. For the scRNA-seq experiment, BECs, hepatocytes and HSC populations were isolated from three AlbCre and three Kansl3 LKO mice. For each population, the samples from each genotype were pooled. The BECs, hepatocytes and HSC populations were mixed in an 1:1:1 ratio. This cell mix was directly subjected to 10x scRNA-seq library preparation. One 10x reaction was performed per genotype. A total of 16,000 cells per genotype were processed using the 10X Genomics protocol CG00052 RevB from the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (PN-120237). The libraries were quantified using a fragment analyzer and pooled for multiplexed sequencing on a NovaSeq 6000. Old liver experiment: 90-week-old control (n=2) and Kansl3 LKO (n=2) livers were isolated and digested in 0.8mg/ml collagenase (Sigma C2674) and 50 U/μl) DNase I (Applichem) in DMEM) at 37°C for 30 min. Cell suspension was cryopreserved in FCS supplemented with 1% DMSO and stored in liquid nitrogen. Frozen sample thawed and viable cells were enriched using the LeviCell 1.0 device (Levitas Bio), selecting the option “large cells”. All samples had a viability of approximately 70%. The cells were then prepared for 10x scRNA-seq library preparation. Two 10x reactions were performed per genotype, one for each animal. A total of 16,000 cells per genotype were processed according to the 10X Genomics protocol CG000204 RevD using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (PN-1000121). Libraries were quantified with a fragment analyzer and pooled for multiplexed sequencing on a NovaSeq 6000.

first: Meike

last: Wiese

first: Cecilia

last: Pessoa-Rodrigues


title: KANSL3 directs transcriptional programs essential for hepatic metabolism and differentiation [ChIP-seq]

overall_design: Hepa1-6 experiment: H4K16ac level in Hepa 1-6 HA-dTAG-KANSL3 cells upon degradation of KANSL3. Hepa 1-6 HA-dTAG-KANSL3 cells were treated for 24hrs with either dTAG-NEG control compound or dTAG13 to rapidly degrade KANSL3. Wildtype liver experiment: Identification of KANSL3 binding targets and histone modifications in wildtype liver tissue.

first: Chiara

last: Bella

first: Yidan

last: Sun


title: Dual edged mechanisms of a tomatine in hepatocellular carcinoma by suppression of Wnt/b Catenin signaling versus RelB driven resistance in tumor therapy

status: Public on Sep 20 2025

city: Shanghai

first: Tianzhen

last: Wang

address: No.500, Dongchuan Road

institute: East China Normal University

summary: Background: The plant-derived steroidal alkaloid α-tomatine has emerged as a promising pan-cancer therapeutic agent, its multifaceted biological effects in HCC remain unexplored. This study aims to decipher α-tomatine’s molecular duality in HCC, resolving its paradoxical capacity to simultaneously activate tumor-suppressive signaling and provoke chemoresistance networks, ultimately establishing synergistic phytotherapy strategies. Methods: HepG2 hepatocellular carcinoma cells were exposed to α-tomatine to evaluate dose-dependent effects on proliferation, migration/ invasion, and cell cycle distribution. Transcriptomic pro ling via RNA sequencing identi ed dysregulated pathways. Pharmacological interventions using Wnt3a (activation) and XAV939 (inhibition) modulated Wnt/β-catenin signaling, while CRISPR/Cas9-mediated RelB knockout and plasmid-based overexpression established isogenic cell models. These interventions were subsequently applied in BALB/c nude mouse xenografts, where tumor volume was longitudinally monitored during α-tomatine treatment. Results: α-Tomatine demonstrated dose-dependent suppression of hepatocellular carcinoma cell proliferation, migration, and invasion, concomitant with G2/M phase arrest. Mechanistically, it exerted Wnt/β- catenin inhibition via β-catenin phosphorylation/degradation while paradoxically inducing RelB-mediated reduction of anti-tumor activity. Wnt activation attenuated therapeutic effects, whereas Wnt inhibitors enhanced ef cacy. Genetic RelB ablation potentiated α-tomatine’s anti-tumor activity, contrasting with resistance in RelB-overexpressing models. Xenografts con rmed enhanced suppression in RelB-de cient tumors. Conclusion: This plant-derived alkaloid exerts anti-HCC effects through Wnt pathway modulation, while compensatory RelB activation constrains therapeutic outcomes. Strategic RelB co-targeting establishes a dual pathway phytotherapy paradigm, synergistically merging botanical pharmacodynamics with precision

overall_design: HepG2 cells were treated with 2uM α-tomatine for 6h, 12h and 24h. The bulk RNA-seq profiling was done to identify the differential expressed genes.

first: Chenyue

first: Yanling

last: Yuan

first: Bianhong

last: Zhang


title: ATAC sequencing analysis of non-irradiated salivary gland organoids

first: Davide

last: Cinat

summary: To identify transcription factors important for salivary gland organoids and associated to salivary gland stem/progenitor cells, we performed ATAC-seq of organoids derived from non-irradiated mice of different ages.

overall_design: Salivary glands from 12-week and 3-month old mice were harvested and used to grow organoids. Organoids from passage 1 (P1) and passage 2 (P2) were used for ATAC-seq analysis.

first: Yi

last: Wu

first: Inge

last: Holtman

first: Rob

last: Coppes


title: Methylome of grape berry reveal tissue specific features associated with metabolic processes [Bisulfite-seq]

first: Yu

last: Ma

overall_design: Bisulfite sequencing (BS-Seq) data of grape berry and grape pulp and berry extracted in F+6W and V+3W

first: P

last: Gallusci

first: Zhaobo

last: Lang


title: Adipocyte autophagy-mediated signals in the control of macrophage phenotype during diet-induced obesity

city: Oxford

first: Klara

last: Piletic

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

summary: A hallmark of obesity is a pathological expansion of white adipose tissue (WAT), accompanied by marked tissue dysfunction and fibrosis. Autophagy promotes adipocyte differentiation and lipid homeostasis, but its role in obese adipocytes and adipose tissue dysfunction remains incompletely understood. Using a mouse model, we demonstrate that autophagy is a key tissue-specific regulator of WAT remodelling in diet-induced obesity. Importantly, loss of adipocyte autophagy substantially exacerbates pericellular fibrosis in visceral WAT. Change in WAT architecture correlates with increased infiltration of macrophages with tissue-reparative, fibrotic features.

overall_design: To investigate the role of adipocyte autophagy in diet-induced obesity, we used Adipoq-Cre ERT2 Atg7fl/fl mice, where autophagy was inducibly depleted with administration of tamoxifen specifically in adipocytes, followed by 16 weeks of high fat diet feeding with a 60kcal% fat diet. Gonadal white adipose tissue was isolated from these mice, mechanically and enzymatically digested and macrophages were isolated using flow-assisted cell sorting (CD11b+ F4/80+ CD64+ markers). We then performed gene expression profiling analysis using data obtained from RNA-seq of macrophages isolated from either WT or adipocyte autophagy KO white adipose tissue.


title: RNA Sequencing (RNA-Seq) analysis of sex-matched neural stem cells derived from early-onset Alzheimer’s disease (EOAD), late-onset Alzheimer’s disease (LOAD), and wild-type controls

city: Richardson

first: Adedamola

middle: Saidi

last: Soladogun

state: Texas

address: 800 W Campbell Rd

department: Biological Sciences

institute: University of Texas at Dallas

summary: Neural stem cells derived from early-onset Alzheimer’s disease (EOAD) patients with PSEN1 mutations, late-onset Alzheimer’s disease (LOAD) patients with APOE4 genotypes, and sex-matched wild-type (WT) controls were cultured and differentiated to neurons. Undifferentiated cells (UD, cultured for 1 day) and differentiated cells (DIF, cultured for 35 days) were compared to study gene expression changes. Oligomeric amyloid beta (Aβ, 0.5 µM) was applied to differentiated WT neurons for 24 hours prior to RNA sequencing. Differential gene expression analysis revealed that genetic background differences between healthy controls, as well as between EOAD and LOAD, contribute as many expression changes as AD-specific mutations. Comparing differentiation-induced gene expression changes between AD neurons and corresponding healthy controls circumvents background variability and highlights disease-specific alterations.Analysis of over 100 AD-associated genes showed altered expression in differentiated EOAD and LOAD neurons, consistent with roles in neuronal functions and AD etiopathogenesis. Notably, LOAD neurons, but not EOAD neurons, exhibited significant deficiencies in heme and redox homeostasis, with reduced expression of genes associated with heme metabolism, oxidative phosphorylation, and NAD/NADH homeostasis. These deficiencies may underlie neuronal dysfunction and contribute to LOAD pathogenesis. Gene Ontology enrichment analysis identified pathways uniquely dysregulated in EOAD and LOAD, offering insights into the molecular mechanisms distinguishing these forms of Alzheimer’s disease. This study emphasizes the critical role of redox and heme homeostasis in LOAD and identifies gene expression patterns altered specifically by AD mutations.

overall_design: RNA sequencing was performed on neural stem cells derived from EOAD patients (PSEN1), LOAD patients (APOE), and male and female wild-type (WT) controls. Conditions included: EOAD (PSEN1): Undifferentiated (UD, 1 day), Differentiated (DIF, 35 days); LOAD (APOE): Undifferentiated (UD, 1 day), Differentiated (DIF, 35 days); WT: Undifferentiated (UD, 1 day), Differentiated (DIF, 35 days), and Differentiated + Aβ (DIF + Aβ, 35 days + 24 hours). Triplicate biological replicates were included for each condition, totaling 30 samples.

first: Chantal

last: Vidal

first: Maria Del Carmen

last: Chacon Castro

first: Heng

last: Du

first: Li


title: Autophagy acts as a brake on obesity-related fibrosis by controlling purine nucleoside signalling

summary: A hallmark of obesity is a pathological expansion of white adipose tissue (WAT), accompanied by marked tissue dysfunction and fibrosis. Autophagy promotes adipocyte differentiation and lipid homeostasis, but its role in obese adipocytes and adipose tissue dysfunction remains incompletely understood. Using a mouse model, we demonstrate that autophagy is a key tissue-specific regulator of WAT remodelling in diet-induced obesity. Importantly, loss of adipocyte autophagy substantially exacerbates pericellular fibrosis in visceral WAT. Change in WAT architecture correlates with increased infiltration of macrophages with tissue-reparative, fibrotic features. We uncover that autophagy restrains purine nucleoside metabolism in obese adipocytes. This ultimately leads to a reduced release of the purine catabolites xanthine and hypoxanthine. Purines signal cell-extrinsically for fibrosis by driving macrophage polarisation towards a tissue reparative phenotype. Our findings in mice reveal a novel role for adipocyte autophagy in regulating tissue purine nucleoside metabolism, thereby limiting obesity-associated fibrosis and maintaining the functional integrity of visceral WAT. Purine signals may serve as a critical balance checkpoint and therapeutic target in fibrotic diseases

overall_design: Gonadal white adipose tissue was isolated from lean C57BL/6J mice, mechanically and enzymatically digested. For primary cell culture, the stromal vascular fraction was enriched for CD11b+ cells with CD11b MicroBeads (Miltenyi Biotec) according to manufacturers’ instructions after red blood cell lysis. 350,000 cells were seeded in 24-well plates in RPMI containing 10 % FBS and 1 % P/S and incubated overnight to allow macrophages to attach. The following day, macrophages were enriched by washing the wells with room temperature PBS and treated with experimental conditions. Macrophages were cultured in RPMI containing 10 % FBS and 1 % P/S and 50 ng/ml M-CSF and treated with 100 µM of either hypoxanthine or xanthine over 72 hours. RNA was extracted using RNeasy Plus Micro Kit (Qiagen) and gene expression profiling analysis was performed on RNA-seq macrophage data.


title: DNA methyltransferase Dnmt3ba-mediated epigenetic modulation of Integrin signaling is essential for hematopoietic stem and progenitor cell development

city: Jinan

first: kang

last: ai

address: 44 Wenhua West Road

institute: Shandong University

summary: In vertebrate embryonic development, hematopoietic stem and progenitor cells (HSPCs) originate from a subset of arterial endothelial cells in the ventral wall of the dorsal aorta through endothelial-to-hematopoietic transition (EHT). Despite extensive research efforts, gaps persist in understanding the establishment of EHT and HSPC generation. In this study, we demonstrate that DNA methyltransferase 3ba (Dnmt3ba), highly expressed in the hemogenic endothelial cells (HECs), plays a crucial role in HEC generation and HSPC development. Depletion of Dnmt3ba impairs HEC survival, which ultimately affects the generation and differentiation of HSPCs in zebrafish. Mechanistically, Dnmt3ba deficiency leads to hypomethylation at the itgα3b and itgα7 loci, diminishing the expression of these Integrins and downstream Akt signaling and Mdm2 phosphorylation, while concurrently triggering HEC apoptosis by upregulation of P53 activity. Manipulation of DNMT3B in an iPSC-derived human hematopoietic differentiation system indicates functional conservation. Collectively, our findings unveil an epigenetic mechanism governed by Dnmt3ba, orchestrating HEC survival through epigenetic modulation of Integrin signaling.

overall_design: Whole-genome bisulfite sequencing (WGBS) and RNA-seq were performed on hematopoietic endothelial cells (HECs) isolated from Danio rerio embryos at 36 hours post-fertilization (hpf). For each experiment, the number of embryos in each group was determined based on the amount required to obtain sufficient RNA or DNA from approximately 5,000 cells for RNA-seq and WGBS, respectively. Three biological replicates were prepared for both the control and dnmt3ba morphant groups. All samples that met the quality and quantity requirements were included in the sequencing analysis.

first: Kang

last: Ai

first: Lei

last: Li

first: Lu


title: Spatial dynamics of brain development and neuroinflammation [Epigenomic_data]

status: Public on Sep 19 2025

city: New Haven

first: Di

address: 55 Prospect St

institute: Yale University

summary: Spatially mapping multiple omics layers across time enables dissection of mechanisms underlying brain development, differentiation, arealization, and disease.  Here, we deploy spatial tri-omics to chart spatiotemporal remodeling in development and neuroinflammation.  We generate a tri-omic atlas of mouse brain from postnatal day P0–P21 and compare corresponding regions in developing human brain.  In cortex, a subset of layer-defining transcription factors shows temporally persistent and spatially spreading chromatin accessibility.  In corpus callosum, myelin genes exhibit dynamic chromatin priming across subregions, and layer-specific projection neurons appear to coordinate axonogenesis and myelination.  In a lysolecithin (LPC) model, we observe molecular programs shared between development and neuroinflammation.  Microglia display conserved and distinct inflammatory and resolution programs and are transiently activated both at lesion cores and at distal sites, presumably via neuronal circuitry.  These data reveal common and divergent mechanisms and provide a resource for studying brain development, function, and disease.

overall_design: Samples consist of mouse brain tissue sections collected across normal postnatal development (P0, P2, P5, P7, P10, P21) as well as from a lysolecithin (LPC)-induced demyelination model at multiple recovery stages (5, 10, 21 days post-lesion). Each sample was processed for spatial multi-omic profiling using DBiT-seq. Biological replicates are included for each developmental stage and lesion condition. Experimental variables under investigation include developmental timepoint, brain region, and lesion status (lesion core, distal white matter, and control). These samples enable comparative analyses of spatiotemporal dynamics in brain development and demyelination.

first: Zhang

last: Di

first: Kirby

last: Leslie


title: Spatial dynamics of brain development and neuroinflammation

last: Zhang

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

The full dataset is available via the NeMO Archive, including controlled-access human data and mouse data. This GEO Series provides a mirror of the mouse subset.

overall_design: Refer to individual Series

first: Leslie

last: Kirby


title: RRBS-seq of single-cell clones of four cell Lines reveals highly-conserved methylated sites in DNA [RNA-Seq]

first: Yicen

last: Ding

address: 800 Dongchuan Road, Shanghai, China

institute: Shanghai Jiao Tong University

summary: DNA methylation is one of the most studied epigenetics, and its effects on embryonic development, cell differentiation, cell development, aging, apoptosis, carcinogenesis, and genomic stability are all im-portant. In the classical epigenetic model, cytosine methylation is steadily transmitted to daughter cells with fidelity as DNA replicates. However, a large number of studies have shown that there are detectable changes in DNA methylation at many CpG sites during DNA replication. In this study, we selected four different types of cell lines, A549, ARPE-19, Jurkat and SW1353. For a single CpG site in a single cell, there are only three methylation states, 100% methylation, 50% methylation, and 0% methylation, and any DNA methylation that deviates from these three results indicates a methylation change. We used reduced representative bisulfite sequencing (RRBS)  to screen out methylation sites.

overall_design: RRBS-seq combined with RNA-seq analysis to find high-fidelity methylation CpG sites in four kinds of cell lines

first: Fei

first: Mengju

last: He

first: Yani

last: Kang


title: Spatial dynamics of brain development and neuroinflammation [Spatial Transcriptomics]

summary: Spatially mapping multiple omics layers across time enables dissection of mechanisms underlying brain development, differentiation, arealization, and disease. Here, we deploy spatial tri-omics to chart spatiotemporal remodeling in development and neuroinflammation. We generate a tri-omic atlas of mouse brain from postnatal day P0–P21 and compare corresponding regions in developing human brain. In cortex, a subset of layer-defining transcription factors shows temporally persistent and spatially spreading chromatin accessibility. In corpus callosum, myelin genes exhibit dynamic chromatin priming across subregions, and layer-specific projection neurons appear to coordinate axonogenesis and myelination. In a lysolecithin (LPC) model, we observe molecular programs shared between development and neuroinflammation. Microglia display conserved and distinct inflammatory and resolution programs and are transiently activated both at lesion cores and at distal sites, presumably via neuronal circuitry. These data reveal common and divergent mechanisms and provide a resource for studying brain development, function, and disease.


title: Proliferative diabetic retinopathy subtypes defined by immune defense and endothelial mitochondrial dysfunction

city: Chicago

first: Andrius

last: Kazlauskas

state: IL

address: 1855 W Taylor Street

department: Ophthalmology & Visual Sciences

institute: University of Illinois Chicago

summary: Proliferative diabetic retinopathy (PDR) is a major complication of diabetes characterized by pathological angiogenesis in the retina. Standard treatment includes vitrectomy to remove these abnormal vessels, and the resulting clinical specimens provide an opportunity to define drivers of PDR. Here, we profiled endothelial and immune cells from such samples to identify disease mechanisms. In some patients, endothelial cells were more abundant, whereas in others, immune cells predominated. Immune cells exhibit gene expression programs directed against pathological endothelium, suggesting an endogenous defense that may explain the scarcity of endothelial cells in certain cases. Preoperative anti-vascular endothelial growth factor (VEGF) therapy altered transcriptional programs in both endothelial and immune cells, indicating that its effects extend beyond the vasculature. A comparison of endothelial signatures from PDR patients and nondiabetic donor retinas revealed a distinct molecular program in PDR, prominently marked by mitochondrial dysfunction. In contrast, endothelial cells from the murine oxygen-induced retinopathy (OIR) model lacked mitochondrial dysfunction, although other features of pathological angiogenesis were shared. These findings suggest that PDR is not a uniform disease but comprises distinct types characterized by either immune-mediated clearance of pathological vessels or endothelial mitochondrial dysfunction. They also revealed that anti-VEGF therapy influences both endothelial and immune compartments, with implications for treatment strategies. Finally, the data clarify both the relevance and limitations of the OIR model for preclinical testing of new therapeutic targets.

overall_design: RNA-Seq analysis of CD31+ cells isolated from vitreous removed from patients with proliferative diabetic retinopathy during vitrectomy.

first: Maximilian

last: McCann

first: Basma

last: Baccouche

first: Yueru

first: Priti

last: Roy

first: Neil

last: Sheth

first: Jennifer

last: Lim

first: William

last: Mieler

first: Felix

last: Chau

first: Lawrence

last: Ulanski

first: Paul

last: Chan

first: Monique

last: Munro

first: Robert

last: Hyde

first: Caitlin

last: Berek

first: Anna

last: Ong

first: Sudeshna

last: De

first: Barbara

last: Siedlecki

first: Ru-Ik

last: Chee

first: Yannek

last: Leiderman

first: Michael

last: Heiferman


title: Transcriptome profiling of porcine valvular interstitial cells undergoing mesenchymal-to-endothelial transition under osteogenic induction

city: shanghai

first: Binglin

last: Li

state: 上海

address: 241 Huaihai West Road, Xuhui District, Shanghai, China

institute: shanghai chest hospital

summary: Calcific aortic valve disease (CAVD) is a progressive disorder characterized by fibrosis, calcification, and endothelial dysfunction. Valvular interstitial cells (VICs) are the predominant cell type within the aortic valve and play key roles in valve remodeling. Recent evidence suggests that VICs exhibit phenotypic plasticity and may undergo mesenchymal-to-endothelial transition (MEndT) under calcific conditions. To explore the transcriptional landscape of this process, we performed RNA sequencing on primary porcine VICs cultured in growth medium (GM), osteogenic medium (OM) for 8 days, and primary porcine valve endothelial cells (pVECs). This dataset provides a resource for understanding the molecular mechanisms underlying MEndT and its potential contribution to CAVD pathogenesis.

overall_design: Primary porcine aortic valve interstitial cells (pVICs) and valve endothelial cells (pVECs) were isolated from healthy pig aortic valves. Three experimental groups were established: pVICs cultured in growth medium (GM) (n = 4 biological replicates), pVICs cultured in osteogenic medium (OM) for 8 days (n = 4 biological replicates), pVECs cultured in growth medium (GM) (n = 4 biological replicates). RNA was extracted from each sample, and sequencing libraries were prepared and sequenced on the Illumina platform. Each group contained four independent biological replicates, yielding a total of 12 samples.

first: Dan

last: zhu


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues

first: Julie

last: Law

summary: DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to anther or ovule tissues. We designate these factors as REM INSTRUCTS METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. Furthermore, we demonstrate that mis-expression of RIM12 is sufficient to initiate siRNA production at ovule targets in anthers. These findings reveal a critical role for genetic information in targeting DNA methylation in reproductive tissues, expanding our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

overall_design: Illumina sequencing of smRNA-seq, mRNA-seq, methylC-seq, and ChIP-seq datasets were generated in this study. For small RNA and mRNA sequencing experiments, three replicates for wild-type plants and two replicates for mutant plants were included.

first: Guanghui

last: Xu


title: Cell-extrinsic controls over neocortical neuron fate and diversity [snRNAseq]

status: Public on Sep 18 2025

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: Neocortical cellular diversity emerges gradually during development. Cell-extrinsic interactions shape this extended maturation, yet cell-type-specific dependence on such cues has not been systematically examined. To address this, we compared how cell identity and diversity unfolds in different conditions during neocortical development. Conditions were modified in vivo using genetically modified mice models in which position or innervation are altered and in vitro using two-dimensional cultures. This approach revealed a molecular hierarchy in which cell class-distinguishing features emerge first, followed by subclass- and type-related characteristics. Acquisition of cellular identity and diversity remained stable across in vivo models. In contrast, in vitro glutamatergic neurons showed decreased expression of identity-defining genes, reduced diversity and alterations in connectivity. Cellular identity and diversity were closest to in vivo values in organotypic cultures. These findings reveal population-specific responses to environmental conditions and highlight the role of extracellular context in shaping cell diversity in the maturing neocortex.

overall_design: Single nucleus transcriptomics of in vivo and invitro models of extrinsic factors of mouse neuronal maturation

first: Natalia

last: Baumann

first: Sabine

last: Fièvre

first: Ilaria

last: Morassut

first: Esther

last: Klingler

first: Giorgia

last: Bartolini

first: Sergi

last: Roig Puiggros


title: CASSIA: a multi-agent large language model for reference free, interpretable, and automated cell annotation of single-cell RNA-sequencing data

city: Madison

first: Yixuan

last: Xie

state: Wisconsin

address: 320 East Wilson Street, 602

department: Department of Biostatistics and Medical Informatics

institute: University of Wisconsin - Madison

summary: Cell type annotation is an essential step in single-cell RNA-sequencing analysis, and numerous annotation methods are available. Most require a combination of computational and domain-specific expertise, and they frequently yield inconsistent results that can be challenging to interpret. Large language models have the potential to expand accessibility while reducing manual input and improving accuracy, but existing approaches suffer from hyperconfidence, hallucinations, and lack of reasoning. To address these limitations, we developed CASSIA for automated, accurate, and interpretable cell annotation of single-cell RNA-sequencing data. As demonstrated in analyses of 970 cell types, CASSIA improves annotation accuracy in benchmark datasets as well as complex and rare cell populations, and also provides users with reasoning and quality assessment to ensure interpretability, guard against hallucinations, and calibrate confidence.

overall_design: Single-cell RNA-sequencing was performed on human brain metastasis tissues obtained during the clinical trial NCT03398694. Samples were collected from patients with confirmed brain metastases originating from non-small cell lung cancer. Tissues were resected, dissociated, and processed using the 10x Genomics Chromium platform. Resulting scRNA-seq profiles were clustered, and marker genes were identified using the FindAllMarkers function in Seurat. These markers were used as input to CASSIA for cell type annotation. Final annotations were validated with quality scores and consensus-based confidence assessments.

first: Elliot

first: Lingxin

last: Cheng

first: Jack

last: Shireman

first: Yujia

last: Cai

first: Jihua

last: Liu

first: Chitrasen

last: Mohanty

first: Mahua

last: Dey

first: Christina

last: Kendziorski


title: Characterization of SARS-CoV-2–Specific B Cell Responses in Breakthrough and Multiple Infection Cohorts

city: New York

first: Patrick

last: Wilson

address: 413 E 69th St

department: Drukier Institute

institute: Weill Cornell Medicine

summary: We analyzed the B cell responses after infection in two cohorts: individuals with breakthrough infections following SARS-CoV-2 vaccination and individuals with multiple SARS-CoV-2 infections.

overall_design: SARS-CoV-2–specific B cells were sorted from PBMCs obtained from both the breakthrough infection cohort and the multiple-infection cohort, and LIBRA-seq was used to assess their antigen reactivity to SARS-CoV-2 and gene expression profiles.

first: Siriruk

last: Changrob

first: Atsuhiro

last: Yasuhara

first: Jordan

last: Chervin

first: Chloe

last: Troxell


title: Cell-extrinsic controls over neocortical neuron fate and diversity [PatchSeq]

first: Denis

last: Jabaudon

overall_design: Chronic optogenetic stimulation of primary cultures, cultures were prepared from E16 brains electroporated at E14 with pCAG-tdTomato plasmid alone or with a mix of pCAG-tdTomato plasmid and pAAV CAG 439 ChR2 E123T T159C 2A tDimer plasmid. Starting at DIV1 cultures were chronically optogenetically stimulated by applying a protocol of train stimulation of blue LED (train of 20 stimulations; 10ms stimulation duration; 50ms stimulation interval; 30s inter-train interval) until Patchseq at DIV17.

first: Natalia

last: Baumann

first: Sabine

last: Fièvre

first: Ilaria

last: Morassut

first: Esther


title: GLP-1 receptor agonism results in reduction in hepatic ethanol metabolism

first: Frhaan

last: Zahrawi

state: CT

address: 300 cedar st

department: Internal Medicine

summary: Glucagon-like peptide 1 receptor (GLP-1R) agonists are used along with ethanol consumption, but their interactions are not understood. Our aim was to determine the effects of GLP-1R agonism on the liver in mouse models of high ethanol consumption. We identified that GLP-1R agonism reduced ethanol consumption, mitigated ethanol-induced upregulation of several liver metabolizing enzymes, including Cyp2e1 and also reduced Cyp2e1 independent of ethanol intake. As expected from a reduction in Cyp2e1, GLP-1R agonism resulted in increased blood ethanol levels. This occurred after a single dose of ethanol when given by gavage, and by the intraperitoneal route. This suggests that GLP-1R agonism can reduce ethanol-mediated hepatotoxicity despite continued ethanol consumption and elevate blood alcohol levels

overall_design: 24 mice were divided into four groups—1) Control (CT), 2) Alcohol-fed (ALC), 3) Alcohol + GLP-1R agonist (ALC + GLP), 4) Control + GLP-1R agonist (CT + GLP). The semaglutide dosage regimen was escalated from 1 to 30 nmol/kg over 16 days. On day 16, mice in the alcohol groups received alcohol gavage, and control groups received dextrin.

first: Suyavaran

last: Arumugam

first: Bubu

last: Banini

first: Wajahat

last: Mehal