title: DPSCs Transfer Mitochondria via TNTs to Drive Hypoxic Angiogenesis

city: Hong Kong

first: Yang

last: Shengyan

address: Prince Philip Dental Hospital, 34 Hospital Road

institute: The University of Hong Kong

summary: The dental pulp resides within a rigid dentin chamber with a limited blood supply, creating a hypoxic environment that impedes tissue regeneration. This study identifies intercellular mitochondrial transfer as a critical endogenous rescue mechanism. Human dental pulp stem cells (DPSCs) actively transfer functional mitochondria to green fluorescent protein-expressing human umbilical vein endothelial cells (GFP-ECs) under hypoxic stress. This transfer significantly reduces hypoxia-induced apoptosis, preserves mitochondrial membrane potential, and enhances the angiogenic capacities of recipient ECs. To uncover the molecular mechanisms driving this phenotype, RNA-sequencing (RNA-seq) was performed on mitochondrial-transferred ECs (Mito(+)) and control ECs (Mito(-)) under hypoxia.

overall_design: RNA-seq profiling was performed on sorted Mito(+) and Mito(−) endothelial cells following 24 h of hypoxic co-culture with DPSCs. Mito(+) ECs received mitochondria from donor DPSCs, whereas Mito(−) ECs did not.

first: Shengyan

last: Yang

first: Waruna Lakmal

last: Dissanayaka


title: RAD51 proximity mapping reveals spatial constraints on homology search during DNA double-stranded break repair

status: Public on Jul 15 2026

city: Zurich

first: Charles

middle: D

last: Yeh

state: ZH

address: Otto-stern-weg 7

department: D-BIOL

country: Switzerland

institute: ETH Zurich

summary: DNA double-stranded breaks (DSBs) are an especially toxic form of damage that can be reversed without loss of genetic information by homology-directed repair (HDR), which copies from an intact template molecule. Finding a correct template within millions to billions of other DNA bases is termed homology search and is mediated by the protein RAD51. A major challenge in understanding homology search is the lack of tools to monitor search itself, rather than the end-stage outcome of HDR. We developed RAD51 proximity identification sequencing (RaPID-seq), a highly sensitive in cellulo method that marks all DNA searched by RAD51, regardless of whether it is chosen as the final template. We find that HDR in human cells is hierarchical. Only DSB-proximal sequences are searched, and even identical sequences outside the proximal window are not efficiently interrogated. Final recombination is unlocked by template homology but only at proximal sequences. We further find that RAD51 efficiently searches exogenously introduced DNA templates, such as those commonly used during genome editing, even those with no homology to the DSB site.  Such highly abundant exogenous templates compete with search of endogenous genome templates. Our data reveal the invisible process of homology search and shed new light on fundamental mechanisms underlying genome editing.

overall_design: Mapping of lentivirus insertion sites (LentiMap) in cell lines doubly-transduced. RaPID-K562 cells were transduced with an expressed BFP and clonally isolated. Thereafter, a non-expressed GFP donor sequence was transduced to generate a pool of cells containing a uniform BFP gene and multiple GFP donor insertions. Cells were treated with CRISPR/Cas9 targeting BFP and optionally with AZD7648; thereafter, cells undergoning BFP-GFP recombination were isolated by FACS and subjected to lentivirus mapping assay.

first: Jacob

middle: E

last: Corn


title: Deep learning design and in vivo validation of Müller glia-specific cis-regulatory elements

city: South San Francisco

first: Oriol

last: Fornes

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: Effective recombinant adeno-associated virus gene therapies require promoters that are compact and cell-type-specific. Ideally, promoters should also exhibit functional conservation when tested in model organisms to ensure that preclinical findings translate reliably to human patients. Here, we introduce a deep learning framework for designing cis-regulatory elements (CREs) meeting these criteria, applied to retinal Müller glia (MG). Using single-cell chromatin accessibility data from human and mouse retinas, we trained species-specific models to predict cell-type accessibility, and designed compact CREs using two complementary strategies. In silico validation predicted that the designed CREs exhibit high MG-specific accessibility (on-target) in both species with minimal off-target accessibility across hundreds of human cell types and tissues. Mechanistic analysis revealed that the predicted MG accessibility is driven by the creation of LHX2 motifs. In vivo validation confirmed that the designed CREs successfully restrict reporter expression to MG in the murine retina. Our deep learning framework is highly generalizable and enables the rapid design of compact, on-target, and species-conserved CREs for precision gene therapy.

overall_design: We performed single-nucleus multiome sequencing, jointly profiling GEX (RNA-seq) and chromatin accessibility (ATAC-seq) in 8 retinas from C57BL/6J mice (11 weeks and 93 weeks old; n = 4 per age group). For each sample, nuclei were isolated from dissected retinas, and unified single-nucleus RNA and ATAC libraries were prepared jointly using the 10x Genomics Chromium Multiome platform to enable simultaneous profiling of GEX and chromatin accessibility within individual cells.

first: Kyung Duk

last: Koh

first: Rebecca

middle: M

last: Marton

first: Jiapei

last: Chen

first: Kevin

middle: A

last: Marroquin

first: Gyeong Jin

last: Kang

first: Sören

last: Müller

first: Gokcen

last: Eraslan

first: Eliah

middle: R

last: Shamir

first: Pratiksha

middle: I

last: Thakore

first: Heinrich

last: Jasper

first: David

last: Garfield


title: Dissection of Poly(A)-binding protein (PABPC) cellular function using degron-mediated depletion with replacement [Nanopore]

city: Cambridge

first: Ryan

middle: Yue

last: Muller

state: Massachusetts

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

summary: Cytoplasmic poly(A)-binding proteins (PABPCs) are essential and highly abundant regulators of mRNA stability and translation, but their cellular functions have been difficult to dissect due to slow turnover and the lethality observed upon loss of both major paralogs, PABPC1 and PABPC4. To enable structure–function analysis of PABPC in human cells, we developed a protein-replacement platform that couples rapid auxin-inducible degradation of endogenous PABPC1 and PABPC4 with doxycycline-controlled expression of engineered PABPC variants. This approach enables acute removal of native PABPC and real-time assessment of how specific domains, paralogs, and sequence alterations support cellular fitness, shape transcriptome profiles, and regulate poly(A)-tail length. Using this system, we show that the RRM4 domain of PABPC1 is essential for growth, whereas post-translationally modified lysines within RRM4 are individually dispensable. Paralogs and variants with heterologous RRM4 domains vary in their ability to substitute for PABPC1, revealing functional divergence among PABPCs. Transcriptome profiling identifies variant-specific regulatory signatures, and dose-controlled rescue further delineates the relationship between PABPC variant abundance and global poly(A) tail lengths in vivo. Together, this platform provides a generalizable strategy for dissecting PABPC biology in the cellular context using rationally designed variants.

overall_design: Tail length measurements following replacement of endogenous PABPC1 and PABPC4 protein with transgenically-expressed PABPC1 or PABP1212 at titrated expression levels. HCT116 polyclonal cell lines were constructed with endogenous mAID degron tags on PABPC1 and PABPC4 and multi-copy transposon-mediated integration of PABPC variant expression constructs. PABPC replacement was induced with 1μg/mL doxycycline and 0.5 mM indole-3-acetic acid (IAA) for 13 days and PABPC variant expression level was sorted using FACS. Four expression levels for each variant and a non-replacement sample was submitted for nanopore sequencing to measure tail lengths.

middle: Y

first: Kiara

middle: X

last: Wang

middle: P

last: Bartel


title: Hemin-induced DEGs in Lung, Kidney of WT and hepatic SR-BI KO mice

city: Lexington

first: Jianyao

last: Xue

state: Kentucky

address: 625 S Limestone APT 223

institute: University of Kentucky

summary: Acute hemolysis can deplete haptoglobin and hemopexin, leaving toxic free heme insufficiently controlled. Here, the authors show that scavenger receptor BI (SR-BI) mediates hepatic uptake of free heme and is essential for protection against heme-induced injury and death. Here we examined gene expression post hemin injections

overall_design: SR-BIfl/fl and AlbcreSR-BIfl/fl mice were treated with hemin at 40 µmol/kg BW, i.p. Twenty-four hours later, a second injection was performed. Thirty-eight hours post the initial injection, RNA was isolated from Kidney, lung and liver using Qiagen RNeasy Mini Kit, and sent to Novogene for RNA sequencing analysis.

first: XiangAn

last: Li


title: SRPK2 overexpression remodels the transcriptome landscape of triple-negative breast cancer cells

city: DaLian

first: Luo

last: Kai

state: Liaoning Province

address: No. 467, Zhongshan Road, Shahekou District, Dalian 116011, China

country: China

institute: The Second Hospital of Dalian Medical University

summary: SRPK2 (SRSF protein kinase 2) is a serine/arginine-rich protein-specific kinase that phosphorylates SR splicing factors and regulates pre-mRNA alternative splicing. SRPK2 is highly expressed in breast cancer and associated with poor prognosis. To characterize how SRPK2 remodels gene expression in triple-negative breast cancer, we performed strand-specific RNA-seq of MDA-MB-231 cells transiently transfected with a SRPK2-FLAG expression plasmid (OE) or the corresponding empty vector (NC).

overall_design: Strand-specific RNA-seq of MDA-MB-231 (triple-negative breast cancer) cells. Two conditions were compared: SRPK2-FLAG overexpression (OE) and empty-vector negative control (NC), each with three biological replicates (six libraries total).

first: Jimeng

last: Guan

first: Linhui

last: Zhang

first: Kai

last: Luo

first: Jia

last: Hou

first: Yinzhao

first: Fei

first: Guixin


title: SRPK2 CLIP-seq reveals direct RNA targets in breast cancer cells

summary: SRPK2 (SRSF protein kinase 2) is a serine/arginine-rich protein-specific kinase that phosphorylates splicing factors and regulates alternative splicing. SRPK2 is highly expressed in breast cancer and associated with poor prognosis, and has been implicated in the post-transcriptional regulation of FASN mRNA. To identify the RNAs directly bound by SRPK2 in breast cancer cells, we performed UV-crosslinked iRIP-seq of SRPK2 in MDA-MB-231 cells.

overall_design: UV-crosslinked iRIP-seq of SRPK2 in MDA-MB-231 (triple-negative breast cancer) cells. Two anti-SRPK2 immunoprecipitation (IP) libraries (SRPK2_IP_1, SRPK2_IP_2) were generated as replicates, each with a matched input control (SRPK2_Input_1, SRPK2_Input_2). Binding peaks were identified by comparing each IP against its corresponding input.

last: Chen


title: Smad4 and Eomes converge on a shared transcriptional program associated with inflammatory CD8 T-cell differentiation

city: Thiruvananthapuram

first: Karthik

last: Chandiran

state: Kerala

address: 3103, School of Biology, Indian Institute of Science Education and Research - Thiruvananthapuram, Maruthamala P.O., Vithura, Kerala 695551

department: Biology

country: India

institute: IISER-Thiruvananthapuram

summary: The ability of CD8 T cells to mediate protective immunity while limiting immunopathology depends on critical transcription factors such as Smad4 and Eomes that regulate differentiation of activated CTLs. Disruption of transcriptional programs mediated by Eomes (30-32) and Smad4 (26, 33, 34) in activated CTLs has been implicated in viral infections, chronic inflammation and cancer. Smad4 and Eomes have been shown to be critical for differentiation of memory cells, particularly TRM cells. To understand the gene regulation programs mediated by Smad4 and Eomes, we have done an integrated RNAseq and ChIPseq analysis using CD8 T cells that are isolated from Smad4KO (S4KO), EomesKO, and Smad3/Smad4-DKO (S34-DKO) mice. We identified overlapping and distinct gene expression programs associated with Smad4 and Eomes that shape activated CD8 T cell identity and functional bias. They act as critical regulators of genes involved in T cell differentiation, metabolic programming and epigenetic control in CD8 T cells. Smad4 and Eomes regulate the genes involved in tissue residency and OXPHOS-linked mitochondrial bioenergetics. Finally, we showed that canonical TGF signaling is active in the absence of Smad4 or Eomes and abrogated only when both Smad3 and Smad4 are deleted. Surprisingly, CD8 T cells lacking both Smad3 and Smad4 are more enriched for TRM signature genes compared to Smad4 or Eomes-deficient CD8 T cells.

overall_design: RNAseq profiling of naïve CD8 T cells isolated from WT, Smad4KO, EomesKO and Smad3/Smad4-DKO and activated with αCD3/αCD28 and expanded further in the presence or absence of exogenous TGFβ

first: Linda

last: Cauley


title: APOBEC3-driven attenuation of the 2022 global outbreak monkeypox virus relative to its clade IIb ancestor

city: London

first: Rebecca

last: Sumner

address: 2nd Floor Borough Wing, Guy's Hospital

department: Department of Infectious Diseases

country: United Kingdom

institute: King's College London

summary: Monkeypox virus (MPXV) is a zoonotic virus endemic to Africa that has recently re-emerged, becoming the first orthopoxvirus with sustained human-to-human transmission since smallpox eradication. The 2022 global epidemic of MPXV was caused by Clade IIb virus (lineage B.1) that derived from the lineage A endemic to West Africa through APOBEC3 microevolution1-3. Here, comparison of lineage B.1 virus with its closest earlier A.1 ancestor reveals that despite only 46 nucleotide differences, lineage B.1 has attenuating phenotypic changes. Both viruses replicated equivalently in cell culture, but B.1 had defects in long-range spread, which mapped to APOBEC3 mutation E353K in OPG057 (F13L). MPXV B.1 was also defective in innate immune control, inducing higher IFNβ and innate immune signalling gene expression, and showing reduced capacity to suppress interleukin-1β-mediated responses, which mapped to APOBEC mutation R48C in OPG047 (F3L). Finally, MPXV B.1 had reduced virulence in a mouse model of MPXV infection relative to the ancestral A.1 strain. Our work demonstrates that the 2022 global outbreak MPXV was intrinsically attenuated, with attenuating mutations that are absent in concurrent, more severe clade IIb outbreaks. Our data also reveal that APOBEC3 editing is a mechanism of MPXV phenotypic variation, potentially contributing to clade evolution and competition.

overall_design: RNA-seq of human foetal foreskin fibroblasts (HFFF) and THP-1-derived macrophages infected with monkeypox virus (MPXV) Clade IIb lineage A.1 or B.1, or mock infected, at 24 h post-infection.

first: Lucy

last: Eke

first: Bruno

last: Hernaez

first: Alasdair

middle: J

last: Hood

first: Telma

last: Sancheira Freitas

first: Hannah

last: Ashby

first: Ailish

last: Ellis

first: Marine

last: Petit

first: Sian

last: Lant

first: Isobel

last: Stokes

first: Preetam

last: Parija

first: Isabel

last: Alonso

first: Francisco

last: Alvarez-de Miranda

first: Alazne

last: Unanue

first: Kevin

last: Maringer

first: Isabelle

last: Dietrich

first: Bryan

last: Charleston

first: Geoffrey

middle: L

last: Smith

middle: O

last: Ulaeto

first: Antonio

last: Alcami

first: Carlos

last: Maluquer de Motes


title: A novel self-organizing embryonic stem cell system reveals the role of Wnt signaling parameters in anterior-posterior patterning of the nervous system

city: Cincinnati

first: Aryeh

last: Warmflash

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

summary: We performed bulk RNA sequencing of cells that are under neural induction with the WNT3A ligand added at 34 hours to induce posterior neural fates. We observed a sequential order of gene activation, from Wnt target genes to WNT8A and then to HOX genes, suggesting that WNT8A acts downstream of the Wnt signaling pathway and upstream of posterior fate markers.

overall_design: Human pluripotent stem cells were seeded at a density of 30,000 cells/cm² in 24-well plates 24 hours before treatment in mTeSR1 medium supplemented with ROCK inhibitor. Cells were differentiated in N2B27 medium containing SB (10 μM) and LDN (100 nM). WNT3A (300 ng/mL) was added at 34 hours. Samples were collected at 34, 42, 50, and 72 hours. Total RNA was extracted using the Invitrogen RNAqueous-Micro Total RNA Isolation Kit. The extracted RNA was stored at −80°C, and RNA quality was assessed using a NanoDrop spectrophotometer, agarose gel electrophoresis, qPCR, and the Agilent 2100 Bioanalyzer. Sequencing was performed by Novogene Co. using the Illumina NovaSeq X Plus platform with paired-end 150-bp reads. An independent biological replicate was generated using the same protocol.

first: Siqi

last: Du

first: Eleni Anastasia

last: Rizou


title: Transcriptomic Profiling of Murine Macrophages During Francisella tularensis Infection

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

summary: Francisella tularensis is a highly virulent intracellular bacterium and the causative agent of tularemia, a severe disease posing a significant bioterrorism threat. During infection, these bacteria rapidly subvert host immune responses, particularly within macrophages, their primary replication niche. However, the temporal dynamics of the host macrophage response remain incompletely characterized. Here, we announce comprehensive time-course RNA-seq datasets that systematically capture the global transcriptional profile of murine RAW 264.7 macrophages across both early and late stages of F. tularensis infection.

overall_design: RNA-seq profiling of Murine RAW 264.7 macrophages uninfected or infected with Francisella tularensis LVS across seven distinct time points (0.5, 1.5, 4, 8, 24, and 48 hours post-infection) in biological triplicates .

first: Ma'ayan

last: Israeli

last: Cohen-Gihon

first: Ofir

first: Ofer

last: Cohen

first: Adi

last: Bercovich- Kinori


title: Characterization of molecular changes associated with aging in the mouse cochlear lateral wall [re-analysis of GSE197634]

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Overall goal of the study was to identify molecular regulators that change in the cochlear lateral wall as a function of aging

relation:
Reanalysis of: GSM5924183
Reanalysis of: GSM5924184
Reanalysis of: GSM5924185
Reanalysis of: GSM5924186
Reanalysis of: GSM5924187
Reanalysis of: GSM5924188

overall_design:
Raw data (fastq files) from GSE197634 were reanalyzed with updated reference indices. Samples from GSE197634 comprised three experimental replicates of lateral wall (LW) from young (2 months) and old (2.5 years) CBA/CaJ mice; the 6 samples are GSM records GSM5924183, GSM5924184, GSM5924185, GSM5924186, GSM5924187, GSM5924188. The fastq files corresponding to those samples were obtained and analyses conducted using Partek Flow software. Reads were aligned by STAR version 2.7.8a to reference index mm39 created 11/06/21. Gene counts were quantified by Partek E/M using an annotation model built from mm39 Ensembl Transcripts release 104. Count data obtained from the reanalysis are archived here.

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

first: Hainan

last: Lang


title: Single-cell analysis reveals impaired Müller glia-mediated intercellular communication and photoreceptor pathology in USH1C retinal organoids

city: Mainz

first: Kerstin

last: Nagel-Wolfrum

address: Hanns-Dieter-Hüsch-Weg 17

country: Germany

institute: Johannes Gutenberg University Mainz

summary: Usher syndrome type 1, caused by pathogenic variants in the USH1C gene, leads to congenital deafness and progressive retinal degeneration resulting in vision loss. While auditory deficits can be compensated by cochlea implants and hearing aids, no treatment exists to prevent retinal degeneration. Here, we generated retinal organoids from induced pluripotent stem cells of two USH1C patients to elucidate the cellular and molecular mechanisms driving ocular pathogenesis. Single-cell RNA sequencing of healthy and USH1C retinal organoids identified differential expression of genes related to phototransduction in photoreceptors, as well as alterations in cell adhesion and canonical Wnt signaling in Müller glia cells. Analysis of intercellular communication revealed an overall reduced signaling efficiency, particularly affecting Müller glia-mediated retinal adhesion processes. Morphological characterization of organoids confirmed transcriptome changes by showing degeneration of the outer limiting membrane and loss of adherens junction architecture. Moreover, photoreceptors revealed increased levels of apoptosis, as well as morphological and functional changes related to phototransduction. Our results demonstrate that disruption of Müller glia signaling contributes to an overall loss of retinal integrity, providing novel insights into USH1C pathogenesis and offering targets for therapeutic interventions.

overall_design: scRNA-seq profiling of healthy-1 and USH1C-1 retinal organoids at 35 weeks of differentitation.

first: Nicole

last: Wenck

first: Mark

last: Zorin

first: Qiang

last: Wang

first: Selina

last: Kröll

first: Anna

last: Justen

first: Katharina

last: Hay

first: Christof

last: Rickert

first: Maria

last: Méndez-Lago

first: Sivarajan

last: Karunanithi

first: Dimitra

last: Athanasiou

first: Kalliopi

last: Ziaka

first: Pietro

last: De Angeli

first: Katarina

last: Stingl

first: Susanne

last: Kohl

first: Michael

last: Cheetham

first: Thomas

last: Mittmann


title: Retina-specific glucocorticoid receptor deletion disrupts rhythmic gene expression in the mouse retina under light-dark conditions

city: Fukuoka

first: Keisuke

last: Ikegami

address: Nishi-ku Motooka 744

country: Japan

institute: Kyushu University

summary: The ocular circadian clock has been thought to be regulated primarily by environmental light. In many peripheral tissues, however, circadian clocks are influenced by temporal information conveyed by adrenal glucocorticoids, while glucocorticoid-dependent regulation of the eye clock, a light-receptive organ, has remained unclear. To investigate this mechanism, we generated retina-specific Nr3c1 (glucocorticoid receptor; GR) knockout mice by crossing Chx10-Cre mice, in which Cre-recombinase is driven by the Chx10 promoter expressed in the developing optic cup, with Nr3c1 flox/flox mice. Using these mice, we performed time-course tissue collection under light-dark conditions followed by time-series RNA-seq analysis. The analysis showed that many rhythmic genes detected in control retina were lost in retina-specific Nr3c1-deficient mice, suggesting that glucocorticoid signaling contributes to rhythmic retinal gene expression.

overall_design: Male 12-week-old WT (Cre-) and retina-specific Nr3c1 cKO (Cre+) mice were maintained under 12 h light/12 h dark (12L:12D) conditions. Whole eyes were collected every 6 hours at 3, 9, 15, and 21 hours after lights-on (ZT3, ZT9, ZT15, and ZT21). At each time point, whole eyes were collected from three WT mice and three cKO mice. Each whole-eye sample was homogenized with a pestle, and total RNA was extracted. Equal amounts of RNA from the three individuals in each genotype/time-point group were pooled and subjected to RNA-seq analysis.


title: OmpW-mediated sensing of MUC2 GalNAc contributes to the ileal tropism of Salmonella Typhi

city: Ithaca

first: Jeongmin

last: Song

state: NY

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

summary: Salmonella Typhi (STy), the causative agent of typhoid fever, preferentially infects the ileum, but the basis for this preference has remained unknown. We show that STy exploits MUC2-derived monosaccharides, such as GalNAc, to upregulate invasion and target the ileum—opposite to the response of closely related S. Typhimurium (STm), whose invasion is inhibited by MUC2. Three STy-specific extracellular residues of the outer-membrane protein OmpW (K141/T142/Q193) engage GalNAc, and a periplasmic relay through the short FepE_STy, RS12510, and TonB transmits this signal to activate the master invasion regulator HilD. Mice lacking MUC2 or gut microbiota lose STy ileal tropism, which is restored by oral GalNAc-containing monosaccharides. An OmpW triple-mutant STy strain establishes a murine oral STy infection model, identifying STy–MUC2 glycan interactions as one of the earliest steps of typhoid pathogenesis and a potential target for prevention.

sample_organism: Salmonella enterica subsp. enterica serovar Typhi

overall_design: A transposon mutant library of Salmonella Typhi PhilD-LacZ (~50,000 insertions) was treated with 0.2% porcine MUC2 and screened on X-gal agar plates. A total of 145 white colonies were selected and pooled for genomic DNA extraction. This dataset contains the high-throughput sequencing data of the pooled DNA used to identify the transposon insertion sites.

first: Chang-Kyu

last: Yoon

first: Gi Young

last: Lee


title: OmpW-mediated sensing of MUC2 GalNAc contributes to the ileal tropism of Salmonella Typhi [STy]

platform_organism: Salmonella enterica subsp. enterica serovar Typhi

overall_design: This includes six RNA-seq samples: three from untreated S. Typhi and three from S. Typhi treated with 0.2% porcine MUC2


title: OmpW-mediated sensing of MUC2 GalNAc contributes to the ileal tropism of Salmonella Typhi [STm]

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: This includes six RNA-seq samples: three from untreated S. Typhimurium and three from S. Typhimurium treated with 0.2% porcine MUC2


title: Organ-Specific Transcriptional and Metabolic Remodelling During Late Mouse Adolescence

city: Freiburg

first: Ahmad

last: Al Ajami

address: Breisacherstr. 153

department: Medical Faculty

institute: University of Freiburg

summary: Mouse models aimed at deciphering human aging have typically focused on early development or late-life stages. Much less is known about the transition from late adolescence to young adulthood, spanning 8 to 12 weeks of age. Here, we show that C57Bl6 mice undergo a comprehensive developmental transition characterized by significant transcriptional and metabolic reprogramming during this time. Transcriptional analysis revealed substantial, organ-specific changes: the heart shifts toward a maintenance-focused phenotype with down-regulated oxidative phosphorylation (OXPHOS) and increased expression of genes supporting structural remodeling. Conversely, the kidney adopts an immunologically active state, reflecting progressive immune cell colonization, while the liver shifts from a hematopoietic role to one dominated by lipid metabolism, detoxification, and ketogenesis. These transcriptional changes correspond to a coherent metabolic maturation driven by the gut-liver axis. Intestinal maturation enhances lipid absorption and microbial fermentation, leading to increased circulating levels of short-chain fatty acids, poly-unsaturated glycerolipids, and sphingomyelins. Elevated hepatic production of ketone bodies, driven by up-regulated fatty acid metabolism genes, provides an efficient alternative energy substrate for peripheral tissues like the heart. Urinary metabolite profiles, marked by increased acylglycines and tricarboxylic acid (TCA) cycle intermediates, further confirm heightened mitochondrial energy turnover and fatty acid beta-oxidation. Collectively, this coordinated maturation from 8 to 12 weeks signifies the transition from a highly plastic developmental state to a stable, energy-efficient, and metabolically flexible adult phenotype.

overall_design: RNA-seq data were generated from three tissues in C57BL/6NCrl mice: heart, kidney, and liver. For each tissue, 12 samples were analyzed, comprising four biological replicates from each age group: 8, 10, and 12 weeks.

first: Qing-xia

last: Huang

first: Eva

last: Kohnert

first: Temel

last: Kilic

first: Christina

last: Engel

first: Melanie

last: Boerries

first: Clemens

last: Kreutz

last: Moos

first: Gerd

last: Walz


title: MicroRNA-34a Promotes Hepatic Lipid Accumulation through RXRα Suppression and Is Reversed by 9-cis-Retinoic Acid in Steatotic Hepatocytes

city: Taichung City

first: Tsai

last: Shih-Chang

address: No. 100, Sec. 1, Jingmao Rd, Beitun Dist

department: Department of Biological Science and Technology

country: Taiwan

institute: China Medical University

summary: Metabolic dysfunction-associated fatty liver disease (MAFLD) is the most common chronic liver disease worldwide and is characterized by excessive hepatic lipid accumulation and metabolic dysregulation. Although microRNA-34a (miR-34a) has been implicated in lipid metabolism, the molecular mechanisms underlying its contribution to MAFLD remain incompletely understood. This study aimed to investigate the role of miR-34a in hepatic steatosis and to identify potential therapeutic targets. An in vitro steatosis model was established using free fatty acid (FFA)-treated HepG2 cells. miR-34a expression was analyzed by RT-qPCR, and direct target interactions were validated using dual-luciferase reporter assays. Proteomic alterations were characterized by iTRAQ-based proteomic profiling, followed by Ingenuity Pathway Analysis (IPA). The therapeutic potential of retinoid X receptor alpha (RXRα) activation was evaluated using 9-cis-retinoic acid (9-cis-RA). miR-34a expression was significantly increased in FFA-treated hepatocytes and directly targeted the 3′-UTRs of PPARα, SIRT1, and RXRα. Integrated transcriptomic and proteomic analyses identified LXR/RXR signaling as a major pathway disrupted by miR-34a overexpression. RXRα was validated as a direct downstream target of miR-34a, establishing a mechanistic link between microRNA dysregulation and nuclear receptor signaling. Pharmacological activation of RXRα by 9-cis-RA markedly attenuated lipid accumulation and reduced the expression of key lipogenic and fatty acid uptake proteins, including FASN, SCD1, and CD36. Our findings identify RXRα as a novel target of miR-34a and reveal a previously unrecognized miR-34a–RXRα regulatory axis governing hepatic lipid homeostasis. Activation of RXRα effectively reverses steatotic phenotypes, highlighting the miR-34a–RXRα axis as a potential therapeutic target for MAFLD.

overall_design: To investigate the molecular mechanisms underlying the anti-steatotic effects of RXRα activation, transcriptomic profiling was performed in FFA-treated HepG2 cells with or without 10 μM 9-cis-retinoic acid (9-cis-RA).

first: Jai-Sing

last: Yang

first: Hong-Yi

last: Chiu

first: Syun-Rong

last: Jhan

first: Yao-An

last: Liu

first: Chao-Jung

last: Chen

first: Shih-Chang

last: Tsai


title: Efficacy, safety, and spatial transcriptomic rationale of orelabrutinib plus obinutuzumab in marginal zone lymphoma

city: Shanghai

first: Jiadai

last: Xu

address: Xuhui District, Zhongshan Hospital Fudan University

institute: Zhongshan Hospital Fudan University

summary: This submission contains raw 10x Genomics Visium HD Spatial Gene Expression FASTQ files from three FFPE mucosa-associated lymphoid tissue lymphoma samples analyzed in the O2 marginal zone lymphoma study. Processed Space Ranger and downstream spatial transcriptomics files will be added before final GEO release. Submitter contact email: lcxujiadai@163.com.

overall_design: Visium HD spatial transcriptomics was performed on three MALT lymphoma biopsy samples from the O2 cohort: gastric MALT lymphoma, thyroid MALT lymphoma, and labial gland MALT lymphoma. Samples were sequenced using paired-end Illumina reads and analyzed with Space Ranger and Seurat-based downstream workflows.

first: Peng


title: Antibody response against Influenza antigens

city: Irvine

first: Li

last: Liang

address: 847 Health Sciences

institute: University of California Irvine

summary: A protein microarray was used to measure antibody response in the plasma of mice immunized with adjuvantged protein vaccine formulations at d14 and d28 post prime immunizations (n = 42). The results demonstrate antigen- specific antibody response was elicited by nanoparticle-adjuvanted protein vaccines.

overall_design: Antibody Profiling Against Hemagglutinin (HA) Antigens from Influenza A Subtypes H1–H18

first: Jiin

last: Felgner

first: Jenny

last: Hernandez-Davies

first: Andriy

last: Yeromin

first: Jui-Lin

last: Chiang

first: Yibo

last: Li

first: Jacob

last: Laster

first: Anthony

last: Gregory

first: Caecilia

last: Basirin

first: Aarti

last: Jain

first: Erwin

last: Strahsburger

first: Algimantas

last: Jasinskas

first: Rie

last: Nakajima

first: D

middle: H

last: Davies

first: Philip


title: Transcriptomic signature of Human Cardiac Fibroblast in Hypertrophic Obstructive Cardiomyopathy

city: Guildford

first: Ayman

last: Ibrahim

state: Surrey

address: Daphne Jackson Road

institute: University of Surrey

summary: Introduction: Hypertrophic Cardiomyopathy (HCM) is a cardiac disorder characterized by an increased interstitial fibrosis and Extracellular Matrix (ECM) remodeling. Cardiac fibroblasts (CFs) have a crucial role in ECM remodeling as well as influencing contractility. There is accumulating evidence that the phenotype of CFs is disease-specific. Here, we investigate the transcriptome signature of CFs in Hypertrophic obstructive Cardiomyopathy (HOCM) patients and its potential functional significance. Methods: Primary CFs were isolated from myectomy specimens of 12 clinically phenotyped HOCM patients and 3 controls. RNA libraries were prepared from cell isolates for subsequent whole transcriptome sequencing. Differential expression analysis was conducted using the Tuxedo pipeline. Pathway and Gene Ontology (GO) enrichment were performed using Protein-protein interaction network analysis and functional clustering were performed using Cytoscape StringApp. Expression of candidate genes and proteins was validated using real time quantitative PCR, Immunocytochemistry, immunohistochemistry, cytokines/chemokines profiling and western blotting, in patient-derived CFs extracts, CFs-conditioned media, and myocardial tissue sections. Results: Whole transcriptome analysis identified 265 significant differentially expressed genes (DEGs) (q-value  ≤ 0.05 and log fold-change ≥ 1.5) in HOCM fibroblasts compared to controls. The most significant GO terms identified were associated with ECM organization and inflammatory response. The most significant GO terms identified were associated with ECM organization and inflammatory response, with circos plot analysis further highlighting pathway-specific gene overlap within inflammatory and structural signaling clusters. The DEGs encompassed gene families such as collagens, proteases, fibulins, inflammatory and signaling cytokines, integrins and signaling receptors and kinases. Notably, MYC was upregulated alongside chemokine ligands and receptors, including CXCR4, CXCL3, CXCL8, CCL2, CCL4 and CCL11, highlighting a potential MYC-linked chemokine signaling axis within the inflammatory HOCM-CFs phenotype. The protein expression of selected ‘extracellular Matrix organization’ and ‘inflammatory response’ genes confirmed the transcriptome results. Conclusion: Transcriptomic profiling of patient-derived HOCM-CFs identified candidate genes and pathways associated with inflammatory signaling, ECM remodeling, and altered cell–cell and cell–matrix communication. These findings show that advanced HOCM-CFs acquire an inflammatory-remodeling phenotype, with the involvement of ECM genes other than collagens.

overall_design: 12 test samples vs 3 controls were used in this study. Cardiac Fibroblasts were isolated from myectomy samples collected from patients with Hypertrophic Obstructive Cardiomyopathy. RNA was extracted from Cardiac fibroblasts (Qiagen). Isolated total RNA was sequenced using TruSeq Stranded Total RNA with Ribo Zero Gold kit 1 (Illumina, San Diego, CA), following manufacture recommendations. Libraries were sequenced as 151 bp pair-end reads on 4 lanes of a NextSeq 550 (Illumina, San Diego, CA) using high-output cartridges.

first: Sarah

last: Halawa

first: Aya

last: Galal

first: Lydia

last: Sidarous

first: Sara

last: Elshorbagy

first: Hasnaa

last: Elfawy

first: Manar

last: Osman

first: Faisal

last: Mohamed

first: Mohamed

last: Roshdy

last: Hosny

first: Mona

last: Allouba

first: Ahmed

last: Mostafa

first: Yasmine

last: Aguib

first: Magdi

last: Yacoub


title: Characterization of the cancer-associated field of injury in the nasal epithelium in never-smokers

city: Boston

first: Minyi

last: Lee

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University Chobanian & Avedisian School of Medicine

summary: Lung cancer in never-smokers represents a distinct and growing clinical challenge, yet early detection strategies largely target smokers. Here, we demonstrate that nasal epithelial gene expression alterations previously associated with lung cancer in current and former smokers are conserved in never-smokers. Notably, immune-related pathways, including interferon signaling, are similarly suppressed in malignant nodules in ever and never smokers. These findings suggest shared molecular mechanisms of lung carcinogenesis in ever and never smokers and should motivate validation of airway-based biomarkers in never-smoker populations.

overall_design:
To be updated by submitter.

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

first: Marc

last: Lenburg


title: Bulk RNA-sequencing of TA in MBNL1/2 KD muscle

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

summary: Myotonic dystrophy type 1 (DM1) is a multisystemic disorder caused by expanded CTG repeats in DMPK transcripts and consequent loss of MBNL protein function. Skeletal muscle in DM1 displays abundant centrally located nuclei despite limited immune-cell–associated fibre necrosis, complicating interpretation of the underlying mechanisms of muscle damage and remodelling. Here, we combine single-nucleus RNA sequencing of human DM1 muscle biopsies with adult-onset, myofibre-specific Mbnl knockdown mouse models to investigate muscle stem cell (MuSC) behaviour in this context. We identify increased numbers of activated MuSCs and a distinct population of myonuclei exhibiting a transitional transcriptional state, including expression of MuSC-associated markers and elevated DMPK levels. In mice, myofibre-restricted MBNL knockdown induces myonuclear accretion in the absence of overt necrosis and promotes analogous transcriptionally distinct myonuclear states. MuSC lineage tracing and ablation demonstrate that MuSC fusion contributes to central nucleation. Together, these findings indicate that MuSC-mediated fusion drives myonuclear remodelling in DM1 muscle, giving rise to centrally located myonuclei with altered transcriptional states. Notably, MuSC ablation did not significantly alter key functional parameters, including myotonia and muscle force, indicating that MuSC-mediated fusion is not a major determinant of overt muscle dysfunction in this model.

overall_design: Muslce was injected with AAV carrying MBNL1/2 KD casette and muscle was collected 10 weeks after injection.

first: Frederique

last: Rau

first: Xavière

last: Lornage

first: Piera

last: Smeriglio

first: Denis

last: Furling


title: Single Nuclei sequencing of mouse model of MBL1 and 2 KD in a Pax7-DTA model

overall_design: Pax7-DTA mice were injected with an AAV vector containing the shRNA for either MBL1 or MBL2. The TA was collected for single- nucleus RNA-sequencing after verfying the downregulation by qPCR. snRNA-seq was perfromed using thr 10x 3' Gene Expression kit.


title: In vitro inhibition of STAT5 signaling limits CD8⁺ T-cell exhaustion and improves outcomes in adoptive T-cell therapy models.

city: Montreal

first: Helene

last: Decaluwe

state: QC

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Sainte Justine

summary: T-cell exhaustion remains a barrier to adoptive cell therapies. Although γc cytokines are widely used to expand T cells, their impact on T-cell states remains incompletely defined. Using an in vitro model of repetitive TCR stimulation, we found that high-dose IL-2 or IL-15 promoted exhausted CD8⁺ T-cell (TEX) differentiation, marked by increased inhibitory receptor expression and loss of stem-like features. During chronic LCMV Clone 13 infection, virus-specific CD8⁺ T cells expressing high IL2Rβ displayed features of terminally exhausted TEX cells, whereas IL2Rβ deficiency favored progenitor-like populations. In TEX cells, IL-2 and IL-15 preferentially induced STAT5 phosphorylation relative to other signaling pathways. Genetic disruption of STAT5 similarly supported progenitor subsets, implicating STAT5 in the progression toward more differentiated TEX states under chronic stimulation. We therefore asked whether transient attenuation of STAT5 signaling during in vitro T-cell expansion could bias differentiation toward progenitor-like populations without compromising functional competence. Transient JAK3 or STAT5 inhibition enriched for TCF1⁺Ly108⁺ progenitor-like cells while preserving cytokine production and degranulation capacity. Following transfer into tumor-bearing mice, cells expanded under STAT5-inhibited (STAT5i) conditions mediated superior tumor control and prolonged survival. Likewise, transient STAT5 inhibition preserved memory-progenitor phenotypes of human CD22 CAR T cells without diminishing cytotoxicity. RNA sequencing of STAT5i-expanded CD8⁺ T cells confirmed reinforcement of stem-like transcriptional programs and reduced enrichment of effector and exhausted signatures. Together, these findings identify the IL-2Rβ–STAT5 axis as a regulator of CD8⁺ T-cell differentiation and support transient STAT5 modulation during ex vivo expansion as a strategy to improve therapeutic T-cell products.

overall_design:
Bulk RNA-sequencing of CD8⁺ T cells expanded for 7 days in vitro with IL-2 or IL-15 ± STAT5i, with naïve CD8⁺ T cells included as reference population.
RNA was isolated from naïve or expanded CD8+ T cells using miRNeasy Mini Kit (QIAGEN).  Poly-A mRNA enrichment was conducted using Dynabeads Oligo(dT) (ThermoFisher), and library preparation was carried out with the KAPA RNA Hyperprep Kit (Roche). RNA sequencing was performed using a NextSeq HighOutput 150 cycles kit (PE75) on the Nextseq500 (Illumina, CA, USA).

first: Mitra

last: Shourian

first: Benoîte

last: Bourdin

first: Nehme

last: El-Hachem

first: Clémence

last: Ruisseaux

first: Alexis

last: Vallée

first: Olivier

last: Gingras

first: Hugo

last: Roméro

first: Edward

last: Kwarteng

first: Elie

last: Haddad

first: Vincent-Philippe

last: Lavallée

first: Jean-Christophe

last: Beltra

first: Hélène


title: In vitro inhibition of STAT5 signaling limits CD8⁺ T-cell exhaustion and improves outcomes in adoptive T-cell therapy models

overall_design:
Virus-specific CD8+ T cells were isolated from mice chronically infected with LCMV Clone 13 at day 21 post-infection. Antigen-specific Tetramer+ CD11a+ CD8+ T cells were sorted into IL2Rβhigh and IL2Rβlow populations based on CD122 surface expression prior to RNA sequencing.
Total RNA was isolated from FACS-sorted CD122high and CD122low virus-specific CD8+ T cells using TRIzol reagent. Poly(A)+ mRNA was enriched and sequencing libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq 2500 platform.


title: Canonical ETI-Dependent and -Independent Pathways Mediate Autoimmunity Caused by Loss of CBP60b Clade Function

city: Liaocheng

first: Lu-shen

last: Li

address: Hunan street

institute: Liaocheng University

summary: To investigate gene expression changes in the cbp60b;c;d;e;f;eds1;pad4;ndr1 (octuple) mutant, aerial parts from two-week-old wild-type (WT), cbp60b;c;d;e;f (quintuple), eds1;pad4;ndr1 (triple), and octuple plants were collected for RNA sequencing.

overall_design: Aerial parts of seedlings were then collected for sequencing. Approximately 20-30 plants per replicate were used for each genotype, and three biological replicates were performed.

first: Sha


title: Transcriptomic analysis of NvpaxA knockdown in Nematostella vectensis

city: Bethlehem

first: Michael

middle: John

last: Layden

state: PA

address: 111 Research Dr

department: Biological Sciences

institute: Lehigh University

summary: To investigate the role of NvpaxA in cnidocyte gene regulatory networks, bulk mRNA sequencing was performed on gastrula-stage Nematostella vectensis embryos (28 hours post fertilization at 24°C) following RNAi-mediated NvpaxA knockdown. Four paired experimental (NvpaxA shRNA) and scramble RNA control replicates were sequenced. Each replicate consisted of approximately 1000 injected embryos.

overall_design: Paired-end bulk mRNA-seq (150bp, Illumina NovaSeq 6000) on 5 NvpaxA shRNA knockdown samples and 5 scramble RNA controls in Nematostella vectensis gastrula embryos (28hpf). Reads were mapped to the Nematostella Nvec200 genome. Differential gene expression analysis performed using DESeq2 on the Galaxy web platform.

first: Layla

last: Alshaer

first: Jamie

last: Havrilak

first: Benjamin

last: Danladi


title: Transcriptomic analysis of NvfoxE-like knockdown in Nematostella vectensis

summary: To investigate the role of NvfoxE-like in cnidocyte gene regulatory networks, bulk mRNA sequencing was performed on gastrula-stage Nematostella vectensis embryos (28 hours post fertilization at 24°C) following RNAi-mediated NvfoxE-like knockdown. Four paired experimental (NvfoxE-like shRNA) and scramble RNA control replicates were sequenced. Each replicate consisted of approximately 1000 injected embryos.

overall_design: Paired-end bulk mRNA-seq (150bp, Illumina NovaSeq 6000) on 4 NvfoxE-like shRNA knockdown samples and 4 scramble RNA controls in Nematostella vectensis gastrula embryos (28hpf). Reads were mapped to the Nematostella Nvec200 genome. Differential gene expression analysis performed using DESeq2 on the Galaxy web platform.


title: Transcriptomic analysis of Nvznf845 knockdown in Nematostella vectensis

summary: To investigate the role of Nvznf845 in cnidocyte gene regulatory networks, bulk mRNA sequencing was performed on gastrula-stage Nematostella vectensis embryos (28 hours post fertilization at 24°C) following RNAi-mediated Nvznf845 knockdown. Four paired experimental (Nvznf845 shRNA) and scramble RNA control replicates were sequenced. Each replicate consisted of approximately 1000 injected embryos.

overall_design: Paired-end bulk mRNA-seq (150bp, Illumina NovaSeq 6000) on 5 Nvznf845 shRNA knockdown samples and 5 scramble RNA controls in Nematostella vectensis gastrula embryos (28hpf). Reads were mapped to the Nematostella Nvec200 genome. Differential gene expression analysis performed using DESeq2 on the Galaxy web platform.


title: Hnf4a Dysfunction in Sepsis: Gene induction by candiate ligand compound MJ041 in WT and KO primary hepatocytes

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Sepsis is a life-threatening condition where a dysregulated host response to infection causes organ dysfunction and the collapse of metabolic and immune functions. Nuclear receptor function is impaired in sepsis, in particular Hnf4a. A screening was performed for Hnf4a ligands, and the primary candiates was profiled with RNA-seq.

overall_design: RNA-seq expression profiling of ptimary hepatocytes in WT or KO genotype trated with vehicle or MJ041 (n=3)

first: Matyas

last: Jelinek

first: Jolien

last: Vandewalle

first: Marah

last: Heyerick

first: Tineke

last: Vanderhaeghen

first: Céline

last: Van Dender

first: Madeleine

last: Hellemans

first: Daria

last: Fijalkowska

first: Martin

last: Guilliams

first: Karolien

last: De Bosscher

first: Claude

last: Libert


title: Effect of depletion of Nsd1 or Ezh2 on gene expression during pluripotency transition

city: 合肥

first: 曹硕

last: 曹

state: 安徽

address: 九龙路

institute: 安徽大学

summary: CRISPR Screen with single-cell RNA-Seq as readout reveals new epigenetic factors regulate pluripotency of m ESCs. This highly sensitive method identified key genes essential for the acquisition and exit from pluripotency, and revealed loss of Nsd1-mediated H3K36me2 delayed exit from the naive state, while loss of Ezh2-mediated H3K27me3 promoted transition to the primed state.

overall_design: Given that knockout of Nsd1 or Ezh2 produced distinct effects on pluripotency, we performed RNA‑seq to characterize the transcriptomic consequences of each depletion.


title: iNOS is a key mediator of anti-PD-1 melanoma therapy response

city: Tampa

first: Youngchul

last: Kim

address: 12902 Magnolia Dr

institute: H. Lee Moffitt Cancer Center

summary: Background: Inducible nitric oxide synthase (iNOS) and its product nitric oxide (NO) were historically linked to poor melanoma outcomes, yet recent evidence shows NO supports anti-tumor immunity. This study examines how iNOS shapes anti–PD-1 efficacy, particularly through interferon signaling. Methods: B16 D5 melanoma tumors were implanted in wild-type (WT) and iNOS knockout (KO) mice to compare tumor growth and response to anti–PD-1 therapy. Flow cytometry, apoptosis assays, and RNA sequencing assessed NO production, PD-L1 expression, and interferon-related gene activation. In vitro, melanoma cells were treated with NO donors (DETA NONOate, SNAP) to assess proliferation and apoptosis. Peripheral blood mononuclear cells from 27 melanoma patients receiving anti–PD-1 therapy were analyzed with multiparameter flow cytometry to correlate NO-associated immune subsets with progression-free survival (PFS). Results: Tumors grew significantly faster in iNOS KO mice, and anti–PD-1 therapy had no effect, demonstrating that iNOS-derived NO contributes to treatment efficacy. NO donors inhibited melanoma proliferation and induced apoptosis in vitro. Transcriptomic analysis showed anti–PD 1 upregulated interferon pathway genes (STAT1, IRF1, IFNB1) in WT but not iNOS KO mice. In patients, a NO-producing dendritic cell subset (DAF FM⁺CD11c⁺) was associated with improved PFS (hazard ratio 0.453; 95% CI=0.270-0.992; p = 0.048), indicating a NO-dependent enhancement of interferon-driven immune activity.

overall_design: RNA-seq data from B16-D5 tumors in WT mice 6 hours post-treatment, comparing them to IgG and untreated controls

first: Markowitz

last: Joseph


title: Spatial Transcriptomic Atlas Reveals that FOXO3-Mediated Mitochondrial Dynamics Imbalance Drives Premature Ovarian Insufficiency in Mice

city: Nanjing

first: Ziwei

last: Song

address: Xianlin street

institute: Nanjing University of Chinese Medicine

summary: Premature ovarian insufficiency (POI) is a major cause of female reproductive aging, yet its underlying mechanisms remain poorly understood. Traditional studies have struggled to reveal the spatial and structural aging patterns of POI ovaries. This study constructed a spatial transcriptomic atlas of POI mouse ovaries to define the spatial and molecular features of granulosa-cell senescence during disease progression. Spatial analysis revealed disrupted follicular structure and distinct granulosa-cell subpopulations with blocked differentiation and senescence-associated gene signatures. Integration of related gene sets identified mitochondrial structural and functional impairment as a central feature of granulosa-cell senescence in POI. These changes were accompanied by excessive mitochondrial fission, reduced fusion, loss of mitochondrial membrane potential(MMP), reduced adenosine triphosphate (ATP) production, and increased reactive oxygen species (ROS). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis implicated the FOXO signaling pathway in mitochondrial dysfunction. Consistently, FOXO3 phosphorylation was significantly reduced in POI ovarian tissues. Pharmacological inhibition of this aberrant FOXO3 activation in a triptolide-induced POI model using KGN cells partially restored mitochondrial morphology and function. Suppressing FOXO3 phosphorylation in normal KGN cells was sufficient to induce mitochondrial dysfunction. Together, these findings demonstrate that FOXO3-mediated disruption of mitochondrial dynamics drives granulosa-cell senescence and contributes to ovarian failure in POI. By combining spatial transcriptomics with functional and mechanistic analyses, this study provides a spatially resolved framework for understanding ovarian aging and identifies FOXO3-regulated mitochondrial pathways as promising targets for diagnosis and therapeutic intervention in POI.

overall_design: POI group: tripterygium glycosides 75 mg/kg intragastric administration for 14 days; untreated mice as blank control.

first: Yaoli

last: Yin

first: Hongxiao

last: Li

first: Meihong

last: Shen


title: Gene expression of Cxcl12 expressing lineage

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: We generated a novel Cxcl12-Cre knock-in mouse model for permanent lineage tracing to investigate the spatiotemporal dynamics of CXCL12-Abundant Reticular (CAR) cells. Using single-cell RNA sequencing (scRNA-seq) and lineage tracing analysis, we found that these cells, representing the Cxcl12-expressing lineage, contribute to the skeleton at adulthood.

overall_design: ZsGreen-positive cells of the Cxcl12-expressing lineage were isolated from the femurs and tibias of Cxcl12-Cre;ZsGreen mice by Fluorescence-activated cell sorting (FACS) and subjected to scRNA-seq.

first: Katsutoshi

last: Hirose


title: IGFBP5 Derived From Endothelial Cells Drive Vascular Invasion and Liver Metastasis of Colorectal Cancer by Activating the ITGB3/PI3K/AKT Axis

city: Beijing

first: Jianqiang

last: Cai

state: Beijing

address: No.17 Nanli, Panjiayuan

institute: Cancer Hospital, Chinese Academy of Medical Sciences

summary: Vascular invasion is a critical step in colorectal cancer (CRC) metastasis, but how specific cells in the tumor microenvironment (TME) regulate this process remains unclear, particularly the role of endothelial cells (ECs). Here, we found that vascular invasion (VascI) is strongly associated with distant metastasis and poor prognosis in CRC patients. Analysis of single-cell RNA sequencing (scRNA- seq) data from 8 colorectal cancer liver metastases (CRLMs), included 4 VascI+ CRLMs and 4 VascI- CRLMs, and identified 10 distinct EC subpopulations. Notably, an IGFBP5+ tipECs significantly enriched in VascI+ CRLMs. High IGFBP5 expression correlated with VascI+ status and poor patient prognosis. Functionally, IGFBP5 overexpression (OE) in human umbilical vein endothelial cells (HUVECs) enhanced EC migration, tube formation, barrier disruption, and endothelial-to-mesenchymal transition (EndMT). In co-culture system, IGFBP5-OE  ECs promoted malignant epithelial cells (MCs) proliferation, migration, and adhesion, and accelerated the growth of patient-derived CRC organoids. Mechanistically, RNA sequencing nominated ITGB3 as a key downstream effector, with activation of the PI3K/AKT signaling pathway. We confirmed a direct ligand-receptor interaction between EC-derived IGFBP5 and ITGB3 on MCs using multiplex immunofluorescence (mIF), co-immunoprecipitation (CO-IP), and proximity ligation assays (PLA). This interaction activated PI3K/AKT signaling in MCs, driving aggressive behavior both in vitro and in vivo, an effect abolished by ITGB3 silencing in MCs. Our findings identify IGFBP5-OE ECs as a key driver of VascI and liver metastasis in CRC via the ITGB3/PI3K/Akt axis, highlighting a potential therapeutic target to suppress metastatic progression.

overall_design: Total RNA was extracted from co-cultured HUVECs and RKO cells using the TRIzol reagent and subjected to mRNA library construction. Libraries were sequenced using an Illumina platform (GeneChem, Shanghai, China). Following sequencing, RNA-seq data were aligned to the human genome, and transcripts were assembled from the alignments. Normalization and DEG analyses were performed using the DESeq2 R package. Based on the identified DEGs, further GO enrichment analysis, KEGG pathway analysis, and GSEA were conducted to identify potential mechanisms.


title: Bulk RNA-seq analysis of human induced pluripotent stem cells and human liver organoids

city: Kanagawa

first: Ryosuke

last: Morozumi

state: --- Select One ---

address: 3-25-26 Tonomachi

institute: National Institte of Health Sciences

summary: This study compares transcriptomic profiles of human induced pluripotent stem cells (iPS cells) and human liver organoids (HLOs) using bulk RNA-seq. Three biological replicates were analyzed for each group. Processed expression values are provided as a gene-level TPM matrix, and differential expression results for iPS versus HLO are provided as a separate processed data table.

overall_design: Bulk RNA-seq was performed on two experimental groups, iPS cells and HLOs, with three biological replicates per group. Differential expression was evaluated between iPS cells and HLOs, and downstream analyses included visualization of differentially expressed genes and gene ontology enrichment.


title: Single cell genomics links targeted functional manipulations to efficacy-associated transcriptional signatures in anti-tumor T cells

city: Denver

first: Kole

last: DeGolier

state: Colorado

address: 1400 Jackson St

department: Immunology and Genomic Medicine

institute: National Jewish Health

summary: Chimeric antigen receptor (CAR) T cells have produced extraordinary remission rates in some hematologic tumors, but these results are yet to be replicated across many malignancies and/or antigens. Modifying CAR architecture or T cell differentiation state can enhance anti-tumor efficacy. However, pooled screening methods are often restricted to in vitro readouts of abundance or transcriptome, limiting projection of long-term T cell fates. We implement barcoded scATAC-seq, tracking transcriptional fates of pooled murine or human CAR T cells with diverse functional modifications. We report stable and transient changes in transcription factor activity programmed by IL-2 concentration during in vitro expansion, and altered in vivo effector differentiation programs driven by combinatorial modifications in CAR antigen binding domain. These data establish use of genetic barcoding to tie targeted functional manipulations to single CAR T cell chromatin profiles in vitro and in vivo, providing insights toward augmented therapeutic efficacy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Murine or human T cells were virally transduced with chimeric antigen receptor (CAR) constructs containing genetic barcodes, and assayed in mixed pools in vitro or ex vivo after transfer into immunodeficient mice bearing leukemia. Cells were then FACS sorted and captured using a custom barcoding protocol for analysis by scATAC-seq.

first: Stephanie

last: DeVoe

first: Marwan

last: Abushawish

first: Angela

last: Prete

first: Terry

last: Fry

first: James

last: Scott-Browne


title: The KIF6-RBP Complex Orchestrates mRNA Transport Required for Sperm Flagellar Assembly

city: changsha

first: tan

last: yueqiu

address: Xiangya School of Medicine, Kaifu District, Changsha, Hunan Province, China.

institute: central south of university

summary: RNA immunoprecipitation sequencing was performed to identify transcripts associated with FMRP-containing ribonucleoprotein complexes in mouse testicular samples. Input and FMRP RIP samples were sequenced and analyzed to define RNA-binding protein-associated mRNA cargoes potentially involved in sperm flagellar assembly and function.

overall_design: RIP-seq was performed using one input sample and one FMRP RNA immunoprecipitation sample from mouse testicular material. Paired-end sequencing data were generated for both samples. Gene-level count/enrichment tables and normalized coverage tracks are provided as processed data.

first: Xie

last: Chunbo

first: Yi

last: Sibing

first: Lin

last: Xinle

first: Zhang

first: Wang

last: Weili

first: Yuan

last: Shimin

first: Meng

last: Lanlan

first: Li

last: Yong

first: Tan

last: Chen

first: Wei

last: Chunjia

first: Yu

last: Yanyan

first: Liang

last: Yaoqiong

last: Huan

first: Hu

last: Liang

first: Lu

last: Guangxiu

first: He

last: Wenbin

last: Qianjun

first: Du

last: Juan

last: Ge

first: Tu

last: Chaofeng

last: Yue-Qiu


title: Spatial and cell type specific molecular genetic investigations of inflammatory myopathies with selective perifascicular injury [RNA]

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary: Idiopathic inflammatory myopathies (IIM) are a heterogeneous group of systemic autoimmune disease often with multisystem involvement. Targeted therapy is still lacking. Efficient serum or histological markers to measure disease activity and predict disease course are missing. Perifascicular myofiber atrophy is a hall mark of dermatomyositis (DM). Despite decades of research, the mechanism of perifascicular atrophy is still incompletely understood. Across other IIM subtypes,  perifascicular myofiber necrosis is also the hall mark pathology for  antisynthetase syndrome associated myositis (ASyS)5, and can be seen in a subset of lupus myositis (LM). We hypothesize that direct comparison between tissue within the diseased perifascicular regions (PF) and the relatively normal centro-fascicular (CF) regions will help narrow down tissue specific drivers underlying the muscle injury (necrosis versus atrophy) in a disease specific manner.

overall_design: Utilizing spatial transcriptome analysis on a small pilot cohort including two muscle samples each from DM-NXP2, DM-Mi2, ASyS, LM, and normal control, respectively, we compared the mRNA and protein expressions within PF vs CF regions. We further stratify the expression profiles within the myofiber (desmin), capillary endothelial cells (CD31) and inflammatory cells (CD45).

first: Cai

last: Chunyu


title: Sex-Dependent Effects of Neonatal Hyperoxia on Prefrontal Cortex Development

city: Kansas City

first: Kaela

middle: Margaret

last: Varberg

state: MO

address: 2401 Gillham Road; CMRI 7902.19

department: Pediatrics

institute: Children's Mercy

summary: Premature infants often require oxygen therapy, which increases the risk of bronchopulmonary dysplasia and long-term cognitive impairment. The prefrontal cortex (PFC), essential for higher-order cognition, may be particularly vulnerable to neonatal hyperoxia, yet the cellular and molecular effects remain unclear. We exposed C57Bl/6 mouse pups to hyperoxia (85% O₂) or normoxia from postnatal days 1–14 and performed single nucleus RNA and ATAC sequencing of the PFC, complemented by oligodendrocyte progenitor cell assays and validation in mouse and human brain tissues. Hyperoxia reduced L4/5 intratelencephalic projecting glutamatergic neurons in females and mature oligodendrocytes in males, accompanied by consistent repression of myelination genes proteolipid protein 1 (Plp1) and myelin basic protein (Mbp) and altered chromatin accessibility. Oligodendrocyte transcription factor 2 (Olig2) was induced in both sexes, whereas lysine demethylase 3A (Kdm3a) activation was female specific. Hyperoxia activated Netrin-1 signaling in males and disrupted tumor protein p53 (TP53)-regulated metabolic pathways in females. Oligodendrocyte progenitor cell proliferation and differentiation were inhibited in vitro, and human bronchopulmonary dysplasia PFC samples recapitulated these core alterations. Together, these findings demonstrate that neonatal hyperoxia disrupts PFC development through sex-dependent effects on neuronal differentiation, oligodendrocyte maturation, and transcriptional regulation. Concordant mouse-human myelination deficits highlight the pathological relevance of oxygen exposure and underscore the importance of considering sex as a biological variable in preterm brain injury.

overall_design: Single nuclei were exracted from postnatal day 14 mouse prefrontal cortex that were exposed to hyperoxia (85% O₂) or room air from postnatal days 1–14. Joint  snRNA-seq and snATAC-seq libaries were prepared using the 10x Genomics platform.

first: Xingrao

last: Ke

last: Yu

first: Carl

middle: F

last: Schreck

first: Joseph

first: Melissa

last: Gener

first: Daniel

last: Louiselle

first: Sheng

last: Xia

first: Sherry

last: Mabry

first: Heather

last: Menden

first: Venkatesh

last: Sampath

first: Robert

last: Lane


title: Spatial and cell type specific molecular genetic investigations of inflammatory myopathies with selective perifascicular injury.


title: Limb cell-fate commissioning is guided by widespread coordinated genome detachment from the nuclear lamina [CUT&Tag]

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell-fate remains a key open question. Here, we address this by mapping a prevalent heterochromatic feature - genome-lamina interactions - relative to transcription in single-cells during mouse embryogenesis. We find that lamina-genome interactions remain relatively uniform following gastrulation but are extensively reconfigured during organogenesis in diverse tissues. Focusing on limb development, we demonstrate that genome-lamina interactions are selectively released at key developmental genes and their surrounding regulatory domains in early multipotent progenitors. Strikingly, this “lamina-release” often precedes later gene expression, suggesting it primes regulatory domains for future potential activation. Lamina-release also coincides with the putative binding of crucial limb transcription factors and so is closely intertwined with the regulatory machinery that drives limb formation. Conversely, we show that CTCF-defined boundaries of topologically-associated domains (TADs) constrains the spread of lamina-release at a limb gene locus. This ensures independent heterochromatin dynamics between neighbouring domains. Together, this suggests a previously unrecognised process where genome-lamina interactions are selectively dismantled at regulatory domains to transition loci toward more permissive chromatin states, thereby potentiating cell-type specific activation. Our work thus reveals how systematic heterochromatin reorganization links to developmental multipotency, providing mechanistic insight into how progenitors traverse diverse cell-fates in vivo.

overall_design:
LMNB1 binding and H3K27me3, H3K9me3 were profiled using CUT&Tag in limb of E8.5, E9.0,E9.5 embryos and ESCs.
In addition, LMNB1 binding, H3K9me3 and H3K27me3 and H3K9me2 were profiled in either WT or DeltaBor E13.5 embryos.

first: Konrad

last: Chudzik

first: Isabel

last: Guerreiro

first: Samy

last: Kefalopoulou

first: Alex

last: Abraham

first: Magdalena

last: Schindler

first: Mario

last: Nicodemi

first: Irina

last: Solovei

first: Andrea

last: Chiariello

first: Stefan

last: Mundlos

first: Michael

last: Robson


title: CCL3 and IL-7 Synergistically Enhance CAR-T Efficacy in Solid Tumors

city: Guangzhou, China

first: Xiaoyun

last: Luo

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

institute: Guangzhou National Laboratory

summary: CAR-T cell therapy has demonstrated remarkable clinical efficacy, but challenges remain in the therapeutic application for solid tumors, primarily due to poor infiltration capacity, suboptimal activity, and tumor antigen escape. Here, we found that the chemokine CCL3 plays a significant role in modulating intratumoral T cell cytotoxicity. However, CCL3 alone is insufficient to sustain durable CAR-T cell mediated tumor killing, largely due to tumor-induced T cell death. In contrast, the combination of CCL3 with IL-7, a cytokine known to enhance T cell survival, exerted a potent synergistic effect. This combination significantly improved CAR-T cell infiltration and longevity in solid tumors, leading to robust anti-tumor efficacy without significant side effects or systemic toxicity. Mechanistically, CCL3 plus IL-7 promoted RUNX3 expression and facilitated the differentiation of CD69+CD103+ tissue-resident memory T (Trm) cells. Furthermore, treatment with CAR-T cells co-expressing CCL3 and IL-7 (3P7-CAR-T) remodeled the immune landscape of solid tumors, marked by an increased infiltration of M1-like macrophages and CD103+ migratory dendritic cells. These changes enhance antigen presentation, thereby promoting the priming of endogenous anti-tumor T cell responses. Taken together, our results demonstrate that CCL3 synergizes with IL-7 to augment CAR-T cell memory and therapeutic effectiveness in solid tumors.

overall_design: C57BL/6J mice were inoculated subcutaneously with 1 × 10⁶ MC38-Trop2 tumor cells (n = 3 / group). At 14 d, 1×106 Ctrl-CAR-T or 3P7-CAR-T cells were injected intravenously without CY pretreatment. On day 21, tumor-infiltrating lymphocytes were harvested, and live CD45⁺ FVS700⁻ cells isolated from the tumors were sorted and subjected to single‑cell RNA sequencing and TCR sequencing seqanalysis.

first: Huanpeng

last: Chen

first: Yujing

last: Ke

first: Huixin

last: Gao

first: Xiaoting

last: Xu

first: Yu

last: Zhan

first: Yingjie

last: Bian


title: Differential physiological, behavioral, and medial prefrontal cortex transcriptomic responses to chronic restraint stress between BALB/c and C57BL/6J mice

city: Saga city

first: Taiga

last: Kurihara

state: Saga (佐賀県)

address: 5-1-1 Nabeshima

institute: Saga University

summary: Multiple factors have been implicated in the pathology of depression and stress resilience. Nevertheless, the molecular mechanisms underlying stress responses are not yet fully elucidated. Chronic restraint stress (CRS) is widely used as a rodent model of stress-induced depressive-like phenotypes. A previous study has demonstrated strain-dependent differences in hair corticosterone and testosterone levels, as well as behavioral responses to CRS, between C57BL/6J and BALB/c mice. However, the mechanisms underlying these differences remain unclear. In this study, male C57BL/6J and BALB/c mice were subjected to CRS for 6 hours per day for 21 consecutive days. Following CRS, behavioral responses were evaluated, and serum corticosterone levels along with oxidative stress-related markers were quantitatively analyzed using LC-MS/MS. In addition, comprehensive gene expression profiling of the medial prefrontal cortex was performed using next-generation sequencing, followed by Gene Ontology (GO) analysis. Control mice without CRS exposure in both strains showed increased body weight. BALB/c mice exhibited significant weight loss and elevated serum corticosterone levels, whereas C57BL/6J mice showed no change in body weight after 21 days and no significant changes in serum corticosterone levels. Oxidative stress analysis revealed a decrease in biological antioxidant potential (BAP) and an increase in derivatives of reactive oxygen metabolites (d-ROMs) in BALB/c mice, whereas C57BL/6J mice showed only an increase in d-ROMs. Behavioral analyses demonstrated that BALB/c mice exhibited increased immobility in the tail suspension test and forced swim test, as well as reduced sucrose preference following CRS. In contrast, C57BL/6J mice showed increased immobility only in the forced swim test. IPA canonical pathway analysis revealed that pathways associated with immune signaling, tissue remodeling, and metabolic processes were elevated in C57BL/6J mice compared with BALB/c mice under basal conditions. Under CRS exposure, pathways related to cell cycle progression, mitotic regulation, DNA damage response, cytoskeletal dynamics, and apoptosis were differentially regulated between the two strains. These results demonstrate marked strain-dependent differences in susceptibility and resilience to CRS. Distinct molecular programs operating at baseline and in response to stress may underlie these differences.

overall_design: Total RNA was extracted from the medial prefrontal cortex (mPFC) of mice following behavioral experiments using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions. RNA samples were subjected to TruSeq Stranded mRNA library preparation (Illumina) and sequenced on an Illumina NovaSeq 6000 platform (2 × 150 bp paired-end reads) with approximately 6 Gb coverage per sample. Gene expression levels were quantified from raw FASTQ files, and processed expression matrices were generated for downstream transcriptomic analysis.

first: Takeshi

last: Uemura


title: Non-invasive electrical stimulation restores corneal nerve density and sensory function in diabetic neuropathy via KCNN-dependent mechanism

city: Boston

first: Menglu

last: Yang

address: 20 Staniford st

institute: Schepens Eye Research Institute, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School

summary: Corneal nerve, originated from trigeminal ganglia, play an important role in conreal sensation and homeotasis. Under disease conditions when corneal nerves are damaged, such as diabetes, corneal injury, or eye surgury, patients suffer from dry eye, pain, delayed wound healing, or urceration. Current treatments are limited, underscoring the need for a regenerative therapy. Here we show that a non-invasive neural modulation therapy, transcutaneous electrical stimulation (ES), significantly restore the nerve density and sensory function in both streptozotocin-induced diabetes mice and keratectomy model. This transcriptomics analysis of TGs from in vivo ES in keratectomy models aims to find mechanistic insights into the ES-induced corneal reinnervation. The results point to ion transport and Ca2+ signaling alteration, alongside activation of neural regeneration pathways. Consistently, membrane potential recording in TGs shows a rapid hyperpolarization upon ES accompanied by increased [Ca2+]i level. Inhibition of potassium intermediate/small conductance calcium-activated channel (KCNN) abolishes the hyperpolarization and neural regeneration effect, whereas activation of KCNN channel significantly enhances nerve regeneration in the STZ model compared with sham treatment. Overall, ES restores corneal nerve density and function via KCNN activation in a diabetic mouse model, offering a novel, non-invasive, and clinically translatable therapeutic strategy for diabetic neuropathy.

overall_design: Female C57BL/6J (8-week-old) TGs under four conditions: untreated (Ctrl), 2 weeks after keratectomy wound (Injury), ES-treated keratectomy for 2 weeks (ES), and ES without keratectomy wound (ES no injury) was collected and subjected to balk RNASeq. Mice were anesthetized using a single intraperitoneal (IP) injection of ketamine 100mg/kg and xylazine 10mg/kg. Anesthetized mice were placed on heating pads to maintain body temperature while sedated and continue to be placed on a warm pad within their cage till recovery. Once sedation is confirmed, the central 1.5 mm diameter area was marked using a biopsy punch and the epithelium and the upper 1/3 of the corneal stroma of a random eye was removed using a rotating spur. A single dose of Ethiqa XR (3.25mg/kg) was injected subcutaneously immediately after the procedure.                                                  In vivo ES was performed using the STG4000 pulse generator (Multichannel Systems, Reutlingen, Germany). Under isoflurane anesthesia, the anode electrode was positioned on the mouse's abdomen through the conductive gel (Spectral 360; Parker Laboratories, Fairfield, NJ, USA). The cathode electrode probe was applied to the skin over the orbital area through a conductive gel interface. For sham controls, electrode probes were applied to the orbital area without delivering an electrical current. A biphasic ramp waveform (300 µA, 20 Hz) was administered for 4 minutes daily over 14 days. To minimize potential confounders, mice were subjected to ES in a randomized order.

first: Anton

last: Lennikov

first: Lu

last: Huang

first: Farris

last: ElZaridi

first: Ningyuan

first: Kai

last: Yuan

first: Amy

last: Li

first: Grace

last: Coyne

first: Wai

last: Tai

first: Dongfeng


city: Guangzhou

first: Huanpeng

address: Guangzhou International Bio-Island, Guangzhou, Guangdong, China

overall_design: 3P7-CAR‑T and Ctrl-CAR‑T cells were co-cultured with MC38-Trop2 tumor cells for 48 hours without cytokine supplementation, after which CAR-T cells were sorted by flow cytometry. CAR-T cells were positively selected and subjected to transcription sequencing. Libraries were sequenced on an MGI BGISEQ-500 platform to assess transcriptional changes in CAR-T cells.

first: Xiaoyun

last: Luo

first: Yujing


title: P3FI-90 activates innate immune responses in triple-negative breast cancer.

city: Jinan

first: Wenhao

address: Wenhua Xi Road No. 107

institute: Qilu Hospital of Shandong University

summary: Immunotherapy has emerged as a promising therapeutic option for cancer management, but its applicability in patients with triple–negative breast cancer (TNBC) is limited by the low efficacy due to the immunosuppressive tumor microenvironment (TME). Here, we identify lysine demethylase 3B (KDM3B) as an essential mediator of immune evasion in TNBC. KDM3B expression is negatively correlated with cytotoxic T lymphocyte (CTL) infiltration. Genetic or pharmacologic inhibition of KDM3B facilitates the recruitment and activation of CD8+ T cells, thereby suppressing tumor growth in TNBC mouse models. Mechanistically, KDM3B targets SHP1 by reducing H3K9me2 levels at its promoter. Suppression of KDM3B attenuates SHP1–mediated STING inactivation, which triggers robust type Ⅰ IFN responses. Strikingly, both KDM3B depletion and treatment with the KDM3B–selective inhibitor P3FI–90 significantly suppresses tumor progression and mitigates resistance to immune checkpoint blockade (ICB) therapy. Taken together, these findings establish KDM3B as a key regulator of immune escape, and targeting KDM3B represents a promising strategy to augment the efficacy of immunotherapy for TNBC.

overall_design: RNA-seq profiling of 4T1 cells treated with DMSO control or P3FI-90 for 24 h.

first: Qifeng

first: Xiaolong

last: Wang


title: Effect of mitochondrial haplotype on gene expression in inter-species composite cell lines formed through cell fusion

city: San Francisco

first: Alex

last: Pollen

state: CA

address: 1651 4th Street RM 473

department: Neurology

institute: UCSF

summary: Inter-species tetraploid composite cells formed by fusing cells from multiple contributor species are a new model system for disentangling cis from trans gene-regulatory divergence. It is unclear, however, how often mitochondria from one or both contributor species are inherited by these cells. We generated a panel of inter-species composite iPSCs by fusing human, chimpanzee, and bonobo contributor cell lines, labeling the composite cell line of origin using MULTI-seq barcodes. We then performed single cell RNA sequencing and demultiplexed cells using the CellBouncer toolkit. After identifying the species of origin of the mitochondria in all cells, we found that human mitochondria tend to predominate over those of other species in fusions including human contributor lines, and that cells containing two species' mitochondria are rare and show signs of apoptotic signaling, along with abnormal mitochondrial gene regulation.

overall_design: Single-cell RNA-sequencing of tetraploid inter-species composite cells formed through fusion of a panel of human, chimpanzee, and bonobo contributor cell lines

first: Nathan

middle: K

last: Schaefer

first: Bryan

last: Pavlovic

first: Matthew

middle: T

last: Schmitz


title: RNA-seq studies in dabrafenib treated endothelial cells

first: Maximiliano

last: Arce

address: Dag Hammarskolds väg 20

country: Sweden

institute: Uppsala University

summary: Cerebral Cavernous Malformations (CCM) constitute the second most common type of intracranial vascular malformations. Cavernomas arise due to somatic or autosomal dominant inherited loss-of-function mutations in KRIT1 (CCM1), CCM2, or PDCD10 (CCM3), forming fragile mulberry-like malformed blood vessel structures, which are prone to leak and break. Treatment is limited to surgical removal of solitary cavernomas. As patients often present with multiple lesions, there is an urgent need to develop non-invasive therapeutic strategies. We performed a high throughput screen of 5200 bioactive molecules followed by image analysis on Ccm3-knockout endothelial cells and discovered that the FDA-EMA-approved BRAF inhibitor dabrafenib, effectively restored cell-cell junctions and vascular barrier properties of CCM-deficient endothelial cells. The potential translatability of dabrafenib was tested in vivo, where it reduced cerebral lesion burden and suppressed lesion permeability, reducing perivascular plasma protein depositions. Dabrafenib also rescued abnormal structural defects present in the developing retina vasculature. Mechanistically, dabrafenib targeted extracellular regulated kinase (ERK)5-Krüppel like factor (KLF)2/4 signaling pathway and suppressed F-actin stress fiber formation, two potentially independent and central molecular processes involved in CCM pathology. Dabrafenib is a kinase inhibitor indicated for the treatment of tumors with BRAF V600E mutations. However, silencing of BRAF did not interfere with dabrafenib-induced KLF2/4 inhibition and restoration of cell-cell junctions, suggesting that its dual therapeutic outcome is independent of BRAF pathway inhibition. In conclusion, dabrafenib is a small molecular weight compound with marked inhibitory effects on cavernoma pathogenesis suggesting that CCMs could be treated with dabrafenib to block cavernoma growth and vascular leakage.

overall_design: HUVECs knocked down for CCM3 (and shControl cells) were treated with dabrafenib or vehicle for 48 hours. Then, RNA was collected and RNA-seq was perfomed to furhter investigate the mechanistical insights of dabrafenib's action upon the pathological pathways upregulated in CCM3-knockdown HUVECs.

first: Arce

last: Maximiliano

first: Sun

last: Ying

first: Peetra

last: Magnusson


title: KDM3B inhibition suppresses SHP1 expression by modulating the epigenetic landscape of the Shp1 promoter.

overall_design: ATAC profiling of shCtrl or shKdm3b EMT6 cells. ATAC profiling of EMT6 cells treated with DMSO or P3FI-90 for 24 h.

last: Yang


title: Spatial resolved single-cell dissection of mouse insula cortex organization, projection and function

first: Yi

last: Zhang

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

summary: Chronic pain is one of the major causes of human suffering with immense clinical and economic impact. Accumulating evidence suggests that the insular cortex (IC) is a central hub that integrates multi-dimensional aspects of pain. While its molecular, cellular, anatomic and connectivity complexity is consistent with its role in regulating multi-dimensional aspects of pain, its cellular composition, organization, and circuit mechanisms underlying its functions in regulating multi-dimensional aspects of pain remain poorly understood. Here we employed the spatial transcriptome profiling technology MERFISH and neural tracing to comprehensively study the organization and connectivity of the IC with single-cell high resolution. A comparative analysis of MERFISH results under normal and chronic pain conditions allowed us to identify neuron subtypes that are most impacted by chronic pain.

overall_design: Mouse brain insula cortex 10μm slices were collected and processed for MERFISH experiments with a panel of 434 genes. The MERFISH imaging was performed on a custom-built machine. For the wildtype male replicate 1 sample, 16 serial sections with 200 μm interval were collected. For all the other samples, 8 serial sections with 400 μm interval were collected.

first: Meng

first: Guoguang

last: Xie


title: Single-cell RNA sequencing of the mouse hippocampus after spared nerve injury (SNI) modeling

city: guangzhou

first: Fanning

last: Zeng

address: Nanshitou Street, Haizhu District

department: Department of Anesthesiology

institute: Zhujiang hospital, Southern Medical University

summary: Chronic pain (CP) affects more than 30% of the global population and is often accompanied by significant cognitive impairments. Although an increasing number of studies have focused on the pathological mechanisms associated with chronic pain-induced cognitive impairments, most have concentrated on the stage after the onset of cognitive impairments. Currently, the course by which chronic pain induces cognitive impairment has not been fully reported. Therefore, single-cell RNA sequencing were conducted in this study in order to map the mice hippocampus altas before and after cognitive impairments induced by spared nerve injury (SNI) on days 3, 7, 14, and 21. After quality control screening, 53852 out of 64207 cells from 11 samples were retained for subsequent analysis. The reliability of the sequencing data was verified through analysis of various evaluation indicators and sequencing alignment rates. Preliminary analysis identified 16 major cell types in the hippocampal tissue, and differential expression analysis revealed transcriptomic changes in hippocampal cells following SNI model establishment, with these early transcriptomic changes being more pronounced in neurons.

overall_design: 8w C57BL/6 WT mice were used for spared nerve injury (SNI) modeling, and hippocampal samples were collected for sequencing at 3, 7, 14, and 21 days post-surgery.

first: Yixin

last: Lin

first: Sophie

last: Xu

first: Xiaojiang

first: Tao

last: Tao


title: Glioblastoma cells utilize evolutionarily adapted cell metabolism to promote their malignant proliferation

city: Helsinki

first: Vasiliki

last: Gkini

address: Haartmaninkatu 8

department: HiLIFE/ Neuroscience Center

country: Finland

institute: University of Helsinki

summary: Glioblastoma is the most aggressive primary brain tumor in adults, with limited therapeutic success and, therefore, poor prognosis. Its malignancy is partly driven by the high proliferative capacity of glioblastoma cells, yet the underlying molecular mechanisms remain unclear. Recent studies have revealed transcriptomic similarities between glioblastoma cells and human fetal neural stem/progenitor cells (NSCs), suggesting that glioblastoma may exploit developmental programs that promote NSC proliferation. Fetal human NSCs rely on glutaminolysis—a metabolic pathway induced by the human-specific mitochondrial protein ARHGAP11B—to sustain proliferation. Here, we show that ARHGAP11B expression correlates with glioma malignancy and is essential for glioblastoma cell proliferation, implicating a critical role of glutaminolysis in tumor growth. Among glutaminolysis-related enzymes, glutamic-oxaloacetic transaminase 2 (GOT2) shows a strong positive correlation with glioma grade and poor patient prognosis. Functional assays reveal that GOT2 knockdown significantly suppresses glioblastoma cell growth, indicating that GOT2-mediated glutaminolysis is critical for their proliferation. Metabolomic profiling further shows that GOT2 is required for nucleotide precursor synthesis, underscoring its role in supporting DNA replication. Consistently, GOT2 depletion reduces the proportion of glioblastoma cells in the S phase of the cell cycle. These findings suggest glioblastoma cells hijack an evolutionarily adapted metabolic program to support malignant growth.

overall_design: Bulk RNA-seq of patient-derived glioblastoma stem cells transduced with GFP-producing lentivirus

first: Maxim

middle: M

last: Bespalov

first: Zeynep

last: Iloglu

first: Seiya

last: Yamada

first: Akira

last: Nemoto

first: Pauliina

last: Filppu

first: Kalevi

last: Trontti

first: Liliia

last: Andriichuk

first: Olli

last: Pietiläinen

first: Vadim

last: Le Joncour

first: Anni

last: Nieminen

first: Pirjo

last: Laakkonen

first: Takashi

last: Namba


title: Comparative transcriptomic profiling of TRI-LC21 and BEAS-2B cells to investigate SMARCA4-deficient undifferentiated tumor

city: Chengdu

first: Hao

last: Luo

address: Xinchuan road

institute: Sichuan university

summary: This study aimed to characterize the transcriptomic features of TRI-LC21. Due to the limited availability of well-defined in vitro models for this tumor type, we sought to investigate gene expression changes associated with SMARCA4 loss and tumor dedifferentiation.  RNA sequencing was performed to compare TRI-LC21 with the normal bronchial epithelial cell line BEAS-2B. Differential expression analysis revealed extensive transcriptional alterations, including activation of neuron-associated pathways and suppression of interferon and p53 signaling. In addition, TRI-LC21 exhibited decreased expression of epithelial markers and increased expression of stemness- and epithelial–mesenchymal transition-related genes, consistent with a poorly differentiated transcriptional state.  These data provide insight into the molecular mechanisms underlying SMARCA4-deficient tumors and support the utility of TRI-LC21 as an in vitro model for further biological and therapeutic studies.

overall_design: To explore the transcriptomic changes in TRI-LC21 cells, the normal bronchial epithelial cell line BEAS-2B was used as a control.Biological replicates were included for each group (n = 3 per group).


title: Lactation accelerates postpartum pelvic floor muscle recovery in a pregnant simulated birth injury model

city: La Jolla

first: Bianca

last: Pena

state: California

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

institute: University of California San Diego

summary: Healthy pelvic floor muscles (PFMs) are essential for proper pelvic floor function. The biggest risk factor for PFM dysfunction is injury sustained during vaginal childbirth, yet the factors that facilitate or impair PFM recovery from birth injury remain unknown. We aimed to assess the impact of the postpartum milieu in the presence and absence of lactation on PFM regeneration following simulated birth injury (SBI) in a pregnant rat model. We determined that lactating rats have a rapid increase in systemic immune markers in response to SBI, which contributes to rapid changes in PFM immune cell infiltration and decrease in pro-inflammatory genes. PFMs in lactating rats have enrichment of anti-inflammatory genes and larger newly formed myofibers that contribute to larger myofiber size after weaning. This suggests that lactation promotes an earlier anti-inflammatory response in injured PFMs that allows for quicker myogenesis and myofiber hypertrophy.

overall_design: Bulk RNA-seq profiling of pubocaudalis muscle after simulated birth injury in a pregnant rat model. Samples are from non-lactating and lactating rats at 1-week and 3-weeks post-SBI.

first: Khushi

last: Diwakar

first: Hillary

last: Tran

first: Selena

last: Cao

first: Celeste

last: Lintz

first: Laila

last: Hayes

first: Marianna

last: Alperin

first: Karen

last: Christman


title: HNRNPU Lactylation Drives Cervical Cancer Growth by Reprogramming Serine Metabolism

city: Chang Chun

first: Zhang

last: Chang

address: yong chang street

department: key laboratory of pathobiology, ministry of education,

institute: jilin university

summary: Cervical cancer remains a major global health burden, yet the molecular mechanisms driving its metabolic reprogramming are incompletely understood. Here, we identify heterogeneous nuclear ribonucleoprotein U (HNRNPU) as a novel non-histone substrate of lysine lactylation that links lactate accumulation to serine metabolism and tumor progression.

overall_design: We demonstrate that lactylation at lysine 181 (K181) stabilizes HNRNPU, enhances its binding to PHGDH mRNA, and maintains the exon 1-containing PHGDH transcript and mRNA stability, thereby sustaining PHGDH expression and activating the serine biosynthesis pathway. This metabolic rewiring promotes redox homeostasis, nucleotide synthesis, and cervical cancer cell proliferation both in vitro and in vivo. Mechanistically, we reveal a competitive interplay between lactylation and NAA50-mediated acetylation at K181, establishing a dynamic post-translational modification switch that fine-tunes HNRNPU function. Importantly, pharmacological inhibition of HNRNPU K181 lactylation by Pazopanib suppresses PHGDH expression and tumor growth, underscoring its translational potential. Collectively, our findings uncover a lactate-driven regulatory axis in which HNRNPU K181 lactylation integrates metabolic signaling with post-transcriptional regulation to promote cervical cancer progression, providing a promising therapeutic avenue for targeting metabolic vulnerabilities in malignancies.

first: Chang

last: Zhang


title: miRNA sequencing of extracellular vesicles derived from rat peripheral nerve fibroblasts

city: Nantong

first: jiahui

last: he

state: Jiangsu

address: 江苏省南通市崇川区启秀路19号

department: 神经再生重点实验室

institute: Nantong University

type: Non-coding RNA profiling by high throughput sequencing

summary: Peripheral nerve fibroblasts were isolated from the sciatic nerves of Sprague-Dawley (SD) rats. Extracellular vesicles were extracted from the culture supernatant of fibroblasts by differential ultracentrifugation and subsequently identified. Small RNA libraries were constructed using total RNA isolated from extracellular vesicles and sequenced using the Illumina miRNA-seq platform. Bioinformatics analyses were performed, including quality control of raw sequencing data, alignment against the miRBase database, quantification of miRNA expression, and screening of differentially expressed miRNAs, to explore the potential roles of extracellular vesicles miRNAs derived from nerve fibroblasts in peripheral nerve regeneration and related physiological and pathological processes.

overall_design: Three samples were prepared from exosomal miRNAs of fibroblasts, and another three samples from intracellular miRNAs of fibroblasts as controls, making a total of six samples.

first: Qianru

last: He

first: Dingding

last: Shen

first: Jiahui

first: Fei

last: Ding

first: Zhenghang

last: Cheng

first: Miaomei

last: Yu

first: Jingya

last: Liu

first: Yue

last: Zhao

first: Shiran

last: Wan


title: NSD2 Degradation Remediates the Oncogenic Cistrome in t(4;14) Multiple Myeloma

city: San Diego

first: Bo

last: Hu

address: 10300 Campus Point Dr

institute: Bristol Myers Squibb

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

overall_design: Refer to individual Series


title: NSD2 Degradation Remediates the Oncogenic Cistrome in t(4;14) Multiple Myeloma [RNA-seq]

summary: The t(4;14) chromosomal translocation drives overexpression of the histone methyltransferase NSD2 and defines a high-risk segment of multiple myeloma (MM) patients. Herein, we report the discovery of NSD2-LDD, a cereblon-recruiting and PWWP1-mediated ligand directed degrader (LDD) that selectively and potently eliminates full length and PWWP1 domain containing NSD2 protein. NSD2-LDD treatment induces global loss of H3K36me2 leading to promoter-proximal spreading of H3K27me3 and re-wiring of cis-regulatory interactions that reverse t(4;14) transcriptional programs. These effects suppress MM disease-associated phenotypes including stromal adhesion, three-dimensional colony growth and paracrine signaling. By integrating patient single cell profiles with model 3D epigenomic and spatial transcriptomics, we delineate t(4;14) disease state and the tumor-intrinsic reprogramming and resultant remodeling of the bone marrow microenvironment upon NSD2 degradation. In cell line derived xenografts and genetically engineered mouse models of t(4;14), NSD2-LDD extends median survival accompanied by tumoral H3K36me2 loss and niche re-modelling. Collectively, this work validates NSD2 as a tractable dependency and supports clinical development of NSD2 degradation as a novel, targeted therapeutic strategy in high-risk MM.

overall_design: Multi-omics profiling of several human mutiple myeloma cell lines either at baseline or upon induced NSD2 degradation via treatment with NSD2-LDD

first: Jacob

last: Edwards

first: Hardik

last: Modi

first: Diana

last: Jankeel

first: Antonia

last: Lopez-Girona

first: Deborah

middle: S

last: Mortensen

first: Lynda

last: Groocock


title: NSD2 Degradation Remediates the Oncogenic Cistrome in t(4;14) Multiple Myeloma [ATAC-seq]


title: Identification of a synovium-specific PRG4high mesenchymal stem cell subset with specialized chondroprotective function

city: Bunkyo-ku

first: Kentaro

last: Endo

state: Tokyo

address: 1-5-45 Yushima

institute: Institute of Science Tokyo

summary: This study aimed to compare human SyMSCs and AdMSCs at single-cell resolution to characterize their cellular heterogeneity and to identify subpopulations associated with chondroprotective function.

overall_design: SyMSCs and AdMSCs were isolated from patients with OA and analyzed using single-cell RNA sequencing.

first: Yuki

last: Hidaka