title: IRG1/itaconate axis modulates lung tumor microenvironment via pentose phosphate pathway [sav25]

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Tumor-associated macrophages (TAMs) are an important component of the immune milieu within the lung tumor microenvironment (TME) and have both tumor-promoting and tumor-inhibiting functions. However, the exact mechanisms underlying TAM-mediated inhibition of tumor development are still unknown. Itaconate is one of the main metabolites produced by the enzyme immune responsive gene 1 (IRG1) during a pro-inflammatory response. Single cell RNA-seq studies show that macrophages are the major immune cells for Irg1 expression in human and mouse lung tumors. Both Irg1-deficient mice and transplantation of Irg1-depleted bone marrow resulted in increased development of lung tumors in Kras and orthotopic mouse models, suggesting the anti-tumor function of Irg1-associated macrophages. On the other hand, 4-octyl-itaconate (octyl-Ita) reduces lung tumor development in lung cancer cell lines in vitro, in vivo models of lung cancer, and ex vivo using human tumor precision-cut lung slices. Mechanistically, IRG1/itaconate induces a metabolic shift in cancer cells and pro-tumor macrophages, specifically through inhibition of the pentose phosphate pathway (PPP). An integrative analysis of metabolomics, transcriptomics and proteomics identified glucose-6-phosphate dehydrogenase (G6PD) as the primary target for the antiproliferative effect of IRG1/itaconate. IRG1/Itaconate inhibited G6PD activity without affecting G6PD expression in Irg1-deficient mice and octyl Ita-treated lung cancer models. The novel inhibitory effects of IRG1/Itaconate and Octyl Ita on G6PD activity and PPP metabolism can not only suppress cancer cell proliferation in a non-cell-autonomous manner, but also re-educate pro-tumor macrophages into anti-tumor macrophages in a cell-autonomous manner. Our results suggest that octyl Ita is an effective anti-tumor metabolite with potential therapeutic application in lung cancer.

overall_design: To check the potential effect of 4-Octyl Itaconate on lung cancer cells, A549 lung cancer cells were treated with 4-Octyl Itaconate (250uM) or DMSO (as placebo) for 48 hours.

first: Siavash

last: Mansouri

first: Rajkumar

last: Savai


title: Nuclear RNA forms an interconnected network of transcription-dependent and tunable microgels

status: Public on Jun 11 2026

city: Edinburgh

first: Nick

last: Gilbert

address: Crewe Rd

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

summary: The human cell nucleus is comprised of proteins, chromatin and RNA, yet how they interact to form supramolecular structures and drive key biological processes remains unknown. Conflicting models have proposed either a fluid-like or solid-like nature for the intranuclear microenvironment. To reconcile this discrepancy, we investigated the 3D structure and properties of the nuclear interior using experiments and computer simulations. We reveal a novel mechanism where newly synthesized RNA interacts with SAF-A (scaffold attachment factor A, or HNRNPU), forming interconnected microgels degraded by the exonuclease XRN2, leading to dynamic cycles of gelation and fluidization. This emergent microgel network depends on transcription, and is disrupted by SAF-A depletion. It also decreases protein mobility and regulates chromatin compaction by modulating micro-phase separation, thereby opening transcriptionally active regions. This tunable intranuclear network exhibits scale-dependent fluid- and solid-like features, that we suggest may regulate transcription by controlling access to regulatory proteins and polymerases.

overall_design: To identify the types of nascent RNA that bind to SAF-A (HNRNPU). To achieve this cells expressing FLAG-SAF-A were exposed to 4sU, with a washout, and then exposed to 365 nm UV light. Cells were then recovered and used for a PAR-CLIP experiment.

first: Ryu-Suke

last: Nozawa


title: IRG1/itaconate axis modulates lung tumor microenvironment via pentose phosphate pathway [sav24]

type: Expression profiling by high throughput sequencing

overall_design: To check the anti-tumor potential of 4-Octyl Itaconate, PBMC-derived macrophages polarized toward pro-tumor macrophages (M2) with IL4 (20ng/ml, 24 hours) followed by treatment with 4-Octyl Itaconate (250uM) or DMSO (as placebo) for further 24 hours. As a positive control, anti-tumor macrophages (M1) were generated with polarization of  PBMC-derived macrophages by LPS (100ng/ml, Sigma) and interferon γ (IFNɣ) (100U/ml, Roche) for 24 hours.


title: SerRS mediates translational readthrough of through engagement of the selenocysteine incorporation machinery

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

summary: Translational readthrough of UGA stop codons by selenocysteine-specific tRNAs (tRNASec) provide the basis for selenoprotein biosynthesis. Seryl-tRNA synthetase (SerRS) charges tRNASec with serine, which is modified into selenocysteine, and delivered to the ribosome by a designated elongation factor (eEFSec). We found that the selenocysteine incorporation machinery, including SerRS, tRNASec, and eEFSec, also mediated translational readthrough of non-selenocysteine genes, including VEGFA, to create C-terminally extended protein isoforms. SerRS bound a subset of non-selenocysteine mRNAs to facilitate serine insertion. SerRS-mediated readthrough is sufficient to reverse premature termination caused by a disease-causing nonsense mutation. Genes involved in hypoxia, angiogenesis, and adhesion are enriched among SerRS-bound genes. This regulatory function of SerRS in mRNA translation is dependent on its enzymatic activity but also a vertebrate-specific domain involved in non-tRNA nucleic acid interaction. Our findings offer an avenue for therapeutic targeting of nonsense mutations through regulation of existing protein synthesis machinery exclusively using unmodified factors.

overall_design: eCLIP-seq for seryl-tRNA synthetase (SerRS) in MDA-MB-231 cells.

first: Justin

last: Wang

first: Brian

middle: A

last: Yee


title: IRG1/itaconate axis modulates lung tumor microenvironment via pentose phosphate pathway

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

overall_design: Refer to individual Series


title: Transcriptomics analysis of host immune response to P. falciparum malaria [Year 2]

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

summary: We performed a genome-wide profiling of  mRNA from human whole blood sample to identify mRNAs responsive to P.falciparum (P.f) infection and/or associated with parasite load.

overall_design: 77 peripheral blood mRNA profiles of children between the ages of (2-12) sampled and profiled during P. falicparum infection 21-day old wild type (WT) and Nrl-/- mice

first: Abdrabou

last: Wael

first: Diawara

last: Aïssatou

first: Dieng

last: Mame Massar

first: Idaghdour

last: Youssef


title: Estrous cycle regulation of the transcriptional landscape of basolateral amygdala cell types

status: Public on Jun 10 2026

city: Birmingham

first: Elizabeth

middle: Kathleen

last: Lucas

state: AL

department: Psychiatry and Behavioral Neurobiology

institute: University of Alabama at Birmingham

summary: Single-nucleus RNA-sequencing data from adult female proestrus, adult female diestrus, and male C57Bl/6J mouse brain basolateral amygdala.

overall_design: This GEO processed-data package contains only the RNA-seq/single-nucleus RNA-seq processed data. Adult C57BL/6J female mice underwent vaginal cytology to determine estrous cycle state for proestrus and diestrus, male animals underwent sham vaginal lavage  (n = 3 per group).

middle: K

first: Peter

middle: J

last: Teravskis


title: Transcription machinery clustering by Integrator synchronizes histone gene expression

city: New York

first: Feiyue

last: Lu

state: NY

department: Institute for Systems Genetics

institute: NYU School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Numerous components of the transcription machinery, including RNA polymerase II (Pol II), accumulate in high-concentration clusters at gene promoters. Whether these clusters assemble on demand during transcription or constitute regulatory units remains unclear. Examining the Drosophila histone locus—where histone genes normally transcribe exclusively during S phase—we unexpectedly found large clusters containing non-chromatin-bound Pol II and elongation factors outside of S phase. When transcription activates during S phase, P-TEFb drives an accelerated turnover of the cluster components. Dispersion of clusters through depletion of the Integrator complex endonuclease module causes histone transcription to have a diminished S-phase peak and instead occur ectopically throughout the cell cycle. We propose that clusters constitute gate-keeping hubs that maintain a poised machinery pool, restricting gene activation to defined temporal windows.

overall_design: CUT&RUN libraries prepared from transcription inhibitors treated Drosophila egg chambers

first: Brandon

last: Park

first: Rina

last: Fujiwara

first: Jeremy

middle: E

last: Wilusz

first: David

middle: S

last: Gilmour

first: Ruth

last: Lehmann

first: Timothee

last: Lionnet


title: EMMIs: Engineered Myometrial Microtissues for Direct Quantification of Oxytocin-Induced Contractility

city: St. Louis

first: Ritu

last: Dave

address: 425 S Euclid Ave

institute: Washington University School of Medicine

summary: Forceful and coordinated contractions of the uterine myometrium are essential for successful labor, delivery, and postpartum uterine involution. Failure of the uterus to generate or sustain contractile force (uterine atony) after delivery results in postpartum hemorrhage, a leading cause of maternal mortality globally. Paradoxically, uterine atony is exacerbated by prolonged oxytocin exposure used to induce or augment labor through a process of contractile desensitization. Despite its prevalent use in obstetrics, the direct impact of oxytocin desensitization on myometrial contractile force generation remains poorly defined. Current model systems are inadequate to address this gap: ex vivo myometrial tissue strips are limited by tissue availability, donor variability, and lack of genetic tractability, while existing in vitro models provide only indirect readouts of contractility without direct force quantification. Here, we introduce engineered myometrial microtissues (EMMIs), a platform enabling the direct, isometric measurement of contractile force in response to physiological agonists like oxytocin. By embedding and molding immortalized human myometrial smooth muscle cells within a collagen hydrogel, we induced significant structural and molecular maturation over six days. Upon maturation, EMMIs were characterized by circumferential cellular alignment, sustained expression of smoothelin, upregulation of connexin-43, and a transcriptomic shift toward a contractile phenotype. Mature EMMIs generated calcium-sensitive, dose-dependent contractions to oxytocin and potassium chloride. Genetic deletion of the oxytocin receptor abolished oxytocin-induced contractility, establishing receptor specificity. Finally, we utilized EMMIs to recapitulate clinical oxytocin desensitization, providing a direct link between prolonged oxytocin exposure and diminished contractile output. Together, these findings establish engineered myometrial microtissues (EMMIs) as a genetically manipulable, and reproducible system for investigating myometrial contractile physiology to improve obstetric outcomes.

overall_design: RNA-seq profiling of EMMIs on Day 1, 3, and 6 of their six-day formation process.

first: Karla

last: Ortega-Sandoval

first: Cailin

last: Gonyea

first: Kaci

last: Mitchum

first: Alana

last: Aristimuno Milan

first: Shriya

last: Suryakumar

first: Antonina

last: Frolova

first: Shreya

last: Raghavan


title: Alternative splicing- and gene fusion-derived neoepitopes in MASLD-associated hepatocellular carcinoma

city: Copenhagen

first: Jesper

middle: Bøje

last: Andersen

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD)-driven hepatocellular carcinoma (HCC) exhibits reduced responsiveness to immune checkpoint blockade compared with viral or other etiologies, suggesting underlying differences in tumor immunogenicity and immune evasion. To characterize the immunogenic landscape of MASLD-driven HCC, we profiled transcriptomic data from 120 liver tissue samples, including healthy controls (n = 12), MASLD samples (n = 13), and MASLD-associated HCC samples (n = 95), and investigated the contribution of transcriptome-derived neoantigens to this altered immune landscape, focusing on alternative splicing and gene fusion events as non-canonical sources of tumor-specific epitopes.

overall_design: RNA sequencing was performed on 120 human liver tissue samples, including healthy controls (n = 12), MASLD liver samples without HCC (n = 13), and MASLD-associated HCC samples (n = 95). The HCC cohort consisted of 47 paired tumor and adjacent non-tumor liver tissues and one additional tumor sample. Transcriptomic analyses were conducted to characterize immune-related alterations and to identify neoantigens derived from alternative splicing and gene fusion events during MASLD-associated hepatocarcinogenesis.

first: Lina

last: Zhao


title: RelB Drives Integrin-Mediated Stress Tolerance and Relapse in High-Grade Serous Ovarian Cancer

city: San Diego

first: Mikella

last: Robinson

address: 5500 Campanile Drive

institute: San Diego State University

summary: High-grade serous ovarian cancer (HGSOC) often relapses after chemotherapy due to chemoresistant cancer stem-like cells (CSCs). NF-κB signaling, previously shown to enhance stemness traits, was investigated for its role in post-treatment tumor regrowth. Here, we found that NF-κB subunits RelA and RelB jointly regulate extracellular matrix genes but differentially control integrin subunits: RelA regulates ITGAV (αV) and RelB regulates ITGB3 (β3). Integrin αVβ3 expression is upregulated on CSCs and this is partially driven by NF-κB activation. In vivo models demonstrate that αVβ3⁺ cells have higher tumor-initiating capacity and comprise over 90% of cells from relapsed tumors. Cells expressing RelB and αVβ3 preferentially grow on mesentery at relapse. Targeting this pathway, combined RelB knockdown and inhibition of αVβ3, eliminated stress-tolerant CSCs, reduced tumor burden, and extended survival. These findings highlight integrins as promising therapeutic targets and reveal distinct roles for NF-κB subunits in regulating metastasis and relapse in HGSOC.

overall_design: RNA-seq profiling of OV90 cells grown in adherent or spheroid conditions with knockdown of RelA or RelB

first: Omar

last: Lujano-Olazaba

first: Nathan

last: Wong

first: Carrie

last: House


title: Transcriptome data of miR-30e-5p overexpression in human aortic endothelial cells

city: Xi'an

first: Chen

last: Wang

address: Yanta West Road No.277

country: China

institute: The First Affiliated Hospital of Xi’an Jiaotong University

summary: To explore the transcriptional changes in human aortic endothelial cells (HAECs) caused by miR-30e-5p overexpression, we transfected HAECs with miR-30e-5p mimics or control miRNA and profiled transcriptomes by RNA-seq

overall_design: HAECs were transfected with miR-30e-5p or control miRNA for 48 hr before RNA isolation followed by RNA-seq analysis

first: Jianqing

last: She

first: John

last: Shyy

first: Zu-yi

last: Yuan


title: Bacteroides Fragilis enterotoxin engagement of the colonic epithelium is associated with early YAP1 activation and colon tumorigenesis

city: Baltimore

first: Franck

last: Housseau

state: MD

address: 1651 E.Jefferson St

institute: Johns Hopkins University School of Medicine

summary: Enterotoxigenic Bacteroides fragilis (ETBF) promotes colonic inflammation and tumorigenesis, but the epithelial signaling events linking toxin (BFT2)-induced junctional injury to tumor development remain incompletely defined. Here, wild-type BFT2, but not catalytically inactive BFT2, induced E-cadherin loss and nuclear accumulation of active YAP1 in colonic epithelial cells.  Deletion of BFT receptors, CLAUDINs 3 and 4 mitigated BFT-associated E-cadherin loss and YAP1 nuclear translocation, supporting a model in which BFT epithelial targeting is linked to early YAP1 activation. In ETBF-colonized Min mice, epithelial YAP1 activation was rapid and transient, whereas STAT3 and NF-kB activation persisted after colonization. Nevertheless, conditional deletion of epithelial Yap1 was sufficient to abrogate colon tumor formation without altering ETBF colonization or abolishing IL-17 colitis. Transcriptomic analyses further associated epithelial Yap1 deficiency with reduced regenerative epithelial programs and increased secretory-cell differentiation signatures. Together, these findings support a model in which BFT engagement of CLAUDINs and toxin catalytic activity are associated with epithelial YAP1 activation, and epithelial YAP1 contributes to ETBF-associated colon tumorigenesis in Min mice

overall_design: RNA was extracted from epithelial cell (Epcam+CD45-) cell sorted from the colon of age and sex-matched  Min mice and VilCre YAPFL Min mice infected 7 days or not by enterotoxigene Bacteroides fragilis. The colons were flushed and cut in small pieces and washed only once in CMF/FBS/EDTA to eliminate debris and dead epithelial cells. Following enzymatic digestion , density gradient was omitted and whole cell preparations were stained for viability, EpCAM, CD45, Thy1.2, and CD19  antibodies, and sorted directly into lysis buffer of the RNeasy Micro Kit by Qiagen. Epithelial cells were characterized as EpCAM+, CD45-, Thy1.2-, and CD19-.  RNA was isolated using the RNeasy Micro Kit by Qiagen fol-lowing the manufacturer protocol. The RNA samples were sent to Novogene for sequencing (Sacremento, CA).

first: Nile

last: Liu

first: Ada

last: Tam


title: Selective insertion of a payload into NK cell checkpoint NKG2A, as a new platform for treating AML.

city: Warminster

first: Maksim

middle: Alexandrovich

last: Shestov

state: Pennsylvania

address: 675 E Street Rd

department: Center for Cellular Immunotherapies

institute: University of Pennsylvania

summary: Natural killer (NK) cells are promising effectors for immunotherapy due to their intrinsic ability to recognize and eliminate malignant cells without prior sensitization. In acute myeloid leukaemia (AML), NK cell function is impaired, in part through inhibitory receptor signalling.  We profiled NK cells from healthy donors and patients with relapsed AML using single-cell RNA sequencing, revealing broad alteration of activating and inhibitory receptor programs in patient NK cells. KLRC1, encoding the inhibitory receptor NKG2A, was co-expressed with effector genes such as granzyme A, granzyme B, and granulysin in NK cells, suggesting its relevance in cytotoxic competence and highlighting it as a targetable locus. Using CRISPR-Cas9, we disrupted KLRC1 and simultaneously integrated either an EGFRt reporter or an anti-CD33 CAR via AAV6-mediated homology-directed repair. KLRC1-deficient (KLRC1 KO ) and CAR-KLRC1 KO NK cells exhibited enhanced cytotoxicity against AML cell lines and primary AML blasts, particularly under limiting effector-to-target conditions. However, KLRC1 disruption imposed proliferative constraints and limited in vivo persistence. To overcome this, we implemented a cis-targeted IL-2 delivery strategy, selectively expanding edited NK cells and restoring long- term persistence in vivo without inducing bystander activation. This dual-editing strategy take advantage of KLRC1 as a versatile genomic platform for inhibitory checkpoint removal and precise transgene insertion, combining enhanced antitumor activity with controlled cytokine support. Collectively, our findings establish a physiologically grounded and adaptable NK cell engineering framework, providing a potent, persistent, and lineage-specific platform for AML immunotherapy.

overall_design: Single-cell RNA sequencing was performed on bone marrow mononuclear cells from 7 relapsed AML patients and 3 normal bone marrow donors. Samples were processed to profile transcriptomic differences between relapsed AML bone marrow and healthy donor bone marrow at single-cell resolution. The study was designed to characterize cellular composition and gene expression programs associated with relapsed AML compared with normal hematopoiesis.

first: Asuncion

last: Borrero Borrego

first: Saar

last: Gill


title: Brain corticogenesis promotes SARS-CoV-2 neuro-glial tropism through lipid-dependent viral replication

city: Gyeongsan

first: Byoung-San

last: Moon

state: Gyeongbuk

address: 280 Deahak-ro

department: Medical Biotechnology

country: South Korea

institute: Yeungnam University

summary: Human induced pluripotent stem cell (hIPSC)-derived cerebral organoids (CBOs) provide a potential in-vitro model to study cellular composition and transcriptional dynamics during human brain development. This single-cell RNA analysis aims to evaluate the capacity of CBOs to reflect key brain developmental stages, assess their transcriptional fidelity against human fetal brain references, and characterize lipid metabolic gene programs associated with brain maturation, collectively providing a transcriptomic framework for understanding coordinated molecular and cellular changes during human brain development.

overall_design: Nuclei were isolated from hIPSC-derived CBOs at two developmental timepoints, embryoid body day 60 (EB60, immature) and day 120 (EB120, mature) and subjected to scRNA-seq. Multiple random cortical regions from different organoids were pooled per timepoint to account for intrinsic organoid heterogeneity.

first: Nhu

last: Mai Thi Quynh

first: Jieun

last: Park


title: Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris

city: Helsingin yliopisto

first: Tanja

last: Pyhäjärvi

state: Finland

address: Department of Forest Sciences

department: Department of Forest Sciences

country: Finland

institute: University of Helsinki

summary: We provide an atlas of gene expression patterns for conifer Pinus sylvestris across five tissues: embryo, megagametophyte, needle, phloem and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level.

overall_design: The plant material was obtained during the growing season of 2016 (May 26th–27th) and consisted of needles, phloem, vegetative buds and seeds from six non-related adult Pinus sylvestris trees. We used data from trees growing in a natural forest population to ensure that the observed patterns of tissue preferential expression and specificity were robust to genotypic and environmental variation. The material was collected at the Punkaharju Intensively Studied Site (ISS) in Southern Finland. Megagametophyte and embryo tissues were obtained by dissecting mature seeds collected from the same mother trees from which the vegetative tissues were obtained. Seeds were stored in the dark at 4 °C until germination was induced by exposure to moisture and continuous light for 48 h.

first: Ojeda

middle: I

last: Dario

first: Cervantes

last: Sandra

first: Ruttink

last: Tom

first: Kujala

middle: T

last: Sonja

first: Kärkkäinen

last: Katri

first: Verta

last: Jukka-Pekka

first: Vuosku

last: Jaana

first: Mattila

middle: M

last: Tiina

first: Pyhäjärvi

last: Tanja


title: Single-Cell Atlas of Photoaged Skin Reveals JAK-STAT Blockade as a Strategy to Reverse Dermal Remodeling

city: Beijing

first: Yuanyuan

last: Liu

address: Medical School of Chinese People's Liberation Army, 100039 Beijing, China.

summary: Chronic ultraviolet exposure superimposes inflammatory and matrix-degenerative insults on intrinsic aging to produce cutaneous photoaging. This study combined a chronic UVA/UVB mouse model with single-cell RNA sequencing of control, UV-exposed, and UV + ruxolitinib-treated dorsal skin to map photoaging at cellular resolution and evaluate topical JAK1/2 blockade as an intervention.

overall_design: Single-cell RNA-seq was performed on full-thickness dorsal skin from female 8-week C57BL/6J mice assigned to control, UV, or UV + ruxolitinib groups. UV-treated mice were irradiated with mixed UVA (315-400 nm, 0.60 mW/cm2) and UVB (290-315 nm, 3.5 mW/cm2) every other day for 12 weeks. The ruxolitinib group received topical 1.5% ruxolitinib ointment after irradiation. Samples were compared across control, UV, and UV + ruxolitinib conditions.

first: Mingwang

last: Zhang

first: Cheng

last: Yang

first: Chenhui

last: Wang

first: Yurui

last: Zou

first: Kai

last: Luo

first: Haima

last: Li


title: In vivo base editing partially rescues bone dysplasia in a mouse model of Hutchinson-Gilford Progeria Syndrome

city: Bethesda

first: Michael

last: Erdos

address: 50 South Dr

department: NHGRI

institute: NIH

summary: Hutchinson-Gilford Progeria Syndrome (HGPS) is a premature aging disorder affecting tissues of mesenchymal origin. Most patients harbor a c.1824C>T/p.G608= variant, commonly described as G608G, in exon 11 of LMNA that leads to aberrant splicing and production of the toxic progerin protein. In addition to cardiovascular, dermal, and adipose tissue deterioration, HGPS mouse models also develop progressive bone dysplasia that occurs in patients. Here we characterize the efficacy of in vivo mutation correction with an adenine base editor (ABE) to rescue structural and functional defects in HGPS transgenic murine bone tissue. Treatment of double-copy transgenic osteoblast cultures with a lentiviral-delivered CRISPR-Cas9 ABE achieved nearly 40% gene correction in vitro, resulting in significant reduction of progerin transcripts and protein, in the absence of selective agents. Furthermore, gene correction improved progeroid osteoblasts’ capacity to deposit and mineralize extracellular matrix compared to untreated cultures. In vivo, a single intravenous dose of AAV9-delivered ABE corrected the mutation, achieving ~14%, ~22%, ~10% and <1% correction in bone by six months of age when administered at P3, P14, 1 and 4 months of age, respectively. Partially rescued bone structural and physical parameters were observed in P14-treated mice with concomitant normalization of gene transcriptional programs and intracellular signaling pathways involved in bone remodeling. This work demonstrates in vivo delivery of a locus-specific DNA base editor to bone tissue, delineates the timing of treatment required for maximum efficacy, and suggests that this system might be tailored for application to other monogenic bone disorders.

overall_design: RNAseq analysis of tibiae from 6-month wild-type, HGPS mice treated with saline and HGPS mice treated with a locus-specific adenine base editor to assess efficacy of gene correction to rescue bone dysplasia.

first: Wayne

last: Cabral

first: Caleb

last: Grenko

first: Diana

last: Yeritsyan

first: Indeevar

last: Beeram

first: Shubham

last: Laiwala

first: Lukas

middle: R

last: Johnson

first: Urraca

middle: L

last: Tavarez

first: Tingfen

last: Yan

first: Stephen

last: Wincovitch

first: Luke

middle: W

last: Koblan

first: Xin

middle: D

last: Gao

first: Meirui

last: An

first: Narisu

last: Narisu

first: Leslie

middle: G

last: Biesecker

first: David

first: Ara

last: Nazarian

first: Francis

last: Collins


title: A pilot study for treatment of chronic cough after COVID-19 infection by nebulization therapy of mesenchymal stem cell (MSC)-derived extracellular vesicles from 3D culture

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

institute: Zhejiang University

summary: RNA-seq of blood cells from patient before and after treatment of chronic cough after COVID-19 infection by nebulization therapy of mesenchymal stem cell (MSC)-derived extracellular vesicles from 3D culture

overall_design:
RNA-seq of blood cells from patient before and 14days after treatment of chronic cough after COVID-19 infection by nebulization therapy of mesenchymal stem cell (MSC)-derived extracellular vesicles from 3D culture

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

first: Jihui

last: Du

first: Zhiyong

last: Zhang


title: Altered Cohesin Dynamics During Cellular Differentiation

city: Oklahoma City

first: Jacob

middle: Gordon

last: Kirkland

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

institute: Oklahoma Medical Research Foundation

summary: The cohesin complex plays essential roles in chromosome organization and gene regulation, yet how cohesin dynamics are controlled during cell-state transitions remains poorly understood. Here, we examined how cohesin regulation is remodeled during the differentiation of mouse embryonic stem cells (mESCs) into the cardiomyocyte lineage using an in vitro differentiation system. We found that core cohesin subunits remain broadly stable at the protein level. In contrast, the levels of cohesin regulators, including the cohesin removal protein WAPL and the cohesin stabilizing protein ESCO1, decline sharply despite modest transcript-level changes. The cohesion maintenance factor Sororin was also reduced. To better understand the net effect of these changes on cohesin dynamics, we use live-cell FRAP of RAD21, which revealed increased cohesin mobility in differentiated cells without a change in recovery kinetics, consistent with reduced stable chromatin engagement or redistribution into a chromatin-unbound nuclear pool. To test functional consequences, we generated homozygous degron alleles for Wapl and Esco1 and induced acute degradation using a dTAG-based system. Loss of WAPL altered cell-cycle dynamics in stem cells and produced a characteristic “vermicelli” chromosome phenotype, consistent with abnormally high and lethal cohesin retention on chromatin. Surprisingly, depletion of ESCO1 had no clear impact on viability and cell cycle progression. Notably, despite loss of detectable WAPL protein in the differentiated cell population, induced WAPL degradation in these cells also resulted in the formation of vermicelli, indicating that the low level of WAPL remains functionally required. Together, these findings identify cohesin regulators, rather than cohesin abundance, as central drivers of changes in cohesin dynamics during differentiation. They further show that even very low levels of WAPL continue to provide critical structural plasticity of chromosomes following cell cycle exit and lineage commitment.

overall_design: For transcriptional analysis, TC1 cells were dissociated either before differentiation or on day 10 of the protocol. Total RNA was extracted from a single-cell suspension using TRI Reagent (Sigma-Aldrich) according to the manufacturer's instructions. Library preparation was done using SMART-Seq Total RNA High Input (RiboGone Mammalian). Libraries will be run on a Tapestation, quantified using a Qubit fluorometer, and sequenced at the OMRF Clinical Genomics Core on a NovaseqX (Illumina).

first: Magdalena

last: Jawor

first: Karol

last: Tchorz

first: Marcin

last: Ostoja-Helczynski

first: Michaela

last: Crossley

first: Susannah

last: Rankin


title: RNA-seq analysis of global gene expression changes in human FSHD immortalized myotubes following treatment with the BAZ1A inhibitor C06

city: Reno

first: Peter

last: Jones

state: NV

address: 1664 N. Virginia St.

department: Pharmacology

institute: University of Nevada, Reno School of Medicine

summary: Facioscapulohumeral muscular dystrophy (FSHD) is caused by epigenetic dysregulation of the disease locus, leading to pathogenic misexpression of DUX4 in skeletal muscle.  We identified BAZ1A (bromodomain adjacent to zinc finger domain protein 1A) as a promising target for FSHD therapeutic development, and identified a small-molecule compound termed C06 that binds BAZ1A in vitro and is a potent repressor of DUX4.  To determine the global specificity of C06 activity, we performed RNA-seq on FSHD myotubes treated with different concentrations of C06, and compared the gene expression profiles.  At low concentrations, C06 returns the DUX4 gene expression signature to a healthier profile without major effects on the muscle transcriptome.  Thus, C06 is a useful tool for potent and specific DUX4 suppression, and a viable candidate for further development.

overall_design: Immortalized FSHD1 myotubes (15Abic) were treated with C06 at 500 nM, 100 nM, or DMSO alone.  4 biological replicates for each treatment groups and 5 biological replicates for each control groups were collected and submitted for sequencing and RNA-seq analysis.

first: Ning

last: Chang

first: Hannah

middle: P

last: Moore

first: Charis

last: Himeda

first: Takako


title: Transcriptomic profiling of Cosmc-silenced Tn+ 4T1 cells-bearing triple-negative tumors in mice

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

summary: Aberrant O-glycosylation and accumulation of the Tn antigen are associated with aggressive phenotypes in triple-negative breast cancer (TNBC). To investigate the transcriptomic consequences of Tn antigen expression, we analyzed gene expression profiles of murine 4T1 breast cancer cells carrying CRISPR/Cas9-mediated silencing of the Cosmc gene (Tn+) compared with parental wild-type 4T1 cells (WT). Total RNA was extracted from 4T1 cells-bearing tumors from mice (Tn and WT)s and subjected to RNA sequencing using Illumina NovaSeq X technology.

overall_design: Tumor tissues were processed for total RNA extraction using the miRNeasy Tissue/Cells Advanced Mini Kit (Qiagen) following mechanical homogenization in RLT buffer supplemented with β-mercaptoethanol. Representative tumor samples from Tn+ and wild-type (WT) groups were selected for transcriptomic analysis, including six biological replicates per condition (n = 6/group), prioritizing samples across different tumor sizes to minimize the impact of intratumoral heterogeneity. RNA quality and integrity were evaluated using the RNA ScreenTape® assay on the Agilent 4200 TapeStation System, and only samples with RNA Integrity Number (RIN) values greater than 7.0 were included for sequencing. Transcriptomic libraries were prepared using the Illumina Stranded mRNA Prep protocol with Illumina DNA/RNA UD Indexes Set B, including poly(A) mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification. Final library quality and fragment distribution were assessed using the D1000 ScreenTape® assay prior to pooled paired-end sequencing on the Illumina NovaSeq X platform, generating approximately 20–30 million reads per sample. Raw sequencing data were processed through a standard bioinformatic pipeline including quality assessment with FastQC, adapter trimming and filtering with fastp, alignment to the Mus musculus reference genome (GRCm39) using STAR, and gene-level quantification using featureCounts.

first: Roger

last: Chammas

first: Teresa

last: Freire

first: Mercedes

last: Landeira

first: Alexis

last: Murillo-Carrasco

first: Tatiane

last: Furuya


title: AETA peptide contributes to Alzheimer’s disease signature of synapse dysfunction

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Alzheimer’s disease (AD), the leading cause of dementia, is characterized by early synaptic dysfunction that precedes overt cognitive decline. While amyloid-β and Tau remain central to AD pathogenesis, molecular triggers of synapse weakening remain unclear. Here, we investigated AETA, a novel brain-secreted peptide derived from amyloid precursor protein (APP), as a potential mediator of synapse dysfunction in AD. We previously identified AETA as a unique modulator of NMDA receptor activity in the healthy brain; however, its role in AD etiology was yet to be explored. Post-mortem analyses of human hippocampal and prefrontal cortex tissues revealed significantly elevated AETA levels in AD patients, particularly in females. To further explore the contribution of AETA to AD synaptic pathology, we analyzed a new mouse model, the AETA-m mouse, exhibiting chronically increased brain AETA expression. Hippocampi of female AETA-m mice display an increase in the number of astrocyte and microglia, but no overt neuroinflammation. RNA sequencing of female AETA-m hippocampi revealed alterations in synaptic gene expression that closely paralleled those observed in vulnerable human AD brain regions, most notably in the hippocampus. These two phenotypes were absent in males. Functionally, hippocampal neurons from AETA-m mice displayed impaired NMDA receptor signaling, dendritic spine loss, and memory deficits especially in females, mirroring early AD-associated synaptic dysfunction. Together, these findings identify AETA as a novel key contributor of synaptic vulnerability in AD and associated memory processing, especially in females. Targeting AETA signaling may, therefore, offer new therapeutic avenues for preventing or mitigating synaptic and cognitive decline in AD.

overall_design: WT vs AETA-m male (5 replicates) and female (4 replicates) mouse hippocampal tissue

first: Jane

last: Dunot

first: Marin

last: Truchi

first: Helene

last: Marie


title: Circulating miRNAs Associated with Frailty in Old People with Cardiovascular Diseases Promote Cellular Senescence and Inflammation

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Circulating microRNAs (miRNAs) have been suggested as candidate biomarkers of frailty, a complex multidomain geriatric syndrome associated with a higher risk of poor outcomes. However, few studies have adopted an unbiased approach to screen for plasma miRNAs associated with frailty independently of common risk factors and little is known relatively to their putative etiopathogenic role. Methods: Leveraging a cohort recruited for a randomized trial testing the effect a remote rehabilitation intervention on frailty in elderlies with cardiovascular diseases (CVD), we tested plasma samples from 24 people, 12 frail and 12 not frail according to the EFT scale and matched for all the other clinical characteristics, to search for miRNAs associated with frailty through small RNA-Sequencing. From this analysis, we selected the 11 most significantly deregulated miRNAs and quantified them in the entire cohort (n=197) through quantitative RT-PCR. Then, we explored the candidate pathways targeted by miRNAs significantly deregulated in frailty through bioinformatics analyses and tested the effect of miR-181b-3p and miR-490-5p overexpression on cellular senescence and inflammation in endothelial cells. Results: We found that plasma levels of miR-181b-3p, miR-490-5p, and miR-500a-5p were increased, while miR-511-5p was reduced, in people with frailty compared with non-frail individuals, also after adjustment for age. Bioinformatics analysis of the frailty-upregulated miRNAs suggested cell cycle and cellular response to DNA damage, two recognized drivers of aging, as regulated biological processes for both miR-181b-3p and miR-490-5p. Overexpression of these two miRNAs through transient transfection in endothelial cells promoted a prototypical cellular senescence response accompanied by a pro-inflammatory phenotype, as assessed through SA-Beta Gal staining and increased expression of multiple senescence and inflammatory markers at both mRNA and protein levels. Conclusions: Overall, these data suggest that circulating levels of miR-181b-3p, miR-490-5p, miR-500a-5p and miR-511-5p might serve as markers of frailty in old people with CVD and that miR-181b-3p and miR-490-5p might be functionally linked to the etiopathogenesis of the syndrome through their effects on cellular senescence and inflammation.

overall_design: Small RNA-seq profiling of plasma samples from frail and not frail in elderlies.

first: Katarzyna

last: Kwiatkowska

first: Francesco

last: Prattichizzo


title: Single-Cell RNA Sequencing of TGF-Treated Human iPSC-Derived Skin Organoids

city: Birmingham

first: Lin

last: Jin

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

summary: Human iPSC-derived skin organoids provide a powerful model for studying skin development and disease. Here, we investigated the effects of TGF-β treatment on human iPSC-derived skin organoids using single-cell RNA sequencing (scRNA-seq). Transcriptomic analysis identified diverse cellular populations, including keratinocytes and fibroblast-like cells, and revealed significant TGF-β-induced changes in cell states and gene expression. TGF-β treatment upregulated profibrotic and extracellular matrix-associated genes and activated pathways related to tissue remodeling and epithelial–mesenchymal transition. These findings demonstrate that iPSC-derived skin organoids recapitulate key features of TGF-β-mediated skin remodeling and provide a useful platform for studying fibrosis and cellular heterogeneity at single-cell resolution.

overall_design: Mature organoids were assigned to three groups: (1) a control group cultured without TGF-βsupplementation, (2) an 8-day treatment group exposed to TGF-β (10 ng/mL) for 8 days, and (3) a 14-day treatment group exposed to TGF-β (10 ng/mL) for 14 days.Medium containing with or without fresh TGF-βwas replaced every other day throughout the experiment. At the end of each treatment period, organoids were harvested for downstream single-cell RNA sequencing (scRNA-seq) analysis to assess cellular composition and transcriptional changes associated with TGF-β-induced skin remodeling and fibrosis.


title: RUNX2 Promotes Fibrotic Activation in Skin Fibroblasts and Is Targetable by Small-Molecule Inhibition

summary: Fibrosis is driven by activated fibroblasts, but key transcriptional regulators remain unclear. We investigated the role of RUNX2 using three human skin fibroblast lines with RUNX2 knockdown (shRUNX2) and matched controls (shControl), treated with or without TGF-β, followed by bulk RNA sequencing. RUNX2 depletion attenuated TGF-β–induced pro-fibrotic gene programs, including extracellular matrix organization and myofibroblast differentiation. In primary fibroblasts, the small molecule F0565-0303 reduced TGF-β–induced fibrotic signatures and decreased RUNX2 expression, partially mimicking RUNX2 knockdown, while showing minimal effects under basal conditions. These results identify RUNX2 as a key driver of fibroblast activation and support its pharmacological targeting as an anti-fibrotic strategy.

overall_design: For knockdown studies, three stable RUNX2 knockdown immortalized fibroblast cell lines (shRUNX2) and three matched control lines (shControl) were cultured under standard conditions. Cells were treated with or without TGF-β (10ng/ml) for 48 hours to induce a fibrosis-like state, followed by RNA extraction for bulk RNA sequencing analysis. For compound testing, primary human skin fibroblasts were treated with TGF-β (10ng/ml) in the presence or absence of F0565-0303 (5 μM), as well as compound-only controls. After 48 hours, cells were harvested and RNA was isolated for transcriptomic profiling.


title: Investigating the Role of RUNX2 Target Genes in Fibrotic Responses

summary: Primary human skin fibroblasts were treated with TGF‑β, and CUT&RUN assays were performed using an anti-RUNX2 antibody to map RUNX2 genomic binding sites under fibrotic conditions.

overall_design: Primary human skin fibroblasts (passages 2–5) were treated with TGF‑β, and CUT&RUN assays were performed using an anti-RUNX2 antibody to identify genomic binding sites. Experiments were carried out with two biological replicates for each condition to ensure reproducibility.


title: DNA repair drives cisplatin-induced neuronal death [SAR-seq]

first: Chuanyuan

last: Chen

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

summary: Cisplatin and similar-acting alkylating chemotherapy agents are the cornerstone treatments for many types of cancers. While effective, these drugs induce long-term side-effects in post-mitotic tissues including the nervous system. There are no known effective pharmacological interventions for chemotherapy-induced neurotoxicity, in part due to our limited understanding of how neurons and other non-dividing cells respond to DNA damage. Here, we show that nucleotide excision repair (NER) is responsible for cisplatin adduct removal in human neurons. However, contrary to its protective role in dividing cells, NER drives neuronal cell death in response to cisplatin. Through excision repair synthesis, NER exhausts low levels of deoxynucleoside triphosphate (dNTP) pools found in post-mitotic neurons. dNTP pools are first consumed to resolve transcription-blocking lesions through transcription-coupled NER. When dNTPs become exhausted, toxic double-strand breaks accumulate across the genome primarily because of incomplete global-genome NER. Supplementation with deoxynucleosides through pharmacological or genetic means protects neurons from cisplatin-induced cell death and reduces cisplatin-induced neuropathic pain in mice. These results identify low levels of endogenous dNTP pools as a vulnerability of post-mitotic cells to DNA damage and suggest nucleoside supplementation as a strategy to protect patients from chemotherapy-induced neurotoxicity.

overall_design: We treated iPSC-derived neurons with the indicated genotypes with cisplatin, EdU, and dN (where indicated) for the specified length of time in each Sample below. Neurons were then processed for SAR-seq, END-seq, S1-END-seq, or RNA-seq.

first: William

last: Nathan

first: Rosy

last: Sakr

first: Bruno

last: Siqueira Mietto

first: Vicent

last: van Batenburg

first: Jeroen

last: van den Berg

first: Josette

last: Wlaschin

first: Ferenc

last: Livak

first: Elsa

last: Callen

first: Nancy

last: Wong

first: Eliza

last: Lloyd

first: Hanna

last: Silberberg

first: Sushma

last: Sharma

first: Raj

last: Chari

first: Tzipporah

last: Freeman

first: Baek

last: Kim

first: Alexander

last: van Oudenaarden

last: Chesler

first: Michael

last: Ward

first: Lisa

last: Boxer

first: Peter

last: McHugh

first: Andrei

last: Chabes

first: Claire

last: Le Pichon

first: André

last: Nussenzweig


title: DNA repair drives cisplatin-induced neuronal death

first: Chuanyuan

last: Chen

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

overall_design: Refer to individual Series


title: DNA repair drives cisplatin-induced neuronal death [END-seq]

first: William

last: Nathan

first: Rosy

last: Sakr

first: Bruno

last: Siqueira Mietto

first: Vicent

last: van Batenburg

first: Jeroen

last: van den Berg

first: Josette

last: Wlaschin

first: Ferenc

last: Livak

last: Callen


title: Effects of  GLI1, GLI3, and GLI1/3 knockdown on rhematoid arthritis synovial fibroblasts stimulated with TNF-alpha

city: Tokyo

first: Tetsuya

last: Saito

state: Select state...

address: 1-5-45 Yushima Bunkyo-ku

department: Rheumatology

country: Japan

institute: Tokyo Medical and Dental University

summary: To investigate effects of  GLI1, GLI3, and GLI1/3 knockdown on rhematoid arthritis synovial fibroblasts (RASFs) stimulated with TNF-alpha, we pre-treated RASFs (n = 3) with siControl (siCtrl) or siGLI1, siGLI3, or GLI1/3 for 72 hours, and then treated them with TNF-alpha (10 ng/mL) for 24 hours and conducted RNA-seq analysis.

overall_design: RASFs (n = 3) were pre-treated with siCtrl, siGLI1, siGLI3, or siGLI1/3 for 72 hours, and treated with TNF-alpha (T, 10 ng/mL), or vehicle control  (Veh) for 24 hours. Total RNAs were extracted and subjected to RNA-seq analysis.

first: Motohiko

last: Sato

first: Shinsuke

last: Yasuda


title: Drought and salinity stress remodel Asian rice (Oryza sativa) leaf development through cell-type specific regulatory programs

status: Public on Jun 22 2026

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

country: Canada

institute: University of Manitoba

summary: Osmotic stressors impair tissue expansion and slow crop development, which can ultimately reduce yield. The mechanisms through which dividing and differentiating cells perceive, integrate, and respond to stress are not well understood. To explore this knowledge gap, we assessed Asian rice (Oryza sativa) seedling responses to drought and salinity stress by performing single-nucleus transcriptome analyses on developing leaves and by assaying ion distribution using ICP-MS and CoroNa Green staining. With a dataset of >125,000 high-quality nuclei, we identified transcriptome signatures of developmental trajectories for each of the major tissue systems, from their origin as dividing cells in the shoot apical meristem to mature cells in epidermal, mesophyll, and vascular tissues. We explored the extensive heterogeneity between cell types with respect to their responses to stress by developing an ensemble-based Perturbation Index and a tool for visualizing pseudobulk expression data and characterizing regulatory modules for different stress responses. Transcriptionally, moderate stress perturbs cells early in development and induces regulatory networks that inhibit cell division, whereas mild stressors primarily disrupt gene expression in differentiated tissues. Overall, these results indicate that leaf development occurring in salt and drought stress conditions are the product of complex interplay of developmental, environmental, and cell-type contexts.

overall_design: Rice seedlings were grown under well-watered, drought, or salinity conditions, with two severities of each stressor. Nuclei were isolated from developing leaves and analyzed with snRNA-seq.

first: Sean

last: Robertson

first: Obaid

last: Maqsood

first: Chi

last: Dang

first: Asher

last: Pasha

first: Claudio

last: Stasolla

first: Nicholas

last: Provart


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

city: Toronto

first: Giacomo

last: Furlan

state: ONTARIO

address: 25 Orde St

institute: Lunenfeld-Tanenbaum Research Institute

summary: Cells and organisms can enter transient dormant states to survive unfavorable conditions during development, physiological adult states and disease. One paradigmatic case of dormancy is diapause, whereby embryos transiently pause development and enter a state of suspended animation. In mammals, diapause occurs pre-implantation at the blastocyst state and involves global growth suppression and metabolic rewiring towards lipid usage as energy source. The molecular regulation of diapause remains poorly understood, including whether it occurs by default or requires active signaling. Here, we identify the canonical TGF-β signaling pathway as an essential driver of transcriptional and metabolic reprogramming in diapause. TGF-β signaling was thought to only be required post-implantation, but we show that the ligand Nodal and its downstream effector Smad2 are essential for the survival of paused embryonic stem cells (ESCs) and blastocysts. Mechanistically, we found that Smad2 represses a Pparg, a transcription factor that is a master regulator of lipid storage, a process incompatible with pausing.  Ablation of Pparg in Smad2-deficient ESCs rescues their survival and prevents excess lipid buildup in pausing conditions. These findings establish Nodal/Smad2 signaling as pivotal for sustaining embryonic diapause and suggest that the crosstalk between TGF-β signaling and the Pparg pathway may be broadly relevant for metabolic rewiring in dormancy contexts.

overall_design: ESCs were grown on gelatin for 24 hours in FBS/LIF media, under control and pausing conditions (200 nM INK128). For each conditions, 4 replicates were collected

first: Furlan

last: Giacomo

first: Collignon

last: Evelyne

first: Ramalho Santos

last: Miguel


title: Evaluation of gene expression changes upon acquired resistance to anti-EGFR targeted therapy in head and neck squamous cell carcinoma

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: We studied molecular mechanisms associated with acquired resistance to anti-EGFR targeted therapy in head and neck squamous cell carcinoma (HNSCC) by comparing gene expression profiles in cetuximab-sensitive and -resistant patient-derived xenograft (PDX) models of HNSCC. We generated and validated several HNSCC PDX models. Resistance mechanisms to anti-EGFR therapy were investigated in one of these PDX models (HNC004). First, sensitivity to cetuximab treatment was tested. This model showed high sensitivity to this drug. We induced acquired resistance to anti-EGFR therapy in this sensitive model by treating it chronically with anti-EGFR monoclonal antibody (cetuximab, 30 mg/kg/week) until resistance ensues. RNA-seq analysis was performed on samples coming from untreated and cetuximab-resistant PDX, revealing major changes of expression at the mRNA level.

overall_design: We induced acquired resistance to anti- EGFR therapy in the a sensitive model by treating it chronically with anti-EGFR monoclonal antibody (cetuximab, 30 mg/kg/week) until resistance ensues. Resistance was defined as continuous tumor growth under cetuximab and an increase in tumor volume of more than 200% compared with baseline. The resistant models were treated continuously with cetuximab without interruption. Cetuximab-resistant PDX were compared with corresponding non-treated (baseline) PDX, with three biological replicates per condition. The study was approved by the ethics committee from UCLouvain (approval ID UCL/MD/2012/09July/314) in accordance with the principles of the Declaration of Helsinki, and all patients gave their written informed consent.

first: Sandra

last: Schmitz

first: Jean-Pascal

last: Machiels

first: Cyril

last: Corbet


title: A single-cell and spatial immune atlas of chronic antibody-mediated rejection reveals autoimmune-shared immune states and a CXCL12-CXCR4 fibroblast-immune niche

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

summary: Chronic antibody-mediated rejection (CAMR) is a leading cause of late kidney allograft failure and shares features of chronic immune activation with systemic autoimmune diseases, but how circulating immune states connect to spatially organized graft injury and whether related immune features recur in autoimmune inflammation remain unclear. Here, we integrated single-cell profiles from peripheral blood and kidney graft samples from patients with CAMR or stable allograft function and healthy controls with independent transplant cohorts, bulk transcriptomic datasets, spectral flow cytometry, multiplex immunofluorescence, high-resolution spatial transcriptomics, and a large blood immune reference spanning autoimmune and inflammatory diseases. CAMR was associated with reproducible myeloid expansion and enrichment of SLC8A1+ monocytes/macrophages, ANK3+CD4+ memory T cells, ZEB2hi T cells, and CD16+ NK cells. These subsets exhibited migratory and tissue-interacting programs characterized by the recurrent expression of CXCR4 and ZEB2. In graft tissue, CXCL12-expressing fibroblasts and CXCR4-expressing immune cells were increased in CAMR. High-resolution spatial transcriptomics localized this fibroblast–immune architecture to perivascular regions marked by endothelial activation and stromal remodeling, and placed CAMR-associated immune states within adjacent immune-rich neighborhoods, supporting a CXCL12-CXCR4 axis that may be associated with local immune accumulation. Comparisons with large-scale blood immune reference data and spatial transcriptomic datasets from rheumatoid arthritis and systemic lupus erythematosus suggested partial recurrence of related immune states and fibroblast–immune organization. Together, this study links circulating CAMR immune remodeling to a spatially organized CXCL12-CXCR4 fibroblast-immune niche, and suggests that elements of this niche recur across alloimmune and autoimmune inflammation.

overall_design:
Integrated analysis of publicly available single-cell RNA-seq datasets from autoimmune and inflammatory disease samples to characterize immune cell states and shared transcriptional programs:
Single-cell RNA-seq of human peripheral blood B cells
Single-cell RNA-seq of human peripheral blood Myeloid cells
Single-cell RNA-seq of human peripheral blood NK cells
Single-cell RNA-seq of human peripheral blood T cells

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

last: Xia

first: Yangjuan

last: Bai

first: Binqi

last: Yang

first: Wei

last: Mao

first: Hongyu

first: Yamei

last: Li

first: Yajiao

last: He

first: Jing

last: Wu

first: Bei

last: Cai

first: Yu

last: Fan

first: Haotian

last: Yu

first: Yang

last: Guo

first: Yanmei

last: Liu

first: Xi

last: Tang

first: Huayun

last: Yan

first: Tao

last: Zhou

first: Yiqi

last: Deng

first: Wanchun

first: Minyuan

last: Cao

last: Shu

first: Yun-Ying

last: Shi

first: Lanlan

last: Wang


title: TRPM4 Expression as a Predictive Biomarker and a Mechanistic Driver of Acetalax Activity in Prostate Cancer: Preclinical Efficacy Studies.

first: Yves

last: Pommier

address: 9000 Rockville Pike

institute: National Cancer Institute

summary: Acetalax, a repurposed ion‐transport–targeting compound, induces rapid oncosis-like cell death selectively in TRPM4-expressing cancer cells. Here, we investigated TRPM4 as a mechanistic driver and predictive biomarker of Acetalax response in prostate cancer. Across prostate cancer cell lines, TRPM4-high cells (PC3, LNCaP, 22Rv1) exhibited Acetalax sensitivity, cell swelling, nuclear enlargement, membrane blebbing, and proteasome-dependent TRPM4 degradation, whereas TRPM4-low DU145 cells were resistant. Chronic Acetalax exposure generated resistant clones characterized by complete loss of TRPM4 expression. RNA sequencing of parental and resistant cells identified TRPM4 loss–associated transcriptomic remodeling, including upregulation of proliferative programs and suppression of inflammatory and stress-response pathways. In TRPM4-positive prostate cancer patient-derived xenograft (PDX) models (LuCaP147 and LuCaP167), Acetalax significantly suppressed tumor growth without inducing body-weight loss. TRPM4 expression was consistently elevated in prostate tumors relative to benign tissues and remained high across disease stages and Gleason grades. Together, these results define TRPM4 as a mechanistic determinant of Acetalax sensitivity and provide a rationale for TRPM4-based patient stratification and the development of Acetalax for treatment-refractory prostate cancer.

overall_design: RNA sequencing was performed on TRPM4-high prostate cancer cell lines (PC3, LNCaP) and their Acetalax-resistant chronic-exposure derivatives (CE). For each line, RNA was collected from parental cells (± short-term Acetalax treatment, 10 µM, 4 h) and CE cells (control and treated), each in biological triplicate. Additional analyses included TRPM4 immunofluorescence, Western blotting, cell swelling/blebbing quantification, and viability assays across prostate cancer cell lines with varying TRPM4 status (PC3, LNCaP, 22Rv1, DU145). Patient-derived xenograft (PDX) models (LuCaP147 and LuCaP167) were treated with Acetalax (100 or 300 mg/kg) or placebo, and tumor volumes and body weights were monitored longitudinally. Gene expression analyses were supplemented with prostate tissue microarrays (TMA) and TCGA/GTEx datasets to assess clinical relevance of TRPM4 expression.

first: Yuka

last: Hoshi-Kadonosawa

first: William

middle: C

last: Reinhold

first: Daiki

last: Tanimaya

first: Yoshitaka

last: Inoue

first: Augustin

last: Luna

first: Suresh

last: Kumar

first: Nai-Yun

last: Sun

first: Yoo Sun

last: Kim

first: Juanjuan

last: Yin

first: Nitin

last: Roper

first: Adam

last: Sowalsky

last: Figg

first: Naoko

last: Takebe


title: Macrophages transfer functional target-cell proteins to their surface during live cell uptake

city: San Francisco

first: Balyn

last: Zaro

state: CA

address: 555 Mission Bay Blvd S, Rm 484

institute: UCSF

summary: A cell’s proteome is assumed to reflect its transcriptional and translational activity. Macrophages regularly acquire xenobiotic material from neighboring cells, which is thought to result in degradation of the material. However, increasing lines of evidence suggest that not all uptaken material is degraded and that other transfer-like processes also occur. Field standard technologies are unable to rigorously report on precisely how and by whom the macrophage protein repertoire is altered during these interactions, leaving unresolved the extent to which non-degradative processes contribute to altered phenotypes. Here, we leveraged chemical tools and proteomics to show that intact target cancer cell surface proteins are transferred to the macrophage cell surface at functionally impactful levels in a manner associated with live cell uptake. Widespread acquisition of proteins during cell uptake reengineers the macrophage cell surface proteome and is a transcriptionally silent, cell non-autonomous process with the potential to alter metabolic uptake.

overall_design: RNA-seq of naive monocyte dervied macrophages (hMDMs, Mac), naive SW620 colorectal cancer cells (SW620), SW620s that were co-incubated with hMDMs but not phagocytosed (Uneaten, UE), macrophages following live-cell uptake of SW620 cells (Eaters, Eat), and macrophages which were exposed to SW620s but did not phagocytose (Non-Eaters, Noneat).

first: Regan

middle: F

last: Volk

first: Amy

last: Fan

first: Sara

last: Casebeer

first: Vishnu

last: Tejus

first: Andrew

last: Condon

first: Bahar

last: Zirak

first: Nayelis

last: Manon

first: Iryna

last: Irkliyenko

first: Danielle

last: Torralba

first: Shao

last: Tao

first: Tommaso

last: Pollini

first: Vijay

last: Ramani

first: Ajay

middle: V

last: Maker

first: Matthew

last: Krummel

first: Hani

last: Goodarzi


title: eIF3 interactions with miRNAs involved in translational control of early T cell activation

city: Berkeley

first: Pooja

last: Mukherjee

state: California

address: 2151 Berkeley Way

institute: University of California, Berkeley

summary: Early T cell activation induces extensive remodeling of the cellular transcriptome and proteome. We previously showed using a transcriptome-wide crosslinking approach that human translation initiation factor eIF3 directly interacts with a select set of immune-related mRNAs shortly after T cell activation. We also found that eIF3 binding to the 3’-untranslated regions (3’-UTRs) of the TCRA and TCRB mRNAs encoding the T cell receptor alpha and beta subunits dynamically regulates a burst in their translation. MicroRNAs (miRNAs) add an additional layer of regulation by fine-tuning both mRNA and protein expression. Although miRNA expression is dynamically regulated during T cell activation, how miRNAs interact with core regulatory pathways in primary T cells remains poorly understood. Here, we reexamined the eIF3-RNA crosslinking experiments in Jurkat cells and probed eIF3 function to investigate miRNA-mediated translational regulation during T cell activation. We found that human eIF3 interacts with multiple mature miRNAs in activated Jurkat cells, including members of the miR-17-92 cluster. These interactions also occur in primary T cells, as shown by RNA immunoprecipitation followed by qPCR (RIP-qPCR). Knocking out the miR-17-92 cluster led to a delay in ILR2A (CD25) cell surface expression in Jurkat cells and reduced activation-associated cell size increase in primary T cells during early T cell activation. In parallel, we used mass spectrometry analysis of activated primary T cells to identify eIF3-interacting factors, and surprisingly found no evidence of Argonaute binding. Together, these findings provide evidence that eIF3-miRNA interactions may play an unappreciated role in translational control during early T cell activation.

overall_design: Bulk RNA-seq was performed on Jurkat T cells to compare transcriptional changes between wild-type (WT) and CRISPR-edited knockout clones (KO-Clone1 and KO-Clone2) at two timepoints: 0h (unactivated) and 5h post-activation. Each condition has 3 biological replicates (18 samples total).

first: Jiwon

last: Shin

first: Cynthia

last: Hermosillo

first: Chi Yin

last: Ching

first: Yumi

last: Koga

first: Aisha Haley

last: Bianchi

first: Dasmanthie

last: De Silva

first: Jamie H.D.

last: Cate


title: Transcriptomic profiling of primary human prostate cancer-associated fibroblasts (CAFs) in response to ADT and Enzalutamide

city: Xi'an

first: Jun

last: Jiang

address: Changle No.169

institute: Air Force Medical University

summary: Cancer-associated fibroblasts (CAFs) are critical components of the prostate tumor microenvironment and modulate therapeutic responses. In this study, we aimed to investigate the transcriptomic alterations in primary human prostate cancer CAFs subjected to different anti-androgen treatments. Primary CAFs were isolated from human prostate cancer tissues and cultured in vitro. The cells were divided into three treatment groups: Vehicle (control), Androgen Deprivation Therapy (ADT), and a combination of ADT plus Enzalutamide (ADT_Enza). High-throughput RNA sequencing (RNA-seq) was performed on 9 samples (3 biological replicates per group) to identify differentially expressed genes and underlying molecular mechanisms. This dataset provides a comprehensive stromal transcriptomic landscape, offering insights into how CAFs react to standard-of-care prostate cancer therapies.

overall_design: Primary human prostate cancer CAFs were cultured and assigned to three groups (n=3 per group): Vehicle, ADT, and ADT+Enzalutamide. Total RNA was extracted from the 9 samples and subjected to bulk RNA sequencing to compare the gene expression profiles across the different treatment conditions.


title: Pulsed Electric Field Ablation Reprograms Tumor Immunity and Stimulates Germinal Center Formation in Tertiary Lymphoid Structures in Patients with Non-Small Cell Lung Cancer

city: Redwood City

first: Dmitry

last: Velmeshev

address: 3200 Bridge Parkway

department: Oncology

institute: Galvanize Therapeutics

summary:
Purpose: This treat-and-resect clinical study evaluated a specialized form of pulsed electric field (PEF) ablation’s potential to modulate antitumor immunity in early-stage non-small cell lung cancer (NSCLC). Tertiary lymphoid structures (TLS) are lymphoid aggregates that recruit immune cells into the tumor microenvironment (TME) and serve as immunity-generating neighborhoods. TLS with germinal centers (GC) have strong prognostic value in most cancers and promote tumor control and responsiveness to immune-based therapies, but no commercially available therapeutics induce their formation. The Aliya System is a proprietary electrosurgical technology that delivers microsecond electrical pulses to tissue, achieving tumor clearance while maintaining stromal architecture.
Patients and Methods: Treatment group patients received ablation immediately after diagnostic biopsy versus a biopsy-only control group. Herein we report on exploratory endpoints examining immune modulation in blood and tumor samples collected from patients in both groups.
Results: Histopathological assessments revealed the presence of TLS with GC in resected tumors. Tissue cytokine assessments and single-cell RNA sequencing demonstrated upregulation of cytokines capable of recruiting and organizing TLS-associated lymphocytes, including CXCL13, and significant increases in GC-related immune populations, including class-switched memory B cells and plasma cells in ablated tumors versus pre-ablation biopsies. Ablation group patients had more tumors containing TLS with GC (47%) vs. control (24%). Ablation group patients exhibited enhanced systemic immunity, with increased serum HMGB1 and circulating cytotoxic T cells.
Conclusions: This specialized PEF may orchestrate multiple simultaneous changes that promote a more immunologically active TME and represent a new approach for improving immunotherapeutic regimen responses in NSCLC patients.

overall_design: BDRhapsody single-cell RNA-seq + AbSeq (Immune discovery panel). Samples were processed in several batches, sequenced on Illumina Novaseq6000 machine and demultiplxed using RbRhapsody pipeline. Single-cell RNA-seq data generated with the BD Rhapsody platform were demultiplexed using the BD Genomics WTA pipeline (Docker machine version 1.9.1). Paired-end FASTQ files from multiple libraries were processed jointly and aligned to the human reference genome (GRCh38) using a pre-built STAR index and GENCODE v29 annotation. Sequencing tags and sequencing run names corresponding individual samples are provided in the "metadata.txt" file.  AbSeq reads were quantified using a dedicated reference file with the sequences specified by BD Rhapsody. The pipeline further carried out UMI error correction, putative cell identification, and generation of gene and protein expression matrices for downstream analyses. Clustering was performed using Seurat. INXBX = biopsy (BX) collected at the index diagnosis visit (INX). RESRT = resection, treatment area, RESRU = resection, untreated tumor, RESRI = resection, indeterminate


title: Polygonum aviculare L. and Its Active Compound Myricetin Inhibit Rheumatoid Arthritis by Targeting Yes

city: Seoul

first: Yong Joon

last: Lee

address: 50 Yonsei-ro, Seodaemun-gu

department: Department of Biotechnology

institute: Yonsei University

summary: Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by synovial inflammation and joint destruction. In RA, fibroblast-like synoviocytes (FLS) acquire a pathogenic phenotype in response to inflammatory cytokines, promoting synovial inflammation and tissue destruction. Thus, targeting pathological FLS activation has emerged as a promising therapeutic strategy. Herein, we aimed to identify novel plant-derived candidates capable of suppressing synovial inflammation. Screening of 327 plants identified Polygonum aviculare L. (PA) as a potent inhibitor of IL-17-mediated synovial inflammation. PA attenuated IL-17-, TNF-α-, and IL-1β-mediated pathological responses in RA patient-derived FLS (RA-FLS) and alleviated clinical symptoms and histopathological changes in an animal model. Transcriptomic analysis revealed that PA reversed IL-17-induced gene expression and suppressed inflammation-related pathways, with NF-κB emerging as a central regulatory axis. UHPLC-based compound profiling combined with AI-driven bioactivity prediction identified myricetin as an active compound of PA with anti-inflammatory and NF-κB inhibitory activity. Myricetin exerted anti-RA effects in RA-FLS, and both PA and myricetin attenuated synovial inflammation in a 3D synovium-like micromass culture system. PA and myricetin targeted Yes and inhibited its activity, with subsequent suppression of SHP-2 phosphorylation and downstream signaling pathways. Notably, myricetin directly bound to the ATP-binding site of Yes. These findings demonstrate that PA and myricetin inhibit pathogenic responses through the Yes–SHP-2 signaling axis and highlight their potential as plant-derived therapeutic candidates for RA.

overall_design: To investigate the effect of Polygonum aviculare L. (PA) on rheumatoid arthritis patient-derived fibroblast-like synoviosytes (RA-FLS), seeded RA-FLS were divided into three groups. Control group: DMSO treated; IL-17 group: IL-17 and DMSO treated; PA group: IL-17 and PA 20 μg/mL treated. After DMSO or PA pretreatment for 1 h, cells were stimulated with IL-17 for 18 h.

first: Sanguine

last: Byun

first: Minju

last: Jeong


title: PPARG governs adipogenic differentiation and cell state plasticity in well-differentiated and dedifferentiated liposarcoma

city: Los Angeles

first: Heather

last: Christofk

address: 615 Charles E Young Dr South

institute: University of California, Los Angeles

summary: Well-differentiated and dedifferentiated liposarcoma (WD/DD LPS) represent a pathological continuum, often coexisting within the same tumor. While the dedifferentiated component is clinically aggressive, marked by rapid growth and metastatic potential, the evolutionary relationship between WD and DD LPS remains unknown. To investigate this, we performed single-nucleus RNA sequencing on matched WD and DD tumor regions. Both compartments shared a predominant population of undifferentiated mesenchymal cells, but only WD regions contained cells expressing adipocytic differentiation markers and PPARG target genes. Given the central role of PPARG in coordinating lipid metabolism during adipogenesis, these findings suggest that loss of this program may underlie the poorly differentiated, proliferative phenotype of DD LPS. Functional studies confirmed that PPARG activation in DD LPS cells induces lipid accumulation, reduces proliferation, and impairs tumor growth in vivo. These support a model in which impaired adipogenic differentiation underlies DD LPS pathology and identify PPARG as a potential therapeutic target to promote differentiation and suppress tumor progression.

overall_design: Single-nucleus RNA sequencing (snRNA-seq) was performed on paired well-differentiated (WD) and dedifferentiated (DD) regions macrodissected from three primary, treatment-naïve WD/DD liposarcoma tumors collected at initial surgical resection. Each tumor contributed two matched samples (WD and DD) that were processed independently to preserve component-specific transcriptional programs. Nuclei were isolated from frozen tissue and used to generate 3′ gene expression libraries using the 10x Genomics Chromium platform, followed by high-throughput sequencing on an Illumina NovaSeq 6000.

first: Brian

last: Kadera


title: Exercise Training Prior To and During Cancer in Mice Preserves Muscle Mass, Reduces Tumor Weight, and Suppresses Molecular Mediators of Cachexia

city: Fayetteville

first: Pieter

middle: Jan

last: Koopmans

state: AR

address: 155 N Stadium Drive

department: Cell and Molecular Biology

institute: University of Arkansas - Fayetteville

summary: We investigated the prophylactic effects of exercise before and during cancer cachexia (CC) using a model designed to mimic endurance and resistance (i.e., concurrent) adaptations. Male and female Balb/c mice were randomly assigned to exercise or control groups whereby exercise groups were subjected to an 8-week voluntary progressive weighted wheel running (PoWeR) program of habitual loading-mediated physical activity beginning at 8 weeks of age. At 16 weeks of age, mice were injected bilaterally with colon-26 adenocarcinoma (C26) cells or PBS, and exercise training was maintained throughout disease progression. Twenty-five days post-tumor induction, we assessed whole-body and muscle phenotype, muscle protein synthesis, a priori targeted gene expression, and transcriptomic adaptations via RNA sequencing. PoWeR training preserved skeletal muscle mass across nearly all muscle groups and maintained tumor-free body and cardiac mass. Muscle mass adaptations related to running volume; and running distance relative to controls was not appreciably reduced by tumor status. Tumor burden was reduced after ~11.5 weeks of PoWeR compared to sedentary, but this was not explanatory for muscle adaptations. PoWeR induced a faster-to-slower muscle fiber type transition in the gastrocnemius and suppressed key protein turnover markers (Redd1, Murf1, Atrogin, Ubc, Gadd45a) as well as the mitophagy-related marker Bnip3 in tumor-bearing muscle; 24h muscle protein synthesis remained stable. PoWeR counteracted tumor-induced impairments in the muscle mitochondrial- and metabolic-related transcriptome. Collectively, physical activity prior to and during cancer preserves muscle mass, reduces tumor growth, and mitigates molecular drivers of CC, underscoring its preventive and therapeutic potential as a lifestyle intervention.

overall_design: Bulk RNA-Seq Profiling of BALB/C mouse gastrocnemius muscle from Exercised/Sedentary, Cancer/Health, Male/Female Mice

first: Koopmans

last: Pieter J

first: Cabrera

last: Ana Regina

first: Tsitkanou

last: Stavroula


title: Umbilical cord blood natural killer cells improve anti-GD2 antibody efficacy in neuroblastoma: from mouse to human [human dataset]

city: Guangzhou

first: Xiya

last: Tan

state: None Selected

address: 51 Dongfeng Road East, Guangzhou 510060, P. R. China.

institute: Sun Yat-sen University Cancer Center

summary: Despite advances in anti-disialoganglioside (GD2) immunotherapy, high-risk neuroblastoma (NB) remains a clinical challenge. Natural killer (NK) cell-mediated antibody-dependent cellular cytotoxicity is a potent mechanism of action of anti-GD2 antibody. However, dose-intensive chemotherapy causes NK cell depletion. Here, a positive association between intratumoral NK cell infiltration and anti-GD2 efficacy was first observed in clinical samples. We then established the unique advantages of ex vivo expanded and activated umbilical cord blood (UCB)-derived NK cells in terms of cytotoxicity, persistence, exhaustion resistance, and safety from preclinical models to clinical cases compared with patient-derived PB NK cells. Anti-GD2 antibody further enhanced the superiority of UCB NK cells in terms of their functional status, persistence, and capacity to remodel an immune-activated tumor microenvironment. Combined treatment with UCB NK cells and anti-GD2 led to synergistic effects in vitro and in mice and achieved complete and partial responses in two patients with relapsed/refractory NB, with no additive toxicity. Mechanistically, anti-GD2 antibody induced a “high activating-low inhibitory” phenotype of UCB NK cells, and donor UCB NK cells showed dynamically lower levels of immune checkpoints but higher levels of memory-like markers than those of recipient NK cells when combined with anti-GD2 therapy. Collectively, this study is the first translational investigation of UCB NK cells combined with anti-GD2 therapy in NB, bridging preclinical mechanistic insights into an early clinical proof-of-concept. A phase I study of UCB NK cell infusion combined with anti-GD2 therapy in children with high-risk, relapsed/refractory NB is ongoing at our center (NCT06631391).

overall_design: Paired design: two bulk RNA-seq libraries (pre-treatment vs post-treatment) from the same subject.

first: Mengjia

last: Song

first: Yingxia

last: Lan

first: Yizhuo

last: Zhang

first: Tong

last: Xiang

first: Juan

last: Wang


title: Transcriptional profiling of sorafenib-resistant and parental sensitive HepG2 and Huh7 hepatocellular carcinoma cells

city: guanghzou

first: wancui

last: zhu

state: State...

address: zhongshan

institute: Sun Yat-sen University

summary: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide, and acquired resistance to sorafenib—the first-line targeted therapy for advanced HCC—remains a major clinical challenge. To investigate the molecular mechanisms underlying sorafenib resistance in HCC, we established sorafenib-resistant sublines of HepG2 and Huh7 cells through continuous exposure to increasing concentrations of sorafenib. We then performed RNA-seq analysis comparing these resistant sublines with their parental sensitive counterparts. Differential gene expression analysis revealed distinct transcriptional signatures associated with sorafenib resistance. Our findings provide a comprehensive transcriptomic resource for understanding sorafenib resistance mechanisms and identify potential candidate genes that may serve as biomarkers or therapeutic targets for overcoming drug resistance in HCC.

overall_design: RNA-seq profiling of sorafenib-resistant (SR) and parental sensitive (WT) HepG2 and Huh7 cell lines.


title: Umbilical cord blood natural killer cells improve anti-GD2 antibody efficacy in neuroblastoma: from mouse to human

overall_design: Bulk RNA-seq was performed to compare transcriptomic changes among four treatment groups in a neuroblastoma model: IgG control, anti-GD2 antibody alone, UCB NK cells alone, and anti-GD2 combined with UCB NK cells. Each group included two biological replicates. Total RNA libraries were sequenced in paired-end mode on an Illumina NovaSeq platform.


title: Differential RNA-seq analyses in MB135iDUX4_KLF18 KO_i3xFLAG-KLF18_AAVSI long and VNTR∆ cell lines

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

summary: DUX4 initiates the first wave of zygotic genome activation (ZGA) in the human embryo and its misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). However, other factors that help regulate ZGA-like transcription in human development and disease are still not fully understood. Here we identify Krüppel-like factor 18 (KLF18) as a component of a DUX4 feed-forward network that is necessary for expression of KLF17 and a subset of the DUX4-regulated totipotency-associated genes. We mapped the genome-wide binding profile of KLF18 downstream of DUX4 and showed that its activity is influenced by DUX4 and chromatin accessibility. We find that in contrast to the rodent ortholog, human KLF18 has a predicted beta-solenoid structure composed of a variable number of tandem repeats (VNTRs) with multiple different structural variants in the human population. Expression of different KLF18 variants in combination with DUX4 showed similar transcriptional activity, whereas assessment of KLF18 structural variants in individuals with FSHD1 showed inconsistent association with disease severity that requires further study as a modifier locus. Together these findings establish the polymorphic transcription factor KLF18 as a critical component of a DUX4-initiated feed-forward network and a candidate locus for human diversity.

first: Danielle

last: Hamm

first: Aidan

middle: B

last: O’Donnell

first: Sean

last: Bennett

first: Richard

middle: J

last: Lemmers

first: Patrick

last: van der Vliet

first: Silvère

last: van der Maarel


title: Epigenetic Subtypes of High-Grade T1 Bladder Cancer Reveal Intra-Tumor Heterogeneity and Distinct Interactions with Tumor Microenvironment [VisiumHD]

city: Boston

first: Yingtian

last: Xie

state: MA

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

summary: High-Grade T1 (HGT1) Non-Muscle Invasive Bladder Cancer (NMIBC) is a clinically heterogeneous disease, characterized by unpredictable treatment responses and limited tools for recurrence prediction. Although molecular classification efforts have been made, patient stratification still primarily relies on clinicopathological features, which offer limited clinical precision. In this study, we integrated chromatin profiling in bulk with single-nuclei(sn) RNA-seq, immunohistochemistry and spatial transcriptomics to define epigenetic subtypes of HGT1, characterize their heterogeneity, and investigate tumor–microenvironment interactions. Our findings reveal distinct chromatin profiles differentiating urothelial (URO) and micropapillary (MP) histological variants of high-risk HGT1. We identified three epigenetic states: two within the URO group, luminal-like inflammatory (LLI) and basal-like (BL), and a separate signature unique to MP tumors. Single-cell and spatial resolution approaches validated intratumoral heterogeneity and provided insight into subtype-specific microenvironmental contexts. Notably, ∼40% of URO tumors exhibited spatially distinct coexisting LLI and BL components. BL regions showed enrichment for angiogenesis and hypoxia pathways and were preferentially located near vascular stroma, while LLI regions showed to be located at the core of the tumor. MP tumors featured a markedly different microenvironment, characterized by diverse populations of cancer-associated fibroblasts (CAFs) and M2-polarized macrophages intermingled with tumor cells, suggesting a more immunosuppressive niche which could account for their worse clinical outcome. URO tumors, by comparison, showed a more immune-excluded phenotype. These findings provide a detailed molecular and spatial map of bladder cancer heterogeneity, highlighting how distinct epigenetic subtypes and histological variants are associated with tumor architecture and microenvironmental interactions. Our data underscore the need for subtype-specific therapeutic strategies to more effectively address the complexity already existing at HGT1 bladder cancer.

overall_design: Spatial transcriptomic profiling was performed using the 10x Genomics Visium HD platform, following the manufacturer’s protocol with minor modifications. Formalin-fixed, paraffin-embedded (FFPE) tissue blocks were sectioned at 5 μm thickness and mounted onto standard glass slides. Sections were then fixed, stained with hematoxylin and eosin (H&E), and imaged using a high-resolution slide scanner to capture detailed tissue morphology. Following imaging, tissue sections underwent permeabilization to facilitate probe access. Subsequently, a probe hybridization step was carried out overnight to target mRNA sequences.After hybridization, the slides were processed using the Visium CytAssist instrument. This step involved aligning the tissue sections on the standard glass slides with the capture areas on the Visium HD slide, enabling the transfer of spatially barcoded probes to the capture areas. The CytAssist instrument facilitates the transfer of spatial information from the tissue sections to the Visium HD slide. Library preparation was then completed using the Visium HD library construction kit, and sequencing was performed on an Illumina NovaSeq system to a depth sufficient for high-resolution spatial gene expression analysis.


title: Effect of depletion of NAMPT in human endothelial cells (B4G12)

city: Beijing

first: Junyi

address: 69th Yongding Road

department: Ophthalmology

institute: The Third Medical Center, Chinese PLA General Hospital

summary: In our study, NAMPT was found downregulated In the corneal endothelium of patients with Fuchs endothelial corneal dystrophy. In this study, NAMPT was knocked down in the human corneal endothelial cell line (B4G12), and significant decreases in corneal endothelial cell viability, as well as the activation of immune-related pathways and extracellular matrix remodeling pathways, were observed. These changes are consistent with the expression profile of corneal endothelium in FECD patients, suggesting that downregulation of NAMPT plays an important role in the pathogenesis of FECD.

overall_design: RNA-seq profiling of human corneal endothelial cell line (B4G12) and their knockdown derivatives (siRNA)

first: Liqiang

first: Luoying


title: Determination of transcriptomic changes associated with freezing-temperature stress in sugar beet plants grown in soil pots

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

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

department: CSRS

institute: RIKEN

summary: We report the gene expression profiles of sugar beet seedlings treated with or without ethanol under freezing-temperature stress condition.

overall_design: Sugar beet seedlings were grown in pots containing horticultural soil at 22 °C with a 16 h light (110 to 140 µmol m-2 s-1 photon flux density) / 8 h dark cycle. Seven-day-old plants grown in pots were used for ethanol pretreatment. The bottoms of the pots were dipped into 80 mM ethanol solution and kept for 3 days. After ethanol pretreatment, the pots were subjected to freezing temperature treatment at -2.1 to -3.5 °C onvernight by a low-temperature incubator. During the freezing temperature stress treatment, the pots were electrically rotated in the incubator to avoid the local effect.

first: Daisuke

last: Todaka

first: Kentaro

last: Nakaminami

first: Maho

last: Tanaka

first: Satoshi

last: Takahashi

first: Do

last: Thi Nhu Quynh

first: Junko

last: Ishida

first: Kyoko

middle: Y

last: Mogami

first: Atsushi

last: Nagano

first: Motoaki

last: Seki


title: Caloric Restriction Reprograms Skeletal Muscle Molecular Pathways in Non-Human Primates: Potential Relevance to Human Aging Biology

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Transcriptomic profiling revealed widespread gene expression differences between CR animals compared to controls. Genes that were overexpressed were mainly involved in pathways related to energy metabolism, mitochondrial function, signaling, and oxidative stress response. Conversely, underexpressed genes were connected to immune response, extracellular matrix organization, apoptosis, and ribosomal RNA processing. Further, we identify alternative splicing as a major mechanism by which caloric restriction modulates genes involved in muscle function, metabolism, and aging.

overall_design:
To investigate the effects of long-term CR on health and longevity. One group is consuming 30% fewer calories (CR) compared to other group (Controls, CTR) throughout their life.
We collected skeletal muscle biopsies (~50-100 mg) both for controls and calorie restricted grouo]ps. We then performed high depth RNA-seqncing using Illumina NovaSeq 6000 system with paired-end reads.
Comparative gene expresiion analysis was conducted between the control and calorie restricted groups.

first: Jayanta

middle: K

last: Das

first: Nirad

last: Banskota

first: Stefano

last: Donega

first: Nader

last: Shehadeh

first: Yulan

last: Piao

first: Nathan

last: Price

first: Julie

middle: A

last: Mattison

first: Julián

last: Candia

first: Rafael

middle: d

last: Cabo

first: Luigi

last: Ferrucci


title: DNA repair drives cisplatin-induced neuronal death [RNA-Seq]

city: Bethesda

first: Chuanyuan

last: Chen

state: MD

address: 9000 Rockville Pike, Building 37

institute: National Institutes of Health

summary: Cisplatin and similar-acting alkylating chemotherapy agents are the cornerstone treatments for many types of cancers. While effective, these drugs induce long-term side-effects in post-mitotic tissues including the nervous system. There are no known effective pharmacological interventions for chemotherapy-induced neurotoxicity, in part due to our limited understanding of how neurons and other non-dividing cells respond to DNA damage. Here, we show that nucleotide excision repair (NER) is responsible for cisplatin adduct removal in human neurons. However, contrary to its protective role in dividing cells, NER drives neuronal cell death in response to cisplatin. Through excision repair synthesis, NER exhausts low levels of deoxynucleoside triphosphate (dNTP) pools found in post-mitotic neurons. dNTP pools are first consumed to resolve transcription-blocking lesions through transcription-coupled NER. When dNTPs become exhausted, toxic double-strand breaks accumulate across the genome primarily because of incomplete global-genome NER. Supplementation with deoxynucleosides through pharmacological or genetic means protects neurons from cisplatin-induced cell death and reduces cisplatin-induced neuropathic pain in mice. These results identify low levels of endogenous dNTP pools as a vulnerability of post-mitotic cells to DNA damage and suggest nucleoside supplementation as a strategy to protect patients from chemotherapy-induced neurotoxicity.

overall_design: We treated iPSC-derived neurons with the indicated genotypes with cisplatin, EdU, and dN (where indicated) for the specified length of time in each Sample below. Neurons were then processed for SAR-seq, END-seq, S1-END-seq, or RNA-seq.

first: William

last: Nathan

first: Rosy

last: Sakr

first: Bruno

last: Siqueira Mietto

first: Vicent

last: van Batenburg

first: Jeroen

last: van den Berg

first: Josette

last: Wlaschin

first: Ferenc

last: Livak

first: Elsa

last: Callen

first: Nancy

last: Wong

first: Eliza

last: Lloyd

first: Hanna

last: Silberberg

first: Sushma

last: Sharma

first: Raj

last: Chari

first: Tzipporah

last: Freeman

first: Baek

last: Kim

first: Alexander

last: van Oudenaarden

middle: T

last: Chesler

first: Michael

middle: E

last: Ward

first: Lisa

last: Boxer

first: Peter

last: McHugh

first: Andrei

last: Chabes

first: Claire

last: Le Pichon

first: André

last: Nussenzweig


title: Differential RNA-seq analysis of MB135iDUX4 with siRNA mediated knockdown of KLF17 and KLF18

first: Stephen

last: Tapscott

first: Danielle

last: Hamm

first: Aidan

last: O’Donnell

first: Sean

middle: R

last: Bennett

first: Richard

last: Lemmers

first: Patrick

last: van der Vliet

first: Silvère

middle: M

last: van der Maarel


title: CB001 bioactive compounds improve intestinal immune disorders caused by simulated microgravity and radiation through anti-inflammatory [scRNA-seq]

first: Zhijie

last: Bai

state: 北京Beijing

address: Taiping Road, Haidian District

institute: beijing institute of radiation

summary: Gastrointestinal discomfort is one of the most common issues during spaceflight, and there is currently a lack of targeted drug treatment strategies. Current research in this area focuses on single-factor modeling, lacking a comprehensive understanding. In the present study, we constructed space flight models based on most important two factors, microgravity and low-dose radiation. Histological, cellular and molecular analyses confirmed the advantage of this dual-factor model in simulating space flight-caused injuries. Upregulated inflammatory and homeostasis disruption were observed in intestines treated by these dual factors. Our data revealed that dual factors enhanced the migration of a Ccr7+ B cells into intestines through upregulating the expression of Cxcr4, which exerted strong activation regulations on leukocytes. We further validated that bioactive compounds of CB001 effectively alleviated intestinal perturbations through recovering the expression of tight junction proteins, suppressing the migration of B cells and downregulating the levels of pro-inflammatory cytokines. Collectively, our work offered CB001 compounds as candidate intervention drug for space flight-induced intestine dysfunctions based on a dual-factor mice model. These data shed lights on special medicine screening for health protection in space flight.

overall_design: The small intestine was isolated and the mesentery and Peyer's patches were removed, and the intestinal contents were flushed with PBS. The treated small intestinal tissues were digested sequentially with HBSS (without Ca2+ and Mg2+) containing 2 mM EDTA and RPMI 1640 medium (containing 20% FBS) containing 1 mg/mL collagenase A and 50 μg/mL DNase I. The digested solution of small intestine was collected and filtered through a 70 μM cell strainer to obtain a single-cell suspension.Single-cells were washed once and subjected for 10x Genomics single-cell sample preparation.


title: let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [mRNA-seq TC5]

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: We examined mRNA levels using mRNA-seq in wild-type (N2), lin-28 mutant animals (HW2705) and animals that have the single GGAG motif (i.e. the putative LIN-28 binding motif) in the lin-46 5'UTR mutated to CTCC (HW3531).

overall_design: N2, HW2705 (lin-28(xe192) I) and HW3531 (lin-46(xe370) V = lin-46(++)) animals were grown at 25°C and collected hourly at 5 to 14 hours after resumption of feeding.

first: Jana

last: Brunner

first: Helge

last: Grosshans


title: let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [mRNA-seq TC3_TC4]

summary: We determined differentially expressed genes in lin-28(xe192) animals in the early developmental time window of 3 to 6 hours collected in three biological replicates, two included here (TC3, TC4) and one as part of a full developmental time course (TC1).

overall_design: Wild-type and lin-28(xe192) animals were grown at 25°C and collected hourly at 3 to 6 hours after resumption of feeding.


title: let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [mRNA-seq TC1]

summary: We examined gene expression changes using mRNA-seq in two different lin-28 mutant strains, lin-28(n719) and lin-28(xe192). Although both are considered genetic null mutants, their expression profiles differ substantially: lin-28(n719) (a point mutation affecting a splice site) shows many more dysregulated genes than lin-28(xe192) (a deletion of the entire lin-28 locus).

overall_design: N2, HW11 (lin-28(n719) I) and HW2705 (lin-28(xe192) I) animals were grown at 25°C and collected hourly at 3 to 6 hours after resumption of feeding.

first: Anca

last: Walczak


title: let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [mRNA-seq TC2]

summary: We examined mRNA levels in wild-type and lin-28(xe192) animals throughout postembryonic development (0-44 h) with hourly resolution. Samples collected at 3 to 6 hours of development were used as one of the three biological replicates used to determine differentially expressed genes in lin-28(xe192) animals.

overall_design: Wild-type and lin-28(xe192) animals were grown at 25°C and collected hourly at 0 to 44 hours after resumption of feeding.

first: Chiara

last: Azzi