title: Motif-directed chromatin repression by BCL11B shapes ectopic targeting and lineage commitment

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

summary: BCL11B encodes a critical T-lineage transcription factor that is implicated as both an oncogene and a tumor suppressor in acute leukemia. Despite its central role in development and malignancy, a basic understanding of the sequence determinants of BCL11B activity remains obscure. Here, we define two functionally distinct modes of BCL11B engagement with chromatin: Most detectable BCL11B binding events are determined by pre-existing patterns of chromatin accessibility and RUNX1 occupancy. In contrast, BCL11B directs chromatin closing at genomic regions enriched for DNA motifs containing the core “TGACC” sequence, which are most prevalent in non-T lineages. These BCL11B-closed target sites cannot be identified from conventional BCL11B chromatin profiling approaches yet represent the primary mechanism by which BCL11B regulates gene expression. We provide evidence that cell of origin impacts the ability of BCL11B to repress lineage-inappropriate gene programs, thereby promoting lineage skewing. Together, these findings define a motif-centered determinant of BCL11B repression and explain how BCL11B controls lineage specification.

overall_design:
This submission includes CUT&RUN data generated in human cord blood-derived CD34+ HSPCs transduced with lentiviral constructs encoding BCL11B, BCL11B-dTAG, or an empty vector (control), and Jurkat cells genetically engineered to express FKBP12F36V-HA-BCL11B (BCL11B-dTAG) or unedited control cells. Cells were either untreated, treated with DMSO (control) or treated with dTAGV-1 for 1 (Jurkat) or 6 (CD34+ HSPCs) hours to induce BCL11B degradation. Two replicates were generated for each experimental condition. For CD34 experiments, CUT&RUN was performed on day 7 of CD34+ expansion, representing 4 days post-transduction. Data sets annoated as "CD34-018" refer to an experiment that tested the effect of untagged BCL11B expression on RUNX1 chromatin occupancy. Data sets annotated as "CD34-016" refer to an experiment that tested BRG1 recrutiment following acute BCL11B degradation.
This submission includes ATAC-seq data generated in human cord blood-derived CD34+ HSPCs transduced with lentiviral constructs encoding BCL11B, BCL11B-dTAG, or an empty vector (control), and Jurkat cells genetically engineered to express FKBP12F36V-HA-BCL11B (BCL11B-dTAG) or unedited control cells. Cells were either untreated, treated with DMSO (control) or treated with dTAGV-1 for 1 (Jurkat) or 6 (CD34+ HSPCs) hours to induce BCL11B degradation. Two replicates were generated for each experimental condition. For CD34 experiments, ATAC-seq was performed on day 7 of CD34+ expansion, representing 4 days post-transduction.
This submission includes RNA-seq data generated in human cord blood-derived CD34+ HSPCs transduced with lentiviral constructs encoding BCL11B, BCL11B-dTAG, or an empty vector (control), and BRU-seq data generated in Jurkat cells genetically engineered to express FKBP12F36V-HA-BCL11B (BCL11B-dTAG) or unedited control cells. Cells were either untreated, treated with DMSO (control) or treated with dTAGV-1 for 1 (Jurkat) or 6 (CD34+ HSPCs) hours to induce BCL11B degradation. Three replicates were generated for each experimental condition for RNA-seq in CD34 cells; two replicates were used for BRU-seq in Jurkat cells. For CD34 experiments, RNA-seq was performed on day 7 of CD34+ expansion, representing 4 days post-transduction.

first: Lindsey

last: Montefiori

first: Qingsong

last: Gao

first: Charles

last: Mullighan


title: The role of Regnase-2 knockout in renal proximal tubules

status: Public on Mar 28 2026

city: Tokushima

first: Kazuhiro

last: Hasegawa

address: 3-18-15 Kuramoto-cho

department: Department of Nephrology

country: Japan

institute: Tokushima University Graduate School of Biomedical Sciences

type: Expression profiling by high throughput sequencing

summary: Regnase-2, an enzyme responsible for suppressing inflammation and producing toxins, including indole. This study used genetically engineered mice to explore the role of Regnase-2 (Reg-2) in kidneys. Using conditional knockout (Conditional KO) mouse models, renal proximal tubule–specific Inmt function was assessed. Gene expression changes, apoptotic cell percentages, and mitochondrial DNA copy numbers were examined by RNA sequencing, histopathology, and various molecular assays. Those analyses were further complemented by immunofluorescence and electron microscopy to investigate cellular and structural alterations.Results: Inmt downregulation induced AKI associated with increased production of reactive oxygen species, and increased tubular apoptosis.

overall_design: Bulk RNAseq using the whole kidneys of Reg-2 conditional KO mice and Control mice.


title: A study for intratumoral heterogeneity of glioblastoma

status: Public on Mar 27 2026

city: Shenyang

first: Sun

middle: Xiang

last: Hao

state: Liaoning

address: puhe road 77th

country: China

institute: CMU

summary: Intratumoral heterogeneity (ITH) is a key driver of therapy resistance in glioblastoma (GBM). This study established a five-gene signature-based gITH classifier through multi-omics analysis, demonstrating robust prognostic predictive value. High-gITH tumors exhibited enhanced molecular complexity, with PDLIM4 identified as the central regulator showing strong correlations with stem-like properties and poor clinical outcomes. Functional validation confirmed that PDLIM4 knockdown suppressed ITH and tumor progression. Our work not only establishes a transcriptome-based quantification framework for GBM heterogeneity, but also reveals PDLIM4 as a promising therapeutic target, offering novel precision medicine strategies.

overall_design: we conducted an integrated study combining multi-region transcriptomics and machine learning. A novel computational framework (gITH score) was developed to objectively quantify transcriptional heterogeneity in GBM. Furthermore, a clinically validated machine learning classifier, derived from heterogeneity levels, was established to stratify patients and predict survival outcomes. Through systematic functional validation, one gene was identified as a central regulator of stemness and developmental plasticity, mechanistically linking it to heterogeneity-driven tumor progression.


title: Matrix Stiffness Induces Midnolin-dependent Lamin B1 Degradation to Control Myoblast Differentiation

city: Shenzhen

first: Qin

last: Peng

address: Gaoke Innovation Center

institute: Shenzhen Bay Laboratory

summary: Cells decode mechanical cues to direct fate decisions through nuclear remodeling, yet nuclear adaptors to mechanical signals remain elusive. Here, we show that soft matrix suppresses myoblast differentiation and induces nuclear abnormality within 30 minutes, accompanied by a greater than 60% reduction in lamin B1 proteins levels. Mechanistically, midnolin interacts with lamin B1 and mediates ubiquitination-independent degradation of lamin B1 on soft matrix, through the Catch domain of midnolin engaging a b-strand within lamin B1’s Ig-like domain. Functionally, moderate lamin B1 expression is essential for myoblast differentiation initiation, as its depletion either by siRNA or CRISPR knockout abolishes myogenic capacity. Our findings reveal that the midnolin-proteasome axis directly converts mechanical inputs into lineage commitment by triggering lamin B1 degradation, defining a novel nuclear mechano-adaptation pathway.

overall_design: RNA-seq profiling for C2C12 cells induced for myogenic differentiation at 0, 6, 24 hours and 7 days. RNA-seq profiling for C2C12 cells seeded on 0.2 kPa and 10 kPa poly-acrylamide (PAA) gel for 12 hours.

first: Liping

last: Guo

first: Yanjing

last: Zhao


title: PATZ1 Condensation Adjacent to PML Nuclear Bodies Suppresses HBoV Transcription as an Intrinsic Antiviral Defense

city: Yinchuan

first: Chuchu

last: Tian

address: 1160 Victory Street

institute: Ningxia Medical University

summary: PML nuclear bodies (PML NBs) are membraneless nuclear compartments that contribute to intrinsic immune defenses against DNA viruses. Here, we identify the host transcription factor PATZ1 as a novel antiviral effector that forms condensates adjacent to PML NBs to suppress human bocavirus 1 (HBoV1) transcription. The viral protein NS1-70, which is essential for HBoV1 DNA replication, triggers the phase separation of PATZ1 into condensates near PML NBs. These condensates act as an intrinsic antiviral defense by recruiting PATZ1 to G-rich regions of the viral genome, thereby repressing viral RNA transcription. To counter this restriction, the alternatively spliced viral protein NS2 interacts with PATZ1, disrupting both PATZ1 condensate formation and its association with the viral genome. Furthermore, PATZ1 also binds G-rich motifs within host gene loci, and NS2-mediated disruption of PATZ1 condensates similarly alleviates transcriptional repression of host genes, thereby facilitating viral replication. Beyond HBoV1, PATZ1 also restricts additional DNA viruses including minute virus of canines (MVC), human parvovirus B19, hepatitis B virus (HBV) and human papillomavirus (HPV), highlighting a conserved antiviral role. Collectively, our findings reveal an unrecognized intrinsic antiviral mechanism involving PATZ1–PML NBs interactions and identify NS2 as a viral antagonist that reprograms host transcription to promote productive infection.

overall_design: RNA-seq analysis was performed on total RNA extracted from 293T cells transfected with wild-type (WT) HBoV1, NS1-mt, or NS1-mt supplemented with NS1, NS2, NS1-70, or an empty vector respectively, at 48 hours post-transfection.

first: Haibin

last: Liu

first: Wuxiang

last: Guan

first: Yuning

last: Sun


title: FABP7 controls radial glial scaffold stability  during human cortical development

city: Nanjing

first: Xu

last: Zhang

address: Longmian Avenue 101

institute: Nanjing Medical University

summary: Radial glial (RG) cells serve as both neural progenitors and structural scaffolds for neuronal migration during cortical development. Although FABP7 has long been recognized as a marker of RG cells, its regulatory function has remained poorly defined. Using human fetal brain slices, embryonic mouse model, cerebral organoids, and assembloids, we demonstrate that FABP7 is essential for maintaining RG scaffold architecture and coordinating neuronal positioning. Single-cell analysis revealed that FABP7 deficiency induces transcriptional dysregulation, particularly affecting cytoskeletal organization, neural fate specification, and stress responses. Furthermore, Transcriptomic features in FABP7 knockdown organoids exhibit convergence with neurodevelopmental disorders such as autism, alongside recapitulation of scaffold defects observed in idiopathic autism organoids. Mechanistically, FABP7 loss suppresses the mevalonate (MVA) pathway, resulting in impaired GTPase-mediated cytoskeletal organization and disruption of radial scaffold integrity. These findings identify FABP7 as a key regulator of cortical development and disease-relevant molecular programs, linking metabolic signaling to neurodevelopmental vulnerability.

overall_design: RNA-seq profiling of CTRL brain organoids cells and their FABP7 knockdown derivatives at Day30  of adipogenic differentiation.

first: Yuanhao

last: Wang


title: Cell Cycle Reprogramming Mediates Acquired Oxaliplatin Resistance in Pancreatic Cancer.

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

country: USA

institute: Baylor college of medicine

summary: Purpose: Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy with limited treatment options. While oxaliplatin-based (Oxa) therapy, such as FOLFIRINOX, has improved outcomes in select patients, Oxa resistance significantly limits its efficacy. This study investigates cell cycle mechanisms driving Oxa resistance and explores targeting these pathways as a therapeutic strategy.  Experimental Design: Murine KPC and human Panc1 oxaliplatin-resistant (Oxa-R) cell lines were established. RNA sequencing, Western blotting, and flow cytometry were used to analyze DNA damage and cell cycle regulators. Viability assays and a murine orthotopic PDAC model were employed to evaluate the therapeutic potential of CDK4/6 inhibition with Oxa.  Results: Oxa-R cell lines exhibited slower proliferation rates, reduced response to Oxa treatment, and significant upregulation of G2/M and E2F1 signaling pathways, findings that correlated with poor survival outcomes in human clinical datasets. In Oxa-sensitive PDAC cells, Oxa treatment activated the ATR-Chk1 pathway, leading to cyclin D1 suppression and apoptosis. In contrast, Oxa resistance was characterized by compensatory upregulation of CDK4/6 signaling, which enabled cells to bypass DNA damage-induced cell cycle arrest. Notably, the addition of CDK4/6 inhibitors restored Oxa sensitivity in resistant cell lines, resulting in enhanced apoptosis in vitro and significantly reduced tumor growth in vivo.  Conclusion: Oxa resistance in PDAC is mediated by cell cycle dysregulation involving cyclin D1 and CDK4/6. Targeting CDK4/6 with Abemaciclib reverses resistance and enhances Oxa efficacy, offering a promising therapeutic strategy for resistant PDAC.

first: Hyun-sung

last: Lee


title: Microglial IL-27 modulates depressive symptoms induced by postnatal immune activation

city: jinan

first: 兴慧

last: 乔

address: 山东大学

institute: 山东大学

summary: Early-life inflammation increases the risk for mental disorders in later life by altering the long-term neuronal spine engulfment capacity of microglia. This process involves a bidirectional, tightly regulated interaction between the nervous and immune systems. However, the mechanisms whereby local immune responses modulate microglial cells are not fully understood. Here we define a critical role of microglial IL-27–IL-27Rα signaling in improving depressive symptoms induced by postnatal immune activation (PIA). IL-27 suppresses excessive microglial phagocytic activity, preserving synaptic density and preventing synaptic loss. Mechanistically, IL-27 activates STAT1 phosphorylation and nuclear translocation, inducing Trem2 expression—a key regulator of microglial phagocytosis—thus restoring synaptic stability. Genetic or pharmacological inhibition of Trem2 abolishes the antidepressant effects of IL-27, confirming the functional importance of this axis. These findings uncover a previously unrecognized IL-27–STAT1–Trem2 signaling axis regulating microglial function and synaptic integrity. Notably, IL-27 treatment also ameliorates behavioral deficits in a prenatal stress (PNS) model, underscoring its broader relevance across early-life adversity paradigms. Toxicological and immunological assessments demonstrate that IL-27 administration is well tolerated, with no significant adverse effects, supporting its translational viability. Together, these results position IL-27 as a promising immunotherapeutic candidate and drug target for mood disorders associated with neurodevelopmental immune dysregulation.

overall_design: We removed the mouse hippocampal tissue and divided it into three groups, control, LPS, and LPS+rIL-27 group, extracted RNA and sent it for sequencing


title: Multi-omic analysis reveals brain-blood concordance and persistent neuroimmune reprogramming with stress and toxicant exposure in a mouse model of Gulf War Illness [ATAC-seq]

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Gulf War Illness (GWI) is a chronic multisymptom disorder associated with prior stress and toxicant exposures. Adult male C57BL/6J mice were exposed to corticosterone (CORT) and diisopropyl fluorophosphate (DFP), followed by repeated intermittent CORT and a later immune challenge with lipopolysaccharide (LPS) or saline. ATAC-seq was performed in hippocampus and frontal cortex to assess chromatin accessibility responses associated with persistent neuroimmune priming.

overall_design: Adult male C57BL/6J mice received CORT in the drinking water for 7 days, followed on day 8 by a single DFP injection and repeated intermittent CORT administration over 5 weeks. On the final day, mice received saline or LPS and hippocampus and frontal cortex were collected 6 h, 12 h, or 24 h later. ATAC-seq libraries represent CORT+DFP+Saline, 6 h baseline controls and CORT+DFP+LPS groups at 6 h, 12 h, and 24 h. One baseline-control subject was excluded because of low read depth. Differential accessibility analyses were performed with csaw within tissue relative to the baseline-control group.

first: Aya

last: Sasaki

first: Kimberly

last: Kelly

first: Lindsay

middle: T

last: Michalovicz

first: David

last: Ashbrook

first: Sanoji

last: Wijenayake

first: James

middle: P

last: O'Callaghan

middle: O


title: Multi-omic analysis reveals brain-blood concordance and persistent neuroimmune reprogramming with stress and toxicant exposure in a mouse model of Gulf War Illness [RRBS]

type: Methylation profiling by high throughput sequencing

summary: Gulf War Illness (GWI) is a chronic multisymptom disorder associated with prior stress and toxicant exposures. Adult male C57BL/6J mice were exposed to corticosterone (CORT) and diisopropyl fluorophosphate (DFP), followed by repeated intermittent CORT and a later immune challenge with lipopolysaccharide (LPS) or saline. Reduced representation bisulfite sequencing (RRBS) was used to profile DNA methylation in whole blood, hippocampus, and frontal cortex collected 6 h, 12 h, and 24 h after challenge.

overall_design: Adult male C57BL/6J mice received CORT in the drinking water for 7 days, followed on day 8 by a single DFP injection and repeated intermittent CORT administration over 5 weeks. On the final day, mice received saline or LPS. Whole blood, hippocampus, and frontal cortex were collected 6 h, 12 h, or 24 h after challenge for RRBS profiling. Processed RRBS files contain CpG-level percent methylation matrices for tissue-specific comparisons of CORT+DFP+Saline, 6 h baseline controls versus CORT+DFP+LPS groups at 6 h, 12 h, and 24 h.


title: Time-resolved transcriptomic profiling of surgical wounds identifies stage-specific therapeutic targets for residual ovarian cancer

city: Seoul

first: Mahesh

middle: Chandra

last: Patra

state: 경기도

address: 241 Gangnam-daero

country: South Korea

institute: Arontier Co. Ltd

summary: Background: The optimal timing of adjuvant chemotherapy after cytoreductive surgery in epithelial ovarian cancer remains uncertain, and perioperative wound-healing responses may transiently create a pro-tumorigenic and drug-resistant microenvironment. This study aimed to characterize time-dependent wound-induced transcriptomic alterations and to identify pharmacologic agents capable of reversing these responses. Methods: An ID8 murine ovarian cancer model was used to compare no treatment, anesthesia alone, and anesthesia plus surgical wounding mimicking futile laparotomy. Tumors were collected at baseline, 1 day (T1), 1 week (T2), and 2 weeks (T3) after intervention. RNA sequencing was performed, and wound-specific differentially expressed genes (WsDEGs) were defined by excluding anesthesia- and progression-related signatures. Functional enrichment analyses were conducted, followed by transcriptome-based drug repurposing using the REMEDY platform to identify compounds predicted to reverse wound-induced gene expression profiles. Results: Surgical wounding significantly increased tumor burden at T1. Transcriptomic analyses revealed distinct, time-dependent wound-associated programs. At T1, WsDEGs were enriched in inflammatory signaling, coagulation, angiogenesis, and immune cell migration, with Vorinostat and Homohar-ringtonine identified as top candidates to counteract these signatures. At T2, pathways related to cell survival, adhesion, and morphogenesis predominated, with LY-2090314, Artesunate, and Birinapant emerging as potential modulators. At T3, cell-cycle regulation and lipid metabolic pathways were dominant, and Fulvestrant, Atorvastatin, Imatinib, and ABT-737 were predicted to inhibit these processes. Conclusions: Perioperative sur-gical wounding induces dynamic, stage-specific transcriptomic programs that may promote ovarian cancer progression and alter drug responsiveness. These findings support time-adapted perioperative pharmacologic strategies to optimize postoperative cancer therapy.

overall_design: RNA-seq profiling ID8 murine ovarian cancer cells without treatment, with only anesthesia, and with anesthesia-cum-surgical wounding at baseline, 1 day (T1), 1 week (T2), and 2 weeks (T3).

first: Seongyun

last: Lim

first: Young-Jae

last: Cho

first: Myeong-Seon

last: Kim

first: Jung-Joo

last: Choi

first: Ji-Yoon

last: Ryu

first: Jae Ryoung

last: Hwang

first: Ju-Yeon

middle: C

first: Mohamed

middle: E

last: Farh

first: Insuk

last: Sohn

first: Jeong-Won

first: Yoo-Young


title: Depletion of IRX3 promotes early cardiac commitment and maturation of human Ipsc-derived cardiomyocytes

city: Sao Paulo

first: Jose

last: Krieger

state: SP

address: Av Dr Eneas C Aguiar 44 10ofl

department: Cardiology

country: Brazil

institute: Heart Institute (InCor)/Univ Sao Paulo Med Sch

summary: The limited regenerative capacity of the adult human heart makes human induced pluripotent stem cell (hiPSC)-based therapies a promising approach for treating myocardial infarction. However, hiPSC-derived cardiomyocytes (hiPSC-CM) display immature features. In this study, we demonstrate that depletion of the transcription factor IRX3 promotes early cardiac commitment and enhances the maturation of hiPSC-CMs. We first established the temporal expression of IRX3 during hiPSC-CM differentiation and subsequently investigated its role by generating two IRX3 mutant hiPSC lines. IRX3-depleted cardiac progenitors exhibited increased expression of GATA4, NKX2-5, TBX5 and Wnt signaling-related genes, along with increased proliferation. Differentiation of IRX3-depleted cells yielded more cardiomyocytes with enhanced expression of TNNI1 and CX43. Notably, IRX3-depleted cardiomyocytes showed improved sarcomere alignment, enhanced cell-to-cell communication, and electrophysiological maturation. Furthermore, in silico analysis suggests that IRX3 regulates cardiomyocyte differentiation by modulating TBX5, GATA4 and NKX2-5 transcription along with their targets. Collectively, our findings underscore the potential of IRX3 depletion in facilitating the molecular and functional development of human cardiomyocytes.

overall_design:
4 samples were analyzed, 2 control samples (Wt_D4) and 2 IRX3-depleted samples (KO_D4)
Total RNA extracted from hPSC commited to cardiomyocytes differentiation protocol in differentiation day 4 of development

first: Agatha

middle: R

last: Silva

first: Nikolas

middle: D

last: Ferreira

first: Caio

middle: M

first: Iuri

last: Valadão

first: Iguaracy

last: de Sousa

first: Ester

last: Bertoldi

first: Vanessa

last: Lima

first: Lauro

last: Turaca

first: Ana

middle: B

last: Barbosa

first: Elida

middle: A

last: Neri

first: José


title: ASCL1 over-expression in neuroblastoma cell lines [RNA-seq]

city: Cambridge

first: Lidiya

last: Mykhaylechko

address: Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way,

country: United Kingdom

institute: University of cambridge

summary: To compare the function of overexpressed ASCL1 in two MYCN-amplified neuroblastoma cell contexts, we have used a doxycycline-inducible lentivirus system to induce ASCL1 overexpression in SK-N-BE(2)C and IMR-32 cell lines, and assessed the transcriptome wide impact of ASCL1 overexpression using RNA-seq.

overall_design: RNA-seq in ASCL1 overexpressing MYCN-amplified neuroblastoma cell lines

first: Laura

last: Woods

first: Anna

last: Philpott


title: Hippocampal CA1 RNA-seq (P14) in mice treated with N-bc2S1P vs saline_RNAseq

city: GuangZhou

first: Hao

last: Liu

state: Guangdong

address: No. 1023-1063 Shatai South Road, Baiyun District

institute: Southern Medical University

summary: RNA-seq was performed on hippocampal CA1 tissue from P14 mice treated with N-bc2S1P or saline (n=3 per group). Single-end 1x150 bp reads were generated on a NovaSeq 6000, aligned to mm10, and provided as a gene-level raw counts matrix.

overall_design: CA1 tissue (~25 mg) was collected from P14 mice (n=3 per group; N-bc2S1P vs saline). Reads were trimmed, aligned to mm10, quantified at the gene level, and summarized as a raw counts matrix.


title: Alterations in chromatin architecture promote totipotent-like features in a DUX-dependent manner [ChIP-seq]

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: 2-cell like cells (2CLC) are a transiently cycling population of cells with totipotent-associated features. Interestingly, CTCF depletion leads to 2CLC conversion in mouse ESC. However, the mechanism underlying this reprogramming or whether totipotent-like conversion depends on chromatin structural alterations or to CTCF-specific effects is unclear. We demonstrate that 2CLC conversion mediated by CTCF loss depends on the transcription factor DUX and correlates with nucleolar integrity. We show that depletion of the cohesin release factor WAPL in ESC also promotes 2CLC reprogramming which is increased by CTCF co-depletion. Single-cell RNAseq/ATACseq analyses in CTCF/WAPL-depleted ESC revealed that chromatin accessibility precedes 2C-associated gene expression. Finally, although distinct transcriptional changes were associated to WAPL or CTCF depletion in human ESC, we did not detect any similarity in their transcriptome with those of early stages of human embryo development suggesting a lack of conservation. Our work revealed an intertwined link between higher-order chromatin organization and totipotency in mice.

overall_design: ChIPseq from ESC-CTCF/WAPL-AID treated with IAA for 0 and 48hour.

first: Ruiz

last: Sergio

first: Tillo

last: Desiree

first: Vega-Sendino

last: Maria

first: Carey

last: Grace I


title: Exit of dormancy is correlated with reactivation of Creb1 that is a potential target to overcome endocrine therapy resistance in ER+ breast cancer cells

city: Chicago

first: Lei

last: Duan

state: IL

address: 1653 W Congress Pkwy

department: Anatomy and Cell Biology

institute: Rush University Medical Center

summary: Estrogen receptor-positive (ER⁺) breast cancers frequently recur years after initial treatment with anti-estrogen therapies such as aromatase inhibitors (AIs), often due to emergence from a dormant state. The molecular mechanisms underlying dormancy and recurrence, especially following endocrine therapy, remain poorly understood. In this study, we identify the transcription factor CREB1 as a critical regulator of tumor dormancy and recurrence in ER⁺ breast cancer. By analyzing longitudinal tumor samples from patients treated with AIs, we identified more than 1,000 “dormancy-downregulated genes” (DDGs) that are downregulated and over 1,000 “dormancy-upregulated genes” (DUGs) that are upregulated during therapy-induced dormancy; notably, DDGs are re-expressed and DUGs are downregulated upon tumor recurrence. Transcriptional profiling and pathway enrichment analyses implicated CREB1, along with ER and E2F1, as central regulators of these genes. These findings were validated in estrogen-deprived ER⁺ cell lines and patient-derived xenograft (PDX) models, where dormancy correlated with reduced CREB1 activity and tumor recurrence coincided with CREB1 reactivation. CREB1 inhibition—via small molecule or siRNA knockdown—effectively reversed CREB1, ER, and E2F1 transcriptional programs by downregulating the DDGs while upregulating the DUGs, and reduced cell proliferation and survival in endocrine- and CDK4/6 inhibitor-resistant ER⁺ breast cancer cells. These findings establish CREB1 as a master regulator of transcriptional reprograming in relapsed ER⁺ breast cancers and highlight it as a promising therapeutic target for overcoming resistance to current endocrine and CDK4/6-based therapies.

overall_design:
RNA-seq profiling of MCF7 cells grown in E2 containing media and MCF7 derivatives that were treated with short-term estrogen deprivation (ED), long-term ED (LTED), LTED plus abemaciclib, and LTED plus the Creb inhibitor 666-15.

***************************************************************
Submitter states that missing raw files are due to file loss: Raw sequencing files are no longer available due to data loss (deleted) on the Novogene’s server.
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first: Kelsey

last: O'Hara

first: Carl

last: Maki


title: Single-Cell Characterization of Anterior Segment Development: Cell Types, Pathways, and Signals Driving Formation of the Trabecular Meshwork and Schlemm's Canal

city: New York

first: Revathi

last: Balasubramanian

state: NY

address: 635 West 165th street

department: Ophthalmology

institute: Columbia University

summary: Morphogenesis of the anterior segment (AS) is crucial for healthy ocular physiology and vision but is only partially understood. The Schlemm's canal (SC) and trabecular meshwork (TM) are essential drainage tissues within the AS, and their proper development and function are critical for maintaining normal intraocular pressure; abnormalities in either tissue can result in elevated pressure and glaucoma. Here, we use single-cell transcriptomic profiling to provide high-resolution molecular detail of AS development with a particular focus on SC and TM. We report transcriptomes for ~130,000 single cells at key developmental stages from postnatal day 2 (P2) to P60. We provide the first annotation of cell types across these developmental stages and crucial information about dynamic changes in pathways/gene expression. Further, we trace developmental trajectories for TM cell and SC endothelial cell (SEC) subtypes and determine genes and signaling networks driving their specific cell fates. We demonstrate dynamic changes in signaling interactions between SC and the TM cells during their synchronized development. Collectively, our data lay a deep molecular foundation for AS development that will direct understanding of normal ocular physiology, glaucoma, and other AS conditions.

overall_design: Pregnant dams were checked daily between 9:00 AM and 12:00 PM for births. The date of birth was recorded as midnight of the day pups were first observed. Mice were collected at the following timepoints: P2.5, P4.5, P6.5, P10, P14, P21, and P60. For each timepoint, eyes from four animals (eight eyes total) were pooled per sample, and two samples were collected per age. All samples consisted of eight eyes, except for one P21 sample, which contained seven eyes due to exclusion of a severely microphthalmic eye. Sex was balanced at each timepoint. Sex was determined by anogenital distance at P21 and P60, and by genotyping at earlier ages. To standardize early timepoint collections, P2.5 and P6.5 harvests were conducted between 7:00–9:00 AM, while all other timepoints were collected between 9:00 AM–12:00 PM. Eyes were enucleated into fresh Dulbecco’s Modified Eagle Medium (DMEM; Gibco) and dissected in the same medium. All dissection tools and surfaces were treated with RNaseZap (Ambion). For dissection, the posterior segment was removed by cutting between the limbus and sclera, followed by lens removal. Finally, we made a small circular cut in the anterior cornea, removing the middle 1/3rd of the area (P2.5–P14), and the middle 2/3rds for P21 and P60. The iris was carefully removed at P21 and P60. The remaining anterior segment tissue (limbal strip) was minced and prepared for enzymatic digestion. Tissues were digested enzymatically (Papain Dissociation System; Worthington Biochemical Corporation) and single cells were loaded into 10× Chromium Single Cell Chips (detailed protocol in Balasubramanian et al.21). Single-cell libraries were generated according to the manufacturer’s protocol. Libraries were sequenced on the Ilumina Novaseq platform. Sequencing data were demultiplexed and aligned using Cellranger software (10× Genomics). Reads were aligned to the mouse mm10 genome.

first: Nicholas

last: Tolman

first: Taibo

last: Li


title: Alterations in chromatin architecture promote totipotent-like features in a DUX-dependent manner.

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Negative regulation of TH17-mediated inflammation by the nuclear receptor REV-ERBβ

city: Jupiter

first: Jonathan

last: Chuck

state: FL

address: 130 Scripps Way, C275

department: Immunology

institute: UF Scripps

summary: TH17 cells play a central role in several human autoimmune diseases.  We and others reported the nuclear receptor REV-ERBα as a cell-intrinsic repressor of TH17-mediated pathogenicity.  REV-ERBβ, REV-ERBα’s closely related family member, is thought to be functionally redundant to REV-ERBα, which we sought to explore in TH17-mediated immunity.  Our data indicate that deletion of REV-ERBβ enhanced TH17-mediated pro-inflammatory cytokine expression and exacerbated disease in mouse models of multiple sclerosis and colitis.  RNA-sequencing indicates REV-ERBβ and REV-ERBα do not have similar transcriptional profiles. REV-ERBβ does not appear to regulate gene expression through interaction with the classic co-repressor NCoR1, which is in contrast to REV-ERBα in TH17 cells, nor does it utilize heme, its known endogenous ligand for its repressive functions.  Our results establish that while REV-ERBβ also acts as a negative regulator of TH17-cell function and pathogenicity, it does so in a manner that is non-redundant, independent, and unique to REV-ERBα.

overall_design: RNA-seq profiling of wildtype and REV-ERBα / REV-ERBβ knockout naive CD4+ T cells or Th17 cells 24 hr post activation.

first: Sean

last: Campbell

first: Sarah

last: Mosure

first: Mohammed

last: Amir

first: Qun

last: Lu

last: Solt


title: CCR5 Governs DNA Damage Repair and Breast Cancer Stem Cell Expansion

city: los angeles

first: XUELIAN

last: CHEN

state: CA

address: 1450 BIGGY ST, NRT 3509

institute: UNIVERSITY OF SOUTHERN CALIFORNIA

summary: The functional significance of the chemokine receptor CCR5 in human breast cancer epithelial cells is poorly understood. Here, we report that CCR5 expression in human breast cancer correlates with poor outcome. CCR5+ breast cancer epithelial cells formed mammospheres and initiated tumors with >60-fold greater efficiency in mice. Reintroduction of CCR5 expression into CCR5-negative breast cancer cells promoted tumor metastases and induced DNA repair gene expression and activity. CCR5 antagonists Maraviroc and Vicriviroc dramatically enhanced cell killing mediated by DNA-damaging chemotherapeutic agents. Single-cell analysis revealed CCR5 governs PI3K/Akt, ribosomal biogenesis, and cell survival signaling. As CCR5 augments DNA repair and is reexpressed selectively on cancerous, but not normal breast epithelial cells, CCR5 inhibitors may enhance the tumor-specific activities of DNA damage response–based treatments, allowing a dose reduction of standard chemotherapy and radiation.

overall_design: RNA seq analysis revealed CCR5 governs PI3K/Akt, ribosomal biogenesis, and cell survival signaling.

first: Richard

middle: G

last: Pestell

first: Xuanmao

last: Jiao

first: George

last: Prendergast

first: Jiang

middle: F

last: Zhong


title: Single-cell profiles delineate immune cell remodeling and enhanced tumor-fibroblast interaction of hepatoblastoma after chemotherapy

city: Shanghai

first: rui

last: Dong

address: 399 Wan Yuan Road

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

summary: Hepatoblastoma (HB), the most common pediatric liver cancer, is typically treated with chemotherapy, yet its impact on the tumor microenvironment (TME) and mechanisms of chemoresistance remain unclear. We perform single-cell RNA sequencing on 32 HB tumors pre- and post-chemotherapy, integrating data from spatial transcriptomics, bulk transcriptomics, multiplexed immunofluorescence, and patient-derived xenografts. Chemotherapy enriches CD69⁺CD8⁺ T cells and shifted myeloid cells toward immune-activating phenotypes. HB tumor cells exhibit both hepatic and mesenchymal features, with hepatic-like cells showing greater chemoresistance. A subset of AFP-high hepatic tumor cells expresses high FGFR4 and showed elevated proliferation. Post-treatment, mesenchymal-like tumor cells and MMP11⁺ cancer-associated fibroblasts enhance FGF-FGFR signaling. FGFR4 inhibition significantly suppressed tumor growth in xenografts. These findings provide a high-resolution landscape of the HB immune TME and highlight cancer–fibroblast interactions, especially via FGF signaling, as key contributors to chemoresistance.

overall_design:
Transcriptomic data were obtained from 32 patients (24 males and 8 females; mean age, 26.3 ± 22.5 months), of which 12 received chemotherapy prior to surgery. Patients who underwent 2–4 cycles of neoadjuvant chemotherapy with cisplatin, vincristine, and 5-fluorouracil according to Pediatric Oncology Group treatment protocols were defined as post-chemotherapy patients. This study was approved by the Institutional Review Board of Children’s Hospital of Fudan University (no. 2020(416)). Informed consent was obtained from each patient or from the guardian of each participant younger than 18 years old. Because of patient privacy and local regulatory restrictions, raw sequencing files are not included in this GEO submission. Processed count matrix, feature, barcode, and cell annotation files are provided.

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

first: Deqian

last: Chen

first: Yong

last: Zhan

first: Jia

last: Wang

first: Kuiran


title: Fibroblast orchestration of inflammaging via NF-kB activation

city: San Francisco

first: Lucile

middle: P A

last: Neyton

address: 505 Parnassus Ave

institute: UCSF

summary: Aged tissue is characterized by chronic inflammation known as “inflammaging”. While this aging immune phenotype supposedly drives some of the most common diseases affecting the elderly, little is known about the structural drivers of inflammaging. In this study, we demonstrate that age-dependent activation of NF-kB in tissue fibroblasts remodels the immune architecture, promoting the emergence of an exhausted T cell population (GZMK+/CD8+) recently identified in normal aging, as well as autoimmunity and cancer. Fibroblast-specific NF-kB activation triggered a fibroblast-macrophage-T cell circuit to form tertiary lymphoid structures in the lung and promoted the emergence of exhausted GZMK+ T cells. Fibroblastic activation of NF-kB increased host susceptibility to acute lung injury and mimics severe pneumonia commonly seen in elderly patients, which was alleviated by deletion of GZMK+ T cells. Our data provide a structural basis for inflammaging, where fibroblasts orchestrate the complex immune aging phenotype in non-immune tissues, increasing susceptibility to age-related diseases.

overall_design:
Cells from tracheal aspirate of COVID-19 patients that were or were not categorized as severe lung injury (on ECMO or with PF ratio <= 100) were analyzed using single-cell RNA sequencing

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

last: Allen

first: Carolyn

middle: S

last: Calfee


title: UFMylation anchors splicing factors at the ER to reprogram nuclear splicing

city: Vienna

first: Yasin

last: Dagdas

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

summary: How organelles communicate stress to the nucleus to coordinate adaptive responses remains a fundamental question in cell biology. Here, we identify a non-canonical retrograde signaling pathway in which stalling-induced UFMylation of ER-associated ribosomes anchors splicing regulators at the ER, directly coupling translational stress to nuclear RNA processing. Phylogenetic profiling linked the UFMylation machinery to a network of nuclear mRNA processing factors. Fractionation-based quantitative proteomics revealed that translational stress triggers UFM1-dependent retention of serine/arginine-rich (SR) splicing factors at the ER, depleting their nuclear pools. Mechanistically, UFMylated ribosomes physically tether SR proteins at the ER surface, driving widespread intron retention that preferentially targets transcripts encoding ER membrane and trafficking components—a response conserved from plants to mammals. These findings reframe UFMylation from a local ribosome repair signal to a systems-level coordinator of ER-nucleus communication that reprograms nuclear splicing and reshapes membrane-associated gene expression with implications for neurodegenerative diseases linked to UFMylation defects.

sample_organism:
Arabidopsis thaliana
Homo sapiens
Mus musculus

overall_design: RNA-Seq transcriptomic profiling was performed on nuclear and cytosolic fractions from 10-day-old Arabidopsis seedlings  and Human RKO cell lines, and  total cell lysate analysis of Mouse neuronal cell lines in WT and UFM1 mutants

first: Ranjith

last: Papareddy


title: The spatiotemporal dynamics of postnatal vascularization in the mouse brain

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

summary: The structure of the cerebral vasculature is immature at birth and undergoes significant post-natal remodeling and expansion. However, how vascularization progresses throughout the brain to integrate volumetric growth with neuronal circuit maturation is unclear. To address this spatiotemporally, we developed LAMBADA—a resource for registering and annotating optically cleared developing mouse brains with high temporal resolution, enriched by aligned spatial transcriptomics. Using this resource, we identified three distinct, brain-wide phases of postnatal cerebral vascular development: (1) an isometric expansion phase, characterized by the expression of well-known transcriptomic signatures; (2) a regional specialization phase, which coincides with neuronal maturation and synaptogenesis; and (3) a refinement phase, marked by the stabilization of vascular networks and synapses. We delineate the molecular and structural mechanisms underlying these phases by correlating vascular remodeling with spatial transcriptomic gene expression. This atlas provides a novel foundation for studying developmental neurovascular interactions and serves as a resource for murine postnatal brain development research.

overall_design: The brains of male C57BL/6J mice on postnatal day 5, 7, 9, 12, 21, and 60 were simultaneously embedded in OCT compound and frozen for cryo-sectioning at a thickness of 10μm and processed for spatial transcriptomics. The tissue preparation followed the protocol provided by the company 10X Genomics more specifically using the Visium Spatial Gene Expression (GEX) and Tissue Optimization (TO) Slide & Reagent Kits (catalog numbers 1000193 and 1000187). Brain sections were done on 3 different planes (anterior, thalamic and brainstem planes).

first: Mathilde

last: Bizou

first: Etienne

last: Doumazane

first: Nicolas

last: Renier

first: Alexandre

last: Dubrac


title: Multiomics immune profiling of a patient-relevant orthotopic lung cancer model using SEPARATE-Seq [MERSCOPE]

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Relevant pre-clinical models are essential for driving progress in cancer therapy research. Here, we developed a pre-clinical study framework using an injectable orthotopic lung adenocarcinoma (LUAD) model (ORTHO) that replicates key features of human LUAD patients and is dissectible into tumoural and non-tumoural adjacent tissue, in analogy with patient samples. We also present SEPARATE-Seq, a technique enabling the partitioning of vascular and intratissue immune cells along with scRNA-Seq. By applying both SEPARATE-Seq and spatial transcriptomics to our dissectible ORTHO model, we confirmed that our model replicates key immune features of human LUAD patients. Similarly to these patients, we observed NK-cell dysfunction and neutrophil dichotomy, and uncovered that these are driven by their vascular/intratissue or tumour/adjacent location, highlighting the need for these spatial distinctions. Additionally, we reveal that several immune populations are restricted to specialised, local niches within the tumour, including a ring of lipid-associated TAMs lining the tumour edge and hubs of interferon-stimulated cells. Overall, our resource, available through an interactive tool, provides a comprehensive multiomics immune characterisation of a reproducible pre-clinical LUAD mouse model.

overall_design: Slides from ITI inoculated LLC-Thy1.1 P2 lungs (n=2) were analysed using the Vizgen MERSCOPE spatial profiling platform, based on MERFISH

first: Pauline

last: Bardet

first: Lize

last: Allonsius

first: Eva

last: Hadadi

first: Damya

last: Laoui


title: Bulk RNA-seq of mouse metastatic mammary cancer cells TUBO

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: A key problem in cancer biology is understanding the phenotypic characteristics of the aggressive cell states present in macrometastases and their molecular underpinnings. Here we report on the cellular constituents of  breast cancer metastases,  revealing that these malignant cells display a gene-expression profile associated to embryonic development of tubular organs.

overall_design: TUBO cells are cultured in petri dishes and then harvested for RNA-seq

first: Robin

last: Caire

first: Giusy

last: Battilana

first: Francesca

last: Zanconato

first: Oriana

last: Romano

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Butyrylcholinesterase alleviates hepatic stellate cell activation via paracrine muscarinic signaling

first: Tao

last: Le

address: LANXI ROAD 164

institute: Shanghai University of traditional Chinese Medicine

summary: Background & Aims: Butyrylcholinesterase (BuChE) is an enzyme involved in Alzheimer’s disease (AD), detoxification and depression. While BuChE expression is reduced in liver cirrhosis, its physiological substrate, acetylcholine (ACh), promotes fibrogenic responses in hepatic stellate cells (HSCs). However, the function of BuChE in liver fibrosis and mechanistic link between these two observations is not known. Methods: BuChE expression and HSC activation were assessed in liver biopsies from patients with liver fibrosis using qPCR and immunostaining. To investigate the functional role of BuChE in fibrogenesis, we employed BucheΔHep, knock-in (BucheKI/KI-Hep) mice, as well as pharmacological inhibition. The inhibitory effect of BuChE on HSC activation was further confirmed using conditioned medium from cells expressing mutant BuChE, in hepatocyte-HSC co-culture experiments, and analyses of recombinant BuChE protein. The release of ACh was measured with patch-clamp and the expression and functionality of its receptor were detected via intracellular Ca2+ influx measurements. The role of the muscarinic acetylcholine receptor 3 (ChRM3) in HSCs was investigated through gain- and loss-of-function experiments, utilizing Chrm3ΔHSC mice and AAV-mediated Chrm3 overexpression driven by the alpha-smooth muscle actin (Acta2) promoter. Results: Buche mRNA expression in livers and enzymatic activity in serum are downregulated in patients and mouse models with liver fibrosis, and show a negative correlation with F stage and ACTA2 expression. Pharmacological inhibition or depletion of BuChE in hepatocytes results in increased HSC activation and aggravates liver fibrosis in various mouse models, whereas its overexpression exerts the opposite effect, indicating a causative role of BuChE downregulation in liver diseases. BuChE is predominantly expressed in hepatocytes in the liver, which can be reduced by TGFβ treatment. Notably, BuChE enzymatic activity is required to prevent HSC activation and fibrogenesis in homeostatic liver. As consequence of the lost BuChE metabolic activity, levels of released unmetabolized ACh are increased, which acts as DAMP to activate HSCs via ChRM3 signaling. This finding was confirmed using Chrm3ΔHSC mice, which exhibit diminished HSC activation and liver fibrosis. Conversely, ChRM3 overexpression in HSCs is promoting the fibrogenic process. Conclusion: Hepatocyte injury disrupts BuChE activity, causing local ACh accumulation and subsequent HSC activation via ChRM3 signaling. This novel cholinergic circuit drives fibrosis and represents a promising new target for therapeutic intervention.

overall_design: Primary hepatic stellate cells were isolated from mouse hepatocytes with Buche knockout

first: Le

last: Tao

first: Nuoya

last: Liu

first: Wei

last: Zhang

first: Zongguo

last: Yang

first: Jianrong

last: Xu

first: Guang

last: Ji

first: Cheng


title: Transcriptomics of MCF-7 cells after corticosterone treatment

city: 郑州

first: yucheng

last: li

state: 河南省

address: 河南省郑州市金水区博学路街道金水东路156号

institute: Henan University of Chinese Medicine

summary: The experiment was divided into two groups: a control group and a corticosterone-treated group, with three replicate samples per group. Following corticosterone treatment, cells were collected for transcriptomic analysis to identify RNAs that were significantly altered after corticosterone exposure.

overall_design: The experiment was divided into two groups: a control group and a corticosterone-treated group, with three replicate samples per group. Following corticosterone treatment, cells were collected for transcriptomic analysis.


title: Multi-omic analysis reveals brain-blood concordance and persistent neuroimmune reprogramming with stress and toxicant exposure in a mouse model of Gulf War Illness [RNA-Seq]

city: Toronto

first: Patrick

last: McGowan

address: 1265 Military Trail

institute: University of Toronto Scarborough

summary: Gulf War Illness (GWI) is a chronic multisymptom disorder associated with prior stress and toxicant exposures. Adult male C57BL/6J mice were exposed to corticosterone (CORT) and diisopropyl fluorophosphate (DFP), followed by repeated intermittent CORT and a later immune challenge with lipopolysaccharide (LPS) or saline. RNA-seq was performed in hippocampus and frontal cortex collected 6 h, 12 h, and 24 h after challenge to define transcriptional responses associated with persistent neuroimmune priming in this mouse model of GWI.

overall_design: Adult male C57BL/6J mice received CORT in the drinking water for 7 days, followed on day 8 by a single DFP injection and repeated intermittent CORT administration over 5 weeks. On the final day, mice received saline or LPS and hippocampus and frontal cortex were collected 6 h, 12 h, or 24 h later. RNA-seq libraries represent CORT+DFP+Saline, 6 h baseline controls and CORT+DFP+LPS groups at 6 h, 12 h, and 24 h. One hippocampus baseline-control library was excluded because of poor sequencing quality.

first: Aya

last: Sasaki

first: Kimberly

last: Kelly

first: Lindsay

last: Michalovicz

first: David

last: Ashbrook

first: Sanoji

last: Wijenayake

first: James

last: O'Callaghan


title: Framework for analyzing bacterial responses to environmental signals: Salmonella’s response to nineteen host associated molecules

city: Rehovot

first: Erez

last: Mills

address: Hertzel 229

country: Israel

institute: The Hebrew University

summary: Most RNAseq studies characterize gene expression in complex environments and long exposure times confounding analysis. Here Salmonella enterica serovar Typhimurium (Salmonella) was exposed in a minimal medium to 19 different metabolites associated with the host for just 10 minutes. This method successfully reduced background processes enabling the identification of compound specific gene changes. Exposure to ten of the compounds resulted in only 1-4 differentially expressed genes (DEGs), while exposure to cysteine and 5-oxoproline resulted in 20 and 34 DEGs respectively. This included transcriptional changes of up to 150-fold. Modulated genes encode import systems or enzymes for the integration of compounds into metabolism. Of note, while some responses were not previously known, many of these DEGs were expected from Escherichia coli data, implying many specific responses are transcription factor mediated. Exposure to seven compounds resulted in no specific responses, implying Salmonella does not sense these compounds, at least in tested conditions. Interestingly, Salmonella specifically down regulated SPI-2 in response to 5-oxoproline exposure, which was the only compound to significantly affect Salmonella growth, implying SPI-2 inhibition might be part of a stress response. Furthermore, the results imply the existence in Salmonella of an unknown tyramine dopamine sensor. Finally, a pipeline was developed which identifies differentially expressed metabolic pathways even when specific genes are not statistically modulated. This pipeline identified a number of expected and unexpected modified pathways. Importantly, in response to propionate exposure Salmonella activated enterobactin biosynthesis implying propionate might inhibit iron bioavailability. To conclude, this work lays the framework for analyzing specific bacterial responses to environmental signals. Such analyses allow resolving bacterial evolutionary programing which can be used to model bacterial transcriptional behavior in complex environments, to develop biosensors, and to engineer ligand specific transcriptional switches for bioengineering.

overall_design: in this work Salmonella enterica serovar Typhimurium stain SL14028 was exposed to 19 different nutrient type compounds. Exposure was limited to only ten minutes, in a defined minimal media, and each time to a specific molecule, to minimize background responses and identify directly modulated genes. each compound had 3 biological replicates.

first: Ron

last: Tovy-Sharon

first: Tali

last: Rosenberg

first: Shir

last: Aharon


title: Transcriptomics of 4T1 cells after corticosterone treatment

address: 河南省郑州市金水区博学路街道金水东路156号


title: Bulk RNA-seq of mouse 4T1 cells with ETV4 KO

first: Silvio

last: Bicciato

overall_design: Control or ETV4 KO cells are cultured in 3D Collagen I gels and then harvested for RNA-seq

first: Robin

last: Caire

first: Giusy

last: Battilana

first: Francesca

last: Zanconato

first: Oriana

last: Romano

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Transcriptomic response to corticosterone treatment in murine osteoblasts.

city: Zurich

first: Ganesh

last: Pathare

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

summary: To assess the transcriptomic response to corticosterone treatment in osteoblasts, we treated differentiated MC3T3 osteoblasts cells with 100 nM corticosterone for 24 hours. Comprehensive RNA-seq analysis was performed to identify differentially expressed genes and pathways associated with glucocorticoid receptor activation, osteoblast activity, and inflammatory responses. This study provides insights into the molecular mechanisms underlying corticosterone-mediated suppression of FGF23 expression and its broader effects on bone metabolism.

overall_design: We included 3 biological replicates in each group, with two groups: Control and Corticosterone


title: ATR and PKMYT1inhibition re-sensitize a subset of TNBC patient-derived models to carboplatin and induce mitotic catastrophe

city: Montreal

first: Mark

last: Basik

address: 3755 Chem. de la Côte-Sainte-Catherine

institute: Lady Davis Institute

summary: Triple negative breast cancer (TNBC) is associated with poor prognosis and is mainly treated with chemotherapy-based regimens, often including carboplatin. Resistance to carboplatin is a common clinical issue that is either initially present or develops with treatment. Overcoming this resistance is a significant clinical challenge, which highlights the need for novel therapeutic strategies. We used a pooled shRNA screening approach with a chemoresistant TNBC patient-derived xenograft (PDX) cell (PDXC) line to identify targets whose knockdown would enhance the efficacy of carboplatin. This screening led to the identification of the ATR (ataxia telangiectasia and Rad3-related) gene as a key therapeutic vulnerability. Inhibiting ATR with BAY1895344 or AZD6738 re-sensitized carboplatin-resistant PDXCs and PDXs to carboplatin, resulting in an increase in DNA damage, and apoptosis. ATR inhibition prevents carboplatin-resistant cells from effectively engaging the S and G2/M checkpoints required for DNA repair, leading to mitotic catastrophe. We further identified that the addition of ATR inhibitors to carboplatin enabled FOXM1-targeted gene program leading to premature passage into mitosis. Moreover, targeting PKMYT1, a regulator of cyclin-dependent kinase 1 (CDK1) controlling the G2/M checkpoint, through knockdown or with the novel PKMYT1 inhibitor RP-6306, also enhanced carboplatin efficacy in our TNBC PDXC. Molecular factors associated with response to the ATR inhibitor/carboplatin combination included low RNA levels of PKMYT1. These results underscore the pivotal roles of ATR and PKMYT1 in mediating resistance to carboplatin in TNBC and support targeting these pathways to overcome carboplatin resistance in this disease.

overall_design: RNA-seq profiling of T-786 patient-derived xenograft cell untreated or treated for 24h with carboplatin (20uM), BAY1895344 (5nM), RP-6306 (100nM, carboplatin+BAY1895344 or carboplatin+RP-6306

first: Juliet

last: Guay

first: Hellen

last: Kuasne

first: Catherine

last: Chabot

first: Kathryn

last: Bozek

first: Yasamin

last: Majedi

first: Marguerite

last: Buchanan

first: Adriana

last: Aguilar-Mahecha

first: Eric

last: Bareke

first: Benjamin

last: Ulmer

first: Tim

last: Kong

first: Kangning

last: Yang

first: Minyan

last: Liao

first: Oluwadara

last: Elubute

first: Ruining

last: Guo

first: Anie

last: Monast

first: Geneviève

last: Morin

first: Sidong

last: Huang

first: Morag

last: Park


title: Kurarinone Ameliorates Experimental Autoimmune Encephalomyelitis by Modulating Gut Microbiota-Indole-3-Acetaldehyde-Aryl Hydrocarbon Receptor Axis in Mice

city: Xian

first: Jiaji

last: Lin

address: No. 1. XinSi Road

department: Neurology

institute: Forth Military Medicial University

summary: Multiple sclerosis (MS) is a central nervous system (CNS) autoimmune disease primarily driven by Th17 and Th1 cells, and the gut microbiota is associated with MS onset and progression. Kurarinone (KU), a key component of the traditional Chinese medicine Radix Sophora Flavesvara, exhibits anti-inflammatory and immune-regulatory effects and can modulate the gut microbiota. However, it is unclear whether KU affects MS via a gut microbiota-mediated mechanism. Herein, we demonstrated that KU significantly alleviated experimental autoimmune encephalomyelitis (EAE), an animal model of MS, by modulating the gut microbiota, particularly by enriching Akkermansia muciniphila. The disease-alleviating effect of KU was achieved in a manner dependent on A. muciniphila. Meanwhile, KU significantly upregulated the tryptophan metabolite indole-3-acetaldehyde (IAAld). The IAAld content was positively correlated with the relative abundance of A. muciniphila and negatively with the severity of EAE in mice. In vitro, A. muciniphila alone could also facilitate the tryptophan metabolism to produce IAAld. Oral IAAld suppresses Th17 and Th1 differentiation to ameliorate EAE. In vitro, IAAld activates AhR and inhibits STAT3/STAT4 phosphorylation, thereby reducing Th17/Th1 differentiation. Collectively, this study identifies a novel mechanism by which KU ameliorates EAE via the gut microbiota-indole-3-acetaldehyde-AhR axis and unveils the potential therapeutic targets for MS.

overall_design: Female C57BL/6 mice aged 6-8 weeks were purchased from GemPharmatech and maintained in the Laboratory Animal Center of Fourth Military Medical University. All mice were maintained under SPF conditions and housed under a 12:12-h light-dark cycle, with humidity of 40-70%, ambient temperature of 26 °C, and sufficient food and water. Mice were group-housed with cage rotation for 2 weeks before the experiments. All animal experimental procedures were approved by the Institutional Animal Care and Use Committee of Fourth Military Medical University. The mice were inoculated with an emulsion comprising incomplete Freund’s adjuvant, MOG35-55 (200 μg) and H37RA (500 μg) at 3 subcutaneous locations on the dorsal surface of the mice. The mice were intraperitoneally injected with 200 ng of pertussis toxin (PTX) on the induction day and 48 h later. EAE clinical scores were assessed daily: 0 (no symptoms), 1 (tail limpness), 2 (hindlimb weakness), 3 (hindlimb paralysis), 4 (tetraplegia), and 5 (moribund/death). On 11 dpi, the KU group was orally administered 100 mg/kg of KU treatment, and the EAE group received PBS until 21 dpi. Feces were collected under sterile conditions and promptly stored at -80 °C. DNA from different samples was extracted using the Stool DNA Kit (Omega, D4015-02) according to the manufacturer’s instructions. The total DNA was eluted in Elution buffer (50 µL) using a modification of the manufacturer’s procedure (QIAGEN) and stored at -80 °C until PCR analysis by LC-BIO Technology Co., Ltd.

first: Xinyan

last: Han

first: Jiaqi

last: Ding

first: Weitai

last: He

first: Xue

last: Kang

first: Cong

last: Zhao

first: Yi

last: Li

first: Di

last: Wu

first: Zonghao

last: Pan

first: Hongzeng

first: Kaixi

last: Ren

first: Jun


title: Gut Microbiota Dysbiosis Remodels the Multi-Tissue Transcriptional Landscape of the Host

city: Hangzhou city

first: Liang

address: 866 Yuhangtang Road Xihu District, Hangzhou Zhejiang Province, China

institute: Zhejiang university

summary: The gut microbiota exerts a profound influence on host physiology, but its systemic impact on gene expression across diverse tissues remains poorly characterized. This study investigated the transcriptional effects of gut microbiota depletion and restoration in mice across six tissues (colon, jejunum, liver, heart, lung, and kidney) using whole-transcriptome sequencing. We found that the presence of gut microbiota significantly altered the transcriptome, with the most pronounced effects in the colon. Using a linear mixed-effects model, we identified 7,365 effector genes. Tissue-specific analysis revealed that these genes were associated with distinct functional pathways, such as immunity in the gut and lung, and metabolism in the liver. Further refinement with LASSO regression pinpointed gut microbiota-mediated key effector genes, whose expression levels were significantly associated with patient survival in corresponding human cancers (e.g., LIHC, LUAD, KIRC). Furthermore, we observed a widespread remodeling of competing endogenous RNA (ceRNA) networks by the gut microbiota. Single-cell data analysis highlighted a potential gut-liver axis interaction, primarily mediated by colonic enterocytes and hepatic cholangiocytes, meanwhile gut microbiota repressed the transcription initiation of Noct in colonic enterocytes, whose expression level was significantly negatively correlated to gut-liver axis interaction. Our findings provide a comprehensive map of the multi-tissue transcriptional landscape shaped by the gut microbiota, revealing tissue-specific regulatory mechanisms and identifying key genes with potential clinical relevance in cancer.

overall_design: 8 weeks-old germ-free (GF) mice, germ-free mice undergoing fecal microbiota transplantation (FMT), and special-pathogen-free (SPF) mice were used, n=3 each group. Collect almost 80 mg heart, liver, lung, kidney, colon and jejunum tissues for whole RNA sequencing. Sequencing were performed by Majorbio (Shanghai, China). Total 771,105,028,366 B raw data were obtained.

first: Shuqi

last: Liu

first: Sai

last: Xiao

first: Yige

first: Shiqi

last: Luo

first: Erjia

last: Hou

first: Yizhen

last: Wang

first: Xin

last: Zong


title: Loss of Neurofascin 186 and Ankyrin G in Purkinje Cells Causes Disruption of Axon Initial Segments, Neurodegeneration and Cerebellar Ataxia

city: San Antonio

first: Manzoor

last: Bhat

state: Texas

address: 7703 Floyd Curl

institute: UT Health San Antonio

summary: The axon initial segment (AIS) is essential for initiating action potentials and maintaining neuronal polarity, yet the developmental roles of its core molecular components—Neurofascin 186 (NF186) and Ankyrin G (AnkG)—remain incompletely defined in cerebellar Purkinje cells. Here, we generated Purkinje cell-specific NF186/AnkG double knockout mice to investigate how these adhesion and scaffolding proteins cooperatively regulate AIS formation, ion channel localization, synaptic targeting, and neuronal survival. We found that combined deletion of NF186 and AnkG markedly disrupted assembly and maintenance of the AIS cytoskeleton during postnatal development. Other AIS-enriched proteins, including βIV Spectrin (βIVSpec), voltage-gated sodium (Nav) and potassium (Kv1.2) channels, failed to properly localize to the AIS and progressively disintegrated between postnatal days 10 and 30. Notably, Kv1.2 clustering in the pinceau synapse was disrupted, and basket cell axons showed misaligned terminal organization, indicating defective inhibitory synapse innervation. By two months of age, degeneration of Purkinje cells was evident, accompanied by cerebellar dysfunction. In addition, our RNA-seq analysis revealed that Purkinje cell-specific loss of NF186 predominantly activated immune-inflammatory pathways, AnkG loss significantly disrupted neuronal developmental and metabolic processes, and the dual loss of NF186/AnkG produced transcriptional changes that were distinct from, and in part intermediate to, those observed in every single knockout. Collectively, our results show that NF186 and AnkG have complementary, non-redundant roles to establish and maintain the Purkinje cell AIS, and that their loss disrupts synaptic organization at the AIS. These findings advance our understanding of AIS development in cerebellar neurons and have implications for diseases involving AIS dysfunction, including cerebellar ataxia and demyelinating neuropathies.

overall_design: Bulk RNA-seq profiling of cerebellar hemispheres from P30 C57BL/6J littermates (mixed sex): NfascFx/Fx;AnkGFx/Fx controls (n=3), Pcp2-Cre;NfascFx/Fx (NF-KO; n=3), Pcp2-Cre;AnkGFx/Fx (AnkG-KO; n=2) and Pcp2-Cre;NfascFx/Fx;AnkGFx/Fx (DualKO; n=3). Single-end 100 bp sequencing.

first: Qian

last: Shi


title: Hippocampal H3K27ac ChIP-seq (P14) in mice treated with N-bc2S1P vs saline

city: GuangZhou

first: Hao

address: No. 1023-1063 Shatai South Road, Baiyun District

institute: Southern Medical University

summary: H3K27ac ChIP-seq was performed on hippocampal tissue from P14 mice treated with N-bc2S1P or saline (n=3 per group). Single-end 1x150 bp reads were aligned to mm10, and H3K27ac enrichment was summarized as a consensus peak count matrix.

overall_design: Chromatin from hippocampal tissue was immunoprecipitated with anti-H3K27ac and sequenced single-end. Reads were trimmed, aligned to mm10, broad peaks were called, and a consensus peak-by-sample count matrix was generated.


title: Base editing restores CDKL5 expression and rescues neuronal deficits in a patient-derived model of CDKL5 deficiency disorder

city: Shatin

first: Yao

last: Zhu

address: CUHK

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: CDKL5 (Cyclin-dependent kinase like 5) deficiency disorder (CDD) is a rare monogenic neurodevelopmental disorder caused by pathogenic mutations in the CDKL5 gene, with approximately 50% of reported variants being point mutations. Base editing presents a promising therapeutic strategy to correct such mutations, restore endogenous CDKL5 expression, and pave the way for novel treatments for CDD. To assess the therapeutic potential of base editing for CDD, we applied adenine base editing (ABE) to correct a CDKL5-R550* (c.1648C>T) mutation in induced pluripotent stem cells (iPSCs) derived from a CDD patient. Isogenic control, CDKL5-R550* mutant, and ABE-corrected iPSCs were differentiated into neurons and the restoration of CDKL5-related and functional recovery were assessed. In this study, we demonstrated that ABE successfully restored CDKL5 protein levels and CDKL5-dependent signalling pathways in edited iPSC-differentiated neurons to levels comparable to the isogenic control. Morphological deficits, and genes expression were normalized in the ABE-corrected neurons. This study provides evidence that ABE can precisely correct pathogenic mutation and functionally rescue some CDD-associated neuronal phenotypes in patient-derived cells, supporting its potential as a valuable gene therapy for CDD. Moreover, these findings underscore the broader applicability of base editing for treating other monogenic neurodevelopmental disorders caused by point mutations.

overall_design: isogenic Control, CDKL5-R550*, ABE-corrected iPSC-induced Day28 cortical neurons

first: Yue

last: Chai

first: Jiayi

first: Mingfeng

last: Guan

first: Zhongyu

last: Zheng

first: Yu

last: Chen

first: Wing Sum

last: Tsang

first: Tao

last: Ye

first: Pak Kan

last: Ip


title: Nuclear-specific reductive carboxylation of alpha-ketoglutarate fuels histone acetylation to induce FOXA1-dependent gene activation [RNA-seq]

city: Buffalo

first: Mark

last: Long

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Mitochondria remain at the core of cell metabolism, whereas the nucleus integrates cellular and environmental signals to activate genes. However, the mechanisms that directly link cellular metabolism to gene regulation are not well understood. In this work, we focused on deciphering metabolic pathways in the nucleus that control acetylation of histone proteins, and identified a moonlighting mechanism that directs local abundance of acetyl-CoA pool by nuclear localization of mitochondrial enzymes, aconitase (ACO2), and isocitrate dehydrogenase (IDH2). Metabolic tracing studies in the isolated nucleus identified reductive carboxylation of α-ketoglutarate catalyzed by IDH2 and ACO2 rapidly synthesize citrate to increase the acetyl-CoA pool. Genetic and proteomic analyses revealed nuclear IDH2 and ACO2, form a complex with KAT2A for histone acetylation, which increased chromatin accessibility and recruited pioneering factor FOXA1 to activate proliferative gene MKI67. In multiple mouse models of cancer, increased nuclear expression of ACO2 and IDH2 was sufficient to develop aggressive tumors indicating the tumorigenic potential of IDH2-ACO2-KAT2A axis. Altogether, our work revealed a paradigm coupling a nuclear metabolic pathway with histone acetylation to control of gene expression that accentuates hyperproliferative phenotype in tumors.

overall_design: Human prostate  cancer cells (LNCaP-C4-2) with or without ACO2-KO were profiled by RNA-seq

first: Abhisha

last: Sawant Dessai

first: Subhamoy

last: Dasgupta


title: The lipoprotein lipase-mediated induction of NADPH oxidase affects small RNA expression in macrophages

city: St. John's

first: Lourdes

last: Peña-Castillo

state: Newfoundland and Labrador

address: 9 Arctic Ave

institute: Memorial University of Newfoundland

type: Non-coding RNA profiling by high throughput sequencing

summary: Lipoprotein lipid hydrolysis products generated by lipoprotein lipase (LPL) (herein, HP) can contribute to the conversion of macrophages into foam cells, but the molecular processes are not well understood. We previously reported that HP from total lipoproteins significantly changed the transcriptome of human macrophages, including an increased representation of small nucleolar RNAs. Cellular stress within cardiomyocytes was previously reported to increase the expression of small nucleolar RNAs through an increase of reactive oxygen species (ROS) generation by NADPH oxidase (NOX). Thus, we hypothesized that the HP induced ROS production through NOX activity, resulting in changes to small RNA transcripts. We examined changes to small RNA expression using RNA-seq in the absence or presence of HP, and whether those changes could be reversed by NOX inhibition. We identified eight differentially expressed small RNAs: three with differed expression in response to HP, and five with differed expression in response to NOX inhibition in the presence of HP.

overall_design: Small RNA-seq profiling of HEK-293 cells after 18 hours of incubation without or with HP, in the absence or presence of NOX inhibitors. P = Cells treated with very low-density lipoprotein (VLDL); L = Cells treated with VLDL lipid hydrolysis products generated by LPL; and G = “L” + the NOX1/4 inhibitor GKT136901.

first: Mariam

last: Tijani

first: Elizabeth

last: Chia

first: Natalie

last: Cotter

first: Robert

middle: J

last: Brown


title: scRNA sequencing revealed HIV-associated inflammatory-mediated lung epithelial dysregulation and fibroblast remodeling

city: Rochester,

first: Khursheed Ul Islam

last: Ganaie

state: New York

address: 601 Elmwood Ave,

department: Environmental Medicine

institute: University of Rochester

summary: HIV infection is a well-recognized risk factor for a wide spectrum of pulmonary diseases, with incidence rates significantly higher in people living with HIV (PLWH). Despite antiretroviral therapy, persistent immune activation and recurrent injury continue to compromise lung integrity in this population. However, the mechanism through which HIV disrupts alveolar homeostasis and reshapes epithelial, immune, and stromal compartments in the lungs remain poorly defined. To characterize the cellular and molecular landscape of HIV infection within the lungs upon tobacco smoking, we performed single cell RNA sequencing (scRNA-seq) on human lung tissues from HIV non-smokers and smokers compared them with HIV positive subjects with and without a smoking history. Integration and Uniform Manifold Approximation and Projection (UMAP) clustering of 54,320 cells from all experimental groups identified 29 transcriptionally distinct clusters upon scRNA seq analyses. HIV infection profoundly altered lung cellular composition, marked by expansion of CD4+, CD8+ T-cells, B cells, and non-classical monocytes, alongside reduced fibroblast abundance. Alveolar Type I and Type II epithelial cells displayed robust HIV-associated transcriptional reprogramming. In AT1 cells,. Fibroblast and smooth muscle cells showed enhanced proinflammatory and stress responsiveness with suppression of extracellular matrix and contractile programs. EMT marker analysis revealed cell type specific shifts with: (a) AT1 cells exhibiting reduced E-cadherin and increased vimentin gene expression, (b) AT2 cells adopting a hybrid epithelial mesenchymal phenotype, and (c) myofibroblast cluster displaying amplified mesenchymal activation. These findings reveal HIV as a potent driver of epithelial dysregulation in the human lung, and suggest that targeting epithelial stress programs and fibroblast remodeling may offer new therapeutic avenues, supporting future efforts to develop therapeutic interventions tailored for PLWH.

overall_design: Performing single cell RNA sequencing (scRNA seq) on Healthy and HIV infected donors with or without smoking history.

first: Khursheed

last: Ul Islam

first: Gagandeep

last: Kaur

first: Sadiya

last: Bi Shaikh

first: Kingshuk

last: Panda

first: Srinivasan

last: Chinnapaiyan

first: Hoshang

last: Unwalla

first: Irfan

last: Rahman


title: SPEG Deficiency Disrupts Excitation-Contraction Coupling in Human Cardiomyocytes via Impaired JPH2 Phosphorylation

city: beijing

first: Hongyue

last: Wang

state: Beijing

address: Mentougou District Fuwai Hospital Western Hills scientific research base

institute: Fuwai Hospital

summary: Dilated cardiomyopathy is a major cause of heart failure, with genetic mutations playing a significant role in its pathogenesis. To explore the molecular mechanisms underlying this condition, we established a striated muscle preferentially expressed protein kinase (SPEG)-deficient human embryonic stem cell-derived cardiomyocyte model to investigate the role of SPEG in cardiac dysfunction. Our findings revealed that SPEG knockout resulted in increased cardiomyocyte volume, disorganized sarcomeres, and upregulated heart failure markers, recapitulating key features of cardiomyopathy. Functional analysis, including calcium transient and contractility measurements, revealed disrupted excitation-contraction coupling in SPEG-deficient cardiomyocytes. Transcriptomic analysis revealed disrupted calcium signaling, while Western blot analysis confirmed reduced phosphorylation of junctophilin-2 (JPH2) as central mechanisms underlying these defects. Pharmacological activation of L-type calcium channels with Bay K8644 effectively restored calcium handling, excitation-contraction coupling delay, and contractile function, offering a promising therapeutic avenue for SPEG-associated cardiomyopathy. This study establishes SPEG as a critical regulator of cardiac function through its role in JPH2 phosphorylation and calcium homeostasis, while the human-relevant model developed here provides a valuable platform for further investigating SPEG-associated cardiomyopathy and exploring potential therapeutic interventions.

overall_design: RNA sequencing was performed by BGI Genomics using the BGISEQ platform. Raw sequencing data were processed and analyzed for differential gene expression using the DESeq2 package. Differential genes were identified based on the criteria of an absolute fold change ≥ 2 and a Q value 0.05. Hierarchical clustering analysis of all differentially expressed genes was conducted using the R package, and heatmaps were generated to visualize the expression patterns. Subsequently, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed on the differentially expressed gene set, with significantly enriched KEGG pathways identified using a Q value < 0.05 as the threshold, to determine the primary cellular pathways associated with the differentially expressed genes. Additionally, Gene Set Enrichment Analysis (GSEA) was conducted on the differential gene set, with significantly enriched pathways identified using a Q value < 0.05 as the threshold, to assess the expression patterns of differentially expressed genes within the enriched pathways.

first: Tianwei

last: Guo


title: Generation of functional salivary gland progenitor cells from extended pluripotent stem cells

city: Beijing

first: Wenpeng

last: Song

address: Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China

department: Department of Stomatology

institute: Capital Medical University

summary: The aim of this study was to use pluripotent stem cells (PSCs) as a starting point to progressively differentiate into induced salivary gland progenitor cells (iSGPCs) by mimicking salivary gland development. In this study, we further explored and optimized the passage strategy and organoid formation protocol of iSGPCs based on our previous studies. After 17 days of differentiation, PSC-derived iSGPCs exhibited a marker expression profile similar to that of adult salivary gland progenitors, including KRT5, KRT14, KRT19, and CD49F. Functionally, iSGPCs exhibit self-renewal capacity, are able to form salivary gland-like branching organoids, and have therapeutic potential in models of radiation-induced salivary gland hypofunction.

overall_design: In this study, a variety of small molecules were used to differentiate pluripotent stem cells into iSGPCs. Bulk RNA-seq was performed on differentiated cells.


title: Mapping neuro-vascular unit communications reveals distinct angiogenic programs across developing brain regions

city: Montréal

first: Gael

last: Cagnone

address: 3175 Chemin de la Côte-Sainte-Catherine

institute: CHU Sainte Justine

summary: Neurovascular unit (NVU) communications guide vascular patterning, BBB maturation, and neuronal homeostasis, yet whether these interactions differ across brain regions during development remains unclear. Here, we combine spatial transcriptomics with region-resolved endothelial single-cell RNA sequencing to map cortical and thalamic NVU communication dynamics. We uncover spatiotemporal divergence of endothelial programs and show that neuronal and glial maturation parallels region-specific angiogenic trajectories. We identify neuronal–endothelial TGFβ2 signaling as an essential regulator of thalamic vascularization during a critical postnatal period. Loss of endothelial TGFβR1 signaling leads to mTOR hyperactivation and thalamus-predominant vascular malformations and hemorrhage within this developmental window, and these defects are rescued by mTOR inhibition. Together, these findings show that circuit maturation and region-specific NVU communication programs coordinate postnatal angiogenesis and vascular maturation, providing a framework for understanding regional vulnerability in neurovascular disorders.

overall_design: Single-cell transcriptomics of fixed endothelial-enriched suspension from thalamus and cortical region of P6, P12 and P60 mouse brain.

first: Mathilde

last: Bizou

first: Joel

last: Howard

first: Alexandre

last: Dubrac


title: Role of Pdk4 in BAPN-induecd aortic dissection in mouse models

city: Suzhou

first: You

last: Yu

state: Jiangsu province

address: No.178 Ganjiang Rd

department: Institute for Cardiovascular Science

institute: Soochow University

summary: Thoracic aortic dissection (TAD) is a life-threatening acute vascular condition with extremely high morbidity and mortality. Endothelial cells (ECs) are critical for maintaining vascular homeostasis, yet the role of Endothelial-to-Mesenchymal Transition (EndoMT)—a key cell fate process in vascular development and disease—in TAD remains poorly defined. Furthermore, the functional significance of EndoMT-gene-program activation mediated by pyruvate dehydrogenase kinase 4 (PDK4) in TAD has not been elucidated. To explore the mechanistic involvement of EndoMT in TAD, a murine TAD model was established through systemic administration of β-aminopropionitrile (BAPN). RNA sequencing was performed to profile the activation landscape of the EndoMT-gene-program in ECs for identifying key regulatory targets. Concurrently, clinical samples from TAD patients and healthy controls were analyzed to quantify mRNA and protein levels of EndoMT-related markers in aortic tissues. Pyruvate dehydrogenase kinase isoenzyme 4 (PDK4) was identified as a critical regulator and validated as a downstream target of EndoMT signaling using an integrated approach combining RNA-seq, luciferase reporter assays, and immunofluorescent staining. The functional role of Pdk4 in TAD was further validated by using conditional knockout (CKO) mouse model. To facilitate better clinical translation, EC-specific Pdk4 deletion or overexpression mouse models were generated via adeno-associated virus (AAV)-mediated delivery and subjected to TAD model. Serum samples from these mice were collected, and enzyme-linked immunosorbent assay (ELISA) was used to measure levels of endothelial injury markers (sICAM1, sVCAM1, sE-Selectin) for assessing endothelial dysfunction. Additionally, the therapeutic potential of dichloroacetate (DCA), a specific PDK4 inhibitor, was evaluated by administering it to BAPN-fed mice to assess its efficacy in ameliorating TAD progression. A significant upregulation of the EndoMT-gene-program was observed in BAPN-fed murine models of TAD, aortic tissues from TAD patients, and HAECs treated with angiotensin II (Ang II). Administration of AAVEndoPdk4 directly induced TAD formation, which was exacerbated by BAPN co-treatment. Conversely, EC-specific knockdown of Pdk4 reduced TAD formation by inhibiting EndoMT signaling. The same results were also obtained in EC-specific conditional Pdk4 knockout mice (CKO, Pdk4flox/flox; Cdh5-CreERT2). PDK4 was identified as a critical factor in both TAD development and EndoMT process, with SNAI1 transcriptionally activating PDK4; vice versa, PDK4 further enhanced the activation of EndoMT signaling in both in vivo and vitro. PDK4 inhibitor, DCA, significantly slowed TAD progression in BAPN-fed mice. Mechanistically, a PDK4-EndoMT feedback loop was identified in TAD, where interruption of this self-reinforcing pathological cycle markedly attenuates the progression of TAD.

overall_design: Bulk RNA-Seq of the aortic tissues from BAPN-fed mice at week 0, 2, 4; To dertermine the role of Pdk4 in the process, AAV-mediated over-expression and knock-down of Pdk4 were analyzed; To investigate the role of PDK4 in endothelial cells, PDK4 overexpression in endothelial cells were also analyzed.

first: Xiangyu

last: Cao

first: Lianbo

last: Shao


title: Single-Cell Spatial Transcriptomics of Archival Human Lung and Breast Tumor FFPE Samples

city: Lausanne

first: Raphael

last: Gottardo

state: Vaud

address: Rue du Bugnon 21

department: Biomedical Data Science Center

institute: Lausanne University Hospital

summary: We profiled human lung and breast tumor fragments using imaging-based single-cell spatial transcriptomics (10x Xenium) and compared the results to sequencing-based spatial transcriptomics (10x Visium) and single-nucleus RNA-seq

overall_design: Single center, translational work on breast and lung cancer samples, CHUV

first: Krisztian

last: Homicsko


title: DNA methylation differences underlying female reproductive aging

city: Atlanta

first: Alicia

middle: K

last: Smith

state: GA

address: 101 Woodruff Circle NE

institute: Emory University

type: Methylation profiling by genome tiling array

summary: Reproductive aging occurs earlier than systemic aging as a woman’s ovarian reserve is depleted as she approaches menopause. There is considerable variability around when a woman reaches menopause, yet few contributing factors have been identified. Assessment of reproductive age involves measuring a woman’s ovarian reserve and oocyte function, which has clearly-defined parameters in in vitro fertilization. As ovarian reserve declines, Anti-Mullerian hormone levels fall and women produce fewer oocytes after ovarian stimulation. Oocyte function also declines, as fewer mature oocytes are produced and have the capacity to be fertilized. The mechanisms of these age-related declines are unclear, but may involve changes in DNA methylation, which are known to occur with age and may reflect the biological processes underlying reproductive aging. We hypothesize that DNA methylation patterns will be associated with ovarian reserve and oocyte function, and that women with poor ovarian reserve and oocyte function will experience epigenetic age acceleration and will accumulate more stochastic epigenetic mutations. To test this hypothesis, we will first perform an epigenome-wide association to examine DNA methylation patterns associated with each measure of ovarian reserve and oocyte function. Then, we will calculate epigenetic age and age acceleration, which are indicators of biological aging, and stochastic epigenetic mutations, which increase with age and may disrupt key biological pathways in an individual.

overall_design: This study examines women who have had an embryo transfer. We  exclude participants with a diagnosis of endometriosis or uterine factor infertility, and those with a history of cancer. At the time of oocyte retrieval, a needle was inserted through the vaginal wall into each ovarian follicle. The oocyte and surrounding follicular fluid were aspirated, and oocytes were separated from the follicular fluid by a qualified embryologist. To capture overall ovarian reserve and oocyte function, follicular fluid from multiple follicles from the same participant were pooled. GCs were separated from follicular fluid via centrifugation and stored at -80C.

first: Smith

last: Alicia

first: Knight

last: Anna


title: BAP1 dysregulation impairs trophoblast differentiation and contributes to placental dysfunction in preeclampsia

city: Madrid

first: Vicente

middle: Pérez

last: García

state: Madrid

address: C/ Nicolás Cabrera 1

department: Tissue and organ homeostasis

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

summary: Preeclampsia, a life threatening hypertensive disorder of pregnancy, is a leading cause of maternal and perinatal morbidity and mortality. Its early onset form (EO PE), requiring delivery before 34 weeks of gestation, is particularly severe and closely linked to defective trophoblast differentiation. Here, we identify BRCA1-associated protein 1 (BAP1) and its cofactors ASXL2 and ASXL3 are upregulated in EO PE placentas. Enforced BAP1 expression in human trophoblast stem cells reinforced epithelial identity, enhanced adhesion, and impaired both extravillous trophoblast differentiation and syncytiotrophoblast formation. Integrated transcriptomic and proteomic analyses revealed suppression of lineage-specific pathways alongside maintenance of progenitor-like and pro-inflammatory signatures. In trophoblast organoids, excess of BAP1 disrupted syncytial maturation and induced interferon-driven pathways overlapping with EO PE transcriptomes. Together, these findings establish BAP1 as a key regulator of human trophoblast differentiation and implicate its dysregulation in the pathogenesis of EO PE, providing mechanistic insight into the cellular basis of placental dysfunction.

overall_design: RNA-seq was performed to investigate transcriptional changes induced by BAP1 overexpression in human trophoblast cells. Gene expression profiles from vector control and BAP1-overexpressing samples were obtained across different trophoblast states, including trophoblast stem cells, syncytiotrophoblasts, extravillous trophoblasts, and trophoblast organoids, enabling the assessment of BAP1-dependent transcriptional programs during trophoblast differentiation.

first: Paula

last: Doria-Borrell

first: Ana

last: Ferrero-Micó

first: Sergio

last: Navarro-Serna

first: Maravillas

last: Mellado-López

last: Pérez-García


title: Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [RAP-seq]

city: Urbana

first: Prasanth

last: Kannanganattu

address: 601 S Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

summary: Hypoxia-induced alternative splicing (AS) controls tumor progression and metastasis. The underlying mechanism specifying hypoxia-responsive AS needs to be determined. We demonstrate the role of nuclear speckle (speckle) nuclear domain (ND) and the long noncoding RNA, MALAT1, in hypoxia-responsive AS. Hypoxia-responsive genes position near speckles, the NDs that enhance splicing efficiency, and their differentially spliced exons harbor features that are characteristic of inefficiently spliced transcripts. Speckle-resident MALAT1, induced in response to hypoxia, boosts hypoxia-responsive AS by regulating the binding of SR-family splicing factor1 (SRSF1) to pre-mRNAs of speckle-associated genes. Mechanistically, MALAT1 facilitates the recruitment of SRSF1 to elongating RNA pol II (RNAP II) by promoting the formation of phase-separated SRSF1 condensates that are preferentially recognized and recruited to pre-mRNA by RNAP II. Our results reveal that MALAT1 boosts hypoxia-induced AS of speckle-associated genes by establishing the threshold concentration of SRSF1 as condensates, thereby promoting RNAP II-mediated recruitment of SRSF1 to pre-mRNAs.

overall_design: MCF7 cells were cultured at 37 degrees Celsius with 5% carbon dioxide and then grown in normoxic or hypoxic (0.2% oxygen) conditions for 24 hours before collection. Cells were fixed with disuccinimidyl glutarate and formaldehyde then lysed. The DNA was fragmented, hybridized to biotinylated RAP probes, then captured using Streptavidin beads.

first: You Jin

last: Song

first: Min Kyung

last: Shinn

first: Sushant

last: Bangru

first: Yu

last: Wang

first: Qinyu

last: Sun

last: Hao

first: Pankaj

last: Chaturvedi

first: Susan

last: Freier

first: Pablo

last: Perez-Pinera

first: Erik

last: Nelson

first: Andrew

last: Belmont

first: Mitchell

last: Guttman

first: Supriya

last: Prasanth

first: Auinash

last: Kalsotra

first: Rohit

middle: V

last: Pappu

first: Kannanganattu


title: Lymphocyte apoptosis and impaired type-17 immunity underlie mucosal candidiasis in DOCK8 deficiency and can be rescued by IL-7 immunotherapy

city: Bethesda

first: Philip

last: Murphy

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: Dedicator of cytokinesis 8 (DOCK8) deficiency is an autosomal-recessive immunodeficiency disorder that manifests with hyper-IgE syndrome and susceptibility to viral, bacterial, fungal, and parasitic infections as well as malignancy, atopy, and autoimmunity. Up to two-thirds of DOCK8-deficient patients develop chronic mucocutaneous candidiasis (CMC), yet the mechanistic basis for this susceptibility remains elusive. Here, we utilized a mouse model of oral candidiasis to investigate the cellular and molecular mechanisms that drive CMC susceptibility in DOCK8 deficiency. We demonstrate that DOCK8 promotes mucosal fungal clearance via the induction of protective type-17 immune responses. Mechanistically, in the absence of DOCK8, the accumulation of IL-17+ and IL-22+ TCRαβ T cells, γδ T cells, and innate lymphoid cells (ILCs) was markedly decreased in the oral mucosa, driven by increased apoptotic cell death, not impaired cell proliferation or recruitment from the blood. Unexpectedly, DOCK8 was required for the cell-intrinsic acquisition of a type-17 phenotype only in oral mucosal γδ T cells, but not in TCRαβ T cells or ILCs in vivo. Concordantly, mice with conditional DOCK8 deletion in all RORγt-expressing IL-17-producing lymphoid cells, but not in CD4+ T cells alone, were susceptible to oral candidiasis. Moreover, prophylactic administration of the gc family cytokine IL-7 rescued lymphocyte apoptosis, increased the number of IL-17+ and IL-22+ cells, and promoted fungal clearance in DOCK8-deficient mice. Thus, we show that mucosal candidiasis in DOCK8 deficiency is driven by multicellular defects in lymphocyte survival and accumulation resulting in impaired type-17 immunity. IL-7 immunotherapy boosts mucosal type-17 responses and ameliorates fungal susceptibility.

overall_design: Bulk RNAseq was performed on Dock8 KO and WT mice, and differential expression between these groups was analyzed.

first: Michael

last: Abers

first: Vasileios

last: Oikonomou

first: Timothy

last: Break

first: Justin

last: Lack

first: Alexandra

last: Wolfarth

first: Byung

last: Ha Lee

last: Freeman

first: Steven

last: Holland

first: Hene

last: Su

first: Jean

last: Lim

first: Sarah

middle: L

last: Gaffen

first: Judith

middle: N

last: Mandl

first: Michail

last: Lionakis


title: Spatially organizing million callus cells identify the core-network enable tomato shoot regeneration [ncRNA-Seq]

city: weifang

first: yongqi

last: liu

state: shandong

address: 699 Binhu Road, Xiashan District

institute: Peking University Institute of Advanced Agricultural Sciences

summary: Plants can regenerate entire organs from somatic cells, offering a powerful system to uncover fundamental principles of cellular reprogramming and self-organization. Unlike animals, depending on pre-existing stem cell niches, plants re-establish pluripotency de novo. Although current understanding emphasizes hormonal control and external environmental cues, a unifying framework that explains how millions of cells coordinate fate decisions across space and time remains elusive. Here, we construct a million-cell spatial transcriptomic atlas of plant regeneration, achieving mesoscale resolution observation for all stages of tomato callus development. This atlas reveals a tripartite stem cell niche architecture: an outer signaling layer, intermediate plastic zone, and a quiescent core, features reminiscent of animal regenerative niches. We uncover a fundamental Inducer-Maintainer-Trigger (IMT) triad model, wherein PI-2 (Inducer) establishes a stem cell activating microenvironment, DCL2/22-nt siRNAs (Maintainer) safeguard pluripotency through post-transcriptional regulation, and EPFL8 (Trigger) initiates stem cell niche establishment. This triad model unifies niche signaling, small RNA-mediated plasticity, and metabolic-state-dependent activation, drawing parallels between plant and animal regeneration. Beyond resolving key questions in plant biology, our findings highlight deep evolutionary convergence in regenerative logic across multicellular life, offering new blueprints for engineering regeneration in synthetic biology, crop science, and tissue engineering.

overall_design: The cotyledons were excised from tomato seedlings at 6 days after sowing and cultured on SIM medium. Samples were collected at 0, 12, 14, and 16 days for small RNA sequencing, with three replicates for each sample.

first: Shaoman

last: Zhang

first: Xiehai

last: Song

first: Zhiliang

last: Yue

first: Yongqi

last: Liu