title: Sp8 and Sp6 regulatory functions in the limb bud ectoderm [ChIP]

status: Public on Jun 24 2026

city: Santander

first: Marian

last: Ros

address: 22nd Albert Einstein St.

institute: IBBTEC-CSIC-SODERCAN

summary: Sp8 and Sp6 are two closely related Sp genes expressed in the limb ectoderm, where they regulate proximo-distal and dorso-ventral patterning. Genetic studies in mice have shown that they act in a dose-dependent manner, with Sp8 exerting a substantially stronger effect than Sp6. Here, we integrate ChIPmentation-seq and RNA-seq analyses to elucidate their genome-wide regulatory networks and mechanisms of action. Our results show that Sp8 has a dual mode of action either directly binding GC-rich motifs or indirectly binding AT-rich motifs through Dlx. In contrast, Sp6 primarily acts through AT-rich motifs, likely via interaction with cofactors such as Dlx5. Both factors regulate key components of the Wnt, FGF, and BMP signaling pathways, central to limb patterning, and display both cooperative and independent roles. We further show that Sp8 and Sp6 can form homo- and heterodimers, as well as interact with Dlx5, revealing a complex regulatory network. Our findings provide molecular insight into limb morphogenesis and have potential implications for understanding congenital limb malformations.

overall_design:
Genome-wide analysis of Sp8 and Sp6 gene regulatory networks in the mouse limb bud ectoderm at E10.5 by ChIP-seq of Sp8 flagged/flagged for Sp8 and WT for Sp6 respectively and RNA-seq of WT and KO embryos

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

last: Castilla-Ibeas

first: Sandra

last: Moreu

first: Rocio

last: Pérez-Gómez

first: Laura

last: Galán

first: Victor

last: Campa

first: Juan

middle: F

last: López-Giménez

first: Álvaro

last: Rada-Iglesias


title: The retrotransposable element-silencing factor Daxx controls microglia identity and function in the adult brain [ATAC-seq]

status: Public on Jun 22 2026

city: Bonn

first: Paolo

last: Salomoni

address: Venusberg-Campus 1, Building 99

country: Germany

institute: DZNE

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Death domain-associated protein (Daxx) is one of the two main H3.3 chaperones in mammalian cells and acts as key repressor of RTEs of viral origin. In present study, we found that Daxx is an IFN-stimulated gene mediating repression of RTEs and IFN-stimulated genes (ISGs) upon inflammatory stimuli in microglia. Using both bulk and single-cell genomics, we demonstrated that shortly after Daxx loss microglia displayed co-expression of DNA damage/p53, IFN/developmental and DAM-like signatures, suggesting lowering of the epigenetic barrier and increased plasticity. With time, Daxx-deficient microglia become restricted to a DAM-like/ApoeHIGH profile, associated with decreased synaptic puncta and altered behavior. Finally, brains from older microglia-specific Daxx KO mice accumulate ApoE protein along with lysosomal markers. Together, our data revealed a role of Daxx in maintenance of the homeostatic state of microglia in the adult brain, with implications for our understanding of the relationship between loss of epigenetic barriers and neuroinflammation and its potential implications for brain function and aging.

overall_design: To investigate the functional role of Daxx in the microglia, we generate a tamoxifen-inducible Daxx conditional knockout mouse by crossing Cx3cr1-CreERT2 mouse line with Daxx conditional allele (Cx3cr1-CreERT2, Daxxflox/flox). The microglia will be isolated from mice brain at 3 days after tamoxifen administration for ATAC-seq analysis.

first: Xin

last: Yan


title: The retrotransposable element-silencing factor Daxx controls microglia identity and function in the adult brain

type: Expression profiling by high throughput sequencing

overall_design: To investigate the functional role of Daxx in the microglia, we generate a tamoxifen-inducible Daxx conditional knockout mouse by crossing Cx3cr1-CreERT2 mouse line with Daxx conditional allele (Cx3cr1-CreERT2, Daxxflox/flox). The microglia will be isolated from mice brain at different time points after tamoxifen administration for RnA-seq analysis.


title: Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency.

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

country: USA

institute: St. Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: Gene expression profile at single cell level of immune cells from C10 tumor in Rag1-/- mice

city: Bethesda

first: Jia

last: Nie

state: Maryland

address: Building 37, Room 3016

department: Center for Cancer Research

institute: National Cancer Institute

summary: Smarta CD4 T cells and CD11b+NK1.1– CD45+ TILs are responsible for tumor control.We used single cell RNA sequncing(scRNA-seq) to dissect their characteristics.

overall_design: Rag1–/– mice bearing C10 tumor  were transferred PBS or Smarta CD4 T cells on day 4. Then, on day 10, Smarta CD4 T cells were isolated from draining lymph nodes and tumors for single-cell RNA sequencing (scRNA-seq). CD11b+NK1.1– CD45+ cells were isolated from PBS-treated tumors or Smarta-treated tumors for scRNA-seq.


title: Unraveling Novel Drug candidate for ALS through an Integrative Network Analysis of approved Drug-Gene Expression Signatures in Human Pluripotent Stem Cell-Based Model

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem

summary: Given the high attrition rates, substantial costs and slow pace of new drug discovery and development, repurposing of 'old' drugs to treat both common and rare diseases is increasingly becoming an attractive proposition. In this study, we evaluated the potential of using human pluripotent stem cells to identify repurposable drug candidates. For this purpose, we treated derivatives from human embryonic stem cells with 50 marketed drugs and we annotated the induced molecular changes by RNA deep sequencing. Focusing on genes previously implicated in monogenic diseases, we identified drugs capable of modulating the expression of PLP1, PMP22, LMNB1 and SQSTM1 genes known to be involved in Pelizaeus-Merzbacher disease (PMP), hereditary neuropathy with liability to pressure palsies (HNPP), adult-onset autosomal dominant leukodystrophy (ALDL) and amyotrophic lateral sclerosis (ALS).

overall_design: Comparative gene expression profiling analysis of RNA-seq data from mesodermal precursor cells derived from the human wild type embryonic stem cell line SA001 treated for 24 hours with 50 different marketed drugs at the concentration of 10 µM. Each drug was tested in triplicates.

first: Sophie

last: Blondel

first: Jean-Marc

last: Paris

first: Jacqueline

last: Gide

first: Laetitia

last: Barrault

first: Johanna

last: Tournois

first: Benjamin

last: Brinon

first: Anne

last: Boland

first: Jean-François

last: Deleuze

first: Didier

last: Auboeuf

first: Marc

last: Peschanki

first: Cécile

last: Martinat

first: Sandrine

last: Baghdoyan

first: Christophe

last: Battail


title: ZNF512B protects critical regulatory regions to safeguard long term genomic integrity. [scRNA-Seq]

city: Odense M

first: Sanjeeb

middle: Kumar

last: Sahu

address: CAMPUSVEJ 55

department: Department of Molecular Medicine

country: Denmark

institute: University of Southern Denmark

summary: Cellular senescence drives aging and disease largely through the senescence-associated secretory phenotype (SASP), yet its regulatory mechanisms remain unclear. Using a SASP reporter combined with a CRISPR-Cas9 screen targeting active regulatory elements, we identify the zinc finger protein ZNF512B as a key suppressor of SASP. ZNF512B loss induces DNA damage, activates cGAS-STING signaling, and triggers inflammatory transcriptional reprogramming. In contrast, ZNF512B promotes preferential DNA repair at regulatory genomic regions, limiting SASP induction. Mechanistically, ZNF512B is rapidly recruited to DNA damage sites via distinct zinc finger domains and facilitates NuRD complex targeting to damaged chromatin, enabling precise repair. In human neuromuscular organoids, ZNF512B deficiency induces inflammation, lineage imbalance, and cytokine secretion resembling ALS-associated pathology. In vivo, ZNF512B overexpression reduces DNA damage and inflammation following acute liver injury. Together, these findings support a mechanism of preferential DNA repair that contributes to maintaining genome integrity to suppress SASP and inflammation.

overall_design: Day 50 Neuromuscular organoids derived from control and ZNF512B knock out human H9 iPSCs were process for single cell RNA sequencing.

middle: K

first: Sudhir

last: Thakurela

first: Mo

last: Li

first: Juan

middle: C

last: Izpisua Belmonte


title: Myc sustains Regional and Sexually Dimorphic Lipid Homeostasis in the Drosophila Intestine

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Organs are not uniform; distinct transcriptional and metabolic territories are apparent in key metabolic organs such as the intestine, liver or pancreas. Whether and why such organ zonation differs between the sexes remains to be explored, despite increasing interest in documenting and functionally interrogating sex differences in physiology. Here, we use the intestine of adult Drosophila to explore mechanisms of adult organ zonation. Through metabolic profiling, we uncover sex and regional differences in intestinal lipid metabolism. Cell type- and adult-specific genetic manipulations reveal a role for the Myc transcription factor in establishing sex-biased and regional intestinal lipid profiles. myc is repressed in male enterocytes by the sex determinant Doublesex, rendering Myc expression female-biased. Genetic gain- and loss-of-function experiments indicate that this Dsx-Myc antagonism in enterocytes underlies the sexually dimorphic and regional intestinal lipid profiles. The actions of Myc in gut enterocytes are physiologically significant: they extrinsically sustain female-biased lipid storage and fecundity. Our findings establish Myc as a new member of the sex differentiation pathway and a key regulator of organ zonation. They also underscore the need to consider the intestine as a previously unrecognised contributor to widely documented sex differences in lipid metabolism.

overall_design: To investigate the effect of dsxRNAi in adult Drosophila midguts from males and females.

first: Irene

last: Miguel-Aliaga

first: Santiago

last: Vernia


title: ZNF512B protects critical regulatory regions to safeguard long term genomic integrity. [screening]

summary: Active regions in the genome are more prone to DNA damage (Schwer et al., 2016), but the mutations occur less often in these regions (Martincorena et al., 2012; Monroe et al., 2022; Xia et al., 2020; Zhang and Yang, 2015), indicating involvement of unknown protective machinery. Chronic DNA damage signaling induces senescence associated secretory phenotype (SASP), which mediates pathophysiological functions of senescent cells during aging (Herranz and Gil, 2018), however, the molecular players governing SASP remain poorly understood. Here we performed a genome wide CRISPR screening by implementing a SASP specific reporter system and a guide RNA library targeting regulatory regions and identify several novel SASP repressors. ZNF512B is one such factor that prioritizes DNA repair around regulatory regions associated with highly expressed genes. ZNF512B selectively recruits NuRD nucleosome remodeling complexes to damage loci and ensure faithful timely manner repair. ZNF512B depletion induces SASP, and its overexpression inhibits SASP in various in vitro and in vivo models by modulating DNA repair. ZNF512B overexpression slows down cutaneous wound healing and reduces damage associated with acute liver injury by repression of SASP. ZNF512B is a known prognostic factor for amyotrophic lateral sclerosis (ALS) (Jiang et al., 2021; Tetsuka et al., 2013; Yang et al., 2015; Yu et al., 2018) and its ablation in human neuromuscular organoids leads to depletion of astroglia compartment, a possible mechanism leading to subsequent defects in neuromuscular pathology in ALS. Taken together these findings have important implications for our understanding of repair bias around functionally constrained regions to safeguard long term genome integrity during aging and age associated pathology.

overall_design: A genome wide CRISPR screening was performed to identify genes/regulatory regions critical for SASP.

first: Alexander

last: Meissner


title: Detecting chromatin accessibility changes that are dependent on ATF4 under mitochondrial stress

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

summary: ATF4 is a stress-responsive gene which is critical for cell survival under stress conditions. ATF4 expression is upregulated under mitochondrial stress and the expression of a few chromatin remodelling genes are regulated by ATF4. ATAC-seq was performed on differentiated neurons after shATF4 knock-down under normal and mitochondrial stress conditions.

overall_design:
To investigate chromatin accessibility changes after shAtf4 knock-down globally, ATAC-seq was performed on cortical neurons under normal and mitochondrial stress conditions.
Lentiviral shRNA was used in the study to knockdown Opa1 and/or Atf4.
Target loci that show chromatin accessibility changes were generated using MACS2 comparing shAtf4 to shControl in normal or shOpa1 conditions.

first: Maria

last: Bilen

first: Ruth

last: Slack


title: ZNF512B protects critical regulatory regions to safeguard long term genomic integrity. [RNA-Seq]

overall_design: siRNA mediated depletion of ZNF512B in human primary lung fibroblast to identifay underlying gene regulatory circuit.


title: ZNF512B protects critical regulatory regions to safeguard long term genomic integrity. [CUT&RUN]

overall_design: To identifay genomic binding loci CUT&RUN assay was performed for ZNF512B, CHD4, MTA2, RBBP4 and GATAD2A


title: Mechanisms of MCM2-7 loading and initial DNA melting at near base-pair resolution [Mcm4-Flag ChIP-Exo]

summary: The loading and activation of the replicative helicase MCM2-7 are key events during the G1-S phase transition. In budding yeast, the origin recognition complex (ORC) binds to the conserved DNA elements A and B1 of the autonomously replicating sequence (ARS). This is followed by the consecutive loading of two MCM2-7 hetero-hexamers into a MCM2-7 double-hexamer (DH). In S-phase the MCM2-7 DH is activated, resulting in two Cdc45-MCM-GINS (CMG) helicases that bidirectionally unwind DNA ahead of the replication fork. Here, we show that MCM2-7 helicase loading across the B1 element displaces ORC from origins. This allows ORC binding and helicase loading at lower affinity binding sites and origins throughout the genome. Furthermore, we mapped the sites of initial DNA unwinding genome-wide and show that these sites appear near the N-terminal domains of the MCM2-7 double-hexamer in proximity of the B1 element. Finally, employing a chemical-biology approach, we establish that during helicase activation the Mcm2/5 interface acts as the DNA exit gate for single-stranded-DNA extrusion. Our work identifies that helicase loading follows a distributive mechanism, allowing for equal MCM2-7 loading across the genome and surprisingly finds that DNA unwinding initiates from the helicase N-terminal interface in proximity to the ARS B1 element.

overall_design: ChIP-Exo 5.0 analysis of the MCM2-7 replicative helicase in G1 vs. 30min release (Mcm2/5 gate mutant)

first: L

middle: M

last: Reuter

first: Sanjay

middle: P

last: Khadayate

first: Christian

last: Speck


title: Mapping of genomic R-loops in the mouse liver

city: Szeged

first: Lajos

last: Mates

address: Temesvari krt. 62.

department: Institute of Genetics

country: Hungary

institute: Biological Research Centre

summary: This study profiles RNA:DNA hybrid formation in the mouse liver.

overall_design: DRIP-seq (R-loop mapping) was performed on mouse liver and liver derived cells.

first: Andrea

last: Nagy

first: Erik

last: Czipa

first: Bálint

last: Vásárhelyi


title: Mechanisms of MCM2-7 loading and initial DNA melting at near base-pair resolution [ssDNA PIP-Seq]

overall_design: permanganate ChIP-seq of Mcm4-Flag tagged cells arrested in in G1 and released into S-phase


title: Pharmacological Destabilization of ZEB2 Attenuates Atherosclerosis via Restoration of Lipid Catabolism

status: Public on Jun 21 2026

city: Shijiazhuang

first: Lingdan

last: Zhao

address: No. 361 Zhongshan East Road, Chang'an District

department: Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education

country: China

institute: Hebei Medical University

summary:
The pathogenesis of atherosclerosis involves phenotypic reprogramming of vascular smooth muscle cells (VSMCs) coupled with profound lipid metabolic dysfunction; however, the critical transcriptional regulators governing this process remain incompletely understood.
Here, we identify zinc finger E-box binding homeobox 2 (ZEB2) as a central regulator linking VSMC phenotypic switching to lipid dysregulation in atherosclerosis. Single-cell transcriptomic trajectory analyses revealed progressive induction of ZEB2 during the transition of contractile VSMCs toward foam-like states, a finding validated in both murine and human atherosclerotic plaques. Genetic and pharmacological inhibition of ZEB2 markedly reduced lipid accumulation in VSMCs and attenuated atherosclerotic lesion burden while improving plaque composition in vivo. Next, we found ZEB2 suppressed fatty acid oxidation programs by transcriptionally repressing melanocortin 2 receptor (Mc2r), thereby limiting Mc2r–cAMP signaling and downstream lipid catabolic gene expression. We further developed TB15, a novel small molecule that selectively destabilizes ZEB2 protein by promoting deacetylation-dependent ubiquitination and proteasomal degradation without affecting ZEB2 transcription. To enable precision therapy, an RGD-functionalized mesoporous polydopamine nanoparticle delivery system was engineered to target phenotypically transformed VSMCs within atherosclerotic plaques, achieving superior therapeutic efficacy with minimal systemic toxicity. Notably, machine learning–based drug response modeling (BFReg-NN) predicted optimal anti-atherosclerotic efficacy when TB15 was combined with fluvastatin or pitavastatin, nominating a rational combination strategy. Together, this work defines the ZEB2-Mc2r axis in atherosclerosis, presents a first_x001E_in_x001E_class ZEB2 degrader, and demonstrates a targeted nanotherapeutic approach with strong translational potential for precision treatment of atherosclerotic disease.

overall_design:
VSMCs were treated with cholesterol (30 μg/ml) for 24 h
VSMCs were treated with H2O for 24 h


title: Mutant p53 binds RNA to drive mitochondrial dysfunction

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: Tumor suppressor protein 53 (p53) is a transcription factor that is deregulated in 50% of cancers. Often termed the guardian of the genome, p53 is responsible for maintenance of genomic stability, cell cycle arrest, DNA repair, senescence, and apoptosis. In cancer cells, deregulation of p53 often occurs through mutations in the DNA binding domain which lead to a loss of the transcriptional activity. While 100’s of somatic mutations in the DNA binding domain are known, a small number of mutants are enriched in cancer, suggesting a gain-of-function role. Here we deploy an intein-based approach to localize µMap photoproximity labeling to p53 to define novel interactions contributing to the loss and gain of function roles of 5 separate hotspot mutants. These data revealed that G245S and R273H binds to RNA through its C-terminal domain. We show through CLIP experiments that mutant p53 has an RNA binding motif that conserved across mutants and is enriched in 3’UTRs, promoting ribosomal localization and labeling of proteins at the mitochondrial surface. We further demonstrate that the RNA binding ability of mutant p53 promotes altered miRNA processing and mitochondrial dysfunction providing mechanistic rationale for historically reported but poorly understood phenotypes.

overall_design: miRNA-seq of HEK cells transiently expressing wild-type or mutant p53, collected in biological triplicates. Untranfected HEK cells served as the control.

first: Alice

last: Long

first: Cameron

middle: J

last: Douglas

first: Dalila

last: Gallegos

first: James

last: Burke

first: David

last: MacMillan

first: Ezgi

last: Hacisuleyman

first: Ciaran

last: Seath


title: High-throughput transcriptome sequencing of DNAJC2-knockdown clear cell renal cell carcinoma cells（shDNAJC2 vs shCtrl）

city: Hangzhou

first: Yunkai

last: Yang

address: Zhejiang provincial people’s hospital

institute: Zhejiang provincial people’s hospital

summary: This project was designed to characterize transcriptomic changes caused by DNAJC2 knockdown in clear cell renal cell carcinoma (ccRCC) cells using high-throughput RNA sequencing. Cells transduced with control shRNA and cells with DNAJC2 knockdown were subjected to next-generation transcriptome sequencing to identify differentially expressed genes and pathways regulated by DNAJC2. This dataset was used to investigate the role of DNAJC2 in ccRCC cell metabolism and ferroptosis-related regulation

overall_design: Stable DNAJC2-knockdown clear cell renal cell carcinoma (ccRCC) cell line (shDNAJC2) and negative control cell line (shCtrl) were constructed via lentiviral shRNA transduction, and knockdown efficiency was validated at mRNA and protein levels. Total RNA was extracted from three biological replicates of each group for library construction and paired-end high-throughput RNA sequencing on Illumina platform. After raw read quality control and genome mapping, gene expression quantification and differential expression analysis between shDNAJC2 and shCtrl groups were conducted. Functional enrichment analyses including GO, KEGG and GSEA were performed on differentially expressed genes to explore transcriptional alterations induced by DNAJC2 silencing, so as to reveal the regulatory role of DNAJC2 in ccRCC cell metabolism and ferroptosis.


title: Malignant epithelial states drive immune dysfunction in ampulla of Vater carcinoma

city: Ulsan Metropolitan City

first: Hyoung-oh

last: Jeong

address: 50, UNIST-gil, Eonyang-eup , Ulju-gun

country: South Korea

institute: Ulsan National Institute of Science and Technology

summary: Background Ampulla of Vater (AoV) carcinoma is a rare malignancy arising at the junction of intestinal and pancreatobiliary epithelium. Its heterogeneous clinical behavior and histological diversity have hindered therapeutic advances, and the cellular basis of this heterogeneity remains unclear. We aimed to construct a single-cell transcriptomic atlas of AoV carcinoma, with a focus on identifying epithelial subtypes and their interactions with the tumor microenvironment (TME). Methods We performed single-cell RNA sequencing on eight primary AoV tumors and four matched normal tissues. Comprehensive clustering and transcriptomic analyses identified cell-type composition, epithelial heterogeneity, and tumor-immune interactions. Findings were validated using deconvolution of bulk RNA-seq data from 62 AoV carcinoma patients. Results Malignant epithelial cells were categorized into four distinct subtypes: Int-Wnt, PB-KRAS, Int-Hypoxia, and Cycling stage. PB-KRAS cells exhibited stem-like transcriptional programs and high genomic instability. Deconvolution analysis of bulk RNA-seq data from the independent AoV cohort revealed that enrichment of the PB-KRAS subtype correlated with tumor recurrence and poor survival. Our immune profiling analysis discovered a significant association between PB-KRAS subtype and GZMK+ CD8+ T cells, which are in a pre-dysfunctional state, alongside SPP1⁺ macrophages exhibiting immunosuppressive traits. Spatial transcriptome data further supports the immunosuppressive natures of TME around PB-KRAS subtype malignant epithelial cells in AoV carcinoma. Conclusions Our study presents a single-cell atlas of AoV carcinoma, highlighting the molecular diversity of malignant epithelium and its association with the immune microenvironment. The PB-KRAS subtype emerges as a stem-like, immunosuppressive tumor state associated with poor prognosis, providing insights for future therapeutic targeting.

overall_design: Transcriptomic profiling of ampulla of Vater (AoV) carcinoma consisting of droplet-based single-cell RNA-seq on primary tumor samples from eight independent patients to investigate intratumor heterogeneity, combined with bulk RNA-seq on an independent validation cohort of 62 AoV carcinoma patients to evaluate the clinical relevance and prognostic utility of identified malignant cell states.


title: Two translocation mechanisms drive neural stem cell dissemination into the human fetal cortex

city: Paris

first: Clarisse

last: Brunet

address: 12 Rue Lhomond

institute: Institut Curie

summary: The strong size increase of the human neocortex is supported by a neural stem cell population, the basal radial glial (bRG) cells. Using live imaging of human fetal tissue and cortical organoids, we identify two translocation mechanisms for bRG cell colonization of the human neocortex. On top of an actomyosin-dependent movement called mitotic somal translocation (MST), we identify a microtubule dependent motion occurring during interphase, that we call interphasic somal translocation (IST). We show that IST is driven by the dynein motor and its activator LIS1, that are recruited to the nuclear envelope by the LINC complex, while MST is controlled by the mitotic cell rounding pathway. 85% of bRG cell translocation is due to IST, for a total movement of 0,67 mm per month of gestation. Our work identifies how bRG cells colonize the human fetal cortex and further shows that IST and MST also occur in bRG-related glioblastoma cells.

overall_design: bulkRNAseq of glioblastoma cell lines obtained from patients to identify transcriptomic similiarities between human radial glia cells (RGCs), neural stem cells of the developing human brain, and glioblastoma-derived cell lines.

first: Ryszard

last: Wimmer

last: Brunet Avalos

first: Alexandre

last: Baffet


title: Multi-omics Analysis of Immune Cells Induced by Artificial Adjuvant Vector Cell (aAVC) Therapy in HPV-Positive Tumor-Bearing Mice

city: Yokohama City

first: Takuya

last: Ishibashi

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

overall_design: Refer to individual Series


title: Multi-omics Analysis of Immune Cells Induced by Artificial Adjuvant Vector Cell (aAVC) Therapy in HPV-Positive Tumor-Bearing Mice [Spatial Transcriptomics]

summary: Immune evasion by tumors highlights the need to activate both CTLs and NK cells against “immune-desert” type of tumor, yet the synergistic potential of dual activation in immune-desert tumors remains unclear. Here, we uncover a spatiotemporal synergy between NK cells and CTLs that drives functional antitumor effects in an immune-desert tumor model.  Using a multi-omics imaging approach integrating spatial transcriptomics, scRNA-seq re-clustering, and multicolor flow cytometry, we show that vaccination rapidly reshapes lymphocyte localization and function in the tumor microenvironment (TME). Early activated IRF8+Klrg1+NK cell infiltration establishes a niche that guides subsequent antigen-primed CXCR3+CTL influx, accompanied by dendritic cell activation and inflammatory monocyte recruitment. This coordinated response relies on structural and chemotactic remodeling of the TME, facilitating NK-CTL interactions at the tumor margin. Our findings demonstrate how integrated multi-omics analyses can uncover previously inaccessible interactions and provide a framework for designing next-generation immunotherapies.

overall_design: Mice were inoculated with HPV-E6 and E7 expressing lung cancer (TC-1) cells and treated with cancer vaccine,  artificial Adjuvant Vector Cells (aAVC) on day7. We collected tumor samples on day3 and day7 after aAVC treatment. Then, we performed sc-RNA-seq and spatial transcriptomic analysis. For spatial transcriptomic analyis, Xenium in situ technology platform (10x Genomics) was employed.

first: Hiroshi

last: Nakazato

first: Kanako

last: Shimizu

first: An

last: Sampei

first: Yan

last: Liu

first: Marin

last: Yanagawa

first: Satoru

last: Yamasaki

first: Jun

last: Shinga

first: Shin-ichiro

last: Fujii


title: Single-cell RNA sequencing reveals Lin28b-dependent immune modulation in the PDAC tumor microenvironment

city: Beijing

first: Minghe

last: Fan

state: Beijing

address: 38 Xueyuan Road, Beijing, China

institute: Peking University Health Science Center

summary: Cancer-associated fibroblasts (CAFs) play a crucial role in shaping the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME). This study investigates the impact of an RNA-binding protein Lin28b on the immune landscape of PDAC. Single-cell RNA sequencing (scRNA-seq) was performed on orthotopic pancreatic tumors from wild-type (WT) and fibroblast-specific Lin28b knockout (Fsp-Cre;Lin28bfl/fl) mice. Our analysis revealed that Lin28b expression in CAFs promotes an immunosuppressive TME characterized by reduced immune cell infiltration and dampened type I interferon (IFN) signaling. Conversely, Lin28b deletion in CAFs resulted in increased infiltration of immune cells, particularly CD8+ T cells and enhanced cytotoxic T cell activity. These findings identify Lin28b as a CAF-intrinsic molecular brake on anti-tumor immunity and provide a rationale for targeting the Lin28 to overcome PDAC resistance to immunotherapy.

overall_design: Wild-type C57BL/6J mice and Fsp-Cre;Lin28bfl/fl mice (6–8 weeks, mixed sex) were orthotopically injected with 15376T pancreatic tumor cells (5 × 10^4 cells) into the pancreas. Single-cell suspensions were prepared using collagenase IV/DNase I digestion and processed with the 10x Chromium Single Cell 3′ v3 kit. Libraries were sequenced on Illumina NovaSeq 6000. FASTQ files were aligned to mm10 using Cell Ranger v7.1; counts matrices and cell metadata are provided.


title: RNA immunoprecipitation sequencing identifies RNA targets of Lin28b in PDAC cancer-associated fibroblasts

summary: This study uses RNA immunoprecipitation followed by sequencing (RIP-seq) to identify RNA targets of Lin28b in PDAC cancer-associated fibroblasts (CAFs). CAFs expressing either Flag-wild-type Lin28b (Lin28b-WT) or an RNA-binding deficient mutant (Flag-Lin28b-MU) were subjected to RIP-seq. Our analysis revealed that STING mRNA, a key component of the innate immune cGAS-STING pathway, is a direct target of Lin28b. This interaction leads to decreased STING mRNA stability and reduced STING protein levels, thereby suppressing type I interferon (IFN) production. These findings provide a mechanistic explanation for the immunosuppressive function of Lin28b in the PDAC tumor microenvironment.

overall_design: RIP-seq was performed on mouse pancreatic CAFs (15376CAFs) overexpressing Flag-tagged wild-type Lin28b (Lin28b-WT) or an RNA-binding deficient mutant (Lin28b-MU).  Lin28b-bound RNAs were immunoprecipitated using an anti-Flag antibody.


title: IRE1 activity regulates tumour and microenvironment cell lineage states while stratifying localised and metastatic prostate cancer

city: Oxford

first: Dimitrios

last: Doultsinos

address: Level 6, John Radcliffe Hospital

department: Nuffield Department of Surgical Sciences

institute: University of Oxford

summary: Prostate cancer (PCa) is an androgen receptor (AR) driven, high-incidence disease significantly contributing to cancer mortality. PCa is in need of better risk stratification at diagnosis and treatment outcomes in patients at high risk of metastasis. The unfolded protein response (UPR) is an AR-dependent process. However, the impact of the UPR transducer IRE1 on AR-dependent biology and treatment resistance has not been defined. We use diverse pre-clinical models of stress response to describe IRE1 activity impact on multiple disease stages and demonstrate its involvement with poor prognosis (RB1 loss), and cell lineage determination (club phenotypes). Integrating clinical transcriptomic datasets, we chart IRE1 activity throughout PCa evolution by developing a PCa-specific, IRE1 activity gene set (IRE1_18) reflecting both tumoral and micro-environmental niches. IRE1_18 can determine tumoral identity, inform androgen deprivation treatment suitability, prognosticate localised and metastatic disease independently from AR activity, and guide IRE1 modulation as a novel combination therapeutic.

overall_design: RNAseq profiling of LNCaP cells and their knockout derivatives (ERN1) grown in full media, charcoal stripped media and/or treated with DMSO, ETOH, R1881, Enzalutamide.

first: Ian

last: Mills

first: Ingrid

last: Tomljanovic

first: Eleftherios

last: Pilalis

first: Aristotelis

last: Chatziioannou


title: Nuclear condensates formed by truncated mutant NEK1s impede ribosomal RNA biogenesis and drive motor dysfunction

city: Suzhou

first: Zongbing

last: Hao

address: 199 Ren-ai Road

institute: Soochow University

summary: NIMA-related kinase 1 (NEK1), a serine/threonine kinase, is a risk variant in amyotrophic lateral sclerosis (ALS). While the full-length NEK1 protein is involved in various cellular processes, such as DNA damage response and microtubule stability, the pathological role of truncated mutant NEK1s in ALS remains elusive. Here, we demonstrated that three truncated forms of NEK1 derived from ALS-related NEK1 nonsense mutations translocated from cytoplasm to the nucleus, exhibited obvious enrichment in the nucleoli, and formed liquid-like nucleoplasmic foci, which are prone to undergo liquid-liquid phase separation in cells and in vitro. Mechanistically, the truncated NEK1s interacted with numerous nucleolar proteins, thereby impairing ribosomal RNA biogenesis and translation. Transgenic flies expressing truncated mutant NEK1s displayed motor dysfunction and reduced survival length. These findings offer new insight in which truncated mutant NEK1s cause cell toxicity via interfering with the phase behavior of nucleolar protein FBL and provide a gain-of-function mechanism in ALS pathogenesis involving NEK1.

overall_design: RNA-seq profiling of 293T cells overexpressing GFP and GFP-812 plasmids, respectively.

first: Yixin

last: Wang

first: Wen

last: Hu

first: Rui

last: Huang

first: Fanmin

last: Wu

first: Haopeng

last: Su

first: Jianye

last: Zang

first: Xiaolei

first: Yanli

first: Haigang

last: Ren

first: Jian

last: Li

first: Min

last: Zhang

first: Yong

first: Guanghui


title: Multi-omics uncovers the immune landscape and molecular signatures associated with antibody-dependent cellular cytotoxicity in SARS-CoV-2 clearance

city: Taipei City

first: Wye-Lup

last: Kong

address: 28, Lane 70, Academia Road Section 2, Nangang District

department: Biodiversity Research Center

country: Taiwan

institute: Academia Sinica

summary: The immune responses to SARS-CoV-2 infection, especially neutralizing antibody generation, have been extensively studied. Beyond direct neutralization, antibodies can eliminate infected cells through engagement with natural killer (NK) cells. However, the molecular and cellular mechanisms by which NK cells collaborate with infection-induced antibodies in vivo during SARS-CoV-2 clearance remain elusive. Here, we analyzed a cohort of patients recovered from the initial SARS-CoV-2 infection to dissect the relationship between viral clearance and antibody-dependent cellular cytotoxicity (ADCC). We found that patients' plasma ADCC capacity was associated with a slower rate of viral clearance and the blood T follicular helper (Tfh) cluster. To elucidate the action of ADCC-inducing antibodies in SARS-CoV-2 infection, we isolated a monoclonal antibody (mAb) with strong ADCC activity. This ADCC-inducing mAb elicited a transcriptional program linked to viral RNA transcription and protein glycosylation. Furthermore, spatial transcriptomics analysis revealed enriched expression of several NK marker genes in discrete spots within the lungs of SARS-CoV-2-infected mice treated with the ADCC-inducing antibody. Consistently, human peripheral blood NK cells ligated with the ADCC-inducing antibody displayed evolutionarily conserved NK cell clusters, similar to those elicited in mice. Together, our study elucidates the temporally coherent action of specific NK cell subsets and ADCC-inducing antibodies in controlling SARS-CoV-2 infection.

overall_design: To elucidate the protective mechanism of strong ADCC-inducing antibody against SARS-CoV-2 infection, we employed transcriptome analysis on K18-hACE2 transgenic mice with 5SB12 mAb pre-treatment and SARS-CoV-2 virus challenge. The experiments were done in 4 different treatment groups in two separate batches for biological replicates, totaling 8 samples. The treatment groups are control (-/-), pre-treated with antibody (+/-), infected with SARS-CoV-2 virus (-/+), and SARS-CoV-2 infected while pre-treated with mAb (+/+). After four days post-infection, lung tissues were harvested and sectioned for 10x Genomics Visium spatial transcriptomics sequencing.

first: Wei-Nan

last: Chen

first: Yu-Chi

last: Chou

first: Jia-Tsrong

last: Jan

first: Deepa

last: Sridharan

first: Mei-Yeh

last: Lu

first: Kuo-I

last: Lin


title: Spatial transcriptomic analysis of head and neck squamous cell carcinoma reveals novel regulators of hybrid epithelial-to-mesenchymal transition

city: St. Louis

first: Sidharth

last: Puram

state: Missouri

address: 4515 McKinley Ave

department: Otolaryngology

institute: Washington University in St. Louis

summary: Head and neck squamous cell carcinoma (HNSCC) is characterized by a high degree of intra- and inter-tumoral heterogeneity. Here we use spatial transcriptomics (ST) to profile both HPV-positive and HPV-negative HNSCC, uncovering distinct patterns of spatial organization of malignant cells and the surrounding tumor microenvironment across groups of tumors. First, we find that HPV-positive HNSCC is characterized by high cellular density in all cellular compartments with distinct expression of hypoxia, senescence, and cell cycle-associated genes in the malignant compartment. In HPV-negative HNSCC, we find two distinct spatial patterns of a partial epithelial-to-mesenchymal transition (p-EMT) program. One pattern is spatially associated with fibroblasts, characterized by p-EMT at the leading edge of tumor nests (“p-EMT edge”), and mediated by TGFB-signaling. The other pattern features high p-EMT expression in the core of tumor nests (“p-EMT core”). In p-EMT core tumors, we observe high co-localization of p-EMT cells with an inflammatory response program including neutrophils and macrophages, as well as differential expression of distinct ligands, including OSM. In vitro experiments demonstrate that OSM can induce the p-EMT state in multiple HNSCC models. Together these findings suggest that multiple p-EMT phenotypes exist across HPV-unrelated HNSCC and are mediated by distinct cell-to-cell signaling mechanisms, highlighting potential novel therapeutic vulnerabilities.

overall_design: To identify effects of tumor microenvironment ligands that stimulate the hybrid epithelial-to-mesenchymal transition in head and neck squamous carcinoma  (HNSCC), we performed RNA-seq on JHU006 and 93VU147T cells treated with vehicle, TGFB, oncostatin M (OSM), SPP1, and IL-1B.

first: Dor

last: Simkin

first: Thomas

last: Barrett

first: Michael

last: Moore

first: Alissa

last: Greenwald

last: Mints

first: Ryan

middle: S

last: Jackson

first: Patrik

last: Pipkorn

first: Jason

middle: T

last: Rich

first: Paul

middle: A

last: Zolkind

first: Richard

last: Harbison

first: Randall

last: Paniello

first: Jose

last: Zevallos

first: Anuraag

last: parikh

first: Douglas

last: Adkins

first: Wade

middle: L

last: Thorstad

first: Rebecca

last: Chernock

first: Itay

last: Tirosh

middle: V


title: A theoretical and experimental framework enables low-coverage sequencing for accurate quantification of genome-wide cytosine modification levels

city: Philadelphia

first: Rahul

middle: M.

last: Kohli

state: Pennsylvania

address: 3610 Hamilton Walk, 502B Johnson Pavilion

department: Department of Medicine

institute: University of Pennsylvania

type: Methylation profiling by high throughput sequencing

summary: 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) regulate gene expression and exhibit dynamic levels during development and disease. While high-depth, base-resolution studies offer the most detailed view of epigenetic landscapes, many open questions are answered by surveying changes in 5mC/5hmC levels across larger cohorts. Nonetheless, current global quantification methods, including mass spectrometry, are typically limited in accessibility, accuracy, or throughput. Here, to evaluate the viability of low-coverage sequencing as an alternative, we first computationally downsampled deeply sequenced data to resolve the three-way relationship between sequencing coverage, modification levels, and measurement error. This relationship allowed us to develop a facile online tool for error calculation and to define experimental targets: <0.24% genome coverage can quantify 5mC and low-abundance 5hmC with minimal and predictable errors (<5%). Importantly, in direct comparisons, low-depth sequencing (Sparse-Seq) demonstrated high accuracy and less variability than mass spectrometry, while distinctively preserving genomic context. Applied serially to developing mouse brains, Sparse-Seq revealed an earlier emergence of 5hmCpG compared to 5mCpH and uncovered previously overlooked, genomic feature-specific epigenetic changes. This work establishes a rigorous foundation for employing Sparse-Seq as a highly accessible approach for 5mC/5hmC quantification, enabling economical first-pass analysis of epigenetic landscapes suited for large cohort studies and new hypothesis generation.

overall_design: To demonstrate the utility of Sparse-Seq, we mapped the levels of 5mC and 5hmC within murine brain cortex at various different developmental stages using Sparse BS/bACE-Seq. We analyzed a total of 48 samples: 24 samples underwent BS-Seq (which measured 5mC and 5hmC as C) and 24 samples underwent bACE-Seq (which measures only 5hmC as C). These samples were collected at 8 developmental timeponts: Embryonic Day 16 (D16), Embryonic Day 18 (D18), Postnatal Day 0 (P0), Week 2 (W2), Week 4 (W4), Week 6 (W6), Week 8 (W8), and Week 10 (W10). Each timepoint was represented by three biological replicates.

first: Christian

middle: E

last: Loo

first: Johanna

last: Fowler

first: Heqiao

last: Zhu

first: Christopher

last: Krapp

first: Ruiyao

first: Marisa

last: Bartolomei

first: Wanding

last: Zhou


title: Mechanism of Nootkatone in U251

first: Qian

last: Wang

state: Zhejiang

address: 2318 Yuhangtang Road

department: School of pharmacy

institute: Hangzhou Normal University

summary: Nootkatone can induce the changes of gene expression in U251 cells

overall_design: The cells were treated with 200μ nootkatone in the experimental group and compared with the control group.


title: Glutamate Ionotropic Kainate Receptors as Therapeutic Targets in Enzalutamide-Resistant and Neuroendocrine Prostate Cancer

status: Public on Jun 20 2026

city: Sacramento

first: Huan

last: Qu

address: 4645 2nd Ave, Research III Bldg

institute: University of California-Davis

summary: Treatment-induced neuroendocrine prostate cancer (t-NEPC) is the major form of re-sistance to androgen receptor signaling inhibitors (ARSI) in advanced prostate cancer, characterized by extremely pronounced invasiveness and lineage plasticity. Through in-depth analysis of clinical cohorts, we found that glutamate ionotropic receptor kainate (GRIK) family members, specifically GRIK2 and GRIK5, are highly expressed in neural lineage plastic prostate cancer cells, NEPC patient derived xenografts, and NEPC patient samples. Their expression positively correlates with neuroendocrine markers and inversely correlates with androgen receptor (AR) activity. Additionally, functional analyses indicated that AR has a direct transcriptional inhibitory effect on GRIK2 and GRIK5, and the absence of AR signaling leads to the upregulation of GRIK2 and GRIK5. Further RNA sequence analysis exhibited that GRIK5 silencing repro-grams the cellular transcriptome, resulting in significant downregulation of AR sig-naling and fatty acid metabolism, while simultaneously activating immune and in-flammatory responses in enzalutamide resistant prostate cancer cells. In both cell line and NEPC organoid models, loss of GRIK5 impairs proliferation and clonogenic for-mation. Notably, GRIK5 also contributes to enzalutamide resistance. Pharmacological evaluation revealed that Pan-GRIK antagonists exhibit anti-tumor activity, although the required relatively high concentrations suggest that more potent therapeutic strategies should be developed. Collectively, this study established GRIK family mem-bers play critical roles in enzalutamide resistance and NEPC progression, highlighting GRIK signaling as a potential therapeutic target for overcoming lineage plasticity in prostate cancer.

overall_design: RNA-seq was performed to profile the transcriptomic changes following GRIK5 knockdown in C4-2B MDVR prostate cancer cells. Samples included cells transfected with control siRNA (siRNA-NC), siGRIK5#1, or siGRIK5#2.

first: Pengfei

last: Xu

first: Joy

last: Yang

first: Fan

last: Wei

first: Leyi

first: Chengfei

last: Liu


title: The T-cell niche tunes immune function through modulation of the cytoskeleton and TCR-antigen forces

city: Atlanta

first: Rachel

last: Fitzgerald

state: GA

address: 1515 Dickey Drive

department: Chemistry

institute: Emory University

summary: Obesity has become a major public health crisis given its rampant growth and association with an increased risk for cancer. Cancer patients who present with obesity tend to have increased tumor burden and decreased T-cell function, yet it remains unclear how obesity compromises T-cell mediated immunity. To address this, we modeled the adipose niche using the secretome of cultured adipocytes and assessed the impact of these factors on T-cell function. We found that these secretomes altered antigen-specific T-cell receptor triggering and activation. RNA-sequencing analysis identified changes in cytoskeletal regulation and actin polymerization in T-cells exposed to the adipocyte secretome. Molecular force measurements were consistent and showed that T-cells exposed to the adipocyte niche display dampened force transmission to the TCR-antigen complex. Conversely, exposure to the control stromal cell secretome lead to enhanced TCR forces. These results were then validated in diet-induced obese mice and human donor T-cells. Importantly, secretome-mediated TCR force modulation mirrored the changes in T-cell functional responses in human T-cells using the FDA-approved immunotherapy, blinatumomab. Thus, the adipocyte niche contributes to T-cell dysfunction through cytoskeletal modulation and reduces TCR triggering by dampening TCR forces consistent with the mechanosensor model of T-cell activation.

overall_design: RNA-seq profiling of isolated RNA from polyclonal CD3+ T cells isolated from C57BL/6 mice after incubation in adipocyte conditioned media, stromal conditioned media or unconditioned media (RPMI) for 4 hours. Differential gene expression analysis of the adipocyte and stromal conditoned media versus unconditioned media was performed to identify transcriptional responses to conditioned media incubation.

first: Maya

last: Jaffe

first: Karmella

last: Haynes

first: Anna

last: Kellner

first: Khalid

last: Salaita


title: Drug repurposing via ultra-high throughput 3D spheroids screening in rare cancer treatment

first: Bing

last: Yao

address: 615 Michael St. Rm 323

department: Human Genetics

summary: Rare cancers comprise over 200 distinct types accounting for 20–25% of U.S. cancer diagnoses yet receive limited therapeutic investment due to small patient populations and resource constraints. Drug repurposing offers a viable strategy, and large-animal models such as minipigs provide physiologically realistic platforms for preclinical evaluation. However, scalable systems for systematically screening large drug libraries in rare cancer models remain unavailable. We developed an integrated pipeline combining a minipig spinal cord glioma (SCG) model with miniaturized ultra-high-throughput screening (uHTS). Primary SCG cells were cultured in 3D platforms for rapid screening of bioactive compounds. Lead candidates underwent validation through 3D spheroid assays, in vivo xenografting, RNA sequencing, immunohistochemistry, and histological analysis. Human SCG tissue samples and population-level datasets assessed translational relevance. uHTS screening identified Clofoctol as a lead compound with potent glioma growth inhibition in both primary SCG cells and xenograft models. Mechanistic studies revealed pleiotrophin (PTN) as a key target, with confirmatory expression patterns in human SCG samples, establishing translational validity. Integration of large-animal cancer models with drug-repurposing pipelines and uHTS platforms is feasible and effective for rare cancer drug discovery. This approach successfully identified Clofoctol, an FDA-approved compound with therapeutic potential for spinal cord gliomas and establishes a scalable model applicable to other orphan cancers.

overall_design: RNA-sequencing All RNA sequencing was performed on the Illumina NextSeq platform by Admera Health (South Plainfield, NJ, USA). Raw data were then transferred to Emory's Department of Human Genetics for further analysis using previously described methods. Briefly, RNA-sequencing data from the minipig SCG were analyzed by aligning reads to a control minipig spinal cord tissue library and, to identify subtype similarities, to a previously sequenced human glioma library. RNA-sequencing data from the Clofoctol-treated xenograft tumor were analyzed by aligning high treatment condition, low treatment condition, and known GBM library reads to the sequencing results of the control xenograft tumor. Alignment of the reads was completed using TopHat 2.1.0. Aligned reads were sorted with Samtools[34], and differential gene expression (DE) analysis was performed using Cuffdiff 2.2.1, with significant DE genes defined by FDR <0.05. Gene Ontology (GO) analysis was conducted via PANTHER[36], and terms were clustered using simplifyEnrichment v3.16. Gene-gene interactions were assessed with STRING and visualized in Cytoscape 3.9.1.

first: Marybeth

last: Yonk

first: Hannah

last: Nuszen

first: Muhibullah

last: Tora

first: Yuhong

last: Du

first: Megan

last: Lim

first: Thais

last: Federci

first: Kimberly

last: Hoang

first: Stewart

last: Neill

first: Yilin

first: Yangping

last: Li

first: Nicholas

last: Boulis

first: Daniel

last: Brat

first: Kecheng

last: Lei


title: CDK7 inhibition suppresses Hippo-YAP signaling to reverse CDK4/6 inhibitor resistance in hormone receptor-positive breast cancer [ChIP-seq]

city: Taipei

first: Yi-Ru

last: Tseng

address: No. 201, Sec. 2, Sh ipai Rd.

institute: Taipei Veterans General Hospita

summary: Hormone receptor-positive (HR+) breast cancer is the most prevalent breast cancer subtype, and cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) are the mainstay of treatment for metastatic disease. Amplification or overexpression of CDK6 is an established driver of CDK4/6i resistance, for which no targeted strategy exists. Through a kinase-inhibitor screen for compounds that suppress CDK6, we identified PIK-75 as an agent that downregulates CDK6 and reverses CDK4/6i resistance in HR+ breast cancer. We found that PIK-75 acts as an inhibitor of CDK7, abolishing phosphorylation of serine 5 on the RNA polymerase II (Pol II) carboxy-terminal domain. The structurally distinct CDK7 inhibitor THZ1 and shRNA-mediated CDK7 depletion both phenocopied the suppression of yes-associated protein (YAP) and CDK6, establishing the effect as CDK7-dependent. Chromatin immunoprecipitation demonstrated that CDK7 inhibition reduced Pol II-serine 5 occupancy at the YAP1 promoter, downregulating YAP1 transcription and YAP-TEAD output. Genome-wide, PIK-75 induced promoter-proximal Pol II pausing that was more pronounced at oncogenic-pathway genes, and transcriptomic and proteomic profiling confirmed a bona fide CDK7-inhibition signature, accompanied by widespread intron retention, rather than a phosphoinositide 3-kinase-dominated response. In CDK6-overexpressing xenografts, PIK-75 combined with abemaciclib reversed resistance and suppressed YAP and CDK6 in vivo. These findings define a transcriptional axis linking CDK7 and Pol II-serine 5 phosphorylation to Hippo-YAP signaling and CDK6, and establish CDK7 inhibition as a rational strategy for CDK4/6i-resistant HR+ breast cancer, supporting evaluation of clinical-stage CDK7 inhibitors in combination with continued CDK4/6 inhibition.

overall_design: ChIP-seq of PolII or CTD-Ser5 in MCF-7 and T-47D cells with PIK75 for 2 h or 24 h

first: Chung-Jen

last: Yu

first: Chih-Yi

last: Lin

first: Yong-Ji

last: Zhuang

first: Chun-Yu

last: Liu

first: Yi-Fang

last: Tsai

first: Chi-Cheng

last: Huang

first: Ling-Ming

first: Ta-Chung

last: Chao

first: Jiun-I

last: Lai


title: CDK7 inhibition suppresses Hippo-YAP signaling to reverse CDK4/6 inhibitor resistance in hormone receptor-positive breast cancer

overall_design:
RNA-seq profiling was performed in (1) T-47D cells with CDK7 knockdown (shCDK7-1 or shCDK7-2) and pLKO controls, (2) CDK6-overexpressing T-47D and MCF-7 cells treated with PIK75, and (3) T-47D cells treated with PIK75 or THZ1.
*** RAW data not provided for GSM9814875-GSM9814882***


title: Human-specific paralogs of SRGAP2 induce neotenic features of microglia maturation and impact synaptic development

city: New Yiork

first: Carlos

last: Diaz-Salazar

state: NY

address: Jerome L Greene Science Center, 3227 Broadway, L8 Quad A

department: Zuckerman Institute

institute: Columbia University

summary: One of the most salient features of human brain development is the considerably prolonged, neotenic, timing of synaptic development compared to other mammals including non-human primates. Microglia play key roles in shaping synaptic connectivity during neural circuits development. However, the structural and functional features of human microglia maturation remain poorly studied. Here, we first demonstrate that human and mouse cortical microglia follow similar developmental trajectories, albeit at strikingly different timescales in vivo. The ancestral gene SRGAP2A and its human-specific paralogs SRGAP2B/C are not only expressed in cortical neurons where they control the timing of synaptic maturation but also that SRGAP2B/C are the only human-specific gene duplications (HSGDs) expressed in human microglia. Using combinations of xenotransplantation of human induced pluripotent stem cell (hiPSC)-derived microglia and mouse genetic models, we demonstrate that (1) HS SRGAP2B/C, by inhibiting SRGAP2A, are necessary and sufficient to induce neotenic features of microglia structural maturation through microglia-specific manipulations, and (2) that induction of SRGAP2-dependent neotenic features of microglia maturation impacts the timing of synaptic development in a non-cell autonomous manner. Taken together with previous studies, our results reveal that, during human brain evolution, the human-specific genes SRGAP2B/C coordinated the emergence of neotenic features of synaptic development by acting as genetic modifiers in both neurons and microglia.

overall_design: The objective of this experiment was to compare the differential gene expression of mouse srgap2-deficient microglia compared to wildtype (WT) littermate controls at steady state in P30 juvenile mice.


title: Differentially expressed genes (DEGs) in HEK-293T cells treated with the culture supernatant of yeast-form Candida albicans

city: Bengbu

first: Jing

last: Wu

address: Donghai road 2600

institute: Bengbu Medical University

summary: The yeast-form of Candida albicansis known to secrete bioactive metabolites that modulate host cellular responses. In this study, we investigated the transcriptional impact of yeast-form C. albicansculture supernatant on human embryonic kidney (HEK)-293T cells. HEK-293T cells were treated with the supernatant, followed by RNA sequencing (RNA-seq) to identify differentially expressed genes (DEGs). Transcriptomic profiling revealed a distinct gene expression signature in treated cells compared to controls. Functional enrichment analysis of these DEGs highlighted significant modulation of pathways associated with cellular stress responses and signal transduction. These findings provide a comprehensive genomic landscape of the host cell response to soluble factors derived from the yeast-form C. albicans, offering insights into the molecular mechanisms underlying fungus-host cell interactions at the transcriptional level.

overall_design: To elucidate the transcriptional impact of soluble factors derived from the yeast-form Candida albicanson host cells, an in vitroexperimental workflow was established. HEK-293T cells were cultured under standard conditions and treated with the supernatant harvested from yeast-form C. albicans(SC5314) cultures grown in YPD medium at 30 °C for 24 hours. As a negative control, HEK-293T cells were treated with cell-free, uninoculated YPD medium processed identically to the experimental condition.

first: Deyan

last: Chen

first: Enhui

last: Yang

first: Yajie

last: Qian

first: Xiancheng

first: Qin

last: Qin


title: Regulation of the transcriptome, miRNAs and alternative splicing in a FSGS zebrafish injury model

city: Hamburg

first: Olga

last: Tsoy

state: Hamburg

address: Alber-Einstein Ring 8-10

institute: Universität Hamburg

summary: Focal Segmental Glomerulosclerosis (FSGS) is a severe kidney disorder with complex and not yet fully understood pathogenesis. To investigate the role of AS in FSGS, we used a well-established zebrafish model, which mimics key human FSGS features, including foot process effacement, matrix accumulation, podocyte detachment and parietal epithelial cell activation. We performed RNA sequencing of isolated glomeruli and whole larvae, followed by integrative bioinformatic analysis to identify AS events and regulatory miRNAs.

overall_design:
NFP-treated and untreated larvae at 5 and 6 dpf (days post fertilization) were dissolved in 1 ml Tri-Reagent (Sigma-Aldrich) according to manufacturer’s instructions and homogenized with ceramic beads (Carl Roth, Karlsruhe, Germany) at 5 m/s for 20 s.
Glomeruli of NFP-treated and untreated larvae were isolated manually at 5 and 6 dpf using two extra-fine precision tweezers (DUMONT, Switzerland) and a fluorescence stereomicroscope (SMZ 18 Nikon, Tokio, Japan). Pools of 10 glomeruli were collected and centrifuged at 1000 x g for 5 minutes at 4°C. Subsequently, the supernatant was discarded and 50 µl of Tri-Reagent (Sigma-Aldrich) were added.
Whole larvae and isolated glomeruli were used for the RNA-sequencing and alternative splicing analysis

first: Francescapaola

last: Mattias

first: Anna

last: Iervolino

first: Stefan

last: Simm

first: Elke

last: Hammer

first: Alexander

last: Gress

first: Tim

last: Lange

first: Florian

last: Siegerist

first: Sabine

last: Ameling

last: Kacprowski

first: Markus

last: List

last: Kalinina

first: Giovambattista

last: Capasso

first: Karlhans

last: Endlich

first: Jan

last: Baumbach

first: Uwe

last: Völker

first: Nicole

first: Felix

last: Kliewe


title: H4R3me2a ChIP-seq in HCT116 cells

city: Nanjing

first: Mu

last: Xu

address: No.32, Gongqingtuan Road,

department: Nanjing First Hospital

institute: Nanjing Medical University

summary: ChIP-seq was performed to profile H4R3me2a occupancy in HCT116 colorectal cancer cells with matched input DNA control. Libraries were sequenced as paired-end 150 bp reads on an Illumina NovaSeq 6000. Reads were aligned to GRCh38 with Bowtie2, peaks were called with MACS2 (q < 0.05), and metagene profiles were generated with deepTools.

overall_design: Two paired-end ChIP-seq libraries were prepared from HCT116 cells: one H4R3me2a immunoprecipitated chromatin sample and one matched input DNA control.


title: Differentially expressed genes (DEGs) in the corneas of Muc13 KO mice versus wild-type controls

first: Jing

last: Wu

summary: The mucosal barrier protein MUC13 plays a critical role in maintaining epithelial homeostasis, yet its function remains poorly defined. In this study, we utilized a combination of genetic knockout models and transcriptomic profiling to elucidate the impact of MUC13 deficiency on tissue responses. Comparative analysis of corneal tissues from 6-week-old male Muc13-knockout (C57BL/6 background) and wild-type (WT) male mice revealed profound transcriptional perturbations in Muc13-/- mouse cornea. RNA sequencing identified a distinct repertoire of differentially expressed genes (DEGs) associated with the loss of MUC13. These findings demonstrate that MUC13 is a pivotal modulator of the epithelial barrier.

overall_design: RNA‑seq–based transcriptomic profiling was performed on corneal tissues collected from 6‑week‑old male C57BL/6 Muc13-knockout (Muc13-/-) mice and age‑/sex‑matched wild‑type (WT) controls.

first: Deyan

last: Chen

first: Enhui

last: Yang

first: Yajie

last: Qian

first: Xiancheng

first: Qin

last: Qin


title: Molecular Basis of Hcp-Dependent Toxin Delivery during Interbacterial Competition

first: Po-Yin

address: 128 Section 2, Academia Road, Nankang

type: Genome variation profiling by high throughput sequencing

summary: The type VI secretion system (T6SS) is a bacterial contractile nanomachine that translocates toxic effectors into neighboring cells, helping bacteria to survive in competitive environments. The core T6SS structural protein Hcp forms the inner tube and mediates the loading and delivery of diverse effectors. Yet, how wide-ranging effectors that lack classical secretion signals are selectively recruited to Hcp remains poorly understood. To better understand, using Pseudomonas aeruginosa H1-T6SS as a model, we performed deep mutational scanning to determine how Hcp accommodates and delivers distinct effectors.

overall_design: Targeted amplicon seq: P. aeruginosa PAO1 ∆hcp1 cells carrying hcp1 mutant library were collected both before and after interbacterial competition against Enterobacter cloacae. Three biolobical repeats were proformed.

first: See-Yeun

last: Ting


title: TGFbeta determines epithelial tissue spacing by regulating mesenchymal condensation

city: Princeton

first: Pengfei

last: Zhang

state: NJ

address: 303 Hoyt Laboratory, William Street

department: ODBI

institute: Princeton University

summary: The branched structure of the vertebrate lung provides a high surface area-to-volume ratio, which increases the efficiency of diffusion-driven gas exchange. Generating this structure requires that the epithelial branches avoid contacting each other as they elongate during development. Previous studies have suggested that the spacing between neighboring branches is intrinsic to growth of the epithelium, but the underlying physical mechanisms remain elusive. Here, we used the embryonic chicken lung as a model system and found that branch spacing is regulated primarily by signaling to the mesenchyme through transforming growth factor-beta (TGFbeta). Although proliferation decreases in epithelial cells that are located in close proximity to an adjacent branch, these patterns surprisingly emerge after regular branch spacing has been established. Instead, we find that TGFbeta promotes the directed migration of mesenchymal cells, which form a condensation that physically displaces the adjacent epithelium and tunes branch spacing. Continuous disruption of TGFbeta signaling prevents mesenchymal condensation and eventually results in contact between adjacent branches. These data suggest that the spacing between epithelial branches results from mesenchymal cell dynamics rather than from epithelial-intrinsic self-avoidance.

overall_design: Spatial transcriptomic mappiog of E5 chicken embryonic lung using an enhanced microfluidic-enabled, deterministic barcoding platform


title: RNA-seq of Lgr5-GFP+ ISCs from KANSL1-deficient mice and control mice.

city: Tianjin

first: Chang

last: Lu

address: 94 Weijin Road, Nankai District

institute: Nankai University

summary: We report the application of RNA-sequence in control  and KANSL1-deleted mice ISCs with 3 biological replicates.

overall_design: Lgr5-EGFP-CreERT2; Kansl1 f/f mice were injected with tamoxifen daily for three or four days. Control mice were injected with corn oil. Lgr5-GFP+ intestinal stem cells (ISCs) were sorted by FACS. Total RNA was extracted for library construction and sequencing.


title: Transcriptomic response of Paraburkholderia busanensis P39 to Colletotrichum scovillei fungal biomass

city: Busan

first: Young-Su

last: Seo

address: Geumjeong-Gu

department: Microbiology

institute: Pusan National University

summary: This study investigated the transcriptomic response of Paraburkholderia busanensis P39 during exposure to fungal biomass of Colletotrichum scovillei KC05. RNA-seq was used to compare P39 grown alone with P39 exposed to fungal biomass, with three biological replicates per condition. The study aimed to identify transcriptional changes associated with fungal-biomass adaptation, nutrient scavenging, cell-envelope remodeling, regulatory responses, and interface-associated functions. Reads were aligned to the Paraburkholderia busanensis P39 genome represented by GenBank accessions CP058248 and CP058249.

overall_design: Comparative paired-end RNA-seq analysis of two conditions: Paraburkholderia busanensis P39 grown alone and P. busanensis P39 exposed to Colletotrichum scovillei KC05 fungal biomass. Three biological replicates were analyzed for each condition.

first: Mannaa

last: Mohamed

first: Seo

last: Young-Su


title: IGF2BP3 promotes epithelial ovarian cancer progression by regulating FASN expression

city: Qingdao

first: Sun

last: Danting

state: Shandong

address: 1677 Wutai Mountain Road, Huangdao District, Qingdao, Shandong Province

department: Department of Gynecology

institute: The Affiliated Hospital of Qingdao University

summary: Ovarian cancer (OC) is the most lethal disease among female reproductive system tumors, particularly epithelial ovarian cancer (EOC). N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic RNA and is involved in gene expression regulation. In OC, high expression of the m6A reader protein IGF2BP3 predicts a poor prognosis, but the target molecules and mechanisms underlying this association remain unclear. This study demonstrates that IGF2BP3 promotes EOC progression by recognizing and stabilizing m6A-modified FASN mRNA, thereby activating the WNT/β-catenin signaling pathway. This activation enhances lipid synthesis, increases mitochondrial membrane potential, shortens S-phase duration, and promotes cell proliferation and metastasis. Mechanistically, IGF2BP3 binds to m6A-modified FASN mRNA to enhance its stability, and pharmacological inhibition of FASN by orlistat reverses IGF2BP3-mediated oncogenic effects and WNT/β-catenin activation. In vivo and in vitro experiments confirm that knocking down either IGF2BP3 or FASN reverses these malignant phenotypes. These findings highlight a novel m6A-dependent IGF2BP3–FASN–WNT axis that drives EOC progression, providing a potential biomarker for targeted therapy.

overall_design: RNA sequencing was performed on OVCAR3 cells overexpressing IGF2BP3 and OVCAR3 cells transfected with a blank viral vector

first: Danting

last: Sun

first: Yuance

first: Jiaze

last: Gao

first: Lin

last: Cheng

first: Yapei

last: Su

first: Yan

first: Junqi

last: He

first: Teng

last: Lv


title: Myelin basic protein is an RNA chaperone in microglial nuclear retro-transport

city: Cambridge

first: John

last: Xu

address: biomedical campus

institute: Cambridge

summary: CNS oligodendrocytes generate myelin, an RNA-containing proteolipid substance that enhances axonal transmission. In multiple sclerosis (MS), myelin debris is phagocytosed by microglia (MG), and prior studies have detected myelin-derived mRNA in MG nuclei, suggesting a retrograde transport pathway. We report myelin basic protein (MBP) is a nucleic acid–binding and trafficking protein. We found that retro-transport of myelin RNA into the MG nucleus was phagocytosis and importin-dependent. Transcriptomic and proteomic analyses of MG nuclei revealed enrichment of myelin mRNAs and proteins, with MBP singularly detected in soluble and chromatin-associated fractions. MBP bound mRNA with high affinity (Kd ≈ 0.30 nM) and was sufficient to facilitate MG RNA nuclear import in vitro and in vivo. Functionally, MBP mediated the delivery of small interfering RNAs for targeted knockdown of toll-like receptor 4. These findings indicate MBP as an RNA-binding protein capable of MG nuclear import, providing insight into neuroinflammatory pathology of MS.

overall_design: RNA-seq profiling of primary rat microglia cells and their subcellular compartments (nuclear and cytoplasmic fractions) were conducted at 24 hours, against fed mouse myelin components. In this dataset, we see nuclear accumulation of myelin-derived RNA in microglia following phagocytic uptake of myelin.

first: Guy

last: Lam

first: Zhaoyang


title: ATAD3A Limits Aortic Dissection via Mito-Lysosome Contacts and Lipoylation

city: Shanghai

first: Jie

last: Lin

state: Shanghai

address: 180 Fenglin Road Street, Xuhui District

institute: Zhongshan Hospital, Fudan University

summary: Background: Aortic aneurysm and dissection (AAD) is a fatal vascular emergency with limited mechanism-based therapies. The mitochondrial AAA⁺ ATPase ATAD3A, enriched at organelle contact sites, has been implicated in mitochondrial signaling, but its role in AAD remains unclear. Methods: AAD was induced in wild-type, ATAD3A knock-in (ATAD3A-KI), and vascular smooth muscle cell (VSMC)-specific knockdown (sh-ATAD3A) mice by 3-week β-aminopropionitrile monofumarate (BAPN) intake or 28-day angiotensin II (AngII) infusion via osmotic minipumps. Aortic dilatation, dissection incidence, rupture-related mortality, and histology were assessed. VSMCs were stimulated with AngII in vitro. Mitochondrial function was evaluated using Seahorse bioenergetics, membrane potential assay, and Ca²⁺ imaging. ATAD3A-dihydrolipoamide s-succinyltransferase (DLST) interaction was examined by co-immunoprecipitation. Pharmacological modulation was performed with the copper chelator tetrathiomolybdate (TTM) and the lipoylation inhibitor Devimistat. Results: ATAD3A expression was upregulated in human thoracic aortic dissection samples and in BAPN-treated mouse aortas, with early downregulation then late upregulation in VSMCs. Systemic ATAD3A overexpression mitigated BAPN- and AngII-induced aortic dilatation, reduced dilation incidence, and improved survival, whereas VSMC-specific knockdown accelerated vascular pathology. Mechanistically, ATAD3A overexpression reduced mitochondria-lysosome contacts, limited mitochondrial Ca²⁺ influx, and suppressed the FDXR/FDX1/LIAS lipoylation pathway, decreasing DLST lipoylation and restraining cuproptosis, thereby preserving VSMC viability and delaying AAD progression. Pharmacological inhibition of cuproptosis using TTM or Devimistat attenuated disease severity in vivo. Conclusions: ATAD3A protects against AAD by coordinating organelle contact and metabolic signaling to restrain mitochondrial Ca²⁺ influx, NADPH flux, and DLST lipoylation-dependent cuproptosis in VSMCs. Targeting the ATAD3A-DLST-cuproptosis axis offers mechanistic insight and therapeutic potential for AAD.

overall_design: RNA-seq profiling of aortic tissues from WT (n=6), WT-BAPN (n=7), ATAD3A-KI (n=5), and ATAD3A-KI-BAPN (n=6) mice, using tissue spanning the ascending aorta to the abdominal aortic bifurcation.

first: Shengjun

last: Xiong

first: Ying

last: An

last: Wu

first: Yuxin

last: Du

first: Yiran

last: E. Li

first: Yujie

first: Zunhui

first: Wenjun

last: Yu

first: Junbo

last: Ge

first: Yingmei

first: Jun

last: Ren


title: Chemotherapeutic Induction of Single-Stranded DNA Accumulation Sensitizes Triple-Negative Breast Cancer to Immunotherapy [RNA-Seq]

city: Houston

first: Shiaw-Yih

state: TX

address: Z10.2030, 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

summary: Despite the widespread adoption of chemo-immunotherapy in triple-negative breast cancer (TNBC), how cytotoxic chemotherapy engages antitumor immunity remains poorly defined. Here, we identify cytosolic single-stranded DNA (ssDNA) accumulation as the mechanistic bridge linking genotoxic stress to immune activation. By integrating in vivo TREX1-deficiency transcriptional signatures, we show that ssDNA-driven immunostimulatory programs—rather than TREX1 expression—robustly predict clinical response to chemo-immunotherapy across independent TNBC cohorts. Through a chemotherapeutic screen, we identify LP-184, an acylfulvene-derived alkylating agent in clinical development, as a potent pharmacologic inducer of cytosolic ssDNA and type I interferon signaling. LP-184 enhances antigen presentation, reduces M2-like tumor-suppressive macrophages, and promotes CD8⁺ T-cell priming, thereby synergizing with anti-PD-1 therapy in vivo. These findings redefine the interface between DNA damage and immune activation, establishing ssDNA-driven immune programs as both a predictive biomarker and a therapeutic axis for next-generation chemo-immunotherapy design.

overall_design: For bulk RNA-seq, two different TREX1-targeting gRNAs were used to generate TREX1 knockout (KO) cells via CRISPR v2 lentiviral transduction in the human triple-negative breast cancer (TNBC) cell line CAL51, and total RNA was harvested for sequencing. Mouse TNBC 4T1 cells were treated with LP-184 for 48 hours, and total RNA was collected for bulk RNA-seq analysis.  For single-cell RNA-seq, 4T1 cells were inoculated into BALB/c mice. One week after tumor implantation, mice were treated with LP-184 (three doses) in combination with either anti–PD-1 (four doses) or control IgG. Tumors from 4–5 mice per treatment group were pooled with equal cell counts, and single-cell suspensions were prepared and processed using the 10x Genomics Chromium platform for scRNA-seq.

first: Yong


title: Chemotherapeutic Induction of Single-Stranded DNA Accumulation Sensitizes Triple-Negative Breast Cancer to Immunotherapy


title: In vivo engineering of hematopoietic stem cells by targeted lipid nanoparticles within humanized mice

first: Rao

last: Shuquan

address: No. 288, Nanjing Road, Heping District,

department: State Key Laboratory of Experimental Hematology

institute: National Clinical Research Center for Blood Diseases Institute of Hematology & Blood Diseases Hospital,

summary: In vivo genetic engineering of hematopoietic stem and progenitor cells (HSPCs) holds the potential to revolutionize the treatment landscape for numerous diseases with unmet clinical needs. An optimal delivery system for genetic medicines must target quiescent human HSCs to ensure long-term therapeutic efficacy. Here, we screened 15 lipid nanoparticles (LNPs) with different PEG-lipid structures and reported an LNP named LNPDP that demonstrated efficient delivery of reporter mRNA to human HSPCs both in ex vivo and in vivo settings, when conjugated with the anti-CD34 antibody (CD34/LNPDP). Using CRISPR/Cas editing cargos, CD34/LNPDP achieved high editing efficiency in human HSPCs ex vivo. Subtle transcriptomic alterations were detected following LNP treatment, primarily attributed to the cellular uptake of exogenous cholesterol. Intrafemoral administration of CD34/LNPDP in humanized mice resulted in efficient editing of the erythroid-specific BCL11A enhancer within human HSPCs, which enables the sustained long-term reactivation of fetal hemoglobin (HbF) expression in erythroid cells. Furthermore, utilizing an additional humanized neutropenia model harboring an ELANE mutation, we demonstrated that intrafemoral administration of CD34/LNPDP can achieve robust editing targeting exon 2 of ELANE in human HSPCs, thereby attenuating the expression of mutant ELANE and partially restoring neutrophil development impairment under long-term observation. Notably, the genetically modified HSPCs exhibited unbiased repopulation of the entire hematopoietic hierarchy following LNP administration. Collectively, targeting CD34 on human HSPCs provides a novel platform to modify HSPCs for in vivo gene therapy without perturbing normal hematopoietic output, making it a promising candidate for clinical translation.

overall_design: RNA-seq profiling of CD34+ HSPCs in two experimental batches: Batch 1: RNA-seq profiling of CD34+ HSPCs treated for 24h with 4 μg/mL of IgG/LNPDP or CD34/LNPDP, compared to untreated controls. Batch 2: RNA-seq profiling of CD34+ HSPCs in a dose-matched comparison where LNPDP, IgG/LNPDP, and CD34/LNPDP were administered at concentrations yielding equivalent transfection efficiency (LNPDP and IgG/LNPDP at 2 μg/mL, CD34/LNPDP at 0.5 μg/mL) for 24 hours, compared to untreated controls. Each condition included biological replicates.

first: Jingjing

first: Zijin

last: Luo

first: Dan

last: Xie

first: Yan

last: Chen

first: Ming

last: Yang

first: Qiang

last: Li

first: Lisha

last: Wang

first: Lu

last: Han

first: Yiming

last: Zhang

first: Haiwei

first: Zilin

last: Lan

first: Haoping

last: Shi

first: Yinghui

first: Fang

last: Dong

first: Yingdai

first: Yao

last: Yao

first: Tao

first: Tuo

last: Wei

first: Shuquan

last: Rao


title: Chemotherapeutic Induction of Single-Stranded DNA Accumulation Sensitizes Triple-Negative Breast Cancer to Immunotherapy [scRNA-seq]

first: Shiaw-Yih

last: Lin

first: Yong

last: Du


title: CLN7 suppression induces apoptosis via mTOR-regulated and chaperone-mediated autophagy in myeloid leukemia cells

city: Hefei

first: Miaomiao

last: Wu

address: 96 Jinzhai Road, Hefei, China

institute: The First Affiliated Hospital of USTC

summary: Refractory disease and relapse continue to impede effective treatment of myeloid leukemia, despite substantial progress in therapeutic approaches. Emerging evidence implicates lysosomal ion channels in the regulation of cell death pathways, highlighting these channels as viable targets for therapeutic intervention. This study identified elevated expression of the lysosomal ion channel CLN7 in myeloid leukemia cells.  Suppression of CLN7 triggered apoptosis, inhibited cellular proliferation, and markedly reduced the abundance of oncogenic proteins. Mechanistically, CLN7 inhibition promoted nuclear translocation of TFEB by downregulating mTOR signaling, thereby enhancing lysosomal biogenesis and macroautophagy. Notably, CLN7 suppression selectively accelerated chaperone-mediated autophagic degradation of BCR-ABL through cathepsin B upregulation. In addition, inhibition of CLN7 induced autophagy-mediated apoptosis, which led to significant impairment of leukemogenic potential. Co-treatment with chemotherapeutic agents and CLN7 suppression enhanced therapeutic efficacy in myeloid leukemia cells. Finally, suppression of CLN7 markedly reduced tumor growth in human xenograft models without compromising normal hematopoietic function. These findings establish CLN7 as a critical regulator of leukemic cell survival, representing a promising therapeutic target for myeloid leukemia.

overall_design: mRNA profiles of human myeloid leukemia cell lines (K562 and OCI-AML3) were generated by deep sequencing using Illumina. We compared the transcriptome of CLN7-knockdown cells (transfected with shRNA targeting CLN7) with control cells (transfected with scramble shRNA). 3 biological replicates of K562  and 4 biological replicates of OCI-AML3 were performed for each condition in these cell lines.

first: Hui

first: Sujun

first: Qianwen

last: Xu

first: Yijing

last: Liao

first: Lili

last: Qu

first: Chunlei

last: Cang

first: Xingbing


title: Maintenance of H3K9me2 heterochromatin in the pollen vegetative nucleus requires ARID1 nuclear body formation

first: Lei

last: Li

address: Xinjiangwancheng

institute: Fudan University

summary: Mature pollen contains a vegetative nucleus with decondensed chromatin and two sperm cells engulfed within the vegetative cytoplasm. Chromatin de-condensation in plants usually accompanies a decrease in heterochromatin markers such as H3K9me2, H3K27me1, and H2A.W. However, H3K9 methyltransferases are detected primarily in the vegetative nucleus. This finding raises two questions: whether heterochromatin persists in the vegetative nucleus, and by what mechanism it is regulated. Here, we show that the vegetative nucleus harbors a basal level of H3K9me2, and that ARID1, an integrator coordinating pollen mitosis and heterochromatin reprogramming during sperm cell formation, promotes the maintenance of this basal level via its C-terminal tail-mediated nuclear body formation. The heterochromatin nature of ARID1 nuclear bodies is further confirmed by their colocalization with H2A.W and H3K27me1. Domain truncation analysis reveals that nuclear body formation of ARID1 depends on its C-terminal forty-nine amino acids. Deletion of this short C-terminal region abolished nuclear body formation and inhibited the interaction with H3K9 methyltransferase SUVH6. Disrupting the nuclear body localization of ARID1 significantly impairs its recruitment to H3K9me2 target loci. Therefore, the ARID1 nuclear body is necessary for maintaining H3K9me2 in the vegetative nucleus, which ultimately influences the regulation of nuclear size. Our findings demonstrate that the vegetative nucleus, despite its decondensed state, maintains a basal level of H3K9me2 that is regulated by nuclear body-localized ARID1.

overall_design: CUT&Tag assays for H3K9me2 and ARID1-GFP were performed with three and two biological replicates, respectively, following the manufacturer’s instructions. Anti-H3 antibody was used as a control, and detailed procedures are described in the manuscript.

first: Yi

last: Zhao

first: Binglian

last: Zheng


title: Nodal/Smad2 signaling sustains developmental pausing by repressing Pparg -mediated lipid metabolism

city: Toronto

first: Giacomo

last: Furlan

state: ONTARIO

address: 25 Orde St

institute: Lunenfeld-Tanenbaum Research Institute

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

overall_design: Refer to individual Series


title: An Optimized Methods for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets [ChIP-exo]

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

summary: We propose an optimized protocol to reconstruct bacterial transcriptional regulatory networks (TRNs) using ChIP-exo and RNA-seq datasets. For the reconstruction of TRNs, the omics datasets were targeted to RpoS and generated in Escherichia coli K-12 MG1655 cultured at mid-exponential phase in M9 glucose media.

overall_design: [ChIP-exo] E. coli K-12 MG1655 cells were grown to mid-exponential phage, cultured in M9 minimal 0.2% glucose with a biological replicate under 37°C with constant agitation.

first: Minchang

last: Jang

first: Joon

middle: Y

last: Park


title: Blockage of Ca2+-permeable AMPA receptors suppresses proliferation of schwannoma cells

status: Public on Jun 19 2026

city: Shinjuku-ku

first: Masahiro

last: Yo

state: TOKYO

address: 35 Shinanomachi

institute: Keio University

summary: Schwannomas are common benign tumors, but management of large or multiple tumors, such as those in NF2-related schwannomatosis, remains challenging due to the risks associated with surgery and radiotherapy. Drug repositioning offers a promising strategy for these slow-growing tumors. While the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor is a known therapeutic target in glioma to prevent seizure and growth, its expression and role in schwannoma have not been fully elucidated. We analyzed the intracellular genetic changes induced by PER treatment using RNA-seq. We treated human fibroblast cell lines (TIG-1) and human schwannoma cell lines (YST-1, HS-PSS) with PER at concentrations of 0 μM (control group), 10 μM, and 30 μM, respectively, and performed RNA-seq after culturing the cells for 7 days.

overall_design: RNA-seq profiling of YST-1 cells, HS-PSS cells, TIG-1 cells treated by pelanpanel 0uM, 10uM, 30uM

first: Utaro

last: Hino

first: Ryota

last: Tamura

last: Toda


title: ARID1B loss remodels the chromatin landscape to promote sorafenib resistance in hepatocellular carcinoma

city: Chapel Hill

first: Jacqueline

last: Brinkman

address: 120 Mason Farm Rd

department: Genetics

institute: Unversity of North Carolina-Chapel Holl

summary: CUT&RUN in HepG2 and HLF HCC cell lines mapping H3K27ac, H3K4me3, ARID1B, FOXA1, FOXA2 occupancy under sorafenib treatment and ARID1B-KO conditions. 2x2 factorial (genotype x treatment), 2 biological replicates per condition. Identifies cBAF-pioneer factor chromatin axis mediating sorafenib sensitivity. Preprint: https://doi.org/10.64898/2026.06.11.731725

overall_design: 2x2 factorial: genotype (WT, ARID1B-KO) x treatment (DMSO, sorafenib 5 µM 48h), 2 replicates, HepG2 and HLF cell lines. Antibodies: H3K27ac, H3K4me3, ARID1B, FOXA1 (HLF), FOXA2 (HLF), IgG control. Paired-end sequencing.

first: Jesse

last: Raab


title: Serine and glycine deprivation-induced gene expression in glioblastoma cell

first: Jong-Ho

last: Lee

address: 37 Nakdong-daero 550 Beon-gil

institute: Dong-A University

summary:
To determine whether glioblastoma cells have altered gene expression profiles under limited serine and glycine conditions of extracellular environment.
We performed gene expression profiling analysis using data obtained from RNA-seq at two conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U87MG cells under serine and glycine deprivation conditions.


title: Pooled CRISPR/Cas9 screen identifies chromatin regulatory genes mediating sorafenib resistance in HepG2 hepatocellular carcinoma cells

summary: Focused pooled CRISPR/Cas9 screen in HepG2 HCC cells. ~6,000 sgRNAs targeting ~750 chromatin/TF genes (~800 non-targeting controls). 4 conditions: T0, DMSO, sorafenib 2.5 µM IC10, sorafenib 4 µM IC50; 3 replicates each. MAGeCK identified ARID1B among top sorafenib-resistance hits. Preprint: https://doi.org/10.64898/2026.06.11.731725

overall_design: 4 conditions x 3 replicates = 12 samples. Single-end 75 bp, Illumina NextSeq 500. MAGeCK sgRNA counting and enrichment analysis.

first: Jackie

first: Jesse R


title: ARID1B loss drives sorafenib resistance through transcriptional reprogramming in hepatocellular carcinoma

summary: mRNA-seq was performed in HepG2 hepatocellular carcinoma cells to characterize transcriptional changes driven by ARID1B loss under sorafenib treatment. Wild-type (WT) and ARID1B-knockout (ARID1B-KO) HepG2 cells were treated with sorafenib (5 µM, 48 h) or DMSO vehicle, with three biological replicates per condition. DESeq2 interaction model identified ARID1B-dependent transcriptional responses to sorafenib. Preprint: https://doi.org/10.64898/2026.06.11.731725

overall_design: 2x2 factorial: genotype (WT, ARID1B-KO) x treatment (DMSO, sorafenib 5 µM 48h), 3 biological replicates per condition, HepG2 cells. Paired-end 75 bp on Illumina NextSeq 100. Salmon quantification against GRCh38/Ensembl 109.


title: Transcriptomic analysis of DHODH inhibition in PIK3CA-mutant colorectal cancer

first: Jun

last: Liang

address: Meilong Road

institute: East China University of Science and Technology

summary: This study investigates the transcriptional consequences of genetic and pharmacological DHODH inhibition in PIK3CA-mutant colorectal cancer. RNA sequencing was performed in RKO cells following either DHODH knockdown (shDHODH versus shNT) or treatment with the DHODH inhibitor HL6 (HL6 versus DMSO) to characterize the transcriptional programs regulated by DHODH and compare the effects of genetic and pharmacological inhibition.

overall_design: RNA sequencing was performed to investigate the transcriptional consequences of DHODH inhibition in colorectal cancer cells. PIK3CA-mutant colorectal cancer cells were treated with vehicle or the DHODH inhibitor HL6 (or transduced with control or DHODH-targeting shRNA) for the indicated duration. Total RNA was isolated and subjected to high-throughput sequencing. Biological replicates were included for each experimental group. Differential gene expression analysis was performed to identify pathways and transcriptional programs regulated by DHODH.

first: J

first: X

last: Liu


title: Female-specific m6A remodeling in the liver correlates with post-transcriptional metabolic adaptation to high fat diet

city: Bronx

first: Ronald

last: Cutler

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

summary: Sex differences strongly influence susceptibility to metabolic dysfunction-associated steatotic liver disease (MASLD), yet the regulatory mechanisms underlying these differences remain incompletely understood. To examine sex-specific hepatic adaptation to high-fat (HF) diet mouse model of MASLD, we integrated proteomics, transcriptomics, and Oxford Nanopore direct RNA sequencing for transcriptome-wide m6A profiling in male and female mouse livers. Female mice were relatively protected from HF diet–induced hepatic steatosis and exhibited distinct proteome remodeling enriched for peroxisomal pathways. In contrast, transcriptomic responses in females were dominated by inflammatory signatures and did not recapitulate the metabolic adaptations observed at the protein level, revealing extensive RNA–protein discordance and post-transcriptional remodeling. Integrated RNA–protein analyses identified female-specific amplification of peroxisomal proteins despite modest transcript-level changes. HF diet also induced sex-specific remodeling of m6A RNA methylation and altered regulation of the m6A methylation system. Notably, reduced 3′ UTR m6A methylation in female peroxisomal transcripts inversely correlated with increased protein abundance relative to RNA expression. Together, these findings implicate m6A-associated post-transcriptional regulation in sex-specific hepatic adaptation to HF diet exposure and the basis for discordance between many of the mRNAs and proteins in the liver.

overall_design: RNA-Seq profiling of homogonized liver to test the effect of high fat diet in male and female mice

first: Krylova

last: Sofia

first: Cutler

last: Ronald

first: Pessin

last: Jeffrey


title: Neurog1 and Neurog2 couple non-IT fate specification with cross-lineage cortical regionalization and bias recruitment into active circuits

first: Alexandra

last: Moffat

state: Ontario

address: 2075 Bayview Ave

institute: Sunnybrook Research Institute

summary: The neocortex comprises diverse neuronal subtypes with distinct projection patterns that emerge through sequential fate transitions. While combinatorial transcription factor (TF) activity is thought to drive this diversification, evidence from single-cell transcriptomics remains largely correlative. Here, by integrating single-cell transcriptomic data mining with double-knockout and split-Cre lineage-specific ablation in mice, we show that co-expression of the proneural TFs Neurog1 and Neurog2 is enriched in, and required to specify, non-intratelencephalic (non-IT) neuronal fates. Lineage tracing further reveals transient Neurog1/Neurog2 expression in intratelencephalic (IT) neurons, inhibitory interneurons, and astrocyte lineages, not specified by these TFs. Consistent with broader regulatory functions, integrative gene regulatory network analysis, single-cell meta-analysis, and spatial transcriptomics identify a Neurog1/Neurog2-co-regulated gene program delineating cortical regional identity. Additionally, lineage-labeled IT neurons show enrichment for immediate-early gene expression, with ~40% co-expressing Fos, suggesting activity-biased recruitment. Taken together, Neurog1/Neurog2 specify non-IT fates and engage gene programs shaping regional identity and circuit integration.

overall_design: To trace cells that expressed Neurog1 and Neurog2, we generated Neurog1^C‑CreKI;Neurog2^N‑CreKI;zsGreen mice by knocking Cre fragments into C‑terminus of the Neurog1 locus and N‑terminus of the Neurog2 locus (a Split‑Cre strategy that reconstitutes functional Cre only in cells co‑expressing both loci). These mice were crossed to a zsGreen reporter to obtain the triple‑transgenic line. At 2 months of age, these transgenic mice were euthanized and the cortex was microdissected under RNase‑free conditions. Cortical tissue was stored at −80 °C until nuclei isolation for snRNA‑seq.

first: Carol

last: Schuurmans


title: Contribution of chromosomal aneuploidy and submicroscopic copy number variations (CNVs) in recurrent pregnancy loss (RPL)

city: Varanasi

first: Ashish

last: Ashish

address: Banaras Hindu University

country: India

institute: MRU Lab

type: Genome variation profiling by genome tiling array

summary: This study investigates the contribution of chromosomal aneuploidy and submicroscopic copy number variations (CNVs) in recurrent pregnancy loss (RPL). Genomic DNA from RPOC samples was analyzed using high-resolution Agilent aCGH arrays (180K). Several clinically relevant CNVs, including deletions and amplifications affecting immune-related and developmental genes, were identified. This suggests a genetic predisposition underlying some cases of RPL.

overall_design: The study aims to investigate the role of chromosomal aneuploidy and copy number variations (CNVs) in the pathogenesis of recurrent pregnancy loss (RPL). Genomic DNA was isolated from products of conception (RPOC) obtained from patients with a history of RPL. High-resolution array Comparative Genomic Hybridization (aCGH) was performed using the Agilent SurePrint G3 Human CGH 4x180K microarray platform, which provides genome-wide coverage of CNVs. The hybridization results were analyzed using Agilent Cytogenomics software to identify chromosomal gains, deletions, and amplifications. Identified CNVs were annotated with respect to gene content, size, cytoband location, and potential pathogenicity. The results contribute to the understanding of genomic alterations associated with RPL and may offer diagnostic and prognostic value in clinical genetics.

first: Royana

last: Singh


title: Deciphering the early events of the transcriptional dialogue between Aspergillus fumigatus and Pseudomonas aeruginosa in a dual-species biofilm

city: Ribeirão Preto

first: Matheus

middle: Mertz

last: Ribeiro

state: São Paulo

address: Av. Prof. Dr. Zeferino Vaz - Vila Monte Alegre, Ribeirão Preto - SP, 14040-900

department: Faculty of Pharmaceutical Sciences of Ribeirão Preto

country: Brazil

institute: University of São Paulo

summary: The polymicrobial biofilm formed by Aspergillus fumigatus and Pseudomonas aeruginosa is clinically significant, particularly in the airways of cystic fibrosis patients, yet the initial transcriptional reprogramming underlying this interaction remains poorly characterized. This study employs dual-species RNA sequencing to decipher the early (48-hour) transcriptional dialogue within a co-culture biofilm model. We reveal that P. aeruginosa adopts a profound state of metabolic arrest and nutrient scavenging when confronted with wild-type A. fumigatus, characterized by a paradoxical downregulation of iron acquisition machinery and a global shift towards transport activity and alternative nutrient catabolism. In response, A. fumigatus exhibits metabolic repression coupled with the induction of stress defense and alternative energy pathways. Disruption of the fungal histidine kinase SlnA, a key signaling component, dramatically alters this interkingdom crosstalk. In the presence of the ΔslnA mutant, P. aeruginosa reactivates canonical starvation responses, including siderophore production and chemotaxis, while the mutant fungus fails to mount an appropriate structural and chemical defense, displaying a transcriptional profile of dysregulated metabolism and vulnerability. Furthermore, the interaction bidirectionally modulates the expression of virulence determinants and secondary metabolite gene clusters in both species, a process significantly influenced by the slnA locus. Our findings define the early transcriptional landscape of this critical fungal-bacterial interaction and establish SlnA as a master regulator of fungal adaptation within a competitive polymicrobial niche.

sample_organism:
Pseudomonas aeruginosa
Aspergillus fumigatus

overall_design: Transcriptomic profiling of Aspergillus fumigatus (WT vs. ΔslnA) and Pseudomonas aeruginosa in dual-species biofilms: influence of the fungal slnA gene on interkingdom interactions

first: Renan

last: Graça-Filho

first: Camila

last: Pinzan

first: Endrews

last: Delbaje

first: Norio

last: Takeshita

first: Steven

last: Kelly

first: John

last: Whitney

first: Gustavo

middle: H

last: Goldman