title: CD4+ T cell-licensed CD8+ T cells drive immunotherapy response in MHC-I negative DNA mismatch repair deficient cancer

city: Groningen

first: Marco

last: de Bruyn

address: Hanzeplein 1

department: Obstetrics&Gynecology

country: Netherlands

institute: University Medical Center Groningen

summary: DNA mismatch repair deficiency (MMRd) occurs in multiple malignancies including 10–15% of colorectal cancers (CRC), where it causes increased tumor mutational burden (TMB) and T cell response. MMRd CRC display multiple mechanisms of immune evasion, yet are highly sensitive to immune checkpoint blockade (ICB), with underlying mechanisms only partially understood. We generated genetically engineered mouse models (GEMM) of hereditary (Lynch syndrome) and sporadic MMRd CRC, and found that accelerated tumorigenesis was accompanied by universal tumor loss of major histocompatibility class I (MHC-I) expression and exclusion of cytotoxic CD8+ T cells, but not helper CD4+ T cells. MHC-I deletion (MHC-IKO) in a syngeneic MMRd CRC model reduced tumor CD8+ but not CD4+ cell infiltrate, and accelerated tumor growth. MMRd MHC-IKO tumors were resistant to anti-PDL1 ICB, but sensitive to anti-PD1 and anti-CTLA4 combination ICB (cICB) with response dependent on both CD4+ and CD8+ T cells, but not γδ-T cells. cICB resistance caused by CD4+ cell depletion was reversed by CD40 agonism, suggesting a mechanism where CD4+ cells license CD8+ cells to kill cancer cells by MHC-I-independent activity. Multimodal analysis revealed that CD4+ T cell help increases the cytotoxic state of CD8+ T cells, potentially lowering their MHC-I-independent activation threshold against cancer cells. Our results underscore the central role of MHC-I loss in tumor immune evasion, and the cooperative role of CD4+ and CD8+ cells in cICB response of MHC-I negative tumors. Our data suggest that MHC-I status may be useful as a biomarker to stratify for ICB monotherapy versus combination therapy.

overall_design: Syngeneic mismatch repair-deficient (MMRd) colorectal tumors were established in mice and treatment was initiated when tumors reached 100–120 mm³. Mice received three doses of immune checkpoint blockade (ICB) with 3-day intervals between treatments. Treatment groups included isotype control antibodies, combined anti-PD1 and anti-CTLA4 therapy, anti-PD1 plus anti-CTLA4 combined with CD4 depletion, and anti-PD1 plus anti-CTLA4 combined with CD40 agonism and CD4 depletion. Mice were sacrificed 48 hours after the final treatment dose. CD4+ and/or CD8+ T cells were isolated from tumors and tumor-draining lymph nodes by flow cytometric sorting and subjected to bulk RNA sequencing to evaluate transcriptional responses associated with immune checkpoint blockade and immune cell modulation.

first: Marta

last: Requesens

first: Luciana

last: Gneo

first: Tijana

last: Tomasevic

first: Nienke

last: van Rooij

first: Annechien

last: Plat

first: Mingjia

last: Xi

first: Charlotte

last: O'Riordan-Moore

first: Katarzyna

last: Kedzierska

first: Noelia

last: Che

first: Mark

last: Glaire

first: Yanshu

last: Cai

first: Monika

last: Madrova

first: Lai Mun

last: Wang

first: Ibrahem

last: Al-Obaidi

first: Matthieu

last: Miossec

first: Marnix

last: Jansen

first: Annabelle

last: Lewis

first: Noemi

last: Perujo Holland

first: Ian

last: Tomlinson

first: Floris

last: Foijer

first: Isabela

last: Pedroza-Pacheco

first: Hans W.

last: Nijman

first: David N.

last: Church


title: A High-Resolution Single-Cell Transcriptomic Atlas of Asexual Budding in the Stony Coral Galaxea fascicularis

status: Public on Aug 10 2026

city: 三亚

first: Xin

last: Huang

address: 海南省三亚市崖州湾科技城用友产业园1号楼

country: China

institute: Ocean University of China

type: Expression profiling by high throughput sequencing

summary: Asexual reproduction via budding is a fundamental process driving the expansion of coral colonies and maintaining reef resilience. This study presents a spatiotemporal single-cell transcriptome atlas of asexual budding in G. fascicularis. We profiled the transcriptomic heterogeneity across four discrete morphological stages: the basal coenosarc, the active budding tip, the early polyp, and the mature polyp.

overall_design: Fresh tissues representing the spatial trajectory of asexual reproduction were micro-dissected and enzymatically digested into single-cell suspensions. Cells were processed using the BD Rhapsody Express Single-Cell Analysis System. The prepared libraries were then sequenced on the GeneMind sequencing platform FASTASeq 300.


title: A transient epithelial plasticity state defines the developmental window for uterine gland specification [Spatial]

city: Columbia

first: Andrew

last: Kelleher

state: MO

address: 1030 Hitt Street

department: Ob, Gyn Womens Health

country: USA

institute: University of Missouri

summary: Uterine gland development and function is essential for reproduction and women's health, yet the epithelial cell states and signaling interactions that govern gland fate specification are not well understood. Here, integration of single cell and spatial transcriptomics with organoid culture, lineage tracing, and genetic and hormonal perturbation models were used to define mechanisms regulating postnatal uterine epithelial differentiation. A developmentally restricted epithelial plasticity state was identified that precedes luminal and glandular cell lineage segregation and accompanied by dynamic reorganization of stromal-epithelial communication during uterine differentiation. Pseudotime analysis revealed progressive acquisition of gland-associated programs, including forkhead box A2 (Foxa2), retinoic acid metabolic genes, and epithelial estrogen receptor alpha (Esr1) expression. Functional studies revealed that ESR1 acquisition and retinoic acid signaling suppress the multilayered organoid phenotype associated with epithelial plasticity, thereby promoting epithelial specification and lineage commitment. Moreover, neonatal hormonal perturbation of adenogenesis and conditional deletion of Foxa2 abolished this organoid phenotype. Together, these findings establish neonatal uterine organoids as a valuable system for investigating mechanisms that regulate glandular epithelial cell fate specification during reproductive tract development.

overall_design: Visium HD spatial transcriptomics (10x Genomics) was performed on FFPE longitudinal sections of postnatal day 5 (PND5) and postnatal day 12 (PND12) mouse uteri to characterize spatial gene expression patterns during postnatal uterine development. Five female C57BL/6J mice were used per timepoint. Sections were processed using Visium HD H1 Slide, HD probe-based v1 chemistry, with the Visium Mouse Transcriptome Probe Set v2.0 (10x Genomics).

first: Jason A.

last: Rizo

first: Sarayut

last: Winuthayanon

first: Thomas E.

last: Spencer

first: Andrew M.


title: A transient epithelial plasticity state defines the developmental window for uterine gland specification

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on uterine and cervical tissues from C57BL/6J female mice across five developmental timepoints — embryonic day 16.5 (E16.5) and postnatal days 1, 5, 12, and 15 (PND1, PND5, PND12, PND15) — to construct a transcriptional atlas of the developing mouse uterus. At each postnatal timepoint, tissues from 2 biological replicates were processed using the 10x Genomics Chromium Fixed RNA Profiling (Flex) platform. Uterus and cervix were collected separately and profiled as distinct tissue compartments. EpCAM-based magnetic sorting was performed prior to library preparation (PND1-PND15) to target an approximately equal ratio of epithelial to non-epithelial cells. Four samples per postnatal timepoint were multiplexed onto a single GEM well using Flex probe barcodes (BC001-BC004): BC001 = biological replicate 1 uterus, BC002 = biological replicate 1 cervix, BC003 = biological replicate 2 uterus, BC004 = biological replicate 2 cervix. E16.5 samples were processed without magnetic sorting or Flex multiplexing due to low epithelial cell viability. A total of 147,440 high-quality single-cell transcriptomes were retained after quality control and doublet removal for downstream analysis.


title: CD4+ T cell-licensed CD8+ T cells drive immunotherapy response in MHC-I negative MMRd cancer

city: Oxford

first: David

address: Roosevelt Drive

department: Centre for Human Genetics

country: United Kingdom

institute: University of Oxford

summary: DNA mismatch repair deficiency (MMRd) causes hypermutation and increased T cell response in multiple tumor types. MMRd colorectal cancers (CRC) display frequent immune evasion, but respond to immune checkpoint blockade (ICB), through uncertain mechanisms. We generated mouse models of MMRd CRC, and found that accelerated tumorigenesis was accompanied by loss of major histocompatibility class I (MHC-I) expression and exclusion of cytotoxic CD8+ T cells, but not helper CD4+ T cells. MHC-I deletion (MHC-IKO) in a syngeneic MMRd CRC model reduced tumor CD8+ but not CD4+ cell infiltrate, and accelerated tumor growth. MMRd MHC-IKO tumors were resistant to anti-PD-L1 ICB, but sensitive to anti-PD1 and anti-CTLA4 combination ICB (cICB) with response dependent on both CD4+ and CD8+ T cells, but not gd-T cells. CD4+ cell depletion-induced cICB resistance was reversed by CD40 agonism, suggesting that CD4+ cells license CD8+ cell cytolysis by MHC-I-independent activity. Investigation of MHC-I status as predictor of cICB vs ICB monotherapy appears worthwhile.

overall_design: RNA-seq profiling of a GEMM model comparing MMR-proficient and MMR-deficient murine polyps, along with profiling of tumours generated by injection of a mutated CT26 murine cell line and treated with immune checkpoint blockade and isotype control

first: Luciana

last: Gneo


title: Influenza A Virus Coinfection Alters Streptococcus pneumoniae Gene Expression during Upper Respiratory Tract Colonization

city: Winston Salem

first: Ming

last: Leung

state: NC

address: 1 Medical Center Blvd

department: Comprehensive Cancer Center

institute: Atrium Health Wake Forest

summary: Streptococcus pneumoniae (Spn) asymptomatically colonizes the upper respiratory tract (URT), which serves as a niche from which it can transmit to another host or cause invasive disease in the same host. While previous studies have modeled pneumococcal gene expression under infection-relevant conditions, the in vivo transcriptional adaptations that occur during nasopharyngeal colonization, particularly during influenza A virus (IAV) coinfection, are poorly understood. Here, we leveraged an established infant mouse model of colonization, shedding, and transmission to perform genome-wide transcriptomic profiling of Spn during early (day 1) and late (day 8) URT colonization and during IAV coinfection. Compared with broth-grown controls, pneumococci isolated from the URT exhibited distinct transcriptional programs, with over 200 genes differentially expressed across time points. Genes involved in carbohydrate uptake and metabolism, glycan degradation, amino sugar and nucleotide sugar metabolism, and amino acid biosynthesis were consistently enriched during colonization, highlighting metabolic adaptation to the nasopharyngeal niche. In contrast, IAV coinfection induced a markedly distinct transcriptional signature, including upregulation of branched-chain amino acid biosynthesis, bacteriocin production, and phosphate acquisition systems. Notably, the pilus islet-1 locus was upregulated during Spn-IAV coinfection. Functional studies demonstrated that while the pilus was dispensable for colonization under mono- and coinfection conditions, it promoted high-shedding events and enhanced inflammatory responses during IAV coinfection. However, reduced inflammation and reduced high shedding events from pups inoculated with a pilus-deficient mutant did not alter transmission frequency in the infant mouse model. Collectively, our findings define the in vivo transcriptional landscape of Spn during URT colonization and reveal distinct bacterial adaptations during viral coinfection, providing insight into mechanisms that influence pneumococcal persistence, inflammation, and transmission.

overall_design: RNA-seq screen of Streptococcus pneumoniae isolated from the upper respiratory tract of infant either at 24 hours post inoculation, 8 days post inoculation, 8 days post inoculation with a concurrent Influenza A infection, all compared to Tryptoc Soy Broth grown Streptococcus pneumonioae. Strain used for the study is TIGR4 a serotype 4 isolate.

first: Noah

middle: A

last: Nutter

first: Alicia

last: Costa-Terryll

first: Lance

middle: M

last: Miller

first: Pengbo

last: Zhang

first: Daniel

last: Fecko

first: M. Ammar

last: Zafar


title: Transcriptional changes in brain leukocytes after myocardial infarction

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

summary: Myocardial infarction (MI) causes systemic inflamamtion in various organs including the brain. However, it is not known how MI causes inflammatory cell accumulation in the brain. In this study, we induced MI by coronary ligation and then sorted leukocytes from the brain four months after MI.

overall_design: Sham or MI surgeries were performed in C57BL/6 mice. Brain single cell suspensions were isolated and stained with antibodies against CD45. Viable CD45+ cells were isolated using FACS.

first: Afaz

last: Uddin


title: Transcriptomic Profiling of Thyroid Eye Disease Orbital Fibroblasts

city: Rochester

first: Collynn

last: Woeller

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary: This project aims to define the persistent transcriptomic alterations in orbital fibroblasts (OFs) derived from patients with thyroid eye disease (TED) compared to non-TED OF controls. Primary OFs were isolated from orbital connective tissue and expanded in vitro under standardized conditions. We performed high-depth RNA sequencing on these cells to characterize the differential expression of genes involved in extracellular matrix remodeling, inflammatory signaling, and metabolic activation. This dataset provides a comprehensive resource for identifying the molecular drivers of orbital remodeling in the context of TED.

overall_design: Primary human orbital fibroblasts from patients with or without thyroid eye disease were cultured and analyzed by RNAseq

middle: F


title: The fungal pathogen Candida auris exposes chitin to trigger IFNg and persist in hair follicles [EDM_bulkRNA-seq]

city: San Francisco

first: Charlotte

last: Hurabielle

state: CA

address: 513 Parnassus Avenue

institute: University of California, San Francisco

summary: Candida auris is an emerging multidrug-resistant fungus that has sparked public health alarm. However, the mechanisms supporting its persistence in skin, a major risk factor for deadly outbreaks, remain unclear. Here, we compared skin colonization by C. auris with that of the related pathobiont C. albicans, illuminating fungal–immune interactions. C. auris exhibited enhanced skin persistence, tropism to hair follicles, and direct binding to hair. Whereas C. albicans triggered a type 3/17-skewed sterilizing antifungal immune response, C. auris triggered a type 1 IFNg-driven response directed toward hair follicles. IFNg unexpectedly enhanced C. auris colonization through direct signaling to keratinocytes, impairing barrier integrity and repressing antifungal defense programs. Genetic and biochemical approaches demonstrated that, in response to skin-associated cues, C. auris upregulates the exposure of cell wall chitin, which is sufficient to trigger type 1 immunity and benefit the pathobiont.

overall_design:
Primary human keratinocytes were isolated from neonatal foreskins and grown as air-lifted 3D epidermal equivalents. Cultures were treated from day 7 with IL-17A (10 ng/mL), IFNg (10 ng/mL), both cytokines, or control medium, then harvested at day 14 for bulk RNA sequencing. Four donors were used; the number of technical replicates per donor varied by treatment group (1-2 per donor).

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

first: Eric

middle: D

last: Merrill

first: Victoria

last: Prudent

first: Pauline

last: Basso

first: Emilie

last: Rapp

first: Parna

last: Moghadam

first: Abram

last: Rodriguez

first: Ethan

last: Hung

first: Jeffrey

last: Cheng

first: Raymond

last: Cho

first: Brook

last: Abegaze

first: Amanda

last: Buck

first: Kennedi

last: Pyper

first: Allessandra

last: Veinbachs

first: Elina

middle: K

last: Wells

first: Tiffany

middle: C

last: Scharschmidt

first: Michael

last: Rosenblum

first: Ari

middle: B

last: Molofsky

first: Suzanne

last: Noble


title: The fungal pathogen Candida auris exposes chitin to trigger IFNg and persist in hair follicles

first: Charlotte

last: Hurabielle

overall_design: Mouse back skin was topically colonized with either C. auris or C. albicans on days 0,2,4,6 and harvested on day 14. Cells were FACS sorted for CD45+ and CD45 negative in a 1:1 ratio, conditions were multiplexed, and scRNA sequencing was performed

first: Eric

last: Merrill

first: Victoria

last: Prudent


title: The fungal pathogen Candida auris exposes chitin to trigger IFNg and persist in hair follicles [scRNA-seq EDM_exp2]

overall_design: Mouse back skin from IFNgKO, IFNgOE (Yeti), IL17afKO and wild type mice was topically colonized with C. auris on days 0,2,4,6 and harvested on day 14. Cells were FACS sorted for CD45+ and CD45 negative in a 1:1 ratio, conditions were multiplexed, and scRNA sequencing was performed

first: Pauline

last: Basso

first: Emilie

last: Rapp

first: Parna

last: Moghadam


title: An engineered bovine mesenchymal stem cell platform enables scalable cultivated meat production

city: Rehovot

first: Sharon

last: Schlesinger

address: Herzl 229

department: Animal Science

country: Israel

institute: Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem

summary: Cultivated meat production requires cell platforms that combine long-term proliferative stability with efficient differentiation and compatibility with scalable manufacturing workflows. Mesenchymal stem cells (MSCs) are attractive in this context because of their adipogenic potential and relative ease of isolation and expansion, but primary MSCs undergo replicative senescence and typically show limited myogenic competence. Here, we developed an engineered bovine Wharton’s jelly derived MSC platform designed to address these limitations. We compared two immortalization strategies, hTERT and SV40 large T antigen, and found that hTERT-mediated immortalization maintained MSC marker expression and robust neutral lipid accumulation consistent with adipogenic induction, whereas SV40 immortalization was associated with marked genomic instability. However, although immortalized MSCs retained robust adipogenesis, myogenic differentiation remained inefficient. To overcome this bottleneck, we introduced an inducible MYOD program into WJ-hTERT cells. Upon doxycycline induction and exposure to a reduced myogenic differentiation cocktail, the engineered cells underwent rapid and efficient myogenic differentiation, with extensive multinucleated myotube formation, actin alignment, and induction of canonical myogenic markers. We further demonstrate that these cells are compatible with long-term 3D spheroid culture, enabling repeated weekly expansion cycles over more than 60 days, and can subsequently be transferred onto edible cellulose scaffolds for lineage-specific differentiation. On scaffolds, the cells supported both adipogenic remodeling and organized myogenic differentiation. In addition, pre-loading scaffolds with myogenic factors reduced the need for repeated growth factor supplementation during maturation, suggesting a route toward lower-cost differentiation workflows. Together, these results establish proof-of-concept modular bovine MSC-based cultivated meat platform in which controlled immortalization, inducible myogenic programming, suspension-compatible expansion, and scaffold-guided tissue formation are each validated and interoperable at the module level.

overall_design: Immortalized bovine MSC line was generated by transient transfection of primary WJ-MSCs with a plasmid encoding the SV40 large T antigen, kindly provided by Prof. Sara Selig. Transfections were performed using the TransIT LT1 transfection reagent (Mirus Bio, MIR 2300) according to the manufacturer’s instructions. Colonies were expanded and subsequently assessed for proliferation, morphology, and genomic stability.

first: Ivana

last: Ribarski-Chorev

first: Shadi

last: Tawil

first: Ilana

last: Vainshtein

first: Dafna

last: Shpatz

first: Yael

last: Gilad

first: Eran

last: Lavi

first: Adar

last: Kfir

first: Ilan

last: Brajzblat

first: Jonathan

last: Giron

first: Oded

last: Shoseyov


title: Valve organoids recapitulate human in vivo organogenesis and pathological processes

first: guang

last: li

address: 530 45th St. 8116 Rangos Research Center

institute: university of pittsburgh

summary: Heart valves maintain unidirectional blood flow, yet most understanding of their development and disease comes from animal models that do not fully capture human valve physiology. We present a human valve organoid model that recapitulates in vivo valve features at cellular and molecular levels. We have profiled the valve cells using single cell mRNA-sequencing at different developmental stages.

overall_design: Valve organoids at different stages including day 8, 11, 14, 26, and 33 were profiled with single cell mRNA-sequencing. The samples at different stages were firstly labeled with an unique MULTI-seq barcode. Afterward, the labled samples were pooled together and profiled with the standard scRNA-seq pipeline.

first: He

last: Yuanhang

last: Haoting

first: Li

last: Guang


title: Transient cell states encode positional information to direct asymmetric growth [MERFISH]

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: How tissues generate asymmetric growth from spatially and temporally restricted signals remains a fundamental challenge in developmental biology. We show that transient cell states encode positional information that instructs asymmetric growth in plants. Using spatial single-cell transcriptomics and multi-omics, we uncover a surprisingly complex landscape of transient cell states in the apical hook, including a previously unrecognized population in the apical hypocotyl region that integrates developmental and hormonal cues and bifurcates into opposing growth trajectories. Gene regulatory network analysis and functional perturbation establish GATA TRANSCRIPTION FACTOR 2 (GATA2) as a central regulator that promotes cell elongation through gibberellin signaling. These results reveal that diverse, spatially localized transient cell states function as regulatory hubs that convert positional information into divergent growth programs, providing a unifying framework for how dynamic cellular states shape organ morphology.

overall_design: MERFISH experiments using a 1,000 target gene panel were performed on 3d-old Arabidopsis etiolated seedlings. Six to ten independent seedlings were embedded and sectioned for each genotype and treatment assayed. Two independent MERFISH experiments were perfored on tissue sections from the same tissue block to ensure biological and technical result replication.

first: Travis

last: Lee

first: Kamonkan

last: Gamnerdsiri

first: Natanella

last: Illouz-Eliaz

first: Tatsuya

last: Nobori

last: Nery

first: Bruce

last: Jow

first: Michelle

last: Liem

first: Caz

last: O'Connor


title: Transient cell states encode positional information to direct asymmetric growth [multiome]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: single-cell multiome


title: Transient cell states encode positional information to direct asymmetric growth [snRNA-seq]

overall_design: snRNA-seq


title: RNA-seq of human iPS cell-derived retinal ganglion cells

city: Aoba-ku, Sendai

first: Seiya

last: Kanno

state: Miyagi

address: 1-1 Seiryo-cho

department: Department of Ophthalmology

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: The integrin family is a key regulator of cellular behavior, transducing adhesion signals through interactions with the extracellular matrix (ECM). Despite its central role in retinal ganglion cell (RGC) survival and neurite outgrowth, the comprehensive expression profile of integrins in human RGCs remains poorly characterized. In this study, we performed RNA sequencing on human iPSC-derived RGCs to elucidate their global transcriptomic landscape. Following a modified Sluch et al. (2017) protocol, RGCs were differentiated from 201B7 iPSCs and isolated at day 40 via CD90.2/Thy1.2-targeted magnetic-activated cell sorting (MACS). Our analysis confirmed robust expression of canonical RGC markers and revealed a significant enrichment of genes involved in ECM-mediated signaling, providing new insights into the molecular basis of RGC-scaffold interactions.

overall_design: Transcriptomic analysis of human RGCs derived from 201B7 iPSCs. RNA-seq was conducted on samples harvested at differentiation day 40. The dataset consists of three independent biological replicates.

first: Masayuki

last: Yamashita

first: Kota

last: Sato

first: Toru

last: Nakazawa


title: Niche-driven plasticity of bipotent basal epithelial cells in the human ocular surface [RNA-Seq]

city: Seattle

first: Yuzuru

last: Sasamoto

state: WA

address: 750 Republican St

department: Ophthalmology

institute: University of Washington

summary: The human ocular surface comprises corneal and conjunctival epithelia separated by the limbus, a specialized niche that maintains corneal transparency through limbal stem and progenitor cells (LSCs). LSC loss or dysfunction causes limbal stem cell deficiency (LSCD), characterized by conjunctivalization, neovascularization, chronic inflammation, and corneal scarring, leading to severe visual impairmen. LSCD may result from injury, autoimmune disease or genetic disorders, yet current treatmens, including limbal transplantation and ex vivo–expanded epithelial grafts, are limited by donor availability and variable long term efficacy. Until now, the limbus has been regarded as a static boundary enforcing lineage segregation between corneal and conjunctival epithelia. Here, we show that the human limbus instead harbors bipotent basal epithelial progenitors that are transcriptionally more similar to conjunctival than corneal basal cells and whose fate is directed by local niche cues. Keratinocyte growth factor (KGF) signaling through FGFR2 promotes corneal epithelial differentiation, whereas epidermal growth factor (EGF) maintains conjunctival identity. This niche dependent epithelial plasticity provides a mechanistic explanation for conjunctivalization in LSCD and identifies KGF–FGFR2 signaling as a potential therapeutic target for corneal epithelium restoration. Together, these findings redefine the limbus as a dynamic progenitor niche with broad implications for stem cell biology and regenerative medicine.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data. We used cultured human corneal epithelial cells treated with different growth factors at different stages (n = 4 donors).

***************************************************************
Raw data cannot be listed here due to the donors' privacy concerns.
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first: Yoshiko

last: Fukuda

first: Shinri

first: Kosei

last: Suzuki

first: Catherine

first: Shoko

last: Kiritoshi

first: Nick

last: Di Girolamo

first: Markus

middle: H

last: Frank

first: Natasha

middle: Y

first: Shuoshuo

last: Wang

first: Sheethal

middle: U

last: Nagalakshmi

first: Ioannis

middle: S

last: Vlachos


title: Principles of cotranslational membrane protein biogenesis by EMC

city: Chicago

first: Qianru

last: Li

state: IL

address: 303 E. Superior Street

institute: Northwestern University

summary: Here we use selective ribosome profiling to reveal the substrate range of EMC and the timing of its association with the ribosome-translocon complex.

overall_design: Selective ribosome profiling of HEK293 cells expressing near-endogenous levels of Flag-tagged EMC6, EMC7, and EMC10. Both the solubilized microsomes ("input") and affinity-purified fractions ("IP") were collected for profiling.

first: Arunkumar

last: Sundaram

first: Yu

last: Wan

first: Josephine

last: Tang

first: Zhe

last: Ji

first: Robert

middle: J

last: Keenan


title: Niche-driven plasticity of bipotent basal epithelial cells in the human ocular surface [scRNA-seq]

first: Yuzuru

first: Yoshiko

last: Sato

last: Lee


title: Next-GenerationPediatric Cancer Models: Patient-Matched Orthotopic Xenografts, 3D Organoids, 2D Cultures, and Cell Lines for Identification of Therapeutic Vulnerabilities in Pediatric Solid Tumors

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

summary: Most pediatric solid tumor cell lines were established decades ago, so patient-matched organoids and xenografts are not available, limiting their translational utility. Here, we present a new approach to generate triads of patient-matched xenografts, 3-dimensional (3D) organoids, and 2D cultures. We have generated 3D organoids from 135 pediatric tumors, including rhabdomyosarcoma, osteosarcoma, neuroblastoma, Ewing sarcoma, Wilms tumor, and retinoblastoma. We have also generated patient-matched 2D cultures (n=82) and cell lines (n=20). When these 3D organoids, 2D cultures, or cell lines were orthotopically implanted into immunocompromised mice, they replicated the molecular and cellular features of the original patient tumor and xenograft. We have completed 352 single-cell and single-nucleus RNA-sequencing experiments (>2.2 million cells) to confirm that our patient-matched triads preserve tumor cell heterogeneity. All samples are renewable and >3,000 vials have been cryopreserved for unrestricted distribution through the Childhood Solid Tumor Network. We demonstrate the utility of patient-matched triads for identifying therapeutic vulnerabilities, providing a powerful tool for advancing pediatric cancer research.

overall_design: Using patient derived orthotopic xenografts (T0), we generated organoids (3D), cell cultures (2D) and established cell culture (CCLF) to model different solid tumors. We were able to validate these models by reinjecting into xenografts and allowing new tumors to grow (VT).

first: Justina

last: McEvoy

first: Melody

last: Allensworth

first: Mariajose

last: Franco

first: Shannon

last: Sweeney

first: Natalie

last: Geiger

first: Juliette

last: Kippen

first: Asha

last: Jannu

first: Stefan

last: Atkinson

first: Ayush

last: Attery

first: Chen

last: Hu

first: Shay

last: Sneed

first: Asa

last: Karlstrom

first: Cynthia

last: Cline

first: Cody

last: Ramirez

first: Antonia

last: Chroni

first: Hongjian

last: Jin

first: Yiping

last: Fan

first: Gang

last: Wu

first: Beisi

last: Xu

first: Abbas

last: Shirinifard

first: Jackie

last: Norrie

first: Brittney

last: Gordon

first: Kaitlin

last: Lord

first: Jakayla

last: Johnson

first: Madison

last: Parks

first: Heather

last: Sheppard

first: George

last: Campbell

first: Jennifer

last: Peters

first: Cam

last: Robinson

first: Carmen

last: Rios

first: Ruvimbo

last: Dzurumi

first: Hannah

last: Golding

first: Lindsey

last: Sheft

first: Anang

last: Shelat

first: Yuen-Yi

last: Tseng

first: Anand

last: Patel

first: Elizabeth

last: Stewart


title: Mysm1 mutations in meander tail mice cause anterior-selective cerebellum malformation

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Mouse meander tail (mea) mutations produce kinked tails and selective malformation of the cerebellum anterior compartment. The anterior cerebellum defects are cell autonomous with respect to granule cell precursors, but the molecular basis has not been known. Myb-like, SWIRM, and MPN domain containing protein 1 (MYSM1) is a chromatin-associated deubiquitinase that promotes gene expression by removing monoubiquitin from histone H2A, among other targets. Loss of MYSM1 function in mice or humans results in bone marrow failure with defective maturation of B cell lineages. Here we show that extant mea alleles have mutations in Mysm1 and cause both neurological and hematological phenotypes, as do new endonuclease-mediated mutations. Multimodal single-nucleus assays show Mysm1 effects on gene expression in several lineages and on the proportion of granule cell precursors by E14.5.  Intriguingly, Mysm1 orthologs have been independently lost in several animal and fungal lineages, including yeast, flies, and nematodes. These results unite previously disconnected literature and demonstrate a requirement for MYSM1 activity in compartment-specific development in developing mammalian brain and suggest potential for compensatory pathways.

overall_design: Multiome comparison of cerebellums from four mutant and wild-type mouse pairs. BKS and FVB mouse strains were used, with two pairs of mice from each strain.

first: Bruce

last: Hamilton

first: Dorothy

last: Concepcion

first: Nathan

last: Zemke

first: Christopher

last: Benner


title: Genome-directed discovery of an octalin-containing polyether ionophore improves diabetic skin wound healing

city: Guangzhou

first: liang

middle: liang

last: Bai

address: 26 Yuancun Erheng Road

institute: The Sixth Affiliated Hospital Sun Yat-Sen University

summary: Chronic hard-to-heal skin wounds in diabetes mellitus are a prevalent and formidable medical challenge, emphasizing the urgent need for innovative therapeutic pharmaceuticals. Herein, we report the identification of a new polyether biosynthetic gene cluster (pdm BGC) from the marine-derived Streptomyces marincola SCSIO 03032 through genome mining. The product of the pdm BGC was increased 48-fold by overexpression of the positive regulator gene pdmRI in this BGC to direct the isolation, structural determination, and biosynthesis analysis of a unique octalin-containing polyether ionophore polydecalinmycin (PDM). Further bioactivity investigations identified PDM as a dual sodium (Na+) ionophore and protonophore. This dual functionality induces a moderate mitochondrial Na+ and H+ leak, thereby enhancing the generation of reactive oxygen species and ameliorating mitochondrial energy metabolism. This novel and comprehensive strategy endows PDM with versatile effects on cells involved in wound healing, facilitating key healing processes such as proliferation, migration, and angiogenesis. Notably, we reveal the promising potential of PDM as a natural agent capable of expediting skin wound healing, especially in chronic diabetic wounds. These findings hold important implications for the treatment of diabetic wounds.

overall_design: RNA-Seq Profiling of  mouse skin Treated with PDM versus DMSO Control

first: Yingjie

last: Li

first: Liangliang


title: E11.5 Branchial Arches RNA-seq from controls and Ehmt1/2 neural crest knockouts

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: GLP and G9a repress alternative fate pathways in the neural crest. Analyses of transcript profiles from 3 control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre) and 3 DKO (Ehmt1f/f, Ehmt2f/f, Rosa26 TdTomato/+, Wnt1-cre) E11.5 embryos demonstrated signficant upregulation of alternative fate programs in DKOs, but no observed difference in the expression of gene sets associated with cellular proliferation, apoptosis, or migration. Control embryos showed enrichment of genes associated with neural crest differentation and positive regulation of osteoblast differentiation. Alternatively, DKOs were signficantly enriched for genes associated with cardiac muscle, endothelial and myofibroblast lineages. Taken together, our RNA-seq data demonstrate that loss of GLP and G9a in the neural crest population leads to aberrant expression of alternative fate genes.

overall_design: Branchial arches from E11.5 control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre) and DKO (Ehmt1f/f, Ehmt2f/f, Rosa26 TdTomato/+, Wnt1-cre) were dissected in cold PBS. The tissues were then dissociated into single cell solutions with papain. Cells were washed twice in PBS, and then flow sorted on endogenous Td Tomato expression. Td Tomato cells were collected and stored in RNAlater until RNA extraction and library prep. RNA was extracted with a Qiagen RNeasy Plus Mini kit, and libraries prepped with  Illumina Stranded mRNA Prep.

first: Diana

last: Fulmer

first: Cheryl

middle: L

last: Smith

first: Rajan

last: Jain

first: Jonathan

last: Epstein


title: Transcriptome profiling of adult zebrafish skeletal muscle at 7 days post-cryoinjury

city: Belgrade

first: Mirjana

last: Novkovic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetic and Genetic Engineering

summary: Skeletal muscle regeneration is a complex, multistep process involving coordinated activation of injury responses, tissue remodeling, and myogenic programs. Adult zebrafish represent a robust model for studying these processes in vivo. We performed transcriptome profiling of adult zebrafish skeletal muscle following severe cryoinjury of the posterior trunk musculature. Gene expression was analyzed at 7 days post-cryoinjury, corresponding to an early stage of repair characterized by completion of muscle degradation and the onset of new muscle fiber formation at the injury site, as previously described by Jazwinska et al (2024). This dataset captures transcriptional changes associated with early regenerative events and provides a resource for investigating molecular pathways underlying skeletal muscle regeneration.

overall_design:
Transcriptome profiling was performed to assess gene expression changes during skeletal muscle regeneration in adult zebrafish following cryoinjury. Severe injury was induced in the posterior trunk musculature (a region lacking body cavities and visceral organs) by applying a liquid nitrogen–precooled cryoprobe to one side of anesthetized fish for 6 s. At 7 days post-injury, fish were euthanized and caudal peduncles were collected for RNA isolation. The cryoinjured group consisted of four biological replicates. Non-injured control samples were derived from a previously deposited dataset (GSE277480).

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

last: Kojic

first: Andjela

last: Milicevic

first: Emilija

last: Milosevic

first: Jovana

last: Jasnic


title: CX3CR1⁺ CD8⁺ Cytotoxic T Cells Drive Tumor Killing in Esophageal Squamous Cell Carcinoma During Neoadjuvant Therapy

city: Beijing

first: Zhihua

last: Liu

state: Beijing

address: State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China

summary: The efficacy of immune checkpoint blockade (ICB) in esophageal squamous cell carcinoma (ESCC) remains highly variable, and the underlying mechanisms driving differential responses are poorly understood. Here, we performed single-cell RNA sequencing (scRNA-seq), T cell receptor (TCR) sequencing, and whole exome sequencing (WES) on 52 ESCC patients from a phase III neoadjuvant clinical trial to characterize the tumor microenvironment (TME) and its association with therapeutic outcomes. We identified a selective expansion of non-exhausted cytotoxic CD8⁺ T cells, particularly CX3CR1⁺ CD8⁺ T cells, in well responders, driven by the CX3CL1-CX3CR1 axis. These cells exhibited high cytotoxicity, clonal expansion, and tumor-killing potential, while exhausted T cell subsets, including CXCL13⁺ CD8⁺ T cells, were reduced in well responders. Pre-treatment tumor mutational profiles revealed that a high cancer cell fraction (CCF) mutation burden and neoantigen abundance were predictive of response, with immune editing reducing immunogenic mutations post-treatment. Additionally, tumor epithelial differentiation (Gp1/Gp2 subtypes) and stromal remodeling influenced treatment outcomes, with Gp2 tumors associated with immune suppression and resistance. Our findings provide new insights into the immune dynamics of ESCC, highlighting CX3CR1⁺ CD8⁺ T cells, the CX3CL1-CX3CR1 axis, and tumor differentiation as potential therapeutic targets to enhance ICB efficacy.

overall_design:
A total of 52 patients with ESCC. All patients were treatment-naïve, and tumors were classified according to WHO criteria. Clinical staging was determined using the UICC/AJCC TNM staging system. For tumor biopsy samples, pre- and post-treatment samples were obtained from the same primary tumor before and after 2 cycle of treatment. Each tumor was punctured by two or three needles, using 16-gauge needles for ESCC. All sample collection procedures complied with the regular routine in clinical practice.

***Submitters state "We removed the tumor stage information (to avoid providing non-compliant clinical data) as the staging information we recorded did not match the official staging system (UICC/AJCC TNM classification)"***

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

last: Zhao

first: Ruixiang

last: Zhang

first: Yang

first: Songming

first: Cheng

first: Zhaoren

last: He

first: Yin


title: Epithelial cells program adaptive immunity through antigen compartmentalization

city: Birmingham

first: Casey

middle: T

last: Weaver

state: AL

address: 1900 University Blvd, THT Building

institute: University of Alabama at Birmingham

summary: Intestinal epithelial cells (IECs) serve as critical interfaces between the host immune system and enteric pathogens, yet their role in orchestrating mucosal immune responses remains incompletely understood. Major histocompatibility complex class II (MHCII) expression on IECs has been proposed to contribute to antigen presentation and T cell priming during intestinal infection, but the cell type-specific transcriptional programs influenced by epithelial MHCII remain unclear. Here, we performed single-cell RNA sequencing (10x Genomics) to comprehensively profile intestinal epithelial and immune cell populations during Citrobacter rodentium infection. We analyzed colonic tissues from H2-Ab1^fl/fl (wild-type) and H2-Ab1^Villin (IEC-specific conditional knockout) mice at naïve baseline and days 9, 14, and 42 post-infection, capturing acute infection, peak response, and memory phases. This dataset enables dissection of MHCII-dependent and -independent transcriptional responses across diverse epithelial lineages and immune cell subsets, providing insights into how IEC-intrinsic MHCII expression shapes mucosal immunity and tissue-resident memory formation during bacterial infection.

overall_design: To investigate the role of MHCII expression on intestinal epithelial cells (IECs) during enteric bacterial infection, we performed single-cell RNA sequencing on colonic tissues from H2-Ab1^fl/fl (wild-type) and H2-Ab1^Villin (IEC-specific MHCII conditional knockout) mice across multiple infection stages. Mice were infected with Citrobacter rodentium strain DBS100 (2×10^9 CFU by oral gavage) and tissues were harvested at four timepoints: naïve (day 0), day 9 (acute infection), day 14 (peak response), and day 42 (memory phase) post-infection. For each condition, mid-distal colons from 2-3 mice were pooled to generate biological replicates. In total, 52 samples were processed, with 2 biological replicates per condition (2 genotypes × 4 timepoints × 3 tissue compartments) except for day 9 IECs, which had 3 replicates per genotype.

first: C. Garrett

last: Wilson

first: M. Pragun

last: Acharya

first: Lennard

middle: W

last: Duck

first: Laura

last: Karsch

first: Nana

last: Twumasi-Ankrah

first: Wang

last: Yuanyou

first: Hongxing

last: Shen

first: Vishal

last: Oza

first: Blake

last: Frey

first: Stacey

middle: N

last: Harbour

first: Yoshiko

last: Nagaoka-Kamata

first: Robin

last: Hatton

first: Jeffrey

last: Moffitt

first: Matthias

last: Gunzer

first: Carlene

last: Zindl


title: The tuberculosis-associated microenvironment promotes HIV-1 persistence by impairing CD8+ T cell-mediated viral control

city: Sydney

first: Jennifer

last: Simpson

address: 176 Hawkesbury Rd

country: Australia

institute: WIMR

summary: Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is the most common coinfection in people living with HIV-1 (PLWH). This coinfection is associated with accelerated HIV-1 disease progression and reduced survival. However, the immunological and virological mechanisms driving this progression are incompletely understood. To address this knowledge gap, using pleural effusion samples from PLWH and TB, we investigated the HIV-1 genetic landscape and the anti-HIV-1 immune response impacted by a TB-associated microenvironment. Our results revealed an enrichment of genetically intact HIV-1 and impaired CD8+ T cell- mediated antiviral response at the site of HIV-1/Mtb coinfection. These findings indicate that the TB-associated microenvironment promotes the persistence of cells infected with replication-competent HIV-1 by creating a niche of reduced antiviral immune pressure, potentially contributing to the worsened clinical outcomes observed in PLWH and TB.

overall_design: Ths study uses single-cell RNA and TCR sequencing of a multiplexed sample (pleural effusion fluid) from an individual living with HIV and TB coinfection. Sequencing was conducted using the BD Rhapsody sequencing pipeline.


title: Roles of RNF213 in temporal resonse to palmitate in HeLa cells

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

summary: We aimed to study roles of RNF213 in palmitate-induced signaling pathways using RNF213-knockout HeLa cells.

overall_design: PolyA-tailed RNA profiles were obtained for paretal and RNF213-knockout HeLa cells stimulated with 0.5 mM palmitate for 0, 1, 3, 6, 12, or 18 h.

first: Qianying

last: Huang

last: Iida

first: Tohru

last: Tezuka


title: Comprehensive transcriptome and epigenome profiling of A2780 models reveals distinct programs of cisplatin, paclitaxel, and dual resistance

first: Wonyoung

last: Choi

address: 3 N Dunlap St

department: Pathology

institute: UTHSC

summary: Ovarian cancer is the most lethal gynecologic cancer, largely because most patients eventually relapse after initially responding to platinum- and taxane-based chemotherapy. To understand how cancer cells adapt to these drugs, we generated cisplatin-resistant (CpR), paclitaxel-resistant (TxR), and dual-resistant (TxCpR) derivatives from the parental A2780 cell line and profiled their transcriptomes and chromatin landscapes using RNA-seq and ATAC-seq. The three resistant lines displayed distinct cellular morphologies, gene expression profiles, and chromatin accessibility patterns. Notably, the dual-resistant state was not simply a combination of the cisplatin- and paclitaxel-resistant states but instead represented a unique regulatory configuration. Integrative analysis of RNA-seq and ATAC-seq identified potential regulators associated with specific drug-resistance of A2780. Furthermore, we suggested resistance-specific distal regulatory regions highly related with transcription factors either directly or indirectly involved in cancer progression, cell plasticity and chemotherapy resistance. Our paired RNA-seq and ATAC-seq datasets provide valuable and comprehensive resources for exploring how enhancer–transcription factor interactions drive chemotherapy resistance and for identifying new therapeutic targets in ovarian cancer.

overall_design: ATAC-seq profiling of control A2780 and their drug-resistant derivatives (Cisplatin-resistant A2780, Paclitaxel-resistant A2780 and Cisplatin and Paclitaxel daul resistant A2780).

first: Choi

last: Won-Young

first: Perkins

last: Rachel

first: Zhang

last: Wenjing


title: Comprehensive transcriptome and epigenome profiling of A2780 models reveals distinct programs of cisplatin, paclitaxel, and dual resistance [RNA-seq]

overall_design: RNA-seq profiling of control A2780 and their drug-resistant derivatives (Cisplatin-resistant A2780, Paclitaxel-resistant A2780 and Cisplatin and Paclitaxel daul resistant A2780).

first: Won-Young

first: Rachel

last: Perkins

first: Wenjing

last: Zhang


title: Effect on gene expression and RNA splicing with CRISPR/Cas9 knockout of PTBP1, PTBP2, or both in MOLM-13, MV4-11, and K-562 human leukemia cell lines

first: Junwei

last: Shi

address: 421 Curie Boulevard

department: Cancer Biology

summary: RNA-modifying enzymes (RNAes) and RNA-binding proteins (RBPs) have emerged as critical gene regulators in both normal physiology and cancer. To systematically evaluate their necessity in cancer, we performed domain-focused CRISPR screens targeting RNAes and RBPs across a broad spectrum of cancer cell lines. These screens identified novel acute myeloid leukemia (AML) dependencies, including PTBP1, with a bias toward KMT2A-rearranged (KMT2A-r) AML, an aggressive subtype with poor clinical outcomes. Genetic and cellular validation confirmed all four RNA-binding domains in PTBP1 are required for KMT2A-r AML proliferation. PTBP1 loss led to cell cycle arrest, apoptosis, and induction of myeloid differentiation programs. Transcriptomic analyses revealed widespread dysregulation of gene expression and splicing. eCLIP-seq further showed PTBP1 binds to a subset of these transcripts critical for AML proliferation, including ACSL4, DPF2, and IKZF1. Our findings demonstrate that PTBP1 supports AML proliferation by fine-tuning the expression and splicing of AML-essential genes and provide a workflow for systematically annotating RNAe and RBP dependencies in cancer.

overall_design: Human KMT2A-MLLT3 fusion AML lines MOLM-13 and MV4-11 or the control human CML line K-562 engineered to express Cas9 were lentivirally transduced in triplicate with sgRNAs targeting PTBP1, PTBP2, both PTBP1 and PTBP2, or a control (the non-targeting Mus musculus ROSA26 locus or the non-expressed EMX1). Cells were harvested at day 5 post-infection for RNA extraction and RNA sequencing.

first: Zhendong

last: Cao

first: Kurtis

last: McCannell


title: Evaluation of PTBP1 binding at transcripts in the human acute myeloid leukemia cell line MOLM-13

overall_design: PTBP1 was immunoprecipitated with two different antibodies from human KMT2A-MLLT3 fusion AML line MOLM-13 for eCLIP-seq evaluation of bound RNAs. Input material was used as a control.


title: Epigenetic training licenses naïve CD8⁺ T cell metabolic fitness and function

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Naïve T cells maintain quiescence yet must respond rapidly to antigens, but how they prime this capacity is unclear. We identify histone variant H2A.Z as a key regulator of an epigenetic training program that licenses quiescent naïve CD8+ T cells for future activation. H2A.Z deficiency disrupts naïve T cell homeostasis and effector responses. Multi-omics reveals that H2A.Z is selectively deposited at OXPHOS gene promoters in quiescent naïve CD8+ T cells, priming the chromatin for rapid transcriptional induction. This training is developmentally instructed by tonic IL-7 signaling and regulated by transcription factor GABPα. Age-related decline in IL-7 signaling reduces H2A.Z occupancy and impairs T cell activation, while IL-7 supplementation or enforced H2A.Z expression rescues this defect. H2A.Z overexpression also enhances CAR-T cell stemness and antitumor efficacy. Our work defines an IL-7R–GABPα–H2A.Z–OXPHOS axis that epigenetically establishes metabolic and functional fitness in quiescent T cells, offering insights for immunotherapy targeting ageing and tumors.

overall_design: Naïve CD4+ T (CD62LhiCD44lo) cells or naïve CD8+ T (CD62L+CD44lo) cells were purified from spleens of WT and H2A.Z-cKO, WT and GABPa-cKO, BCL2+ WT and BCL2+ IL-7R-cKO mice. Then the sorted naïve T cells were stimulated with anti-CD3 and anti-CD28 antibodies (Abs) for 24 h, RNA-seq were performed before or after stimulation (3 biological replicates).

first: Mengjie

last: Lv

first: Jiyu

last: Ding

first: Haizhen

last: Long

first: Qian

last: Chai

first: Guohong

last: Li


overall_design: Naïve CD8+ T (CD62L+CD44lo) cells were purified from spleens of  WT and H2AZ-cKO. The sorted naïve T cells were stimulated with anti-CD3 and anti-CD28 antibodies (Abs) for 6 or 24 h.  Then the naive CD8 T or activated CD8 T cells were collected for ATAC-seq and CUT&Tag assay.


overall_design: Immature single-positive CD8+ T cells, mature single-positive CD8+ T cells, and naive CD8+ T cells were isolated from the thymus and spleen of wild-type (WT) mice. Naive CD8+ T cells (defined as CD62L+CD44lo) were purified from the spleens of WT and IL-7R-cKO mice, BCL2-expressing WT and BCL2-expressing IL-7R-cKO mice, as well as young and aged mice. For CUT&Tag-seq, DNA was fragmented and tagged using the H2A.Z antibody (Abcam, #ab4174) via the Target & Tagmentation approach in T cells. Genomic DNA was subsequently extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, #TD904). Additionally, chromatin immunoprecipitation (ChIP) assays were performed using the ULI-NChIP protocol to assess H2A.Z enrichment in naive CD8+ T cells from young and aged mice.


title: Pro-inflammatory role of granzyme K producing bystander CD8 T cells in acute myeloid leukemia

city: Paris

first: Yannick

last: Simoni

address: 22 rue Mechain

country: France

institute: Institut Cochin

summary: This study investigates the composition, antigen specificity, and functional characteristics of CD8⁺ T cells in acute myeloid leukemia (AML). Using paired blood and bone marrow samples from AML patients, we performed single-cell transcriptomic (CITE-seq) and T cell receptor (VDJ) profiling to identify immune cell subsets and their clonotypes.

overall_design:
CITEseq/5' V(D)J sequencing: Mononuclear cells from peripheral blood or bone marrow aspirations from AML patients were thawed and stained with TotalSeq™-C Human Universal Cocktail, V1.0. Viable CD8 T cells were sorted using FACS Aria III
Please note that the Cell Ranger output processed data files generated from both ADT and GEX samples are linked to the corresponding GEX sample records.

first: Lisa

last: Aziez

first: Nicolas

last: Deredec

first: Ismael

last: Boussaid

first: Carolyn

middle: G

last: Shasha

first: Romain

last: Vazquez

first: Chloé

last: Friedrich

first: Ania

last: Alik

first: Kanchanadevi

last: Manasse

first: Zoé

last: Fremont-Debaene

first: Alexandra

last: Barthelemy

first: Cyril

last: Catelain

first: Philippe

last: Rameau

first: Marguerite

last: Vignon

first: Justine

last: Decroocq

first: Olivier

last: Kosmider

first: Dorothée

last: Selimoglu-Buet

first: Evan

last: Newell

first: Eric

last: Solary

first: François

last: Delhommeau

last: Herault

last: Tartour

first: Rudy

last: Birsen

first: Didier

last: Bouscary

first: Michaela

last: Fontenay

last: Chapuis


title: Regulatory Effect of Traditional Chinese Medicine Active Extracts on the Transcriptome Profile of RAW264.7 Macrophages

first: Zhaokun

last: Yin

state: Guangdong

address: 132#, Waihuan Dong Road

institute: Sun Yat-Sen University

summary: This study, based on RNA-seq technology, systematically compared the transcriptomic differences between the normal control group, LPS model group, and LPS + Traditional Chinese Medicine extract treatment group. The aim was to screen key differential genes (DEGs) and their enriched core pathways under drug intervention. The results showed that the active extract of Traditional Chinese Medicine significantly reshaped the gene expression profile in RAW264.7 cells related to biological processes such as metabolic reprogramming, ferroptosis, inflammation response, and immune regulation, suggesting its potential for multi-target and multi-pathway immune-metabolic regulation.

overall_design: Transcriptional data from three groups of RAW264.7 cells (normal, LPS model, and LPS + Traditional Chinese Medicine extract) were collected. Through differential expression and pathway enrichment analysis, the overall regulatory effect of the Traditional Chinese Medicine extract on the cell gene expression profile was systematically evaluated.

first: Shiqi

last: Luo

first: Zhiyan

last: Qin

first: Jianxun

last: Song

first: Lei

last: Zhang

first: Min

last: Huang

first: Jing

last: Jin


first: Mingzhao

last: Zhu

overall_design: Naïve CD8+ T cells (CD62L+CD44low) were purified from the spleens of wild-type (WT) and H2A.Z-cKO mice, as well as WT and GABPα-cKO mice. For CUT&Tag-seq, DNA was fragmented and tagged under the Target & Tagmentation workflow using antibodies against H2A.Z, GABPα, and H3K27ac in T cells. Genomic DNA was isolated using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, #TD904). Additionally, CUT&Tag assays were performed in WT Jurkat cells and in Jurkat cell lines with knockout of H2A.Z or GABPα.

first: Mengjie

last: Lv

first: Jiyu

last: Ding

first: Haizhen

last: Long

first: Qian

last: Chai

first: Guohong

last: Li


title: Transcriptomic analysis of CAFs with silencing of TERRA lnRNA

city: Charlestown

first: Gian Paolo

last: Dotto

state: MA

address: 149 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hsopital

summary: The tumor microenvironment is essential for cancer progression, yet the nuclear mechanisms that reprogram stromal fibroblasts into cancer-associated fibroblasts (CAFs) remain to be defined. Here, we identify a telomere-derived RNA–protein signaling axis that links genome integrity and fibroblast plasticity. We show that the long non-coding RNA TERRA, transcribed from telomeres, is upregulated in CAFs across multiple human skin cancers following loss of androgen receptor (AR) expression. Elevated TERRA enhances telomeric DNA damage and activates a CAF-specific transcriptional program. Through proteomic profiling, we identify the RNA-binding protein NONO as a critical TERRA effector. TERRA and NONO form nuclear complexes selectively in CAFs, while in normal fibroblasts NONO associates with AR. Disruption of the TERRA-NONO complex, either by genetic silencing or a small-molecule inhibitor of NONO, reverses CAF activation and suppresses tumor-stroma cells expansion in vitro and in vivo. These findings uncover a telomere-encoded mechanism of stromal reprogramming and identify the TERRA–NONO complex as a targetable point of vulnerability in the tumor microenvironment.

overall_design: Gene expression of CAFs with ASO TERRA silencing were analyzed and compared to correspondent ASO SCR controls. Experiments were run on 3 biological replicates.

first: Emery

last: Di Cicco

first: Dotto

last: Gian-Paolo


title: Transcriptomic analysis of CAFs with silencing of NONO

overall_design: Gene expression of CAFs with NONO silencing were analyzed and compared to correspondent siCTR. Experiments were run on 2 CAF strains using 2 targeting siRNAs.


title: Dysregulated Proline Metabolism Contributes to Subretinal Fibrosis in Neovascular AMD: Therapeutic Potential of Prolyl-4-Hydroxylase Inhibition

city: Eveleigh

first: Ting

state: NSW

address: C81 Biomedical Building, 1 Central Ave

institute: The University of Sydney

summary: Subretinal fibrosis is a key pathological feature of late-stage neovascular age-related macular degeneration (nAMD), often leading to irreversible vision loss. To investigate early molecular changes underlying subretinal fibrosis, we performed transcriptomic analysis on JR5558 mice, a spontaneous model of retinal neovascularisation, at 4 and 8 weeks of age. Age-matched C57BL/6J mice were used as controls. Bulk RNA sequencing was performed on whole retinas to identify differentially expressed genes and enriched biological pathways.

overall_design: Whole retinas were dissected from JR5558 mice and age-matched wild-type C57BL/6J controls at 4 and 8 weeks of age. Each group included three biological replicates, with each replicate consisting of a retina from a separate mouse. RNA was extracted using the GenElute™ RNA Purification Kit (Sigma-Aldrich), and RNA integrity was confirmed before sequencing. Library preparation and RNA sequencing were performed by Novogene (Illumina platform, paired-end). Differential gene expression analysis was performed using standard pipelines.

first: Yue

last: Zeng

first: Elisa

last: Cornish

first: So-Ra

last: Lee

first: Michelle

last: Yam

first: Mark

last: Eminhizer

first: Jingwen

first: Jialing

first: Shaoxue

first: Xian

last: Wei

first: Jinliang

last: Yang

first: Meidong

first: Andrew

last: Chang

first: Meixia

first: Jianhai

last: Du

first: Ling

first: Mark C.

last: Gillies


title: Autophagy maintains HEV identity and function during inflammation.

city: Leuven

first: Gabriele

last: Bergers

address: Herestraat 49

department: Department of Oncology

country: Belgium

institute: KU Leuven-VIB CCB

summary: High endothelial venules (HEVs) play a crucial role in immunological responses by facilitating lymphocyte entry into the lymph node through display of peripheral node addressins (PNAd). During inflammation, the HEV network expands and upregulates additional adhesion molecules for proper T cell influx, but the underlying mechanisms remain poorly understood. Here we report that autophagy is essential for the proper expansion and functioning of HEVs using single-cell transcriptomics, intravital imaging, and novel inducible HEV tracer mouse models. We demonstrate that lack of autophagy leads to a loss of HEV phenotype and functionality through reduced lymphotoxin beta receptor and Unfolded Protein Response activation, which contribute to decreased production of PNAd. This autophagy-dependent mechanism maintains HEV identity during inflammatory stress. These findings reveal that blocking HEV expansion can be exploited therapeutically, as demonstrated in a psoriasis model where it resulted in less severe disease phenotype.

overall_design: We performed single-cell RNA sequencing to investigate the impact of autophagy deficiency on endothelial cells (ECs) and immune cells during inflammation. The study included 12 samples from conditional autophagy knockout mice (ATG12 Cre- and Cre+ mice) under three experimental conditions: Vehicle control, oxazolone (OX) treatment day 3, and OX day 7. Both CD45-CD31+ endothelial cells and CD45+ immune cells were analyzed. Mouse strains included C57BL/6 background mice with various genotypes: ATG12 fl/fl x CDH5 CreER (endothelial-specific autophagy knockout), ATG7 fl/fl x CDH5 CreER, LC3B-RFP-GFP reporter mice, CHST4 CreER Tomato reporter mice, and ATG12 fl/fl x CHST4 CreER (HEV-specific autophagy knockout). Inflammation was induced using 4% oxazolone applied topically, and tissues were collected at day 3 (peak inflammation) and day 7 (resolution phase) post-treatment. Single-cell suspensions were prepared from lymph nodes using enzymatic digestion, and endothelial cells were enriched by CD45 depletion before 10X Genomics single-cell RNA sequencing.

first: Kathryn

middle: A

last: Jacobs

first: Yichao

last: Hua

first: Patrizia

last: Agostinis


title: Comprehensive Profiling of the GlycoRNA Landscape in Extracellular Vesicles

city: Xiamen

first: chao

middle: jie

last: hao

state: Fujian

address: No. 422, Siming South Road

institute: Xiamen University

type: Non-coding RNA profiling by high throughput sequencing

summary: Glycosylated RNAs (glycoRNAs) have recently been identified on the cell surface, yet their intercellular transfer mechanisms remain unclear. Given the central role of extracellular vesicles (EVs) in cell–cell communication, here, we investigated the presence, composition, dynamics, and trafficking of EV-associated glycoRNAs. Combining metabolic glycan labeling with high-throughput sequencing, we constructed an EV glycoRNA library, revealing subsets not previously detected in cell surface glycan studies.

overall_design: RNA sequencing libraries from the RNA fractions of Ac4ManNAz treated MCF-7 EVs. RNA samples were isolated from bulk RNAs or Ac4ManNAz-enriched.

first: Xiaodie

last: Chen

first: Ting

first: Chaojie

last: Hao

first: Ximing

first: Jiaheng

last: Zhu

first: Yuqian

last: Zhang

first: Hongyu

last: Lin

first: Yanlin

last: Song


title: A Scalable Microarrayed Organoid Platform for Precision Modeling of Intestinal Epithelial Damage and Recovery

city: Lausanne

first: Aline

last: Roch

address: EPFL Innovation Park Building L

country: Switzerland

institute: DOPPL SA

summary: Chronic inflammatory bowel diseases (IBD), including Crohn's disease, are characterized by relapsing-remitting intestinal inflammation associated with a dysfunctional intestinal epithelial barrier. Existing preclinical in vitro models of IBD have limitations in accurately reproducing the dynamic processes of epithelial barrier dysfunction and repair, which hinders the translation of research findings into new therapeutic approaches. Here, we established a scalable, microarrayed 3D human intestinal organoid platform that enables high-throughput, single-organoid resolution modeling of inflammation-induced epithelial damage and subsequent regenerative responses, recapitulating both morphological and transcriptional signatures of biopsy-derived mucosal tissues from Crohn’s disease patients. Employing time-resolved morphological imaging, transcriptomics, and a novel quantitative epithelial recovery metric, introduced as the 'Intestinal Organoid Recovery Score (IORS),' we distinguished responder organoids to preventive and therapeutic bioactives, notably dexamethasone (DEX), nicotinamide (NAM), and β-hydroxybutyrate (BHB). These interventions effectively mitigated inflammation-induced barrier disruption and promoted regenerative epithelial barrier programs to restore barrier function. Transcriptomic analysis further revealed differential modulation of pathways associated with epithelial integrity and inflammatory responses in DEX and NAM interventions, highlighting distinct regenerative mechanisms of action that may be utilized for future combinatorial therapies. Collectively, this robust, single-organoid resolution approach offers an unprecedented opportunity for precision medicine-driven screening and therapeutic development in the context of chronic gastrointestinal diseases.

overall_design: RNAseq profiling of human primary small intestine organoids grown for 12 days and exposed on day 4 to inflammatory cytokines, with or without pre-treatment with bioactives dexamethasone and niacinamide, and compared to organoids non-exposed to inflammatory cytokines

first: Marine

last: Meyer

first: Juliane

last: Dervaux

first: Laurent

last: Ferrier

first: Evarist

last: Planet

first: Julien

last: Duc

first: Camilla

last: Ceroni

first: Brice

last: Chambrin

first: Jens

last: Stolte

first: Sylviane

last: Métairon

first: Abhilash

last: Kannan

first: Sylke

last: Hoehnel-Ka

last: Kraus

first: Patrick

last: Descombes

first: Nathalie

last: Brandenberg

first: Mario

last: Noti

first: Omid

last: Mashinchian


title: Hippo Signaling Regulates Spontaneous Human Trophoblast Syncytialization in 3D Cultures

city: London

first: Stephen

last: Renaud

state: ON

address: 1151 Richmond Street

department: Anatomy and Cell Biology

country: Canada

institute: University of Western Ontario

summary: Human trophoblast stem cells were grown as 2D or 3D cultures. RNA-seq was then utilized to determine global transcriptomic changes between 2D and 3D cultures. This study provides insight into the molecular mechanisms regulating the development of trophoblast subpopulations in 3D cultures.

overall_design: Transcriptomic profile of 2D and 3D human trophoblast stem cell cultures.

first: Michael

last: Zheng

first: Lin

last: Zhao

first: Richard

last: Xi

first: Jahdiel

last: DeNobrega

first: Mary

last: Tammo

first: Peeyush

middle: K

last: Lala


title: Gene identification for ocular congenital cranial motor neuron disorders using human sequencing, zebrafish screening, and protein binding microarrays

city: Boston

last: Gisselbrecht

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

type: Genome binding/occupancy profiling by array

summary: Through exome and genome sequencing of a genetically unsolved human oCCDD cohort, we previously identified variants in 80 strong candidate genes. Here, we further prioritized a subset of these (43 human genes, 57 zebrafish genes) using a G0 CRISPR/Cas9-based knockout assay in zebrafish and generated F2 germline mutants for seventeen. We tested the functionality of variants of uncertain significance in known and novel candidate transcription factor-encoding genes through protein binding microarrays.

overall_design: One variant allele was examined for each of three human TFs. Each variant was assayed in parallel with its reference allele (in separate chambers of the same slide) in biological duplicates (on separate slides, on separate dates).

first: Julie

last: Jurgens

first: Paola

middle: M

last: Ruiz

first: Jessica

last: King

first: Emma

middle: E

last: Foster

first: Lindsay

last: Berube

first: Wai-Man

last: Chan

first: Brenda

last: Barry

first: Raehoon

last: Jeong

first: Elisabeth

last: Rothman

middle: C

last: Whitman

first: Sarah

last: MacKinnon

first: Cristina

last: Rivera-Quiles

first: Brandon

last: Pratt

first: Teresa

last: Easterbrooks

first: Fiona

last: Mensching

first: Silvio

last: Di Gioia

first: Lynn

last: Pais

first: Eleina

last: England

last: de Berardinis

first: Adriano

last: Magli

first: Feray

last: Koc

first: Kazuhide

last: Asakawa

first: Koichi

last: Kawakami

first: Anne

last: O’Donnell-Luria

first: David

last: Hunter

first: Caroline

middle: D

last: Robson

first: Martha

last: Bulyk

first: Elizabeth

last: Engle


title: Post-transcriptional Modifications of the Large Ribosome Subunit Assembly Intermediates in E. coli Expressing Helicase-inactive DbpA Variant

city: El Paso

first: Eda

last: Kocui

state: TX

address: 500 W. University Avenue

department: Chemistry and Biochemistry

institute: University of Texas at El Paso

summary: RNA post-transcriptional modifications are ubiquitous across all organisms and serve as fundamental regulators of cellular homeostasis, growth, and stress adaptation. Techniques for the simultaneous detection of multiple RNA modifications in a high-throughput, single-nucleotide resolution manner are largely lacking in the field. Given the crucial role of RNA modifications in cellular metabolism, developing such techniques is of paramount importance. We used the Escherichia coli ribosome as a model system to develop novel techniques for RNA post-transcriptional modification, leveraging its extensive and diverse array of modifications to enable the simultaneous interrogation of multiple modification types. For modification detection, we performed reverse transcriptase reactions in the presence of Mn²⁺ and quantified the reverse transcriptase deletions and misincorporations at modification positions using Illumina next-generation sequencing. In the absence of chemical treatment, we simultaneously detected the following modifications in ribosomal RNA: 1-methylguanosine (m¹G), 2-methylguanosine (m²G), 3-methylpseudouridine, N⁶,N⁶-dimethyladenosine, and 3-methyluridine. Furthermore, subjecting the RNA samples to 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate followed by alkaline conditions allowed us to simultaneously detect pseudouridine, 7-methylguanosine (m⁷G), 5-hydroxycytosine (OH⁵C), 2-methyladenosine, and dihydrouridine (D). Finally, subjecting the rRNA samples to KMnO₄ followed by alkaline conditions allowed us to simultaneously detect m⁷G, OH⁵C, and D. Our findings reveal that m¹G, m²G, m⁷G, and D are incorporated before the accumulation of the 27S, 35S, and 45S in cells, suggesting that the enzymes responsible for these modifications complete their functions before these three intermediates are populated.

overall_design: The ribosomal particles were isolated using sucrose gradients from cells  expressing the wild type DbpA or the R331A DbpA construct.

last: Koculi


title: Spatial transcriptomics unveils the in situ cellular and molecular hallmarks of the lung in fatal COVID-19

city: Barcelona

first: Manel

last: Esteller

state: Barcelona

address: Carrer de Sant Quintí, 77, Horta-Guinardó, 08041 Barcelona

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: IR Sant Pau

summary: Severe Coronavirus disease 2019 (COVID-19) induces heterogeneous and progressive diffuse alveolar damage (DAD) highly disrupting lung tissue architecture and homeostasis, hampering disease management leading to fatal outcomes. Characterizing DAD pathophysiology across disease progression is of ultimate importance to better understand the molecular and cellular features driving different DAD patterns and to optimize treatment strategies. To contextualize the interplay between cell types and assess their distribution, spatial transcriptomics (ST) techniques have emerged, allowing unprecedented resolution to investigate spatial architecture of tissues. To this end, post-mortem lung tissue provides valuable insights into cellular composition and their spatial relationships at the time of death. Here, we have leveraged VisumST technology in post-mortem COVID-19 induced acute and proliferative DAD lungs including control samples with normal morphological appearance, to unravel the immunopathological mechanisms underlying DAD, providing novel insights into cellular and molecular communication events driving DAD progression in fatal COVID-19. We report a progressive loss of endothelial cell types, pneumocytes type I and natural killer cells coupled with a continuous increase of myeloid and stromal cells, mostly peribronchial fibroblasts, over disease progression. Spatial organization analysis identified variable cellular compartments, ranging from major compartments defined by cell type lineages in control lungs to increased and more specific compartmentalization including immune-specific clusters across DAD spectrum. Importantly, spatially informed ligand-receptor interaction (LRI) analysis revealed an intercellular communication signature defining COVID-19 induced DAD lungs. Transcription factor (TF) activity enrichment analysis identified TGF-B pathway as DAD driver, highlighting SMAD3 and SMAD7 TFs activity role during lung fibrosis. Integration of deregulated LRIs and TFs activity allowed us to propose a downstream intracellular signaling pathway in peribronchial fibroblasts, suggesting potential novel therapeutic targets. Finally, spatio-temporal trajectories analysis provided insights into the alveolar epithelium regeneration program, characterizing markers of pneumocytes type II differentiation towards pneumocytes type I. In conclusion, we provide a spatial characterization of lung tissue architecture upon COVID-19 induced DAD progression, identifying molecular and cellular hallmarks that may help optimize treatment and patient management.

overall_design: We leveraged the recently developed Visium spatial transcriptomics (VisiumST) technology in a cohort of 23 lungs,  including those with normal histology (n=4) and those that underwent DAD upon the course of fatal COVID-19 (n=19). To further untangle the precise and topographically located gene expression changes underlying the disease, both acute (n=7) and proliferative (n=12) stages of DAD were studied using the single-cell RNA expression data of a human cell atlas of the lung to annotate cell types.

first: Carlos

last: Garcia-Prieto

first: Eva

last: Musulen

first: Veronica

last: Davalos


title: Characterizing the role of fibroadipogenic progenitor in experimental model of pancreatic cancer cachexia

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

institute: University of British Columbia

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

overall_design: Refer to individual Series


title: Characterizing the role of fibroadipogenic progenitor in experimental model of pancreatic cancer cachexia [RNASeq_KPC_KPCScr_and_miR-27a-KD]

summary: The experiment aims to understand the effect of miR-27a knockdown in pancreatic cancer cells and investigate if the knocking down miR-27a delays tumor progression.

overall_design: Two groups- KPC scrambled and KPC-miR-27 KD (n=4) were utilized and subjected to RNA Seq (n=4)

first: Ashok

last: Narasimhan

first: Lin

last: Tung

first: Tara

last: Stach


title: An aging-sensitive compensatory neuroprotective factor that confers cognitive resilience

city: Quechee

first: Michael

last: Steinbaugh

state: VT

address: PO Box 1520

institute: Acid Genomics

summary: Endogenous compensatory changes influence trajectory of brain aging, cognitive decline and Alzheimer’s Disease (AD) risk, however, the identities of underlying mechanisms have remained elusive. A screen for hippocampal dentate granule cell (DGC) synapse loss-induced factors identified a secreted phospholipase, Pla2g2f, whose expression increases in DGCs during aging. Pla2g2f deletion in DGCs exacerbates aging-associated synapse loss, emergence of inflammatory microglia, reactive astrogliosis, lipid dysregulation and memory impairment. Boosting Pla2g2f in DGCs during aging prevents these pathophysiological impairments and modifies trajectory of cognitive decline. In human microglia-neuron coculture experiments PLA2G2F mediates intercellular signaling to decrease lipid burden. Boosting Pla2g2f expression in an aging-sensitive AD model reduces amyloid load and preserves memory. Thus, PLA2G2F functions as a compensatory neuroprotective factor that counteracts aging-associated cognitive decline.

overall_design: The dentate gyrus of Ctrl and Experimental groups were dissected and processed for Illumina next-generation sequencing (n=5 Ctrl, n=7 Experimental).

first: Cinzia

last: Vicidomini

first: Kathleen

last: McAvoy

first: Travis

last: Goode

first: Matheus

last: Victor

first: Liam

last: Evans

first: Zon

last: Lai

first: Marina

last: Lyon

first: Manuel

middle: R

last: Fernández San Silvestre

first: Gracia

last: Bonilla

first: Ruslan

last: Sadreyev

first: Robert

middle: V

last: Farese Jr.

first: Tobias

last: Walther

first: Shannan

middle: H

last: Sui

first: Takaomi

last: Saido

first: Kei

last: Yamamoto

first: Makoto

last: Murakami

first: Li-Huei

last: Tsai

first: Amar

last: Sahay


title: Characterizing the role of fibroadipogenic progenitor in experimental model of pancreatic cancer cachexia [RNASeq_FAP_KPCScr_and_miR-27a-KD]

first: Fabio

last: Rossi

summary: The study aims to understand if modulating miR-27a-3p reduces tumor burden and alleviates muscle wasting and FAP dysregulation using an experimental model of pancreatic cancer cachexia.  KPCY- a murine pancreatic cancer cell line was utilized for the study.

overall_design: FAPs were sorted from hind limb muscle from control, KPC scrambled and miR-27a KD samples and were subjected to RNA Sequencing.

first: Ashok

last: Narasimhan

first: Lin

last: Tung

first: Tara

last: Stach


title: Characterizing the role of fibroadipogenic progenitor in experimental model of pancreatic cancer cachexia [RNASeq_FAP_timeseries]

summary: The study aims to understand if fibroadipogenic progenitors are dysregulated in cancer-associated muscle wasting, also known as cachexia. To that end, RNA was isolated from freshly sorted FAPs at different time points including day 14, day 21, and day 26.

overall_design: FAPs were sorted from hind limb muscle from control and KPC samples at all three time points and were subjected to RNA Sequencing.


title: Characterizing the role of fibroadipogenic progenitor in experimental model of pancreatic cancer cachexia [snRNASeq_whole_muscle]

summary: The study aims to understand the alterations in different cell types in skeletal muscle during cancer associated muscle wasting (also known as cachexia). To that end, we performed single nuclear RNA sequencing using quadriceps muscle.

overall_design: DAPI+ nuclei were sorted from quadriceps muscle from control and KPC mice and were subjected to single nuclear RNA Sequencing.


title: LCK deficiency in CD8 T cells leads to reduced proliferation and increased effector T-cell formation in mice [scRNA-seq]

status: Public on Aug 09 2026

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

summary: LCK is an SRC-family kinase that mediates the initial steps in T-cell antigen receptor signaling and governs positive and negative selection during thymocyte development. While its developmental role is well established, its functions in peripheral T-cell responses remain poorly defined. Here, we investigated the responses of wild-type and LCK-deficient TCR-transgenic OT-I T cells across two infection models and an autoimmune diabetes model. LCK-deficient T cells exhibited reduced antigen-induced proliferation but, paradoxically, displayed enhanced effector differentiation in vivo. This phenotype likely reflects dysregulation of specific TCR signaling pathways, as LCK was more critical for ERK and NFAT activation than for NFκB, AP-1, or AKT/mTOR signaling. T cells deficient in a related kinase FYN also showed a slight increase in effector cell formation, suggesting that effector differentiation is regulated by their combined activity rather than distinct non-redundant roles. Our results reveal that LCK has two intrinsic roles in T-cell responses – promoting proliferation while restraining effector differentiation. These findings provide new insight into the molecular mechanisms of T-cell activation in vivo with implications for understanding the pathophysiology of LCK deficiency in humans and optimizing adoptive T-cell therapies.

overall_design: The experiment compares CD8+ T cells taken from the spleens of cLCK KO and WT mice.

first: Valeria

last: Uleri

first: Veronika

last: Niederlova

first: Ondrej

last: Stepanek


title: The splicing factor UAP1 exhibits a conserved function in cold stress responses among three dicotyledonous species

city: hefei

first: Xinwei

last: Zhao

state: anhui

address: changjiang strest

institute: anhui agricultural university

summary: Cold stress is a major environmental factor limiting the productivity and geographical distribution of horticultural crops. Here, we identified the spliceosome U4/U6.U5 tri-snRNP-associated protein 1 (UAP1) as a pivotal negative regulator of cold tolerance in both tomato (Solanum lycopersicum) and soybean (Glycine max). Using CRISPR/Cas9-mediated gene editing, we generated UAP1 knockout orthologs in three dicotyledonous species: tomato, soybean and Arabidopsis. The sluap1 and gmuap1 mutants exhibited significantly enhanced cold resilience, characterized by reduced membrane damage, lower reactive oxygen species accumulation, and higher survival rates after cold stress. To elucidate the underlying molecular mechanism, we further characterized the uap1 mutants in Arabidopsis, which similarly displayed a cold-tolerant phenotype. Transcriptome-wide analysis revealed that the loss of AtUAP1 results in widespread differential alternative splicing under cold stress. Notably, we identified a critical intron retention event in the circadian clock gene AtPRR3, leading to a truncated, non-functional protein. Genetic evidence confirmed that atprr3 mutants mimic the cold-tolerant phenotype of atuap1, and heterologous expression of SlUAP1 or GmUAP1 effectively rescued the atuap1 mutant, demonstrating high functional conservation. Our findings establish the UAP1-mediated splicing module as a conserved thermoregulatory mechanism across diverse species and position UAP1 as a promising universal target for the biotechnological improvement of cold resilience in horticultural and field crops.

overall_design: Experimental materials are whole seedlings of Arabidopsis thaliana Col-0 cultivated on MS medium. All seedlings were cultured normally for 11 days on MS medium at standard growth temperature. Two sample treatment groups were set up: 1. Control group: seedlings continuously cultured under normal conditions for a total of 12 days without cold treatment; 2. Cold stress treatment group: 11-day-old seedlings subjected to 4 °C cold stress treatment for 24 h to obtain 12-day equivalent-age materials. Each treatment group contains three genotypes: wild-type Col-0, uap1-1 mutant and uap1-2 mutant. Four independent biological replicates were prepared for every single genotype in both control and cold-stressed groups.

first: Jianhua

last: Zhu


title: Spatial transcriptomics reveals microenvironmental heterogeneity in osteoarthritic subchondral bone

city: New Orleans

first: Weiqiang

last: Lin

state: LA

address: 1324 Tulane Ave

institute: Tulane University

summary: Although increasing evidence implicates subchondral bone alterations in osteoarthritis, the spatial organization of subchondral bone remodeling remains unclear. Applying spatial transcriptomics on human subchondral bone, we identify a spatially conserved osteogenic core-halo architecture that displays transcriptional reprogramming in sclerotic microenvironments. Spatial dependency and a customized cell-cell communication framework reveal disrupted osteoblast-osteoclast spatial coupling, enhanced osteoblast-mesenchymal interactions, and identify FN1-SDC2 and COL1A1-DDR2 as candidate stromal-osteogenic signaling axes that may contribute to aberrant bone remodeling. Additionally, we present the first in situ transcriptional landscape of osteocytes and reveal its potential regulatory role in aberrant bone remodeling. We further delineate a continuum of spatial ecotypes exhibiting distinct enrichment, spatial topology reorganization, and inter-ecotype communication rewiring across pathological states. Metabolic flux inference additionally reveals substrate-limited, stressed states across multiple ecotypes in sclerotic microenvironments. Collectively, our findings provide critical insights into aberrant subchondral bone remodeling in osteoarthritis and offer a valuable framework for future mechanistic studies and therapeutic exploration.

overall_design: Human femoral head specimens were collected from patients undergoing hip arthroplasty, processed into formalin-fixed, EDTA-decalcified, paraffin-embedded tissue blocks, and profiled using both 10x Genomics Visium HD platforms. FFPE sections were processed on the CytAssist instrument, followed by H&E staining, probe extension and library construction according to the manufacturer’s protocols with minor adaptations. Libraries were sequenced on an Illumina NextSeq 2000 platform.

first: Xinyi

last: Xiao

first: William

last: Sherman

first: Fernando

last: Sanchez

first: Chuan

last: Qiu

first: Zhe

last: Luo

first: Qing

last: Tian

first: Hui

last: Shen

first: Hongwen

last: Deng


title: A Nanomolar-Affinity Antibody Enabling Sensitive Labeling and High-Resolution Genomic Mapping of O-GlcNAc

city: Beijing

first: Xiaoyang

last: Guo

address: 5 Yiheyuan Road, Haidian District

institute: Peking University

summary: High-affinity O-GlcNAc-specific antibodies are crucial for the sensitive detection and functional study of O‑GlcNAcylation. Here, we report the development of a pan-specific, nanomolar-affinity O-GlcNAc antibody named EPR19847 by using a degenerate O‑GlcNAcylated peptide as the immunogen. The EPR19847 antibody can be used for O‑GlcNAc detection, imaging, isolation, and chromatin immunoprecipitation. Using this novel antibody, O-GlcNAcylated proteins were enriched and identified in mouse embryonic stem cells (mESCs). Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) demonstrates that O-GlcNAc is enriched around the promoters of highly expressed genes, and that its genomic distribution is positively correlated with transcription-activating marks including H3K4me3, H3K9ac, and RNA Pol II in mESCs. Further analysis suggests a high occupancy of O-GlcNAcylation within super-enhancers. We anticipate that EPR19847 will serve as a powerful tool for the highly-sensitive detection and systematic functional dissection of O-GlcNAc.

overall_design: ChIP-seq profiling of mESCs by newly developed EPR19847 at various usage amount. O-GlcNAc antibody RL2, Isotype IgG and Input were also included as controls.

first: Weiyao

last: Hong

first: Che

last: Zhang


title: Global regulatory role of stringent starvation protein SspA in modulating IncX3 plasmid fitness cost in Escherichia coli

city: Hangzhou

first: Ziyi

last: Liu

address: Wusu Road 666

institute: Zhejiang A&F university

summary: The IncX3 plasmid is a primary vector for disseminating carbapenem resistance globally, yet the chromosomal regulatory mechanisms governing its fitness cost remain poorly understood. Our previous work identified the stringent starvation protein SspA as a modulator of IncX3 plasmid fitness in Escherichia coli via flagellar biosynthesis. Here, we elucidate the global regulatory role of SspA and verify whether its effect is mediated through the master regulator H-NS

overall_design: ChIP-seq of SspA-6xHis in Escherichia coli C600 carrying the IncX3 plasmid pL53T. Two samples were sequenced: an Input control (C600_input) collected before bead incubation, and an SspA-immunoprecipitated sample (C600_WT_ChIP) enriched via Ni-NTA magnetic bead pull-down. EMSA was performed to assess direct SspA-DNA binding to the hns promoter region. Motif analysis, GO enrichment, and KEGG pathway analysis were conducted on SspA-bound peak-associated genes.

first: Ying

last: Tang

first: Chenggang

last: Xu


title: LCK deficiency in CD8 T cells leads to reduced proliferation and increased effector T-cell formation in mice [Bulk RNA-seq]

first: Juraj

last: Michalik

overall_design: The experiment compares cLCK KO and WT mice CD8+ T cell behavior under different treatment: notably activation by OVA and inhibition by IP38, inhERK and Cyclosporin.

first: Valeria

last: Uleri

first: Veronika

last: Niederlova

first: Ondrej

last: Stepanek


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Pseudomonas aeruginosa PAS57 vs PAS96 and PAS57 vs PAS79 Transcriptomes

city: Guangzhou

first: Wenru

last: Li

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of P. aeruginosa PAS57 (RNA-seq) to transcriptome profiling of P. aeruginosa PAS96 and PAS79 and to evaluate protocols for optimal high-throughput data analysis.

overall_design: Methods:LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAS57, PAS96, and PAS79 at a concentration of 1.0E8 CFU/mL in triplicate. All nine experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the  nine experimental groups. The cell precipitates were separately snap-frozen at -80ºC.  Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol.

first: Wen-Ru

first: Zhi-Qing

first: Xu-Bin

last: Huang

first: Kang

last: Liao

first: Xiao-Bao

last: Xie

first: Xing

last: Lu

first: Zong-Bin

last: Cui


title: Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming [CUT&Tag]

city: Rehovot

first: Yonatan

last: Stelzer

address: Procurement Division 234 Herzl St.

institute: Weizmann Institute of Science

summary: Genomic imprinting secures parent-specific gene expression through differential DNA methylation at imprinted control regions (ICRs). However, how unmethylated alleles resist de novo methylation remains unclear. Using an allelic Dlk1-Dio3 ICR methylation reporter and genome-wide loss-of-function screening, we identify the zinc finger protein GZF1 that binds the unmethylated maternal ICR and protects it from de novo methylation via a regulatory element containing GZF1 and ZFP57 motifs that mediates mutually exclusive, methylation-dependent binding. Loss of either factor causes reciprocal imprinting failure: Gzf1 loss induces maternal allele methylation, H3K4me3 depletion, and silencing of maternal transcripts, whereas Zfp57 loss results in maternalization. Remarkably, GZF1 protects the unmethylated ICR from de novo methylation in both oocytes and embryos, and its loss leads to perinatal death consistent with paternalization of the maternal allele. Together, our findings establish a reciprocal mechanism that maintains parental epigenetic asymmetry across both imprint establishment and embryonic reprogramming.

overall_design: H3K4me3 CUT&Tag profiling in wild-type and Gzf1-knockout mouse embryonic stem cells (RGM background). H3K4me3 was profiled by CUT&Tag (anti-H3K4me3) for each genotype, and genome-wide H3K4me3 was compared between wild-type and Gzf1-KO (differential peak analysis) to assess changes at the Dlk1-Dio3 IG-DMR.

first: Arik

last: Toren

first: Liron

last: Hoffman

first: Irina

last: Miodownik

first: Yoav

last: Mayshar

first: Raz

last: Ben-Yair

first: Ayelet-Hashahar

last: Orenbuch

first: Hernan

last: Rubinstein

first: Aviezer

last: Lifshitz

first: Roni

last: Stok Ranen

first: Alexander

last: Wainstein

first: Daoud

last: Sheban

first: Liran

last: Shlush

first: Amos

last: Tanay

first: Ariel

last: Afek


title: Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming [bulk RNAseq]

overall_design: Wild-type (n=4) versus Gzf1-knockout (n=5) mESC lines; bulk RNA-seq; differential expression (DESeq2). Samples were generated across two sequencing batches (run1 and run2; see 'batch' column).


title: Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming [ChIP-seq]

overall_design: Chromatin was immunoprecipitated with anti-Flag M2 (Sigma F1804) or anti-GZF1 (LSBio LS-C429273); H3K27Ac ChIP used anti-H3K27Ac (Thermo Fisher MA5-23516). On-bead Illumina library construction was performed as previously described: end-repair, A-tailing, ligation of indexed adapters, crosslink reversal, SPRI purification, and KAPA HiFi amplification.


title: Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming [CRISPRscreen]

overall_design: Two independent screens (Exp1, Exp2). Reporter mESCs transduced with Cas9 + a genome-wide sgRNA library (19,674 genes) were puromycin-selected, passaged to P6 and FACS-sorted by Tom/GFP into Tom+GFP+ (PP, enriched), Tom-GFP- (MM), Tom+GFP- (PM, control) and unsorted (US); T1 is an early unsorted baseline. sgRNA abundance was quantified with MAGeCK count and tested (PP & MM vs US/PM/T1) with MAGeCK.


title: HMGCS2-PPARα signaling activates the prolongevity gene CISD2 to delay liver aging

city: Taipei

first: Yi-Long

last: Huang

state: Not US or Canada

address: No.155, Sec.2, Linong Street, Peitou

department: Center for Healthy Longevity and Aging Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Aging is a major risk factor for metabolic liver disorders, yet the molecular mechanisms driving hepatic aging remain incompletely understood. Here, we identify an HMGCS2-PPARα signaling pathway that regulates the prolongevity gene CISD2 and liver aging. Using naturally aged mice, we show that late-life administration of the citrus flavonoid hesperetin restores hepatic CISD2 expression, improves liver pathology, and partially reverses aging-associated transcriptomic alterations. Mechanistically, we identify HMGCS2 as a molecular target of hesperetin and demonstrate that HMGCS2 interacts with PPARα to activate CISD2 transcription through a PPAR response element (PPRE) in the CISD2 promoter. Genetic and transcriptomic analyses reveal that the protective effects of hesperetin are largely CISD2-dependent, as they are significantly attenuated in hepatocyte-specific Cisd2 knockout mice. Consistent with these findings, PPARα and CISD2 expression decline with age in human liver tissues. Together, our results define a signaling axis linking HMGCS2, PPARα, and CISD2 that regulates liver aging and suggest that targeting this pathway may represent a strategy to mitigate age-associated hepatic dysfunction.

overall_design: This submission includes two bulk RNA-seq experiments using mouse liver samples. The natural aging experiment compared three groups: young, old, and old mice treated with hesperetin (PZ19b). The Cisd2 hepatocyte-specific knockout experiment compared four groups: Cisd2 f/f control, Cisd2 f/f treated with hesperetin, Cisd2 hepatocyte-specific knockout (Cisd2 hKO), and Cisd2 hKO treated with hesperetin.

first: Zhao-Qing

last: Shen

first: Tsai-Wen

last: Teng

first: Ting-Fen

last: Tsai


title: Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming [Bisulfite]

first: Yonatan

last: Stelzer

type: Methylation profiling by high throughput sequencing

overall_design: Per-locus CpG methylation compared between wild-type and mutant genotypes in vitro and in vivo.

first: Arik

last: Toren

first: Liron

last: Hoffman