title: SWI/SNF Remodeling Complexes Regulate 3D Chromatin Architecture by Antagonizing CTCF and Cohesin

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

summary: The BAF (mammalian SWI/SNF) chromatin remodeling complexes play a fundamental role in nucleosome positioning and transcription factor binding. Despite the well-established role of the three BAF complexes in chromatin remodeling (cBAF, PBAF and ncBAF), no common mechanism has been identified that would explain widespread occurrence of BAF complex loss-of-function mutations across cancers and genetic disorders in diverse tissue types. Given that BAF complex regulates accessibility of both ubiquitous and tissue-specific transcription factors, we set out to determine whether a unifying chromatin regulatory mechanism of BAF remodeling across tissues exists. To investigate this, we profiled chromatin accessibility after inhibiting all BAF complexes across a panel of cancer-derived and non-cancer cell lines, encompassing lymphoid, myeloid, neuronal, epithelial, embryonic, and other lineages. We found that the only commonality between tissues was a striking increase in chromatin accessibility at CTCF sites, observed in most tissue types. This effect was most pronounced in lymphoid and myeloid tissues, tissues that also exhibited the highest baseline levels of CTCF. Chromatin immunoprecipitation in these tissues revealed increased CTCF and cohesin (SMC3) binding, demonstrating a previously unknown antagonistic binding relationship between cBAF and CTCF-cohesin complexes on chromatin. Genetic deletion of the cBAF-specific subunit ARID1A reproduced the chromatin accessibility changes observed upon pan-BAF complex inhibition, demonstrating that cBAF loss is the principal driver of increased CTCF accessibility. To determine the functional consequences of the observed CTCF gain, we investigated its impact on topologically associated domains (TADs). High-resolution chromatin capture (Micro-C) showed strengthening of existing TAD boundaries, increasing intra-domain interactions, and splitting larger domains into smaller, more insulated structures, demonstrating how BAF loss reshapes 3D chromatin architecture. To identify remodelers that help CTCF recruitment to chromatin in absence of cBAF, we identified CTCF interacting complexes and found that CTCF directly interacts with fully assembled PBAF, but not cBAF, stabilizing CTCF binding in the absence of cBAF. Furthermore, we show that upon cBAF loss, the PBAF complex is recruited to sites of increased CTCF occupancy, showing for the first time a functional shift in chromatin regulation by the antagonism of these remodelers. We further determined the functional consequence of this antagonism in vivo. Conditional Arid1a deletion in primary mouse B cells led to the expansion of highly proliferative cells with increased CTCF binding. To determine whether CTCF drives this phenotype, we generated a dual knockout model by crossing Arid1a- and Ctcf-conditional knockout mice. Strikingly, Ctcf deletion fully reversed the proliferative phenotype of Arid1a loss, establishing a direct functional in vivo link between ARID1A loss and CTCF gain. Finally, linking this phenotype to 3D chromatin structure, we found that loss of cBAF rewires chromatin looping by converting distal enhancer–promoter interactions into shorter, promoter-proximal loops via increased CTCF binding. This shift in loop anchors alters transcriptional programs, underscoring a unified mechanism by which cBAF loss redefines 3D chromatin organization and gene regulation

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design:
CtcfHet GC cells from splenocytes were sorted and underwent the manufacturer's nuclei preparation procedure. Then, about 20,000 nuclei were placed into a 10x Chromium X instrument. The remainder of the library preparation steps were conducted in accordance with the manufacturer's protocol
Micro-C was performed in RIVA cells using two ARID1A wild-type (WT) clones and two ARID1A heterozygous (HET) clones to map chromatin interactions at single nucleosome resolution. Comparisons between ARID1A HET and WT samples were used to assess the role of ARID1A in 3D genome organization.
Cell lines or primary mouse B-cells of different genotypes were subject to Omni ATAC-Seq protocol (Corces et al., 2017; Nature Methods). Each genotype was assessed in at least triplicates. Results from mutant samples were compared to WT samples to identify differences in chromatin accessibility after deletion of ARID1A, CTCF, or both ARID1A and CTCF.
Cells were treated for 24h with a BAF inhibitor or DMSO, and subject to Omni ATAC-Seq protocol (Corces et al., 2017; Nature Methods). Each condition was assessed in triplicates. Results from inhibitor-treated sampels were compared to DMSO samples to identify differences in chromatin accessibility after BAF inhibition.
Cells of different genotypes (ARID1A WT or ARID1A HET), or WT cells treated with either 100 nM of SMARCA2/4 inhibitor FHD-286 or DMSO for 24h were subject to ChIP. Each condition was assessed in at least duplicate per batch. Results for samples with heterozygous mutation were compared to WT cells, whereas results for inhibitor-treated samples were compared to DMSO-treated samples to elucidate the role of cBAF in the binding of PBRM1, BRD7, CTCF or SMC3.
Cells were treated for 24h with a BAF inhibitor, dTAG or DMSO where indicated, and subject to Omni ATAC-Seq protocol (Corces et al., 2017; Nature Methods). Each condition was assessed in triplicates unless otherwise noted. Results from inhibitor-treated sampels were compared to DMSO or WT samples to identify differences in chromatin accessibility after BAF inhibition.
Micro-C was performed in RIVA cells using two ARID1A wild-type (WT) clones and two ARID1A heterozygous (HET) clones to map chromatin interactions at single nucleosome resolution. Comparisons between ARID1A HET and WT samples were used to assess the role of ARID1A in 3D genome organization.
Cell lines were subject to the joint 10x genomics nuclear isolation protocol. Then, about 20,000 nuclei were placed into a 10x Chromium X instrument. The remainder of the library preparation steps were conducted in accordance with the manufacturer's protocol
Cells of different genotypes (ARID1A WT or ARID1A HET), or WT cells treated with either 100 nM of SMARCA2/4 inhibitor FHD-286 or DMSO for 24h, or dTAG-13 or DMSO for 6h were subject to ChIP. Each condition was assessed in at least duplicate per batch. Results for samples with heterozygous mutation were compared to WT cells, whereas results for inhibitor-treated samples were compared to DMSO-treated samples to elucidate the role of cBAF in the binding of PBRM1, ARID1A / ARID1A-HA, CTCF and SMC3.

first: Debek

last: Sonia

first: Meydan

last: Cem

first: Chin

last: Christopher

first: Melnick

last: Ari

first: Barisic

last: Darko


title: Simultaneous orthogonal cell engineering by a single CRISPR-Cas9 polyfunctional editor [BiSulfite-seq]

status: Public on Apr 06 2026

city: Milano

first: Sara

last: Valsoni

state: MI

address: via Olgettina 60

department: TIGET

country: Italy

institute: SR-TIGET

type: Methylation profiling by high throughput sequencing

summary: The parallel disruption of multiple genes coupled with targeted transgene insertion offers a powerful strategy for more effective and precise cell engineering. However, such orthogonal editing involves the induction of multiple DNA breaks, raising safety concerns related to the risks of chromosomal translocations. Here, we present a polyfunctional CRISPR-Cas9-based strategy that enables both transgene insertion and epigenetic silencing at distinct genomic loci in a single treatment without inducing reciprocal chromosomal translocations. This is accomplished through an optimized all-in-one epigenome editor equipped with a catalytically active Cas9, whose endonuclease activity is selectively disabled at epigenetically silenced loci by the use truncated gRNAs. As a proof of concept, we demonstrated that this platform enables efficient multi-locus editing, including functional replacement of the endogenous TCR with a tumor-selective one, targeted insertion of a prototypic CAR with either a selectable marker or an immunomodulatory receptor into a TCR locus or a ubiquitously expressed gene, and durable, multiplexed epigenetic silencing of clinically relevant genes in primary human T cells. Polyfunctional editing establishes a versatile and safe framework for orthogonal editing, broadening the scope of genome and epigenome engineering in cancer immunotherapy and beyond.

overall_design: Analysis of B2M or TET2 CpG island methylation status of K-562 cell line or T cells treated or not with different ETRs

first: Deborah

last: Cipria

first: Tania

last: Baccega

first: Miriana

last: Rizzo

first: Piergiuseppe

last: Quarato

first: Alice

last: Reschigna

first: Rita

last: El Khoury

first: Martino

middle: A

last: Cappelluti

first: Sandra

last: Ammann

first: Valeria

last: Mollica Poeta

first: Matteo

last: Conti

first: Pietro

last: Spinelli

first: Ivan

last: Merelli

first: Toni

last: Cathomen

first: Monica

last: Casucci

first: Angelo

middle: L

last: Lombardo


title: Function of PLAGL1 during osteogenesis of mandible [RNA-seq]

city: Shanghai

first: Jiahui

last: Du

address: Zhizaoju Road 639

country: China

institute: Shanghai Jiao Tong University

type: Expression profiling by high throughput sequencing

summary: We show that PLALG1 promotes osteogenesis.

overall_design: We detected the function of PLAGL1 in mouse mandibular periosteal progenitors during osteoblastic differentiation with b-glycerophosphate (b-GP) (5 mM), ascorbic acid (50 ug/ml), and dexamethasone (100 nM) in a-MEM.


title: A stem cell-derived neuronal culture model for mouse species variation in neurite growth

city: Berkeley

first: Rachel

middle: B

last: Brem

state: CA

address: 321 Koshland Hall

department: Plant and Microbial Biology

country: USA

institute: UC Berkeley

summary: Stem cell-derived neurons represent a powerful experimental system for the study of axon growth and regeneration, cutting cost and technical challenges. We developed an in vitro system using stem cell-derived motor neurons to investigate phenotypic differences in neurite growth between mouse subspecies. Previously, neurons in CAST/EiJ mice (Mus musculus castaneus) were reported to regrow CNS axons after injury to a greater degree than other strains. Here, we assayed neurite outgrowth from stem cell-neurons in a fully in vitro system, in the abscence of injury signals. In this system, CAST/EiJ neurons grew longer axons than those of C57BL/6J and 129S6/SvEv origin. Additionally, CASTx129 hybrid neurons exhibit comparable neurite growth to CAST/EiJ, indicating a dominant genetic effect.

sample_organism: Mus musculus domesticus x Mus musculus castaneus

overall_design: To assess the transcriptional identify of the various cell lines used, we sequenced undifferentiated pluripotent stem cells and differentiated motor neurons. Samples were sequenced from a C57BL/6J, CAST/EiJ, 129S6/SvEv, and hybrid CASTx129 lines.

first: N

middle: M

last: Simon

first: M

last: Frier

first: Y

last: Kim

first: D

last: Bautista

first: J

middle: R

last: Dutton

first: R


title: C2orf74 Orchestrates Germ-Leydig Crosstalk to Reprogram White Adipocyte Identity II

city: HeFei

first: zhao

last: li

address: Daoxiangcun

institute: ustc

summary: Gender differences in obesity is widely reported, however, identification of gender specific obese gene and characterization of its role in obesity remain elusive. Here, we identify a germ cell specifically expressed gene C2orf74 and demonstrate that C2ORF74 promotes high-fat diet (HFD) induced obesity in male but not female male. Loss of C2ORF74 protects male mice from obesity by boosting testosterone levels and enhancing energy expenditure and browning of white adipose tissues (WAT). We demonstrate that spermatogenic C2ORF74  suppresses testosterone biogenesis in Leydig cells through germ-cell secreted BPIFA3, whose maturation and secretion is dependent on DPM1-mediated glycosylation. Collectively, these findings define a role of spermatogenic C2ORF74 in energy expenditure and adipose browning in a gender specific manner.

overall_design: high fat diet fed WT and C2orf 74 mice at 8 weeks old for 12 weeks and isolated white adipose tissues ,extract RNA for RNA seq


title: Cellular Origin and Molecular Mechanisms of Lung Metastases in Patients with Aggressive Hepatoblastoma

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: Lung metastases are dangerous for patients with aggressive hepatoblastoma. Here we characterize a dramatic increase in cancer-associated fibroblasts and neuron-like cells that are released into the bloodstream and are found in lung metastases. Using RNAseq of fresh tumor samples taken from hepatoblastoma patients, and cells cultered from those tumors, we observe the rapid proliferation of metastasis-initiating pathways.

overall_design: Comparative gene expression analysis of fresh tumor samples obtained from hepatoblastoma patients, and cells cultured from those tumors.

first: Nicolai

last: Timchenko

first: Ruhi

last: Gulati


title: MRE11 proximal polyadenylation site-mediated looping impacts transcription and genomic stability [RNA-seq]

city: Boston

first: Dipanjan

last: Chowdhury

state: MA

address: 4 Blackfan Circle

institute: Dana-Farber Cancer Institute

summary: MRE11, a key regulator in maintaining genome integrity, has two main polyadenylation sites (PAS) in 3’UTR. There is a ~3 Kb difference between the proximal PAS (pPAS) and the distal PAS (dPAS). Therefore, using the pPAS can result in a ~3 Kb shorter MRE11 transcript which lacks a significant number of regulatory motifs in the 3’UTR. Analysis of the Cancer Genome Atlas revealed (10/160) mutations in MRE11 3’UTR, and intriguingly all these mutations are localized in pPAS. We observed that deletion of pPAS (~150 bp) using CRISPR caused ~50% reduction of MRE11 protein and mRNA. We hypothesize that pPAS regulates transcription of the MRE11 gene via ‘DNA looping’ where this cis element in the 3’UTR regulates the canonical MRE11 promoter. MRE11 hypomorphism in AT-like deficiency (ATLD) cells is well characterized, and MRE11pPAS-/- phenocopy these cells. Cell cycle analysis revealed that MRE11pPAS-/- cells grow slower with increased proportion of cells in the S/G2 phase with a concurrent decrease in the G0/G1 population. The most intriguing phenotype was in the context of G1/S checkpoint. Overgrown wild-type RPE1 cells when confluent exit the cell cycle and stop replicating. In contrast, MRE11pPAS-/- cells continued replicating leading to rapid cell death. Next, we systematically synchronized cells in G0/G1, and observed that EdU labeling in these G0/G1-paused cells shows increased BrdU+ population only in MRE11pPAS-/- cells. Induction of MRE11 in MRE11pPAS-/- cells can ‘rescue’ the ectopic replication of confluent cells, confirming that the phenotype is indeed due to reduced MRE11 expression. This suggests that optimal MRE11 is necessary for preventing unlicensed DNA replication in completely distinct scenarios. Our study highlights the importance of the 3’UTR in transcriptional regulation of MRE11 and its profound impact on genomic stability and cell growth.

overall_design: To invesitgate the role of pPAS on gene regulation, we knockout MRE11pPAS and then perform RNA-seq to find deregulated gene after MRE11pPASKO.

first: Kaimeng

last: Huang


title: Epigenetic modulation of polyamine biosynthetic pathways rectifies T cell dysfunction to enhance anti-tumor immunity in lung cancer

city: Taipei City

first: Nai-Wen

last: Chang

address: 2F., No.7, Zhongshan S. Rd., Zhongzheng Dist.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: T cell exhaustion (TEX) represents a critical target for immunotherapy in cancer. Nevertheless, T cells exhibit diminished responsiveness to immune checkpoint inhibitors once they transition to a terminally-exhausted state. In this study, we employed Single-cell RNA-seq to demonstrate BETis reduced terminal TEX while promoting progenitor TEX through activation of the MYC-ODC axis.

overall_design: MPE CD3+ T cells were treated with or without 500 nM JQ1 for 3 days (D3R3, n=3). Multiplex single-cell sequencing analysis was performed using TotalSeq™-B antibodies (394645, 394647, 394635, and 394637, BioLegend) as per the manufacturer’s instructions. Briefly, 2 × 10^6 cells were resuspended in Cell Staining Buffer (BioLegend) and incubated with Human TruStain FcX™ Fc Blocking Reagent (BioLegend) for 10 minutes at 4°C. TotalSeq™-B antibodies were then added to each cell suspension and incubated for 30 minutes at 4°C. After antibody labeling, the samples were pooled, filtered through a 40 µm Flowmi™ Cell Strainer (BAH136800040, Sigma), and the cell concentration and viability were assessed using a Countess II FL Automated Cell Counter (Invitrogen™). Single-cell libraries were constructed using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics, CG000206 Rev D), incorporating Feature Barcoding technology for cell surface protein analysis. To target a recovery of 10,000 cells, the cell suspension was adjusted to 700–1,200 viable cells per microliter before generating single628 cell gel beads in emulsion (GEM). Libraries were sequenced on a NovaSeq 6000 System (Illumina) using paired-end 150 bp reads, generating at least 80 GB of data per sample for gene transcriptome sequencing and 20 GB for hashing tags.


title: C2orf74 Orchestrates Germ-Leydig Crosstalk to Reprogram White Adipocyte Identity I

summary: Gender differences in obesity is widely reported, however, identification of gender specific obese gene and characterization of its role in obesity remain elusive. Here, we identify a germ cell specifically expressed gene C2orf74 and demonstrate that C2ORF74 promotes high-fat diet (HFD) induced obesity in male but not female male. Loss of C2ORF74 protects male mice from obesity by boosting testosterone levels and enhancing energy expenditure and browning of white adipose tissues (WAT). We demonstrate that spermatogenic C2ORF74 suppresses testosterone biogenesis in Leydig cells through germ-cell secreted BPIFA3, whose maturation and secretion is dependent on DPM1-mediated glycosylation. Collectively, these findings define a role of spermatogenic C2ORF74 in energy expenditure and adipose browning in a gender specific manner.

overall_design: high fat diet fed WT and C2orf 74 mice at 8 weeks old for 12 weeks and isolated testicular leydig cells ,extract RNA for RNA seq


title: ROS1 regulates blueberry fruit ripening in a negatively ABA manner (WGBS)

city: Beijing

first: Zejia

last: Wang

address: Yanyuan Street

institute: Peking University

summary: Characterization of WGBS and RNA-seq in  blueberry fruits

overall_design: This dataset contains 15 WGBS data and 15 RNA-seq of cultivated blueberries.

first: Yangyan

last: Zhou

first: Qikun

last: Liu


title: C2orf74 Orchestrates Germ-Leydig Crosstalk to Reprogram White Adipocyte Identity

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

overall_design: Refer to individual Series


title: Cell clusters during mandibular bone regeneration [scRNA-seq]

first: Jiahui

last: Du

summary: We show 14 cell clusters during mandibular bone regeneration.

overall_design: We detected 14 cell clusters, including  granulocytes, monocytic cells, B cells, Erythrocytes, NK cells, endothelial cells, mesenchymal lineage cells during mandibular bone regeneration.


title: RNA-seq of wild-type human iPSC-derived retinal organoids at different developmental stages

status: Public on Apr 05 2026

city: Manchester

first: Jacob

last: Sampson

address: Oxford Road

country: United Kingdom

institute: University of Manchester

summary:
Human retinal organoids derived from pluripotent stem cells provide an in vitro system to model key aspects of early human retinal development and to investigate mechanisms underlying developmental eye disorders. Congenital eye diseases, such as microphthalmia, anophthalmia and coloboma, arise from disruptions in gene regulatory programs that control retinal progenitor specification and neuronal differentiation. However, studying these processes in humans is challenging due to limited access to developing retinal tissue.
Here we present a temporal bulk RNA sequencing dataset of retinal organoids collected across multiple stages of differentiation (days 0, 35, 60, 90, 120, and 150). These timepoints span early retinal lineage specification through progressive neuronal differentiation and maturation of retinal cell types. The dataset captures dynamic gene expression changes associated with retinal development and provides a transcriptional framework for studying genes implicated in congenital and developmental retinal disorders.

overall_design: RNA-seq of wild-type human iPSC-derived retinal organoids at days 0 (iPSC), 35, 60, 90, 150 and 180 of organoid differentiation.

first: Srishti

last: Silvano

first: Rick-Lenze

last: van Annika

first: Milena

last: Zitnik-Sergeant

first: Jamie

last: Ellingford

first: Manning

last: Cerys


title: Bile acid uptake activates STAT signaling and impairs natural killer cells in metabolic dysfunction–associated steatohepatitis

city: Jerusalem

first: Johnny

last: Amer

address: Ein kerem

country: Israel

institute: Hadassah Hospital

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) encompasses a spectrum of fatty liver diseases ranging from steatotic liver disease to metabolic dysfunction-associated steatohepatitis (MASH), and its prevalence is increasing worldwide due to the pandemic of obesity. Approximately 20–30% of MASLD patients develop MASH, leading to liver cirrhosis and associated complications, including hepatocellular carcinoma. Liver damage, such as cholestatic conditions in which bile secretion and flow are disturbed, is associated with impaired innate and adaptive immunity. NK cells play a crucial role in inhibiting liver fibrosis. However, how bile acids affect natural killer (NK) cells remains unknown. We aimed to assess the impact of bile acid concentration on NK cell functionality and identify the molecular and metabolic NK cell signaling pathways that influence liver fibrosis pathogenesis. To this end, we studied peripheral NK cells from patients with MASH, healthy donors, and a mouse model of MASH. Sodium+/taurocholate cotransporting polypeptide (NTCP) expression was 2.5-fold higher in peripheral blood NK cells from MASH patients with advanced liver fibrosis than in those from early liver fibrosis patients and healthy donors. Greater taurocholic acid (TCA) uptake was observed in peripheral NKNTCP+ cells from the early and advanced liver fibrosis MASH patient groups than in NKNTCP- cells from the same patients. It was associated with increased levels of exhaustion markers and decreased activity. Moreover, single-cell RNA sequencing and functional analyses demonstrated that NTCP⁺ NK cells in advanced MASH adopt stress- and exhaustion-associated transcriptional programs with reduced translational activity, accompanied by increased STAT3 activation and diminished STAT1 signaling, highlighting their impaired cytotoxic function. Following STAT3 inhibition, trNKNTCP+ cells presented significantly reduced NTCP expression, reduced NK cell exhaustion, and restored NK cell activity. In MASH mice, epigallocatechin gallate-mediated inhibition of NTCP expression reduced TCA uptake and attenuated liver fibrosis. Additionally, in immunodeficient liver fibrosis model mice, reconstitution with trNKNTCP- cells alleviated liver fibrosis, decreased proinflammatory and profibrotic cytokine levels, and ameliorated lipid homeostasis. Our findings suggest that enhancing immune responses by restoring NK cell activity through NTCP antagonism may offer a clinically beneficial strategy to prevent liver fibrosis in patients with metabolic disorders, autoimmune diseases, and chronic viral hepatitis.

overall_design: Peripheral NK cells were isolated from two representative F3/F4 advanced liver fibrosis MASH patients (A and B) selected based on age and sex and were sorted on the basis of positive/negative NTCP expression.

first: Ahmad

last: Salhab

first: Lu

last: Yinying

first: Rifaat

last: Safadi


title: Effect of hydrolyzed corn starch treatment on the gene-expression profiles

city: Tokyo

first: Hitomi

last: Hagawa

address: 7-2-1 Hirai, Edogawa-ku

department: Research & Development Headquarters

country: Japan

institute: Lion Corporation

summary:
This study investigates the transcriptional response of normal human epidermal keratinocytes (NHEKs) to treatment with hydrolyzed corn starch containing maltotetraose.
NHEKs were treated with 2.0% hydrolyzed corn starch for 24 h, and total RNA was subjected to gene expression profiling using a Clariom S human array.

overall_design: NHEKs were cultured in 6-well plates and treated with either culture medium alone (control) or medium containing 2.0% hydrolyzed corn starch for 24 h. Total RNA was extracted from cells and hybridized to Clariom S human arrays. The dataset includes n=3 control samples and n=3 treated samples.

first: Eri

last: Ichikawa

first: Keiko

last: Otake


title: Molecular Characterization of auditory nerve with Versican deficiency [re-analysis]

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Overall goal of the study is to identify molecular regulators of auditory nerve development and maintenance. A reanalysis was done for sequencing data (fastq files) deposited under GEO record GSE122045. These samples were prepared from auditory nerve tissue isolated from Young adult C57BL/6 wildtype and Young adult Versican V0/V2 isoform knockout mice (n=3). This reanalysis was done to identify genes differentially expressed in auditory nerve between wildtype and versican deficient mice.

relation:
Reanalysis of: GSM3453625
Reanalysis of: GSM3453626
Reanalysis of: GSM3453627
Reanalysis of: GSM3453628
Reanalysis of: GSM3453629
Reanalysis of: GSM3453630

overall_design:
The original study examined auditory nerve samples from young adult C57BL/6J wildtype and Young adult Versican V0/V2 isoform knockout mice. Each group used three independent samples. For the reanalysis, fastq files corresponding to those archived in record GSE122045 were obtained and analyzed anew, using Partek Flow software. Briefly, alignment was performed using STAR 2.7.8a and a mm39 reference index, gene counts were quantified to annotation model (Partek E/M) using a transcript model built from mm39 Ensembl Transcripts release 111, and normalized counts and differential expression metrics were obtained by DESeq2.

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

first: Hainan

last: Lang


title: Effect of MEK inhibiton on KrasQ61R mutant Lgr5-positive intestinal stem cells

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

summary: We have previously shown that KRAS hyperactivation depletes the Lgr5-positive intestinal stem cells. Here, we aim to address whether reducing the MAPK pathway output, by using a MEK inhibitor (Cobimetinib) is sufficient to restore expression of Lgr5-positive intestinal stem cell markers.

overall_design: RNAseq profiling of Kras Q61R (Rosa26CreERT2) mice treated with combimetinib for 5 days, and harvested at Day 10 post-tamoxifen adminstration.

first: Amanda

last: Moore

middle: P

first: Frederic

middle: J

last: de Sauvage


title: Remembering heat: How the unicellular alga Cyanidioschyzon merolae establishes a molecular stress memory that boosts its thermotolerance

city: Berlin

first: Teresa

last: Kowar

address: Königin-Luise-Str. 12-14

country: Germany

institute: Freie Universität Berlin

summary: A powerful way to enhance heat tolerance is by establishing a stress memory through exposure to a heat stress that is strong enough to induce a molecular stress response without causing irreversible damage, followed by a recovery phase. While this has been extensively studied in multicellular organisms, we demonstrate that heat stress memory is also present in the unicellular red alga Cyanidioschyzon merolae. We show that, similarly to more complex organisms, thermomemory in this alga is underpinned by transcriptomic reprogramming, with the chloroplast emerging as the main site of gene trainability. Additionally, we find a conserved small heat shock protein (sHSP)-encoding locus in the nuclear genome to be heat-trainable, likely by histone depletion and modification through the repressive mark H3K27me3. We show that of C. merolae’s two sHSPs, only CmsHSP2 is necessary for proper HS memory establishment, and that the two sHSPs localize to different cellular compartments during heat stress. Finally, comparative RNA-Sequencing of an Enhancer of zeste mutant reveals a role for the H3K27me3-transferase in adapting the transcriptome to recurring heat exposures, beyond regulating the trainable sHSP locus.

sample_organism:
Cyanidioschyzon merolae
Cyanidioschyzon merolae strain 10D

overall_design:
RNA-seq profiling of Cyanidioschyzon merolae 10D cells and the Polycomb mutant line Cme(z)-1 under (repetitive) heat stress regime to investigate putative heat stress memory on transcriptomic level. RNAseq was performed on three biological replicates for each condition on an  Illumina NovaSeq 6000. Control samples (N) were published in Hisanaga et al., 2023, Current Biology 33, 4367–4380 | https://doi.org/10.1016/j.cub.2023.08.073.;  GEO Number GEO: GSE221632 previously. As control samples the following GSM sample accession numbers were reanalyzed: GSM6891998, GSM6891999, GSM6892000, GSM6892001, GSM6892002, GSM6892003. Albeit control samples were published earlier, all the samples were generated at the same time.

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

last: Kerckhofs

first: Léa

last: Faivre

first: Martha

last: R. Stark

first: Ruth

last: Lintermann

first: Ana-Belen

last: Kuhlmann

first: Stephen

last: D. Rader

first: Daniel

last: Schubert


title: Posterior explants of Stage 26 embryos treated with picrotoxins

city: Fujisawa

first: Masaki

last: Hachiman

state: Kanagawa

address: 5322 Endo

department: Graduate School of Media and Governance

institute: Keio University

summary: This dataset contains RNA-seq profiles from the posterior explants of Xenopus laevis embryos at stage 26. Explants were sectioned posterior to the otic vesicle and treated with 0.5 mM picrotoxin for 3 h to inhibit Gamma-Aminobutyric Acid (GABA) signaling, followed by removal of the ventral yolk. Two biological replicates were prepared for each condition, with each replicate pooling explants from three embryos. RNA-seq was performed to identify transcriptional changes associated with GABA signaling during tailbud-stage body axial elongation. The dataset includes raw FASTQ files and metadata, enabling the analysis of differential gene expression patterns under GABA inhibition.

overall_design: Stage 26 embryos were transversely sectioned posterior to the otic vesicle along the anteroposterior axis. The obtained posterior explants were treated with picrotoxin (0.5 mM) for 3 h, followed by the removal of the ventral yolk. For each condition, two biological replicates were prepared; each replicate consisted of pooled explants from three individual embryos.

first: Hiroki

last: Kuroda


title: Aqueous Artemisia argyi extract mitigates acute lung injury by coordinating gut microbiota, metabolic homeostasis, and pulmonary inflammatory signaling

city: ALAR

first: 海宏

last: 焦

address: Tarim University

institute: Tarim University

summary: Background: Artemisia argyi is a traditional medicinal herb with established anti-inflammatory and immunomodulatory properties. Its aqueous extract (AEAA), enriched in water-soluble bioactive constituents, exhibits favorable safety and bioavailability; however, its potential protective effects against acute lung injury (ALI) and its associations with systemic immunometabolic regulation remain incompletely understood. Methods: An LPS-induced ALI mouse model was established following 28 days of AEAA pretreatment. Lung histopathology, pulmonary edema, and inflammatory cytokines were evaluated. Integrated multi-omics analyses—including gut microbiota profiling, untargeted metabolomics of colonic contents and serum, and lung transcriptomics—were performed to characterize treatment-associated microbial, metabolic, and transcriptional alterations.Results: Lung transcriptomic profiling suggested attenuation of LPS-associated transcriptional signatures related to NF-κB, MAPK, Toll-like receptor, and PI3K–AKT signaling pathways. Cross-omics integration further revealed coordinated associations among microbial shifts, metabolic remodeling, and pulmonary inflammatory gene expression.Conclusion: These findings suggest that aqueous Artemisia argyi extract is associated with mitigation of LPS-induced acute lung injury, accompanied by coordinated alterations in gut microbiota composition, host metabolic profiles, and pulmonary inflammatory gene expression. Although causal relationships were not established, this integrated multi-omics analysis provides a systems-level, hypothesis-generating framework supporting the potential of AEAA as a multi-target botanical candidate for ALI.

overall_design: Seven-week-old male C57BL/6 mice were randomly assigned to five groups: control, LPS, LPS + low-dose AEAA (0.5 mg/mL), LPS + mid-dose AEAA (1 mg/mL), and LPS + high-dose AEAA (1.5 mg/mL). AEAA was administered in drinking water for 28 consecutive days. On day 29, mice in the LPS and AEAA groups received intratracheal LPS (5 mg/kg), while control mice received sterile saline. Lung tissues were collected 8 h after challenge for RNA-seq analysis. Representative samples from each group were analyzed (n ≥ 4 per group).

first: Huixiang

last: Wang

first: Haihong

last: Jiao


title: Effect of depletion of SPAST exon17 on gene expression in human embryonic stem cells (hESC) and cortical organoids (COs)

city: Daejeon

first: Mi-Ok

last: Lee

address: 125, Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: To investigate neurodegenerative disease, we established SPAST exon17 knock-out in hESCs in which target gen have been knocked down by CRISPR/Cas9, differentiated into COs.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of in hESCs (two WT, three of SPG4 exon17 KO lines) and COs (three WT, four SPG4 exon17 KO)  .
Comparative gene expression profiling analysis of RNA-seq data for hESCs (two WT, three of SPG4 exon17 KO lines) and COs (three WT, four SPG4 exon17 KO)

first: Onju

last: Ham

first: Mi-OK


title: SnRNAseq of tumors isolated from Apc cKO; Kras-mutant animals

first: Sandra

last: Melo

summary: Here, we performed snRNAseq on flash frozen tumors isolated from VilCre; Apc fl/fl; Kras-mutant animals.

overall_design: Single-nuclei sequencing of Apc cKO; Kras-mutant tumors. Single nuclei were extracted from a panel of Apc fl/fl; Kras-mutant tumors. snRNA alibraries were prepeared using the 10x Genomics platform.

first: Amanda

last: Moore

first: Frederic


title: GPR35+ tumor-associated neutrophils promote tumor growth in hepatocellular carcinoma.

first: Ning

last: Li

state: Shanghai

address: Fenglin Road 180

institute: Zhongshan Hospital, Fudan University

summary: Bulk RNA-seq profiling of tumor-associated neutrophils from Hepa1-6 mouse hepatocellular carcinoma (HCC) models. Neutrophils were isolated from mice HCC tissues and classified as GPR35+ or GPR35- subsets (n=3 per group). Differential expression analysis revealed significant upregulation of MAPK signaling pathway and pathways associated with neutrophil migration and cytokines production in GPR35+ neutrophils. These data support the pro-tumorigenic role of GPR35+ neutrophils in HCC.

overall_design: RNA-seq profiling of GPR35+ and GPR35- tumor-associated neutrophils in Hepa1-6 mouse hepatocellular carcinoma models


title: Effect of treating AKPS organoids with either single agent KRAS G12C inhibition, TEAD inhibiton or APC restoration, or dual and triple combination on gene expression.

summary: We have previously shown that single agent treatment with either divarasib (KRAS G12Ci) or APC restoration, results in cell plasticity. Here, we aim to evaluate the effects on combination treatment and if gene expression changes can be enhanced with TEAD inhbiiton.

overall_design: RNAseq profiling of AKPS organoids treated with divarasib, GNE-7883 or APC-restoration (dox), or dual or triple combination for 24h.

first: Thi Thu Thao

last: Nguyen

last: de Sauvage


title: Expression of Kras isoforms in Kras-mutant conditional knock-in alleles.

summary: We have generated a novel Kras-LSL-Q61R allele. Here, we aim to evaluate the expression of the Kras isoforms and if the mutant Kras alleles (G12D and Q61R) express similar levels to one another and Kras WT.

overall_design: RNAseq profiling of Kras wild-type, Kras G12D and Kras Q61R (Rosa26CreERT2) at Day 10 post-tamoxifen adminstration.

first: Shiva

last: Malek


title: Effect of treating DLD1 organoids with either single agent MEK (cobimetinib) inhibition or APC restoration on chromatin accessibility.

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We show that single agent treatment with either cobimetinib or APC restoration, results in cell plasticity.

overall_design: ATACseq profiling of DLD1 cells treated with cobimetinib or APC-restoration (dox), or the combination for 72h.


title: Multiome analysis of tumors isolated from Apc cKO; Kras-mutant animals

summary: Here, we performed multiome on flash frozen tumors isolated from VilCre; Apc fl/fl; Kras-mutant animals.

overall_design: Multiome sequencing of Apc cKO; Kras-mutant tumors. Single nuclei were extracted from a panel of Apc fl/fl; Kras-mutant tumors. Joint snRNA and scATAC libraries were prepeared using the 10x Genomics platform.


title: Multiome analysis of Kras-mutant intestinal epithelium 10 days post-recombination

summary: Here, we used multiome on flash frozen ileal tissue isolated from VilCre; Kras-mutant animals 10 day post-tamoxifen induction.

overall_design: Multiome sequencing of ileal tissue harvested for animals 10 days post-tamoxifen induction.


title: Effect of treating AKPS organoids with either single agent KRAS G12C inhibition or APC restoration, or  combination on chromatin accessibility.

summary: We show that single agent treatment with either divarasib (KRAS G12Ci) or APC restoration, results in cell plasticity.

overall_design: ATACseq profiling of AKPS-iAPC organoids treated with divarasib or APC-restoration (dox), or the combination for 48h.


title: Evaluation of mutational changes in tumors arising in VilCre; KrasQ61R mice

summary: We observed a number of small intestinal tumors arising in Kras Q61R animals. Here, we sought to determine if there are any mutations to explain the development of these tumors.

overall_design: Whole-exome profiling of a 5 individual tumors from 3 mice and an adjacent normal control.


title: Nanoplastics induces Arrhythmia in Human Stem-cells derived Cardiomyocytes [mouse hearts]

city: Singapore

first: Jeremy

last: Pang

address: 61 Biopolis Drive

country: Singapore

institute: A*STAR

summary: Nanoplastics (NPs), plastic particles ranging from 1–1000 nm, form through weathering and are considered more hazardous than larger plastics due to their ability to penetrate cell barriers and be internalised by biological systems. Most research on NPs has focused on animal models, examining effects on the brain, lungs, and gastrointestinal tract. To enhance physiological relevance, this study investigated the impact of NPs on human cardiomyocytes (CMs) derived from human embryonic stem cells (hESCs). We observed significantly higher cellular uptake of 50 nm NPs compared to 500 nm particles, with dose-dependent accumulation over 3, 5, and 7 days of treatment. This accumulation induced oxidative and endoplasmic reticulum (ER) stress, culminating in arrhythmias by day 7. Complementing these in vitro findings, transcriptome profiling of mice exposed to NPs for 8 weeks revealed disrupted RNA splicing, dysregulated protein translation, and defective protein folding. These molecular changes led to ER stress, apoptosis, and impaired transmembrane ion conductance, contributing to the arrhythmic phenotype. Our findings highlight the detrimental effects of NPs on the human heart. Further research is needed to fully elucidate the mechanisms underlying NP-induced toxicity and to develop strategies for mitigating their adverse effects. This study underscores the urgency of addressing NP pollution to protect human health.

overall_design: RNA-SEQ of Wild Type adult male mice treated with Polystyrene-Nanoplastics over 8 consecutive weeks and control group administered with distilled water.

first: Shirley Pei Shan

last: Chia

first: Jeremy Kah Sheng

first: Winanto

last: Winanto

first: Boon-Seng

last: Soh


title: Multiple Myeloma Surviving T Cell Therapies Exhibits a CD45+ Immune Evasive Phenotype

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: Multiple myeloma (MM) is an incurable plasma cell malignancy where relapse is inevitable, even after the advent of transformative T cell redirecting therapies (TCRT) such as chimeric antigen receptor (CAR)-T cells and bispecific T cell engaging (TCE) antibodies. Identifying and characterizing MM cells that persist after these therapies is critical to improving outcomes. Here, we demonstrate that MM persisting through CAR-T and TCE treatments upregulate CD45 as part of a resistance-associated gene expression program. Bone marrow samples from MM patients were treated ex vivo with TCEs elranatamab and SAR442257, as well as anti-BCMA CAR-T and activated T cell alone. MM cells surviving were analyzed via flow cytometry, and the phenotypes observed were validated using samples from patients before and after clinical treatment with idecabtagene vicleucel CAR-T. Across all treatments, MM cells persisting after treatment with TCRT exhibited new surface expression of CD45. Imaging flow cytometry revealed CD45 expression in discrete focal patches on the MM cell surface. Mechanistic studies implicated secreted HSP70 as a key driver of this effect. Bulk-RNA-Seq revealed a concurrent increase of LAG-3 and IFNγ signaling mRNAs alongside CD45 mRNA. These findings were confirmed at the protein level, where PD-L1 upregulation was also observed. Our results suggest that selective pressure from TCRT drives the emergence of an immune evasion phenotype in MM, marked by CD45 upregulation and immune checkpoint activation. These findings highlight the potential for combining TCRT with checkpoint inhibitors to counteract resistance in relapsed or refractory MM.

overall_design: To avoid contamination from PBMCs in the H929 sequencing data, conditioned media from H929-PBMCs co-cultures with or without SAR442257 was applied to fresh H929 cells. Increased CD45 protein levels were confirmed via flow cytometry, and bulk RNA-seq was performed on the remaining cells

first: Alana

last: Keller

first: Dennis

last: Kady

first: Sarah E

last: Parzych

first: Zachary J

last: Walker

first: Amanda J

last: Novak

first: Catherine

last: Pham-Danis

first: Tanisha N

last: Medha

first: Jeremy T

last: Rakhola

first: Meher P

last: Boorgula

first: Eric M

last: Kohler

first: Daniel W

last: Sherbenou


title: Epigenetic modulation of polyamine biosynthetic pathways rectifies T cell dysfunction to enhance anti-tumor immunity in lung cancer [ATAC-seq]

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

summary: T cell exhaustion (TEX) represents a critical target for immunotherapy in cancer. Nevertheless, T cells exhibit diminished responsiveness to immune checkpoint inhibitors once they transition to a terminally-exhausted state. Here, we employed an epigenetic drug screen and identified BET inhibitors (BETis) as enhancers of effector functions in primary exhausted T cells from malignant pleural effusions in lung cancer patients. Transcriptomics, metabolomics, and ATAC-seq analyses revealed that BETis reinvigorate TEX by activating the polyamine biosynthesis pathway, expanding intracellular polyamine pools, and altering chromatin accessibility. Genetic and pharmacological inhibition of ornithine decarboxylase (ODC), a key enzyme in this pathway, abolished BETi-mediated immunopotentiation. Single-cell RNA-seq demonstrated BETis reduced terminal TEX while promoting progenitor TEX through activation of the MYC-ODC axis. BETi treatment or adoptive transfer of BETi-treated T cells suppressed malignant pleural effusion formation in a syngeneic lung cancer model. These findings highlight an epigenetic-metabolic approach to enhance TEX plasticity and offers insights for novel cancer immunotherapies.

overall_design: CD3+ T cells were isolated from malignant pleural effusions (MPE) of two lung cancer patients and treated with mock and JQ1 (500nM) for 24-72 hr. At day 7, CD8+ T cells were further isolated from mock- and JQ1-treated CD3+ T cells for ATAC-seq to analyze the chromatin accessibility.

first: Hsing-Chen

last: Tsai


title: HDAC5 Deficiency Induces Intrinsic Resistance to KRASG12D Inhibition by Disrupting c-Myc Acetylation-Ubiquitination Homeostasis

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: We found that HDAC5 deletion significantly enhances intrinsic resistance to MRTX1133 in KRASG12D mutant pancreatic cancer. Mechanistic studies show that HDAC5 deletion promotes resistance to KRASG12D inhibitors by sustaining the activation of the MAPK signaling pathway.

overall_design: ChIP-seq was performed on PANC-1 cells transfected with siControl or siHDAC5 to investigate the impact of HDAC5 knockdown on MYC chromatin binding.

first: Zhou

last: Yingke

first: Yu

last: Haixin


title: TP53INP2 promotes mitophagic degradation of YAP to impede dedifferentiated liposarcoma development

city: Nanjing

first: yixuan

last: wang

state: Jiangsu

address: No.163, Xianlin Avenue

institute: Nanjing University

summary: Dedifferentiated liposarcoma (DDLPS) constitutes 15-20% of liposarcoma (LPS) and has high rates of local recurrence and distant metastasis. Abnormal yes-associated protein (YAP) signaling has been implicated in DDLPS development. However, the mechanisms that drive aberrant YAP signaling remain largely unknown. Here, we show that tumor protein p53 inducible nuclear protein 2 (TP53INP2) is a potential negative modulator for DDLPS malignant progression. The levels of TP53INP2 protein expression in tumor tissues from 79 patients with DDLPS decreased progressively. Compared with primary tumors, the recurrent tumors also showed reduced TP53INP2 expression. More importantly, low TP53INP2 expression correlates with poor prognosis. TP53INP2 gain- or loss-of-function experiments in DDLPS cell lines showed profoundly inhibitory properties towards cancer malignancy. Mechanistically, TP53INP2 mainly located in mitochondria and promoted mitophagic degradation of YAP depending on VDAC1. The WW domain in YAP and the PPXY motif in VDAC1 were required for their interaction. Taken together, these data demonstrate that TP53INP2 represses DDLPS malignant progression by inactivating YAP via a mitophagy-dependent mechanism, and that TP53INP2 expression may represent a novel prognostic biomarker for the patients with advanced DDLPS.

overall_design:
To investigate the regulatory role of TP53INP2 in the malignant progression of DDLPS, we established a plasmid-overexpressing TP53INP2 gene in the SW872-S cell line.
Subsequently, we conducted gene expression profiling analysis using RNA-seq data from two different cell sources.

first: Yixuan

last: Wang

first: Liwei

first: Ying

last: Huang

first: Zhixiu

last: Chen

first: Xiang

last: Feng

first: Lin

last: Zhou

first: Jiawen

last: Yang

first: Guoyu

last: Li

first: Rui

first: Qiang

last: Xu

first: Yan

last: Shen


title: Human bladder cancer tissues: tumor VS adjacent normal

city: Shanghai

first: Bo

last: Peng

address: 301 Yanchang Road

department: Department of Urology

institute: Shanghai Tenth People’s Hospital, School of Medicine, Tongji University

type:
Methylation profiling by array
Expression profiling by array
Non-coding RNA profiling by array

summary: m6A Epitranscriptomic Microarray nanlysis was conducted to investigate m6A methylation level and expression level profiling of the lncRNAs between bladder cancer tissues and adjacent normal tissues.

overall_design: human bladder cancer: tumor tissues VS adjacent normal tissues. Biological replicates: Three paired tumor tissues and normal tissues.

first: Jinbo

last: Xie


title: GPSM1 restricts CD73+CD103+ Treg cells in adipose tissue, critical for promoting obesity-related metabolic deterioration

city: shanghai

first: Xiaorui

last: Lyu

state: shanghai

address: 600 Yishan Road

department: Shanghai Diabetes Institute

institute: Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Regulatory T cells (Tregs) have been considered as a key regulator of adipose homeostasis and metabolic health. However, the underlying regulatory mechanisms remain unclear. Here, we report G-protein-signaling modulator 1 (GPSM1) expression in CD4+ T cells of peripheral blood or visceral fat is significantly correlated with human obesity and glucose dysregulation. CD4+ T or Treg cell-specific deletion of GPSM1 mice exhibit increased numbers of Treg in adipose tissues, restrained inflammation and improved insulin and glucose tolerance under a high fat diet. These effects are mediated through maintaining a new CD73+CD103+ Treg subpopulation we identified that mainly accounts for enhanced adipose thermogenesis and suppressive inflammation after GPSM1 deletion, which is revealed by single-nucleus RNA sequencing. By contrast, CD4+ T cell-specific GPSM1 overexpression mice have less numbers of Tregs and are more prone to adipose tissue dysfunction and metabolic deterioration. Mechanistically, RHOA-cell stiffness-TAZ axis mediates the effects of GPSM1 on the abundance of Treg. Furthermore, adoptive transfer of GPSM1-deficent Tregs promotes energy expenditure and improve metabolic performance in Rag1-/- mice, suggesting a therapeutic potential for Treg against obesity and related disorders.

overall_design: SnRNA-seq of the  scWAT of GPSM1f/f (n = 3) and GPSM1ΔTreg (n = 3) mice

first: Ruibing

last: Qi

first: Yanli

last: Hua

first: Wei

first: Jing

last: Yan

first: Weiping

last: Jia

first: Cheng

last: Hu


title: A Unique System of Paired PDX Models to Investigate the Progression of Potentially Lethal to Lethal Prostate Tumors at a Multi-omic Level

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

summary: Prostate cancer (PCa) exhibits substantial heterogeneity in aggressiveness among patients, with significant lethality in its advanced metastatic stages. Defining the molecular mechanisms underlying rapid disease progression remains a pressing unmet need. Here, we present a comparative analysis of a longitudinally paired patient-derived xenograft model of aggressive PCa progression before and after therapeutic intervention. Using multi-omic analysis, we characterized the MDA PCa 177-B (androgen receptor [AR]-negative, basal) and MDA PCa 189-1 (AR-positive, luminal) models, which exhibit distinct transcriptomic profiles yet originate from a shared clonal lineage. Targeted and single-cell DNA sequencing revealed that these models share 71.5% of copy number variations, tracing back to a common ancestral cell population. Targeted bisulfite sequencing of both models revealed epigenetic marks unique for aggressive disease compared to normal/benign prostate. Next, through single-cell RNA sequencing, we identified a subset of cells exhibiting a low differentiation profile, present in both PDX models and characterized by a unique molecular signature associated with adaptive immune responses and metastasis-related pathways. Further integrative analysis using data from a broad spectrum of disease samples demonstrated that, within this pair of aggressive PDX models, these low-differentiation clusters are exclusive to stem-like tumor cell populations. These findings support the hypothesis that a continuum of epigenetic, transcriptomic, and phenotypic transitions occurs during the progression of PCa from its potentially lethal to lethal stages. We suggest that this continuum can be captured through well-characterized, longitudinal PDX models derived from the same patient. Our multi-omic approach underscores the value of such models in uncovering the dynamic and adaptive mechanisms of PCa aggressiveness.

overall_design: Fresh tissue from  PDXs MDA PCa 177-B and MDA PCa 189-1PDXs was harvested and tissue dissociation to single cell suspension was performed using the enzymatic mix solution Accumax (Thermofisher, Cat. No.: 00-4666-56) for 20 min at 37°C under rotation. The cells were washed twice with PBS through cell strainer (70 μm) and centrifuged at 1,500 rpm for 5 min. The single cell suspensions were diluted in PBS with 0.4% BSA and transferred to the MDACC ATGC facility of MDACC for scRNA library processing using the Chromium Single Cell Gene Expression 10X Genomics protocol

first: Souzana

last: Logotheti

first: Ana

last: Aparicio

first: Rama

last: Soundararajan

first: Marcos

last: Estecio


title: Combined dopamine receptor inhibition and radiotherapy target mesothelioma-initiating cells and increase survival in a mouse model of mesothelioma [scRNA-Seq]

status: Public on Apr 04 2026

city: Los Angeles

first: Frank

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

summary: Malignant pleural mesothelioma (MPM) is a rare thoracic cancer associated with poor prognosis and low survival rates. In solid cancers, repurposed dopamine receptor antagonists have been shown to have anti-cancer effects. Moreover, in combination with radiotherapy, quetiapine (QTP), a dopamine (D) 2/3 receptor antagonist, has been shown to interfere with self-renewal capacity in glioma-initiating cells and increase survival in mouse models of glioblastoma. In this study we explore combined treatment effects in MPM. Using mesothelioma cell lines, MSTO-211H, H2052, and H2452, and MSTO-211H-derived orthotopic xenograft mouse model of MPM we examined how QTP combined with radiation affects mesothelioma-initiating cells (MICs) in vitro and survival in vivo. Subsequently, bulk and single cell RNA sequencing was used to characterize the transcriptomic landscape of MSTO-211H treated with combined radiation and QTP. We demonstrate that combining QTP with radiation reduces MIC self-renewal capacity and stem cell frequency. In vivo, this combination therapy significantly extends the median survival of mesothelioma-bearing mice. Clonogenic survival assays revealed that QTP does not enhance radiosensitivity in the tested mesothelioma cell lines. Sequencing data revealed, combined treatment upregulated genes involved in cholesterol homeostasis, depleted cancer stem cells, and increased cellular senescence. Taken together, our study highlights the therapeutic potential of radiation with QTP in the treatment of MPM.

overall_design: MSTO-211H mesothelioma-initiating cells were seeded in suspension in a flask. Cells were treated with QTP (10 uM) or vehicle control and irradiated with 4 Gy the next day. 48 hours after the irradiation, RNA was isolated.

first: Cardenas

last: Anjelica


title: Simulated microgravity models sex differences in knee osteoarthritis through a CD36-regulated mechano-metabolic circuit

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

country: Canada

institute: University of Alberta

summary: Leveraging the unique conditions of space microgravity, our research offers groundbreaking insights into osteoarthritis (OA), a degenerative joint disease impacting over three million Canadians and predominantly affecting load-bearing joints such as the knee. With knee OA (KOA) known for its higher incidence and severity among females—a phenomenon not fully explained by existing risk factors—the application of simulated microgravity (SMG) presents a novel approach to understanding the disease's progression and the biological sex differences in response to it. By employing rotating wall vessel (RWV) technology to simulate spaceflight conditions on Earth, our studies focus on the biomechanical unloading experienced in microgravity, which has been observed to induce OA-like changes in articular tissues. This innovative research strategy allows us to explore the potential mechanisms of OA development and progression in a controlled environment, mimicking the microgravity of space to provide new perspectives on the disease's molecular underpinnings. Initial results from our investigations reveal that SMG significantly alters the molecular expression profiles in engineered meniscus constructs derived from non-KOA patients, notably influencing genes related to chondrocyte hypertrophy and OA progression while downregulating protective genes. Further analysis has illuminated sex-specific molecular responses to SMG, demonstrating pronounced differences between male and female specimens. This highlights the importance of considering biological sex in OA research, as it significantly influences disease development and response to microgravity conditions. Extended RNA sequencing under SMG conditions has identified distinct molecular signatures for different sex-based groups, pointing towards an OA-like transcriptome profile in females particularly responsive to SMG. One of the most significant findings from our microgravity studies is the modulation of CD36, a transmembrane protein implicated in lipid metabolism and OA pathogenesis. Its altered expression under SMG conditions and known upregulation in KOA patients underscore the potential mechanisms by which microgravity-induced cellular responses can mimic and inform us about OA development, particularly in terms of sex-specific disparities.

overall_design: we employed age-matched young mice, encompassing both sexes, including CD36 knockout (ko) mice and their C57Bl/6 strain control counterparts, as our animal model. Meniscus tissues were extracted from these mice, including both medial and lateral sections, leading to the creation of four distinct experimental groups: 1.Female CD36 ko mice 2.Female C57Bl/6 control mice 3.Male CD36 ko mice 4.Male C57Bl/6 control mice. These isolated meniscus tissues underwent a 3-week culture in simulated microgravity (SMG) conditions, utilizing a rotating wall vessel bioreactor. A control group was concurrently maintained under standard gravity conditions for comparative analysis. Following the culture period, tissue constructs from each group were randomly selected for a series of analyses, including RNA sequencing (RNAseq) and reverse transcription-quantitative polymerase chain reaction (RT-qPCR), bone mineral quantification, histology and immunofluorescence assessments, shotgun proteomics, and evaluations of DNA and cartilaginous glycosaminoglycan (GAG) content

first: Haiming

last: Lin

first: Daniel

last: Young

first: Aahil

last: Ansari

first: Melanie

last: Kunze

first: Maria

last: Febbraio

last: Graf

first: Antoine

last: Dufour

first: Adetola

last: Adesida


title: The placentalia specific histone H3.4 promotes germ cell development and reproductive fitness

city: Basel

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

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

overall_design: Refer to individual Series


title: Transcriptome analysis of sham-operated, MI-injured and FGF17-treated MI mice hearts (MI)

city: Wenzhou

first: Chao

last: Niu

address: 109 Xueyuan West Road, Lucheng District

institute: Wenzhou Medical University

summary: Fibroblast growth factor (FGF) signal transduction plays essential roles in cardiac repair following myocardial infarction (MI). Among which, FGF17 was demonstrated to regulate epicardial epithelial-mesenchymal transition to provide new vasculature for muscle regeneration during the process of myocardial repair in zebrafish. However, little is known about its function in the mammalian cardiovascular system. This study investigated whether FGF17 signaling exerts cardioprotective effects in ischemic mice hearts, and attempted to elucidate the underlying mechanisms.

overall_design: Neonatal mice were subcutaneously injected with adeno-associated virus  of serotype 9  carrying mouse Fgf17 gene and its control vector. Until 8 weeks old, mice were subjected to a permanent ligation of the left anterior descending artery (MI injury) or to a sham operation without ligation. We then performed gene expression profiling analysis using data obtained from RNA-seq of sham-operated hearts, MI-injured hearts transduced with AAV-FGF17 or control vector at two time points (3 and 14 days post-MI).


title: Microarray analysis of liver-specific  Sirt1 knockout mice lung tissue

city: Xi'an

first: Yiwei

last: Cao

address: Hanguang Road

institute: Xi'an Physical Education University

summary:
To explore the pathology of liver-specific Sirt1 knockout mice.
To specify, the liver-specific Sirt1 knockout mice commenced high blood glucose within three months. When the mice age extended to one year, the mice present surprising higher lung tumor vulnerabilities in contrast to wild type, we explore the underlying mechanism of the symptom

overall_design: Total RNA obtained from liver-specific Sirt1 knock out mice lung tissue at 3 months old compared to wild type.

last: CAO

first: Ruihong

last: Wang


title: Effect of LINC01535-204 (BLACAT3) knockdown on gene expression in bladder cancer T24 cells

first: Bo

last: Peng

summary: To investigate the target genes and biological functions regulated by BLACAT3, we constructed a T24 cell strain stably knocking down BLACAT3 by shRNA.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq.

first: Jinbo

last: Xie


title: Transcriptome analysis of sham-operated, MI-injured and FGF17-treated MI mice hearts (Normal)

summary: This study investigated whether FGF17 signaling exerts cardioprotective effects in un-injured normal mice hearts.

overall_design: Neonatal mice were subcutaneously injected with adeno-associated virus of serotype 9 carrying mouse Fgf17 gene and its control vector. Until 8-10 weeks old, mice were sacrificed and the hearts were harvested. We then performed gene expression profiling analysis using data obtained from RNA-seq of AAV-FGF17 or its control vector transduced mice hearts.


title: 2-Cys peroxiredoxins and the chaperone cpHSP70 act in concert in chloroplast biogenesis in Arabidopsis seedlings

city: Sevilla

first: Fernando

last: Rodríguez-Marín

state: Sevilla

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

summary: The redox balance between NADPH-dependent thioredoxin reductase C (NTRC) and 2-Cys peroxiredoxins (PRXs) help chloroplast photosynthetic performance acclimate rapidly to environmental cues. The Arabidopsis (Arabidopsis thaliana) 2cpab mutant, which lacks chloroplast 2-Cys PRXs A and B, shows impaired embryogenesis and cotyledon development. This phenotype indicates that these enzymes have a relevant function at early stages of plant development, although this function is poorly understood. Here, we show that the albino cotyledons of the 2cpab mutant have unstructured chloroplasts and decreased chloroplast lipid contents, revealing a key function of 2-Cys PRXs in cotyledon chloroplast differentiation. These phenotypes are mimicked by NTRC overexpression, whereas loss of NTRC function has no effect. RNA-Seq analyses showed transcriptomic changes resembling the response to proteotoxic stress in 2cpab seedlings, which was confirmed by the high sensitivity of 2cpab seedlings to heat stress. In de-etiolating seedlings 2-Cys PRXs interact with chloroplast-localized chaperone heat shock protein 70 (cpHSP70); moreover, Arabidopsis seedlings simultaneously lacking 2-Cys PRXs and cpHSP70-1 exhibit a dramatic alteration of seedling development. Based on these results, we propose that 2-Cys PRXs contribute to cotyledon chloroplast differentiation by affecting organellar proteostasis. This function is exerted in concert with chaperone cpHSP70 and is essential for seedling establishment.

overall_design: For transcriptomic analyses, six-day-old wild-type, and green and albino seedlings of the 2cpab mutants grown in MS medium supplemented with sucrose (0.5% w/v) under continuous light at 125 µE m-2 s-1 were collected.

first: Antonia

last: Gallardo-Martínes

first: María

last: Hernández

first: María-Cruz

last: González

first: Francisco

last: Cejudo

first: Juan

last: Pérez-Ruiz


title: Robust and highly efficient generation of functional chimeric antigen receptor engineered murine macrophages that alleviate cardiac fibrosis

city: Hangzhou

first: Hengxing

last: Lu

state: Zhejiang

address: 1369 Wenyi West Road, Yuhang District

institute: Zhejiang University

summary: To investigate the therapeutic potential of chimeric antigen receptor engineered macrophages (CAR-Ms), studies in immunocompetent mouse models are essential. However, due to the low editing efficiency and limited proliferative capacity of primary murine macrophages, efficient generation of functional CAR-Ms remains a technical challenge, hampering the advancement of this promising immunotherapeutic approach. Here, we established immortalized mouse monocytes using the DHFR-HOXB8 system, in which the presence of overexpressed HOXB8 protein is controlled by trimethoprim (TMP), allowing for conditional immortalization and subsequent macrophage differentiation. Transcriptomic and functional analyses confirmed that DHFR-HOXB8-derived cells retain bona fide monocyte and macrophage identity, closely resembling primary cells. Using this platform, we achieved CAR editing efficiencies exceeding 95% in monocytes/macrophages and showed that CAR expression conferred potent phagocytic and cytotoxic activity upon DHFR-HOXB8-derived macrophages against target cells. Adoptive transfer of FAP-targeted CAR-Ms in mouse models of myocardial infarction (MI) and transverse aortic constriction (TAC) attenuated cardiac fibrosis and improved cardiac function, demonstrating their in vivo activity and underscoring their therapeutic potential across diverse cardiac pathologies. This study thus provides a potent platform for generating genetically engineered macrophages suitable for preclinical murine studies.

overall_design: We compared the transcriptome of the iMonos, iMacs, BMDMs, and RAW264.7 cells  by RNA-Seq.

first: Jishou

last: Zhang

first: Hailing


title: Comparative circadian transcriptome analysis reveals dampened and phase-advanced rhythms in sun-exposed skin

city: Manchester

first: Qing-Jun

last: Meng

address: A.V. Hill Building, Oxford Road

department: Faculty of Biology, Medicine and Health

institute: The University of Manchester

summary: Daily molecular rhythms modulate skin physiology. However, the effects of chronic sun exposure on these rhythms remain unstudied. This study aimed to identify and compare rhythmic genes and pathways in photoprotected and chronically photoexposed human skin in vivo. Skin biopsies were taken from photoprotected (upper buttock) and photoexposed (dorsal forearm) skin of 20 subjects at noon, 6PM, midnight, and 6AM, across a 24-hour cycle, and gene expression was quantified with RNA sequencing. Cosinor analysis identified cycling genes along with their amplitudes and peak expression phases. We found that fewer genes met the criteria for cycling in the photoexposed skin as compared to the photoprotected skin, and transcripts that cycled in both sites had lower amplitudes and advanced peak times in photoexposed skin as compared to photoprotected skin. We identified 480 genes with significantly different rhythmic properties between the skin sites. Genes involved in DNA repair, MYC targets, E2F and G2M checkpoint pathways were enriched among those that showed higher amplitude oscillations in photoprotected skin. Genes involved in epithelial mesenchymal transition and apical junction pathways showed higher amplitude oscillations in photoexposed skin. These results suggest that chronic UV exposure may disrupt and/or reprogram circadian output rhythms to further alter skin physiology.

overall_design: RNA-seq profiling of skin biopsies from photoprotected (upper buttock) and photoexposed (dorsal forearm) skin of 20 subjects at noon, 6PM, midnight, and 6AM, across a 24-hour cycle.

first: Michael

last: Saint-Antoine

first: Zeyad

last: El-Houni

first: Victoria

last: Newton

first: Eleanor

last: Bradley

first: Shruthi

last: Ramesh

first: Hamish

last: Hunter

first: Mike

last: Bell

first: Alexander

last: Eckersley

last: Sherratt

first: Ron

middle: C

last: Anafi


title: Genome-wide identification of vitamin D receptor–regulated enhancer RNAs reveals epigenetic regulation of CYP24A1 transcription

city: Iwaki

first: Takahiro

last: Sawada

state: Fukushima

address: Jobankamiyunagayamachi Kaminodai57

institute: Research Institute of Innovative Medicine

summary: Vitamin D (VD) exerts diverse physiological and pathological effects primarily through the vitamin D receptor (VDR), a ligand-dependent transcription factor. However, the limited number of known VDR target genes does not fully explain the broad spectrum of VD actions. In this study, we performed a comprehensive genome-wide analysis to identify enhancer RNAs (eRNAs) involved in VD-dependent gene regulation. Using integrated ChIP-seq, RNA-seq, and NET-CAGE analyses in human HCT116 and HaCaT cells, we mapped VDR binding sites and identified VD-responsive transcripts. VDR binding was strongly dependent on vitaminD and predominantly localized to enhancer regions marked by H3K27ac, indicating association with active chromatin. Through stepwise filtering, we identified a limited number of high-confidence eRNA candidates associated with VDR-bound regulatory regions. Among these, eRNAs located at the CYP24A1 locus were robustly induced by VD and correlated with strong transcriptional activation of the gene. Functional analyses using BET inhibition and LNA-mediated knockdown demonstrated that these eRNAs contribute to VD-dependent transcription. Furthermore, CRISPR/dCas9-mediated induction of specific eRNAs enhanced CYP24A1 expression, supporting a direct regulatory role. In contrast, newly identified target genes such as DLX2 and SYT8 exhibited modest, cell type–dependent responses to VD. Our findings reveal that VDR-mediated gene regulation involves a limited but functionally significant set of eRNAs, particularly at super-enhancer regions, and highlight a unique epigenetic mechanism underlying VD action.

overall_design: Examination of 4 different method in 2 cell types.

first: Koki

last: Nojiri

first: Yoshiak

last: Kanemoto

first: Thi-Ngoc

middle: T

last: Nguyen

first: Yusuke

last: Hakozaki

first: Tomoyuki

last: Kurokawa

first: Shigeaki

last: Kato


title: Chromatin binding of nuclear transport factor Importin α in human cultured cancer cells

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: Micronuclei (MN) are membrane-enclosed structures that contain DNA or chromatin, and their presence can lead to genomic instability.  We found that importin α, a key nuclear transport factor, is highly concentrated in the MN in cultured human cancer cells. Notably, importin α is not uniformly distributed across all MN; it is localized to approximately 40% of them. This selective localization is characterized by an uncorrelated distribution relative to importin β1, CAS/CSE1L, and Ran, suggesting uncontrolled its nuclear-cytoplasmic recycling. Additionally, along with an association with euchromatin regions, we identified chromatin-regulating molecules as potential interactors with importin α and noted a significant reduction in the mobility of importin α within MN, indicating the establishment of a unique microenvironment in these importin α-enriched structures. These results indicate that importin α serves as a previously unrecognized molecular marker for assessing the quality control of MN in human cancer cells.

overall_design: Chromatin immunoprecipitation sequence (ChIP-seq) analysis on whole MCF7 cells using two different importin α1 antibodies.

first: Yoichi

last: Miyamoto

first: Masahiro

last: Oka

first: Kazumitsu

last: Maehara


title: Epigenetic modulation of polyamine biosynthetic pathways rectifies T cell dysfunction to enhance anti-tumor immunity in lung cancer [RNA-seq]

first: Chia-Lang

last: Hsu

institute: National Taiwan University Hospital

summary: T cell exhaustion (TEX) represents a critical target for immunotherapy in cancer. Nevertheless, T cells exhibit diminished responsiveness to immune checkpoint inhibitors once they transition to a terminally-exhausted state. Here, we employed an epigenetic drug screen and identified BET inhibitors (BETis) as enhancers of effector functions in primary exhausted T cells from malignant pleural effusions in lung cancer patients. Transcriptomics, metabolomics, and ATAC-seq analyses revealed that BETis reinvigorate TEX by activating the polyamine biosynthesis pathway, expanding intracellular polyamine pools, and altering chromatin accessibility. Genetic and pharmacological inhibition of ornithine decarboxylase (ODC), a key enzyme in this pathway, abolished BETi-mediated immunopotentiation. Single-cell RNA-seq demonstrated BETis reduced terminal TEX while promoting progenitor TEX through activation of the MYC-ODC axis. BETi treatment or adoptive transfer of BETi-treated T cells suppressed malignant pleural effusion formation in a syngeneic lung cancer model. These findings highlight an epigenetic-metabolic approach to enhance TEX plasticity and offers insights for novel cancer immunotherapies.

overall_design: CD3+ T cells were isolated from malignant pleural effusions (MPE) of three lung cancer patients and treated with mock and JQ1 (500nM) for three consecutive days. At day 7, total cellular RNA was extracted for RNA-seq.

first: Hsing-Chen

last: Tsai


title: Beckwith-Wiedemann spectrum exhibiting a 46,XY karyotype caused by genome-wide paternal uniparental heterodisomy

city: Saga

first: Satoshi

last: Hara

address: 5-1-1 Nabeshima

institute: Saga University

summary: Patients with genome-wide paternal uniparental disomy (GWpUPD) usually exhibit clinical features of Beckwith-Wiedemann syndrome (BWS) and a 46,XX karyotype, with all chromosomes showing isodisomy. Here, we report the case of a boy with classical BWS features harboring a 46,XY karyotype. Genetic analysis of autosomes and sex chromosomes revealed two distinct paternal genomes in peripheral blood leukocytes, whereas a normal biparental genome was detected in oral swabs under chimeric conditions. These findings indicated that the patient had genome-wide paternal uniparental heterodisomy (GWpUPhD). To our knowledge, this is the first reported case of a GWpUPhD chimera with a 46,XY karyotype. We therefore propose a potential mechanism underlying this phenomenon.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood and oral swab samples.

first: Tomohiko

last: Sato

first: Osamu

last: Shimokawa

first: Ritsuko

last: Pooh

first: Yayoi

last: Watanabe

first: Musashi

last: Kubiura-Ichimaru

first: Hidenobu

last: Soejima


title: 4-1BBL suppresses the induction of anti-inflammatory responses by regulating the metabolic reprogramming of macrophages

city: Sunnyvale

first: Young

middle: Jun

last: Kang

address: 428 Oakmead Pkwy

institute: Molecular Medicine Research Institute

summary: Integration of intracellular signaling and metabolic reprogramming is critical for macrophage polarization and the induction of pro- or anti-inflammatory responses. However, the molecular switches that govern macrophage polarization remain incompletely defined. While 4-1BB ligand (4-1BBL), a member of the TNF superfamily, is known to promote sustained pro-inflammatory responses in macrophages, its role in anti-inflammatory macrophage responses has not been elucidated. This study identifies 4-1BBL plays a role as a negative regulator of anti-inflammatory macrophage polarization. Genetic deletion or pharmacological inhibition of 4-1BBL significantly enhanced the expression of anti-inflammatory cytokines and markers in mouse macrophages. In IL-4R signaling, 4-1BBL restrained JAK1 (Janus kinase 1) and STAT (signal transducer and activator of transcription) 6 phosphorylation, thereby modulating transcriptional programs associated with anti-inflammatory macrophage activation. Consistently, 4-1BBL deficiency elevated mitochondrial oxidative phosphorylation and fatty acid oxidation, accompanied by increased expression of metabolic genes in anti-inflammatory macrophages. Transcriptomic analysis further revealed a shift toward anti-inflammatory and oxidative metabolic gene signatures in IL-4-treated 4-1BBL-deficient macrophages. Importantly, inhibition of 4-1BBL signaling also augmented anti-inflammatory responses in human monocytes and facilitated the transition from pro-inflammatory to anti-inflammatory phenotypes. Collectively, these findings establish 4-1BBL as a molecular switch that regulates macrophage polarization by integrating inflammatory signaling with metabolic reprogramming, highlighting 4-1BBL as a potential therapeutic target for promoting inflammation resolution.

overall_design: To investigate the role of 4-1BBL in regulating anti-inflammatory responses, mouse bone marrow-derived macrophages (BMDMs) from wildtype (WT) or 4-1BBL-deficient (4-1BBL KO) mice were obtained and immortalized by infection with the retroviruses encoding v-raf and v-myc. Cells were stimulated with IL-4 for 24 hours and total RNAs were prepared.

first: Young Jun


title: Fusobacterium nucleatum FadA promotes the progression of esophageal squamous cell carcinoma through binding to TFRC

city: Chengdu

first: Xueji

last: Shi

address: Guoxue Ln, Wuhou District

institute: Sichuan University

summary: In China, esophageal squamous cell carcinoma (ESCC) represents the major histopathological form of esophageal cancer. Fusobacterium nucleatum (F. nucleatum, Fn) has been reported to be associated with ESCC. FadA has been identified exclusively in F. nucleatum. However, the potential role and underlying mechanism of FadA in ESCC remain unclear. Whole genome sequencing (WGS) data of ESCC tissue from NCBI database were analyzed to characterize the microbial composition of ESCC. The relative expression of Fn and FadA was validated by qPCR in another ESCC tissue cohort. An E. coli BL21 (DE3) expression system was utilized to express FadA. After purification, FadA was co-cultured with KYSE150 cells. Cell migration, proliferation, and invasion were evaluated by wounding-healing, CCK-8, and Transwell migration and invasion assays. RNA and proteomic sequencing analysis were performed to identify the altered molecule initiated by FadA treatment. TFRC was further validated by knockout and overexpression in KYSE150 cells. Molecular docking, molecular dynamics simulations, and normal mode analysis (NMA) were used to predict and evaluate the interaction between FadA and TFRC. ESCC tissue exhibited decreased α-diversity and distinct microbial composition, with significant enrichment in F. nucleatum. FadA expression was significantly elevated in ESCC tissue samples. Functional assays illustrated that FadA promoted the migration, proliferation, and invasion of ESCC cells. Integrated RNA and proteomic sequencing identified TFRC as a key upregulated target after FadA treatment, which was further confirmed by TFRC overexpression and knockout. Computational analysis supported a stable interaction between FadA and TFRC. FadA is upregulated in ESCC and promotes the migration, proliferation, and invasion in ESCC through TFRC. FadA may serve as a potential biomarker and therapeutic target in ESCC.

overall_design: RNA-Seq profile of KYSE150 cells treated or not treated with FadA, which was a secret protein from Fusobacterium nucleatum, for 48 hours.

first: Mengyuan

last: Song


title: Mitochondrial Phosphatase PGAM5 Negatively Regulates the Induction of Anti-inflammatory Macrophages

summary: Mitochondrial metabolism plays a crucial role in determining the functional polarization of macrophages, yet how mitochondrial signaling differentially regulates the induction of pro- and anti-inflammatory macrophages remains incompletely understood. Phosphoglycerate mutase 5 (PGAM5), a mitochondrial outer membrane phosphatase, has been implicated in promoting pro-inflammatory macrophage responses through a Dynamin-related protein 1(DRP1)-dependent metabolic reprogramming. This study identifies a distinct role for PGAM5 as a negative regulator of anti-inflammatory macrophage responses. Knockdown of PGAM5 markedly enhanced IL-4-induced expression of anti-inflammatory cytokines and M2 marker genes, including Il10, Tgfb, Arg1, Fizz1, and Ym1, as well as surface markers CD163 and CD206. PGAM5 knockdown also augmented mitochondrial oxidative metabolism and increased the expression of fatty acid oxidation/oxidative phosphorylation genes. Mechanistically, PGAM5 selectively regulated IL-4-induced phosphorylation of JAK1 without affecting STAT6 activation, as JAK1 phosphorylation was enhanced in PGAM5 KD macrophages. However, DRP1 was indispensable in IL-4-mediated induction of anti-inflammatory responses and mitochondrial respiration, indicating that PGAM5 negatively regulates anti-inflammatory macrophage polarization through DRP1-independent pathway. Collectively, these findings establish PGAM5 as a central regulator that oppositely controls macrophage polarization, highlighting its potential as a therapeutic strategy to modulate macrophage-driven inflammation and resolution.

overall_design: To investigate the role of PGAM5 in regulating the induction of anti-inflammatory responses, immortalized mouse bone marrow-derived macrophages (BMDMs) were infected with PGAM5 or DRP1-targeting shRNA to knock down PGAM5 or DRP1. PGAM5- or DRP1-KD iBMDMs were stimulated with IL-4 for 24 hours and total RNAs were prepared.


title: Monocyte Chemokines Enhance Atherosclerotic Plaque Necrosis After Bacterial Kidney Infection

city: Bonn

first: Georg

last: Sendtner

address: Venusberg Campus 1a

department: Medical Clinic 1, Nephrology Section

institute: University Hospital Bonn

summary: Urinary tract infections (UTI) are frequent and highly inflammatory. Using a pyelonephritis mouse model, we investigated the impact of pyelonephritis on the development of atherosclerosis. Bulk RNA sequencing analysis of kidneys and aortas harvested four weeks post-infection was performed to identify key molecular markers and delineate differentially regulated inflammatory pathways in both organs. Our results show an upregulation of inflammatory mediators in kidney and aorta, providing a possible mechanistic link between pyelonephritis and atherosclerosis.

overall_design: Female Ldlr-/- mice were infected with uropathogenic E. coli strain 536, which was instilled into the bladder twice at a 3-hour interval. One week after infection, mice were placed on high fat diet for three weeks. Kidneys and aorta were harvested four weeks hours after the second infection. Control mice received urethral instillation with PBS.

first: Lena

last: Possenriede

first: Peyman

last: Falahat

first: Marie

last: Foerster

first: Georg W

first: Julia

last: Miranda

first: Leonie

last: Richard-Strophal

first: Uta

last: Scheidt

first: Christian

last: Kurts

first: Florian

last: Wagenlehner

first: Ekaterina K

last: Koltsova

first: Sibylle

last: von Vietinghoff


title: Regulation of germinal center B-cell homeostasis by Deltex-1 (Dtx1) [scBCR]

first: Michael

last: Green

state: Texas

address: 7455 Fannin Street

department: Department of Lymphoma/Myeloma

institute: The University of Texas MD Anderson Cancer Center

summary: Germinal centers (GC) are sites for the clonal expansion and affinity maturation of B-cells that is coordinated by interaction with follicular dendritic cells (fDCs) and T follicular helper (TFH) cells. Loss of GC homeostasis can contribute to the development of B-cell malignancies and autoimmunity. Here we sought to investigate the GC-specific function of Deltex-1 (Dtx1), a gene that is highly expressed in GC B-cells and is a prominent target of aberrant somatic hypermutation. Dtx1 conditional knock-out (cKO) led to a competitive advantage in the GC reaction and marked GC hyperplasia accompanied by expansion of, and dependence upon, the fDC network. Dtx1 cKO GC B-cells bore transcriptional evidence of Notch and Myc pathway activation, and genetic inhibition of Notch activity led to resolution of GC hyperplasia. Together, these data implicate Dtx1 as a critical regulator of fDC-derived Notch signaling and GC homeostasis.

overall_design: GC B cells were isolated from mice spleens at day 10 post-immunization using the Germinal Center B Cell (PNA) MicroBead Kit (Miltenyi Biotec, #130-110-479), and sorted by FACS, followed by single-cell BCR sequencing


title: Regulation of germinal center B-cell homeostasis by Deltex-1 (Dtx1) [scRNA]

overall_design: GC B cells were isolated from mice spleens at day 10 post-immunization using the Germinal Center B Cell (PNA) MicroBead Kit (Miltenyi Biotec, #130-110-479), and sorted by FACS, followed by single-cell RNA sequencing


title: Zona-pellucida-inspired cellular microenvironment induces the formation of human blastoids from primed human pluripotent stem cells

city: Abu Dhabi

first: Satoshi

last: Imamura

address: Saadiyat Campus, C1-L0-RL5-27

department: Science

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Human blastoids provide an in vitro, embryo-free model for human implantation; however, current protocols depend on genetically unstable naïve human pluripotent stem cells (hPSCs). Here, instead of using naïve hPSCs, we report a hydrogel-based strategy that directly generates human blastoids from standard primed hPSCs. A 10% w/v poly(N-isopropyl-acrylamide)–PEG matrix mimics the zona pellucida by providing negligible adhesion and gentle confinement. Within nine days, aggregates cavitate and form epiblast, primitive endoderm, and trophectoderm—including a CCR7⁺ polar subset—attach to the extracellular matrix, secrete hCG, and initiate extravillous differentiation. Single-cell RNA-seq and RNA velocity analyses reveal early pruning of paracrine networks, preservation of an FGF2 core, and later lineage-specific reconnection. Comparative interactomics place hydrogel blastoids closest to day-5–7 embryos and show marked suppression of VEGF, PDGF, and CXCL inflammatory cues typical of naïve-cell models. This minimal, feeder-free niche enables scalable production of blastoids containing EPI, PrE, and TE-like cells from primed hPSCs.

overall_design: Raw gene expression matrices from RNA-seq analysis of bTSC, bEVT, and bST cells were imported for analysis. Transcript abundance was quantified as transcripts per million (TPM), followed by log2 transformation [log2(TPM + 1)] to stabilize variance. PCA was performed using the top 2,000 most variable genes, based on a centered and scaled expression matrix. The first two principal components (PC1 and PC2) were used for dimensionality reduction and visualization. Lineage-specific marker genes for TSC, EVT, and ST were curated and subjected to row-wise Z-score normalization. These normalized expression values were used for hierarchical clustering and heatmap visualization. In addition, the mean marker gene expression ± standard deviation was displayed as grouped bar plots in log2(TPM + 1) units to compare lineage enrichment across trophoblast subtypes.

first: Xiaopeng

last: Wen

first: Shiho

last: Terada

first: Akihisa

last: Yamamoto

first: Kaori

last: Mutsuda-Zapater

first: Kei

last: Iida

first: Giuseppe-Antonio

last: Saldi

first: Nataliya

last: Sakharova

first: Kyoko

last: Sawada

first: Koki

last: Yoshimoto

first: Motomu

last: Tanaka

first: Ken-ichiro

last: Kamei


title: Hcn1-dependent engram neurons in the PVN encode gastric inflammatory memory [gastritis]

city: Jinan

first: E

last: Liu

state: Shandong Province

address: No. 44, West Wenhua Road, Lixia District, Jinan City, Shandong Province, China

institute: Shandong University School of Basic Medicine

summary: The brain encodes peripheral inflammatory signals, yet the mechanisms underlying the storage and retrieval of stomach-specific immune information remain unclear. This study reveals a novel pathway through which Fos-positive neurons in the paraventricular nucleus of the hypothalamus (PVN) regulate gastritis via a PVN–dorsal motor nucleus of the vagus–stomach neural circuit and the hypothalamic-pituitary-adrenal (HPA) axis. Using activity-dependent genetic labeling, chemogenetics, and optogenetics, we demonstrate that FosPVN neurons are essential for gastritis progression and can be activated by stress to drive chronic inflammation. Single-nucleus RNA sequencing (snRNA-seq) revealed significant upregulation of hyperpolarization-activated cyclic nucleotide-gated channel 1 (Hcn1) in FosPVN neurons during gastritis. Inhibiting Hcn1 reduced neuronal excitability and ameliorated gastric pathology. Crucially, repeated activation of FosPVN neurons forms a specific "inflammatory memory" leading to the persistence of disease, while stress can exacerbate gastric inflammation through these FosPVN neurons. Our findings elucidate the central neural mechanisms encoding gastric inflammation and identify Hcn1 as a potential therapeutic target for neuromodulatory treatment of chronic inflammatory diseases.

overall_design: Single-nucleus RNA-sequencing of male mice with oral gavage of  HCl/ethanol solution (gastritis group).

first: Xijia

last: Xin

first: Weikai

last: Han

first: Qingyu

last: Ren

first: Yaqi

last: Tang

first: Qingwei

last: Yue

first: Jinhao

last: Sun


title: Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors

city: Shanghai

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

summary: Depression is a globally prevalent disabling mental illness with serious social hazards. Previous studies suggest that neuroinflammation plays an important role in the pathogenesis of depression, but the underlying mechanism remains elusive. Endogenous retrovirus (ERVs) is a type of transposable elements (TEs), consists around 8% of human genome but are mostly silenced in vivo. Repressive histone modifications H3K9me3 mediated by the methyltransferase SETDB1 plays a key role in maintaining silencing of ERVs. In this study, we constructed Setdb1-CK-cKO (KO) transgenic mice. Behavioral tests showed that the KO mice exhibited anxiety-depression-like behaviors compared to wild type (WT). Cortex snRNA-seq analysis revealed significant changes in astrocytes in addition to excitatory neurons, with the emergence of a new sub cluster of astrocytes in the KO whose transcriptional profile exhibited specific ERVs activation. We observed a large number of GFAP-positive cells in the KO cortex and striatum by Immunostaining, suggesting reactive astrogliosis. Transcriptomic analysis of astrocytes revealed significant upregulation of genes associated with inflammation in the KO cortex, including multiple chemokine genes. To investigate the potential molecular mechanism underlying "endogenous" neuroinflammation in KO mice, we focused on the purinergic receptor P2X7R, which has been reported to play an important role in mediating neuroinflammation and emotional behaviors. Most importantly, we found that the expression of P2rx7 was significantly upregulated in the KO neuron. We applied multiple epigenomic methods (RNA-seq, ATAC-seq, H3K9me3 ChIP-seq) to analyze in detail the molecular mechanism by which SETDB1 regulates the P2rx7 gene expression, and identified a novel enhancer fragment, mE1. We further constructed a SETDB1 knockout human 293T cell line and examined chromatin accessibility by ATAC-seq. We found a regulatory fragment hE1 with enhancer activity, which was present at a similar location in the human P2RX7 locus, suggesting that this mechanism is conserved between human and mouse. Knockout of P2X7R effectively ameliorated neuroinflammation and partially alleviated neuronal dysfunction as well as behaviors in Setdb1-CK-cKO mice.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: H3K9me3 ChIP-seq of sgSETDB1 and control 293T cell line, 3 samples for sgSETDB1 and 2 sample for control. H3K9me3 ChIP-seq of Setdb1-CK-cKO cortex neuronal nuclei, 3 samples per group.

first: Yueyan

last: Zhu

first: Daijing


title: Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors [snRNA-seq]

overall_design: Nuclei were isolated from the cortex of wildtype and Setdb1-CK-cKO mice, two animals for each group.


title: Metastatic triple-negative breast cancer secretes heme metabolites to alter macrophage immune suppression and function

city: Aurora

first: Andrew

last: Goodspeed

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: A promising approach to improve immunotherapy options for metastatic breast cancer is therapeutic inhibition of metabolic pathways that regulate both pro-tumorigenic and immune suppressive signals. The heme breakdown, or catabolism, pathway is often elevated in aggressive cancers; however, the effects of this pathway on the breast tumor microenvironment (TME) remains understudied. We revealed that the heme catabolizing enzyme heme oygenase-1 (HO-1/HMOX1) is elevated in aggressive triple-negative breast cancer (TNBC) specimens where it positively correlates with immune suppressive macrophages. In mouse TNBC-like mammary tumors, pharmacologic inhibition of HO-1 did not impact primary tumor growth, but knockdown of Hmox1 in tumor cells significantly decreased primary tumor growth and spontaneous lung metastasis. Analysis of tumor interstitial fluid and matching plasma from these animals revealed that levels of the heme metabolite bilirubin were significantly higher intratumorally, but they were depleted with tumor cell Hmox1 knockdown. To test if bilirubin impacts immune cells, mouse bone-marrow derived macrophages (BMDM) were treated with exogenous bilirubin that decreased macrophage efferocytic capacity, or dead cell engulfment, in a dose dependent manner. Conversely, bilirubin treatment significantly increased the ability of BMDM to suppress activation of CD8+ splenocytes. Macrophages isolated from 66Cl-4 mammary tumors treated with SnMP to deplete intratumoral bilirubin were unable to suppress production of cytotoxic molecules Granzyme-B and Perforin in stimulated CD8+ splenocytes. 66Cl-4 mammary tumors harboring HO-1 knockdown had a significant decrease in growth rate and number of pro-metastatic CD206+ macrophages after treatment with αPD-1. Together these results suggest that tumor HO-1 supports macrophage dysfunction and immune suppression during TNBC progression via bilirubin. Further, depletion of intratumoral bilirubin levels has the potential to dynamically impact macrophage populations, particularly in combination with immunotherapy, demonstrating an underappreciated role for this metabolic pathway and metabolite as a pro-metastatic, immunomodulators in cancer.

overall_design: Primary bone marrow cells isolated from 4 different 8-week-old Balb/cJ mice and differentiated into bone marrow-derived macrophages (BMDM) via M-CSF were treated with 2.5 uM bilirubin or vehicle control for 48 hours.  Cells from different mice were cultured separetly to  observe hetergenity between animals. After treatment, mRNA was harvested using TriZol and sequencing was conducted using the NOVASEQ 600 platform.

first: Michelle

last: Williams

first: Jennifer

middle: K

last: Richer

middle: E

first: Meher Preethi

last: Boorgula