title: Divergent Macrophage-Regulated T cell States Determine Response to Bacillus Calmette-Guérin (BCG) in High-Risk Bladder Cancer

city: Chicago

first: Joshua

last: Meeks

address: 303 East Superior Street

institute: Northwestern University

summary: The primary therapy for high-risk bladder cancer (BCa) is repeated instillations of the tuberculosis vaccine, Bacillus Calmette-Guerin (BCG). While BCG decreases the risk of recurrence by more than half, the concerted mechanisms of immune activation from BCG are unknown. Our objective was to investigate how the immune response differs between responders and non-responders to BCG therapy. We performed single-cell RNA-sequencing of isolated immune cells adjacent to high-risk bladders before and after BCG in BCG responders and non-responders. We identify an increase in Th17-like Th1 cells in BCG responders, characterized by greater expression of pro-inflammatory cytokines. Alternatively, non-responders had increased CD8+ T-cell exhaustion and T-regulatory cells. We identify that the primary mechanism of divergent T cell activity is driven by altered polarization and immunosuppressive signaling with myeloid cells. Through a machine-learning-based approach, we identified a Th17-like Th1 cytokines, such as IL17, IL21, and IL26, were predictive of a response, which were then validated in a separate BCG-treated BCa cohort. Together, this suggests that dynamic regulation of myeloid-T cell interactions can be targeted to improve BCG activity.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) of isolated immune cells adjacent to high-risk bladders in BCG responders and non-responders before and after BCG. We also compared concurrent scRNA-seq profiles of circulating immune cell populations with those of bladder immune cells.

first: Andrew

last: Houston

first: Mairah

last: Khan

first: Ryan

last: Brown


title: Anticancer activity of RAS-GTP inhibition in cholangiocarcinoma [Mouse_hKPR.KPCHR_Sep25]

status: Public on Mar 30 2026

city: Pamplona

first: Silvestre

last: Vicent

address: Avenida Pío XII 55

department: Oncology

country: Spain

institute: Center for Applied Medical Research (CIMA)

type: Expression profiling by high throughput sequencing

summary: About 25% of cholangiocarcinoma (CCA) patients harbor KRAS mutations, being potentially amenable to direct KRAS inhibitors. Here, we investigated the activity of RAS(ON) multi-selective inhibitors, which target the active, GTP-bound state of both mutant and wild-type variants of canonical RAS isoforms, in CCA preclinical models and patients. RAS(ON) multi-selective inhibitors yield strong anticancer responses in cell- and patient-derived xenografts and in immunocompetent allograft models. Consistently, we describe responses to the RAS(ON) multi-selective inhibitor daraxonrasib in two KRASG12X patients with advanced CCA. RAS-GTP inhibition also potentiates the activity of the current standard-of-care CCA therapy to prolong survival in cell-derived human xenografts and mouse allografts. Furthermore, we demonstrate that both intrinsic and acquired resistance to RAS(ON) multi-selective inhibitors mainly rely on reconstitution of RAS signalling. Overall, our findings indicate that KRAS mutant CCA is addicted to RAS signalling for proliferation and support the potential clinical evaluation of RAS-GTP inhibition in CCA.

overall_design: In vivo generated resistant cell lines (hKP117-RR, KPCh972-RR, KPCh993-RR) and parental (hKP and KPCh) were assessed for altered biological pathways.

first: Rodrigo Entrialgo

last: Cadierno

first: Konstantina

last: Morali

first: Silve


title: Anticancer activity of RAS-GTP inhibition in cholangiocarcinoma [Mouse_iAKP_Abr24]

overall_design: KPCh cells and iAKP cells were treated or not with 100nM of RMC-7977 for 24hrs to assess alterations in biological pathways upon treatment.


title: Anticancer activity of RAS-GTP inhibition in cholangiocarcinoma [Human_Abr24]

overall_design: HUCCT-1 cells and KKU-213 cells were treated or not with 100nM of RMC-7977 for 24hrs to assess alterations in biological pathways upon treatment.


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation

city: Worcester

first: Chun-Hao

last: Chao

address: 364 Plantation St. LRB560D

department: MCCB

country: USA

institute: UMass Chan Medical School

summary: R-loops—RNA:DNA hybrids that often form co-transcriptionally—are emerging as key regulators of genome function, yet their roles in shaping chromatin architecture and developmental potential remain incompletely defined. Here, we use inducible Rnaseh1 expression in mouse embryonic stem cells (mESCs) to achieve acute, global R-loop depletion and systematically interrogate their impact on chromatin structure and lineage specification. We find that R-loop loss has minimal effect on steady-state gene expression or self-renewal. Instead, it leads to a striking reduction in H2A.Z occupancy at both active and bivalent promoters, accompanied by increased nucleosome density—revealing a previously unrecognized role for R-loops in maintaining promoter architecture. During gastruloid differentiation, R-loop-depleted mESCs exhibit accelerated ectodermal differentiation, along with dysregulation of lineage-specific transcription factors and impaired cell-cell signaling. Consistent with these alterations, R-loop-depleted cells show widespread perturbations in gene regulatory networks across several early cell types. These findings uncover a critical role for R-loops in shaping the H2A.Z chromatin landscape and preserving balanced lineage trajectories during early development, offering new insights into the epigenomic regulation of stem cell fate.

overall_design: Rnaseh1-inducible cells with or without Dox treatment were subjected to DRIPc-seq.

first: Thomas

last: Fazzio


title: Transcriptomic responses to acute or chronic ethanol exposure observed across five brain regions in male mice

city: St. Louis

first: Gabor

last: Egervari

email: gabor@wustl.edu, egervarilab@gmail.com

state: MO

address: 4515 McKinley Ave, Couch Building

department: Genetics, Biochemistry and Molecular Biophysics

institute: Washington University School of Medicine

summary: Alcohol use disorder (AUD) has been consistently linked to transcriptomic dysregulation in the brain. Alcohol itself produces transcriptomic changes in the brain, and resulting molecular changes may contribute to the progression or maintenance of AUD. However, little is known about how ethanol-induced transcriptomic outcomes differ between acute and chronic exposure. Here, we systematically investigated the transcriptomic effects of ethanol exposure across key brain regions relevant to AUD and how these outcomes differ between acute and chronic exposure. To this end, RNA sequencing was done for the cortex, dorsal hippocampus, ventral hippocampus, dorsal striatum, and ventral striatum of adult male mice that were given a daily i.p. dose of ethanol or saline for 1 day (acute) or 10 days (chronic). Both ethanol exposure paradigms resulted in dysregulated expression (gene and transcript) and splicing in the investigated brain regions. Transcriptomic dysregulation varied across regions and was more robust following acute than chronic ethanol exposure. Paradigm-dependent transcriptional effects of ethanol were limited in most regions but were striking in the ventral hippocampus, suggesting alcohol's transcriptomic effects in this region might play a relevant role in the transition from limited to chronic alcohol consumption. Overall, this systematic study illuminates alcohol's effects on transcriptional regulation in the brain and how these effects differ across brain regions and by extent of exposure, ultimately providing valuable insight for developing novel therapeutics for AUD.

overall_design: RNA-seq samples are from adult male C57BL/6J mice 8-10 weeks of age that were given a daily i.p. dose of 2 g/kg ethanol or saline (control) for 1 day (acute) or 10 days (chronic) and sacrificed 4 hours after the final injection. Five brain regions were investigated: cortex (CTX), dorsal hippocampus (dHPC), ventral hippocampus (vHPC), dorsal striatum (DS), ventral striatum (VS). Experimental conditions are defined by paradigm (acute or chronic) and treatment (saline or ethanol): acute saline (AP), acute ethanol (AE), chronic saline (CP), chronic ethanol (CE). Each sample corresponds to a biological replicate (mouse); there are n=3-4 biological replicates (mice) per group.

first: Erica

middle: M

last: Periandri

first: Kala

last: Dodson

first: Mariana

last: Lopes

first: Francisca

middle: N

last: de Luna Vitorino

first: Anjola

last: Ola

first: Joanna

last: Gongora

first: Benjamin

middle: A

last: Garcia

first: Karl

last: Glastad


title: Identification of  Therapeutic Targets for Low-Grade Serous Ovarian Carcinoma [EM-seq]

city: Melbourne

first: Kathleen

last: Pishas

state: Victoria

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

type: Methylation profiling by high throughput sequencing

summary: Low-grade serous ovarian carcinoma (LGSOC) is a rare, indolent ovarian cancer subtype with limited effective therapies. Approximately 40% of cases lack canonical MAPK/ERK or PI3K/AKT/mTOR pathway alterations and are classified as having no specific molecular profile (NSMP). These patients have poor responses to chemotherapy, MEK inhibitors, and hormonal therapies, highlighting the need for alternative strategies. This study aimed to identify novel therapeutic targets in NSMP LGSOC. A high-throughput drug screen of over 3,500 compounds (including FDA-approved, clinically tested, and investigational agents) was conducted across 12 LGSOC and one control ovarian epithelial cell line. EGFR inhibitors emerged as selective hits in NSMP cell lines and were further tested in two NSMP and two MAPK-mutant lines in combination with standard-of-care chemotherapy agents, carboplatin and paclitaxel. EGFR expression was assessed using RNA sequencing, DNA methylation profiling, and immunohistochemistry in primary tumours, followed by survival analysis based on expression levels.

overall_design: We aimed to profile the whole genome methylation landscape of 12 Low Grade Serous Ovarian Carcinoma patient derived cell lines and compared this to two normal cell lines

middle: I

first: Hannah

last: Kim

first: Marta

last: Llaurado-Ferandez

first: Mark

middle: S

last: Carey

first: Ian

middle: G

last: Campbell

first: Dane

last: Cheasley

first: Raunak

last: Shrestha


title: Identification of  Therapeutic Targets for Low-Grade Serous Ovarian Carcinoma

overall_design: RNA-sequencing of 12 LGSOC cell lines and two normal controls (no treatment)

first: Timothy

last: Semple


title: Durable control of autoimmunity requires sustained stimulation of regulatory T cells [TCR scRNA-Seq]

city: Miami

first: Thomas

middle: R

last: Malek

state: Florida

address: 1600 NW 10th Avenue

department: Microbiology and Immunology

institute: University of Miami Miller School of Medicine

summary: Low-dose recombinant interleukin-2 (rIL-2) therapy holds significant promise for treating autoimmune and inflammatory disorders by selectively expanding the endogenous pool of CD4⁺Foxp3⁺ regulatory T cells (Tregs). However, clinical benefits are limited by the suboptimal pharmacokinetic profile of rIL-2, which fails to support sustained Treg activation. Here we investigated the efficacy of a long-lasting IL-2-based biologic mIL-2/CD25 to limit type 1 diabetes in female NOD mice when administered in a manner to cause periodic versus continual increases in Tregs. We find that the latter is highly effective in limiting autoimmunity and leads to substantial remodeling of the pancreatic islet immune landscape, which has important implications for advancing IL-2-based therapies for autoimmunity.

overall_design: Evaluation of the pancreatic islet T cell repertoire landscape of female NOD mice utilizing 10X Chromium single-cell RNA sequencing (scRNA-seq). Starting at 12 weeks of age, female NOD mice were i.p. treated with PBS or 5 μg mIL-2/CD25 twice per week for 3 weeks. 3.5 days after the last mIL-2/CD25 injection, pancreatic islet-infiltrating T cells were isolated and sorted as CD45+CD19- CD4+ and CD8+ cells and subjected to 5' scRNA-seq gene expression and T cell receptor V(D)J sequencing (islets were pooled from 5-6 mice/group).

first: Janika

last: Põder


title: Effect of HNF1A-MODY on stem cell islets [scRNA-Seq]

city: Bergen

first: Lucas

last: Unger

address: Haukelansbakken 15

country: Norway

institute: University of bergen

summary: This project investigates the impact of the hotspot mutation P291fsinsC in HNF1A-MODY (Maturity-Onset Diabetes of the Young) on stem cell-derived islets. RNA sequencing (RNA-seq) was performed on islets differentiated from mutant and control HNF1A-MODY stem cells to study the mutation's effect on gene expression. By comparing the transcriptomic profiles of these islets, the study aims to uncover molecular mechanisms underlying the dysfunction caused by the P291fsinsC mutation during islet development and maturation.

overall_design: HNF1A-MODY stem cells with the P291fsinsC hotspot mutation and wild-type controls were differentiated into the posterior foregut stage.

first: Simona

last: Chera


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [ZX-1 CUT&Tag]

first: Chun-Hao

last: Chao

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Rnaseh1-inducible cells or ZX-1 with or without Dox treatment were subjected to CUT&Tag with antibodies/proteins including H2A.Z, H3K4me3, H3K9me3, H3K27me3, H3K27ac, H3K36me3, RNAPIISer2P, H3.3, H4ac and IgG

last: Fazzio


title: West Nile virus and Zika virus infections induce aggresome formation in human neural progenitor and A549 cells

city: Atlanta

first: Emilio

middle: E.

last: Espínola

state: Georgia

address: 145 Piedmont Ave SE

department: Biology

institute: Georgia State University

summary: ZIKA viral replication vesicles (VRVs) were previously observed to cluster asymmetrically on one side of the nucleus in infected Huh7, A549 and human neural progenitor cells (h-NPCs). West Nile virus (WNV) infections in these cells also induce asymmetrically clustered VRVs. The sequential cell responses leading to asymmetric clustering of the WNV and ZIKV VRVs were investigated. Both infections activated the cellular unfolded protein response (UPR) as indicated by increased expression of HSPA5 (GRP78), the master regulator of endoplasmic reticular stress, and activation of the PERK branch of the UPR (p-PERK–p-eIF2α–GADD34). Increased microtubule (MT) acetylation was also detected. As the infection progressed, the level of ubiquitinated proteins increased and GRP78, HDAC6, ubiquitinated proteins and VRVs clustered at the cellular microtubule organizing center (MTOC) and became surrounded by a vimentin “cage.” The components involved in the formation of asymmetric virus replication complexes are characteristic of aggresome formation, an additional cellular response that copes with excessive misfolded proteins when the UPR is overwhelmed. During aggresome formation, HDAC6 links polyubiquitinated proteins to the dynein motor complex for transport along MTs to the MTOC where they aggregate and are surrounded by a vimentin cage. HDAC6 knockdown prevented the asymmetric clustering of the viral replication complexes and resulted in activation of the p-PERK–p-eIF2α–CHOP apoptotic pathway. The threshold for triggering aggresome formation varied with the infecting orthoflavivirus and cell type. The formation of aggresome-like, asymmetric VRVs in A549 cells and h-NPCs infected with WNV or ZIKV prolonged cell survival and increased the viral yield.

overall_design: RNA-seq profiling of A549 cells infected with Zika virus (ZIKV) PRVABC59, or West Nile virus (WNV) NY99, at 16 and 32 hours post-infection.

middle: E


title: Durable control of autoimmunity requires sustained stimulation of regulatory T cells

overall_design: Longitudinal evaluation of the pancreatic islet immune landscape of female NOD mice utilizing 10X Chromium single-cell RNA sequencing (scRNA-seq) technology. Starting at 10 weeks of age, female NOD mice were i.p. treated with PBS or 5 μg mIL-2/CD25 once or twice per week for 5 or 20 weeks. 3.5 days after the last mIL-2/CD25 injection, pancreatic islet-infiltrating CD45+ immune cells were isolated and subjected to scRNA-seq (islets were pooled from 3 mice/group). Additionally, scRNA-seq analysis was carried out on islet-infiltrating CD45+ immune cells from a cohort of 10-week-old untreated mice ("Untreated baseline" group) and on a cohort of 30-week-old mice that received 5 μg mIL-2/CD25 twice/week for 5 weeks followed by a 15-week "off-therapy" period.


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [CUT&Tag]

overall_design: Rnaseh1-inducible cells or ZX-1 with or without Dox treatment were subjected to CUT&Tag with antibodies/proteins including H2A.Z, H3K4me3, H3K9me3, H3K27me3, H3K27ac, H3K36me3, RNAPIISer2P, H3.3, H4ac, IgG


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [scRNA-Seq]

overall_design: Rnaseh1-inducible cells were differentiated into gastruloids with and without Dox treatment. Samples were collected at Days 0 (0 hr), 3 (72 hrs), and 5 (120 hrs) for scRNA-seq


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [RNA-Seq]

overall_design: Rnaseh1-inducible cells were differentiated into gastruloids with and without Dox treatment. Samples were collected at Days 0 (0 hr), 3 (72 hrs), and 5 (120 hrs) for bulk RNA-seq


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [CUT&Run]

overall_design: Rnaseh1-inducible cells or ZX-1 with or without Dox treatment were subjected to CUT&RUN or MapR with antibodies/proteins including  CTCF, RHD-MNase, IgG


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [MNase-Seq]

overall_design: Rnaseh1-inducible cells with or without Dox treatment were subjected to MNase-seq with different amount of MNase for the digestion.


title: R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation [ATAC-Seq]

overall_design: Rnaseh1-inducible cells with or without Dox treatment were subjected to ATAC-seq


title: Investigating the role of muscle fibers in the early stage of nerve regeneration within a Muscle-in-Vein graft

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

summary: Background: Every year, many people experience a reduced quality of life due to peripheral nerve damage, resulting in significant healthcare costs, with painful neuroma formation as a common drawback following improper nerve regeneration. The Muscle-in-Vein (MIV) technique, consisting of a vein enriched with skeletal muscle fibres, offers a promising approach to nerve repair, in which the vein serves as a conduit, while muscle fibres avoid vein collapse and provide essential growth factors. The MIV-technique advantages include natural axon guidance through muscle fibre basal laminae, enhanced Schwann cell migration, reduced scar formation and a lower incidence of neuroma formation compared to synthetic conduits. This research aims to explore the role of muscle fibres in the early stages of nerve regeneration - an essential yet understudied phase - within the MIV graft in a rat median nerve injury and repair model. Methods: The study was performed in vivo inducing an 8 mm gap in the rat median nerve, subsequently repaired through the Muscle-in-vein technique. Regenerating nerves were harvested at 3-, 7-, 14-, and 21-days post-injury for comprehensive molecular and morphological analyses, with particular emphasis on the vascularization process, identified as an emerging key factor in nerve regeneration. Results: Immunofluorescence data reveal complete macrophage colonization and a well-structured vascularization throughout the entire graft 7 days post-injury. RNA sequencing analysis on early time points further confirms the pathways involved in vasculature development among the most enriched ones and provides insights into the behaviour of specific angiogenesis- associated genes. A deep evaluation of differentially expressed genes suggests that endothelial cell differentiation occurs in the early stages, as confirmed by the expression profiles of subtype-specific endothelial cell markers. Conclusions: Our data supports the hypothesis of a partial anastomosis between the vessels of the nerve stumps and those of the muscle guided by macrophages. This insight enhances our understanding of the MIV technique and provides valuable guidance for improving tissue engineering approaches for developing more effective treatments for peripheral nerve injuries.

overall_design: The median nerves of adult female Rattus norvegicus were transected to create an 8 mm gap and repaired using 10 mm muscle-in-vein graft. Regenerating nerves were collected at 3 and 7 days for RNA extraction, which was sent to Novogene SRL for Illumina Next-Generation sequencing.

first: Federica

last: Zen

first: Alessandro

last: Crosio

first: Debora

last: Molinaro

first: Giulia

last: Ronchi

first: Stefano

last: Geuna

first: Giovanna

last: Gambarotta

first: Stefania

last: Raimondo


title: The NAMPT/SIRT7/SOD2 axis regulates alveolar progenitor cell renewal and pulmonary fibrosis [bulkRNA-seq]

city: Los Angels

first: Xuexi

last: Zhang

state: California

address: AHSP A9404, 8700 Beverly Blvd

department: Medicine

institute: Cedars Sinai Medical Center

summary: We employed bulk RNA sequencing using the UCLA Technology Center for Genomics &Bioinformatics platform to investigate the role of nicotinamide phosphoribosyltransferase (NAMPT), a key enzyme in NAD+ biosynthesis, in AT2 cells in the lung. NAMPT has been implicated in regulating stem cell function, mitochondrial bioenergetics, apoptosis, and senescence in neurodegenerative diseases, endothelial cells, and human iPS cells. We used CRISPR/Cas9 system to knockout or activate NAMPT in immortalized IPF AT2 cells.

overall_design: To study the function of NAMPT in IPF AT2 cells, we used CRISPR/Cas9 system to activate NAMPT in immortalized IPF AT2 cells. We then performed bulk RNA-seq analysis with NAMPT KO (EV1, EV2, EV3) and control (KO1, KO2, KO3) in healthy AT2 cells; NAMPT activated (N1, N2, N3) and control (E1, E2, E3) IPF AT2 cells.

first: Jiurong

last: Liang

first: Paul W

last: Noble

first: Dianhua

last: Jiang

first: Xue

last: Liu


title: The NAMPT/SIRT7/SOD2 axis regulates alveolar progenitor cell renewal and pulmonary fibrosis [scRNA-seq]

summary: We employed single-cell RNA sequencing using the 10x Genomics platform to investigate the role of nicotinamide phosphoribosyltransferase (NAMPT), a key enzyme in NAD+ biosynthesis, in AT2 cells in the lung. NAMPT has been implicated in regulating stem cell function, mitochondrial bioenergetics, apoptosis, and senescence in neurodegenerative diseases, endothelial cells, and human iPS cells. Single-cell lung suspensions were prepared from Nampt AT2 conditional knockout and control mice at day 0 and day 4 post-bleomycin injury. scRNA-seq was performed on FACS-sorted Epcam+ and CD45+ live cells, and purified cells were clustered to evaluate NAMPT function in AT2 and immune cells.

overall_design: To study the function of Nampt in mouse AT2 cells, we isolated individual cells (CD45/31/34-EPCAM+ and CD45+ mixed cells) from Nampt AT2 conditional knockout and control mice at day 0 and day 4 after post bleomycin injury (2.5 U/kg). Then performed single cell analysis using the 10x Genomics Chromium platform.


title: Effect of HNF1A-MODY on stem cell islets [scRNA-seq]

first: Lucas

last: Unger

overall_design: HNF1A-MODY stem cells with the P291fsinsC hotspot mutation and wild-type controls were differentiated into pancreatic islets. RNA sequencing was performed on these islets to compare gene expression profiles and assess the impact of the mutation on islet development and function.

last: Chera


title: Effect of HNF1A-MODY on stem cell islets

first: Simona


title: Adaptive cellular evolution in the intestinal tracts of hyperdiverse African cichlid fishes [RNA-Seq]

city: Basel

first: Antoine

last: Fages

address: Vesalgasse 1

country: Switzerland

institute: University of Basel

summary: Adaptations relating to how nutrients are acquired and processed play a central role in the colonization of novel ecological niches and, therefore, in organismal diversification. While the evolution of feeding structures has been studied extensively in this context, the nature of dietary adaptations in the digestive tract remains largely unexplored. Here, we investigate the cellular and molecular basis of dietary adaptations in the massive radiation of cichlid fishes in Lake Tanganyika using comprehensive single-cell transcriptomic data derived from the intestines of 25 African cichlid species with distinct habitats and diets. We show that, at the cellular level, dietary adaptations are primarily driven by anterior enterocytes, and that both the abundance and gene expression profiles of these cells have evolved in response to dietary specializations. These dietary adaptations in enterocytes are driven by rapidly evolving cell population-specific genes, suggesting that alterations in gene regulatory programmes and cell-state specification promote ecological diversification.

sample_organism:
Haplochromis burtoni
Eretmodus cyanostictus
Lepidiolamprologus attenuatus

overall_design: bulk RNAseq data from intestinal tracts of African cichlid fishes


title: The nuclear cap-binding complex safeguards stress-resistant protein synthesis and proliferation of stem cells [CLIP-seq and mRNA-seq]

city: Daejeon

first: Jeeyoon

last: Chang

address: 291 Daehak-ro, Yuseong-gu, Daejeon

department: Life Science

country: South Korea

institute: Korea Advanced Institute of Science & Technology

summary: The integrated stress response (ISR) suppresses global translation while allowing the selective translation of key regulatory genes. However, the mechanisms behind sustained protein synthesis during ISR activation remain unclear. In eukaryotic cells, the 5′-cap of most mRNAs is bound either by the nuclear cap-binding complex (CBC) or by the cytosolic cap-binding protein eIF4E. Our study reveals that under stress conditions, CBC-bound mRNAs utilize eIF2A, an alternative translation initiation factor, to maintain protein synthesis when translation of eIF4E-bound mRNAs is significantly inhibited. Human embryonic stem cells (hESCs), which inherently exhibit ISR, continue active proliferation due to a compensatory increase in eIF2A expression. This increase ensures CBC-dependent translation (CT) and supports the synthesis of essential cell cycle proteins during stress. Furthermore, we identify YAP, a master regulator of cell proliferation, as a critical target of CT, driving stress-resistant proliferation in stem cells. Collectively, our findings highlight CT as a crucial pathway that protects protein synthesis and supports stem cell proliferation during stress.

overall_design: CLIP-seq and mRNA-seq profiling of H9 hESCs.

first: Seyoun

last: Oh

first: Jiwon

last: Jang

first: Yoon Ki

last: Kim


title: Adaptive cellular evolution in the intestinal tracts of hyperdiverse African cichlid fishes [scRNA-Seq]

sample_organism:
Oreochromis niloticus
Tropheus moorii
Haplochromis burtoni
Bathybates ferox
Callochromis pleurospilus
Cyphotilapia frontosa
Petrochromis orthognathus
Boulengerochromis microlepis
Lepidiolamprologus elongatus
Neolamprologus brichardi
Perissodus microlepis
Neolamprologus brevis
Telmatochromis vittatus
Triglachromis otostigma
Simochromis diagramma
Eretmodus cyanostictus
Haplotaxodon microlepis
Xenotilapia spiloptera
Limnotilapia dardennii
Lepidiolamprologus attenuatus
Julidochromis ornatus
Benthochromis horii
Cyprichromis coloratus
Trematocara zebra
Shuja horei

overall_design: single-cell RNAseq data from intestinal tracts of African cichlid fishes


title: Antiviral Tfh response by “tolerant” congenitally infected virus carriers drives antibody-mediated viral load control [scRNA-Seq]

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

summary:
Congenital infection can result in viral persistence as commonly observed for hepatitis B virus in humans. The accompanying “neonatal tolerance” state remains immunologically ill-defined and treatment options are unsatisfactory.
Studying congenital lymphocytic choriomeningitis virus infection, the prototypic mouse model of neonatal antiviral tolerance, we observe antibody-mediated suppression of viral replication. These responses are driven by canonical antiviral CD4 Tfh responses, whereas CD8 T cells are irrelevant for viral load control. Viral epitope-specific CD4 T cells of congenitally infected animals are less abundant than in adult infection. They exhibit reduced clonal diversity and distinct differences in gene expression patterns. Importantly, exogenous supplementation of T help augments antiviral germinal center B responses of congenitally infected mice.
These findings reveal that humoral immune defense is partially exempt from neonatal tolerance and remains effective against congenital infection. Imperfect virus control by limited CD4 Tfh responses may offer opportunities for a functional cure by immunotherapy.

overall_design: 1. Experimental group, "neonat.": Neonatal, intercranial infection (i.c.) (within first 24h after birth) with artLCMV (Kallert et al., Nat.Comm., 2017) leading to life long virus carriage, harvest of splenocytes 8 weeks post infection. 8 biological replicates 2. Experimental group, "chronic": Intra venous (i.v.) infection of adult animals at 7 weeks age with LCMV(Cl13/WE-GP) leading to chronic infection, harvest of splenocytes 24 days post infection. 6 biological replicates In both groups, LCMV GP66-77 tetramer+, CD44hi, CD4+T cells were subjected to scRNA- and scTCR-sequencing.

first: Katrin

last: Martin

first: Peter

last: Reuther

first: Florian

last: Geier

first: Anna-Friederike

last: Marx

first: Tiago

last: Abreu-Mota

first: Jonas

last: Fixemer

first: Anna

middle: L

last: Kastner

first: Karen

last: Tintignac

first: Karsten

last: Stauffer

first: Ingrid

last: Wagner

first: Doron

last: Merkler

first: Daniel

middle: D

last: Pinschewer


title: Antiviral Tfh response by “tolerant” congenitally infected virus carriers drives antibody-mediated viral load control [scTCR-Seq]

overall_design: 1. Experimental group, "neonat.": Neonatal, intercranial infection (i.c.) (within first 24h after birth) with artLCMV (Kallert et al., Nat.Comm., 2017) leading to life long virus carriage, harvest of splenocytes 8 weeks post infection. 8 biological replicates 2. Experimental group, "chronic": Intra venous (i.v.) infection of adult animals at 7 weeks age with LCMV(Cl13/WE-GP) leading to chronic infection, harvest of splenocytes 24 days post infection. 6 biological replicates In both groups, LCMV GP66-77 tetramer+, CD44hi, CD4+T cells were subjected to scRNA-and scTCR-sequencing.


title: The nuclear cap-binding complex safeguards stress-resistant protein synthesis and proliferation of stem cells

first: Jeeyoon

last: Chang

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

overall_design: Refer to individual Series


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome

city: Piscataway

first: Joshua

middle: K

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

institute: Rutgers University

summary:
Sirtuins are deacetylases implicated in stress responses and longevity in mammals. Although their differential impact on disease for the two sexes have been noted, underlying reasons are not known. Here, using Sirtuin 7 (SIRT7) as a model in mice, we probe mechanisms leading to sex differences and find that Sirt7-/- females have decreased fitness throughout the lifespan. Intriguingly, SIRT7 preferentially localizes to the sex chromosomes. In females, SIRT7 loss affects “X-chromosome inactivation” (XCI), the 1st arm of dosage compensation that equalizes X-linked gene expression between males and females. Xist is overexpressed and gene silencing becomes more efficient. Surprisingly, however, SIRT7 loss has greatest impact on the active X (Xa). The Xa becomes hyperacetylated on H3K36ac, structurally disorganized, prone to DNA damage, and overexpressed. Increased Xa expression leads to genome imbalance and augmented “X-chromosome upregulation” (XCU) — the 2nd arm of dosage compensation that balances X-chromosome versus autosomal gene expression. These data reveal an essential crosstalk between sirtuins and the sex chromosomes, with SIRT7 safeguarding X-chromosome integrity and dosage balance with autosomes. We propose that the sex bias in Sirtuin 7 biology can be explained in part by unequal effects on the sex chromosomes.

This SuperSeries is composed of the SubSeries listed below.

first: Nicolas

last: Simonet

first: Barry

last: Kesner

last: Guitart-Solanes

first: François

last: Serra

first: Maria

last: Espinosa-Alcantud

last: Lappala

first: Laia

last: Marín-Gual

first: Cristina

last: Marín-García

first: Uri

last: Weissbein

first: Josema

last: Castelló-García

first: Moritz

last: Bauer

first: Danni

last: Wang

first: Llorenç

last: Rovirosa

first: Jay

last: Tischfield

first: Lourdes

last: Serrano

first: Bernhard

last: Payer

first: Aurora

last: Ruiz-Herrera

first: Berta

last: Vazquez

first: Biola

last: Javierre

first: Alejandro

last: Vaquero

first: Jeannie

middle: T

last: Lee


title: The nuclear cap-binding complex safeguards stress-resistant protein synthesis and proliferation of stem cells [RNA-seq]

first: Jeeyoon

last: Chang

summary: Various cellular stresses lead to an inhibition of steady-state translation driven by the cytoplasmic cap-binding protein eIF4E via the integrated stress response (ISR) in order to mitigate stress-induced damage. A caveat is that essential proteins for cell survival or maintenance should be expressed even under ISR-activated conditions. Here, we find that when global translation is compromised due to eIF2α phosphorylation during ISR, eIF2A takes over the function of eIF2α for Met-tRNAi delivery. Notably, preferential association between eIF2A and cellular factors involved in the pioneer round of translation driven by nuclear cap-binding protein complex (CBP20/80) allows the pioneer translation to occur during ISR. We also observe that ISR is activated in growing human embryonic stem cell (hESC) colonies. Under these naturally arising ISR conditions, eIF2A-mediated pioneer translation is active and safeguards self-renewal and differentiation of hESCs. Collectively, we unravel the molecular mechanism underlying translation that secures protein synthesis under cellular stress.

overall_design: Ribo-seqs and mRNA-seqs were performed in both HEK293T cell and hESCs with or without knock-down of endogenous eIF2A. In HEK293Ts, mRNAs bound to either CBP80 or eIF4E were IPed and then subjected to ribo-seq.

first: Seyoun

last: Oh

first: Sung

last: Jang

first: Jiwon

first: Yoon

last: Kim


title: The nuclear cap-binding complex safeguards stress-resistant protein synthesis and proliferation of stem cells [Ribo-seq]


title: Intratumoral CD40 agonist sotigalimab in combination with pembrolizumab induces rapid activation of antigen presenting cells and drives anti-tumor responses in non-injected tumors in metastatic melanoma: Results of a phase 1/2 study

status: Public on Mar 29 2026

city: Houston

first: Salah-Eddine

last: Bentebibel

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: Checkpoint inhibitors (CPIs) benefit metastatic melanoma (MM) patients, but resistance remains a challenge. This phase 1/2 (NCT02706353) study evaluated intratumoral sotigalimab (an anti-CD40 agonistic antibody) with pembrolizumab in 32 CPI-naïve MM patients. Primary endpoints included determining safety and tolerability, the recommended phase 2 dose (RP2D) of  sotigalimab, and the objective response rate (ORR). The most common adverse events (AEs)  related to sotigalimab were injection-site reactions, pruritus, and fatigue. The ORR was 47% and the disease control rate (DCR) was 91% for all patients, and 50% and 92% at the RP2D, respectively. Multiomic biomarker analyses of tumor and blood samples collected before and during treatment demonstrated that sotigalimab effectively engaged the CD40 pathway, boosting the infiltration and activation of myeloid cells, including CD11c+DC-LAMP+ dendritic cells (DCs) and macrophages. The combination therapy activated both innate and adaptive immunity, in both  injected and non-injected tumors. TCR sequencing analysis showed increased T-cell clonality  with expanded new clones shared between injected and non-injected tumors. Clinical responses correlated with these immunologic changes, but not with baseline immunological features  associated with response to anti-PD1 monotherapy. In the B16 melanoma mouse model, single- cell RNA sequencing analysis showed that the combination therapy enhanced antitumor immunity and reduced the immunosuppressive tumor environment. These findings suggest that intratumoral sotigalimab may enhance anti-PD1 therapy, supporting the need for further randomized phase 2 trials to better evaluate its therapeutic potential in the 'in situ' immunization  approach.

overall_design: Preclinical study: single cell RNA-seq was performed on 4 samples of CD45+ live immune cells sorted from tumors. Each sample contained intratumoral immune cells collected from 6 mice per each experimental group. Experimental groups: control (IgG-treated), CD40 Ab-treated, PD1 Ab-treated, and Combo (CD40 Ab & PD1 Ab-treated)

first: Jingjing

last: Liu

first: Jianhua

last: Zhang

first: Barbara

last: Pazdrak

first: Heather

last: Sonnemann

first: Adi

last: Diab

first: Gregory

last: Lizee


title: Ketogenesis promotes leukemia development by inhibiting ferroptosis in leukemic stem cells [ATAC-Seq]

city: guangzhou

first: Songqi

last: Zhu

state: guangdong

address: No. 74, Zhongshan 2nd Road, Yuexiu District

country: China

institute: Sun Yat-sen University

summary: Hepatic ketogenesis generates ketone bodies as an alternative energy source during carbohydrate restriction or ketogenic diets, yet its role in non-hepatic cell types remains poorly defined. Here, we show that leukemic stem cells (LSCs) in acute myeloid leukemia (AML) engage elevated ketogenesis, driven by fatty acid oxidation (FAO), to produce D-β-hydroxybutyrate (BHB). LSCs express high levels of 3-hydroxymethylglutaryl-CoA synthase 2 (HMGCS2), the rate-limiting enzyme in ketogenesis than blast cells and normal hematopoietic stem cells (HSCs). Deletion of Hmgcs2 in AML cells markedly decreases BHB levels, disrupts LSC function, and impairs leukemia progression in both mouse and human AML models, while largely sparing normal hematopoiesis. Mechanistically, BHB suppresses ferroptosis by limiting pro-ferroptotic phospholipid remodeling through epigenetic regulation of fatty acid desaturase 2 (FADS2). Together, these findings identify autonomous ketogenesis as a critical metabolic program that protects LSCs from ferroptotic cell death and sustains leukemia progression.

overall_design: ATAC-seq profiling of LICs derived from two groups of C57BL/6J mice: AML and AML with Hmgcs2 knockout (HMGCS2 KO). This study aims to elucidate autonomous ketogenesis as a critical metabolic mechanism that protects LICs from ferroptotic cell death and supports leukemia progression.

first: Xue

last: Han

first: Kexin

last: Wang

first: Weiwei

last: Ma

last: Guan

first: Xiaobin

last: Tian

first: Zhuangzhhuang

last: Zhao

first: Linjia

last: Jiang


title: Ketogenesis promotes leukemia development by inhibiting ferroptosis in leukemic stem cells [RNA-Seq]

overall_design: RNA-seq profiling of LICs derived from three groups of C57BL/6J mice: AML, AML with Hmgcs2 knockout (HMGCS2 KO), and AML HMGCS2 KO supplemented with BHB. This study aims to elucidate autonomous ketogenesis as a critical metabolic mechanism that protects LICs from ferroptotic cell death and supports leukemia progression.


title: Sex-Dependent Effects of Glutamatergic Disruption on Dopaminergic Neuron Subtype Vulnerable in Parkinson’s Disease

city: Bethesda

first: Mark

last: Cookson

state: MD

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

summary: Aldehyde dehydrogenase 1A1-positive (ALDH1A1+) dopaminergic neurons are selectively vulnerable in Parkinson’s disease (PD), yet how their activity is shaped by presynaptic inputs is unclear. We investigated the role of glutamatergic input by conditionally deleting Grin1, encoding a critical NMDA receptor subunit, in ALDH1A1+ neurons. Grin1 conditional knockout mice showed normal locomotion and motor learning, but females exhibited increased operant reward acquisition along with excessive feeding and weight gain after food restriction. To determine regional contributions in female mice, we selectively knocked down Grin1 in ALDH1A1+ neurons of the ventral tegmental area (VTA) or substantia nigra pars compacta. VTA-specific knockdown in females reproduced the post-restriction feeding and weight gain phenotype. Bulk whole-brain mRNA sequencing revealed significant gene expression changes based on sex primarily in Grin1 conditional knockout mice following food restriction. Many of the differentially expressed genes were associated with energy production, metabolic responses, and glial function. These findings reveal a sex-specific role for NMDA receptor–mediated glutamatergic input to ALDH1A1+ VTA neurons in regulating feeding behavior, providing mechanistic insight into how dysfunction of this vulnerable subpopulation may contribute to PD-related non-motor symptoms.

overall_design: mRNA-seq was used to characterize the sex- and feeding state-dependent transcriptomic effects of impaired glutamatergic input to ALDH1A1+ midbrain dopaminergic neurons following conditonal knockout of the Grin1 gene. The brains of female and male Grin1 conditional knockout and control mice were collected either: 1) prior to any food restriction, 2) immediately after two consecutive nights of food restriction, or 3) after two consecutive nights of food restriction followed by three consecutive days of free access to food via an automatic feeding device.

first: Kathleen

middle: F

last: Carmichael

first: Gavin

last: Riccobono

first: Victor

last: Martinez Smith

first: Jinhui

last: Ding

first: Lisa

last: Chang

first: Lixin

last: Sun

first: Lupeng

first: Huaibin

last: Cai


title: Single-cell multi-omic analysis of post-transplant mesenchymal cells reveals molecular signatures and regulators of lung fibrosis (scRNA-seq)

city: Ann Arbor

first: Lu

last: Lu

state: MI

address: 100 Washtenaw Ave.

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan, Ann Arbor

summary: Chronic lung allograft dysfunction (CLAD) is a critical challenge in lung transplantation. Dysregulated gene expression and epigenomic states in lung mesenchymal cells (MCs) play a key role in these conditions. We performed single-cell multi-omic profiling on MCs isolated from human bronchoalveolar lavage samples of lung transplant recipients with CLAD, compared with time-matched controls. Our results provide deeper insights into the transcriptomic and epigenomic changes in post-transplant MCs, nominating biomarkers and disease-associated factors with implications for future therapeutic efforts.

overall_design: We collected and performed scRNA-seq on cells from human lung autopsy samples, including one from a CLAD patient and two from healthy controls. Due to the low number of MCs detected in these initial samples, we sequenced two additional samples (one from the same CLAD patient and one from the same healthy control) after CD45+ depletion.

first: Aidan

middle: P

last: McLinden

first: Natalie

last: Walker

first: Ragini

last: Vittal

first: Michael

last: Combs

first: Joshua

last: Welch

first: Vibha

last: Lama


title: Single-cell multi-omic analysis of post-transplant mesenchymal cells reveals molecular signatures and regulators of lung fibrosis (RNA-seq)

overall_design: We used cells from the same CLAD MCs samples as our single-cell multiome profiling, along with an additional line not included in the multiome profiling. These cells were treated with either a C/EBPD-targeting siRNA (treated group) or a scrambled siRNA (control group) for 16 hours. To measure the gene expression changes induced by C/EBPD silencing, we performed bulk RNA-seq on both the treated and control groups across the four CLAD samples.


title: Real-time quantitative PCR analysis of Triticum aestivum leaves under heat stress

status: Public on Mar 28 2026

city: Giza

first: Marwa

last: Sanad

address: 33 El Bohouth St, Dokki

department: Genetics and Cytology

country: Egypt

institute: National Research Centre

summary: Triticum aestivum leaves were collected under heat stress compared to non stressed plants during anthesis stage to assay peroxiosme biogenesis genes (pex11.3, pex11.4, Fis1A, DRP5B), antioxdant gens (CAT and SOD), and heat shock proteins (HSP90, and HSP101)

overall_design: Comparative Ct experiments, 3-5 leaves on the each biological replicate were bullked to extract the RNA, 3 random biological plants were sampled per treatment and RNA isolated, notmalized, and cDNA synthesized, and equal amount of synthesied cDNA for each sample has used to assay the qPCR

first: Joseph

last: Shenoda

first: Aida

last: Rizkallah

first: Mona

last: Hussein

first: Salah

last: El-Assal


title: Bulk RNA-seq of SIT1 knockout and control T cells from human healthy donors

city: Oslo

first: Pu

last: Chen

address: Gaustadalléen 21

department: Norwegian Center for Molecular Biosciences and Medicine

institute: University of Oslo

summary: The transmembrane adaptor protein SIT1 is a negative regulator of T cell receptor (TCR) signaling, but its role in human immunity remains poorly characterized. We performed bulk RNA sequencing (RNA-seq) on T cells derived from human healthy donors. SIT1 knockout (KO) was generated in primary T cells, and transcriptomic profiles were compared between SIT1 KO and control cells. This dataset enables the characterization of gene expression changes associated following SIT1 loss. Due to applicable data privacy regulations, identifiable information, including raw sequencing data from the participants, cannot be deposited in public repositories. Qualified researchers may request access to the data by submitting a formal application demonstrating compliance with the participants’ consent conditions. The consent signed by the study participants enables the use of data for study of rare immunological and hematological diseases. Requests should be directed to j.s.saarela@ncmbm.uio.no Processed gene expression data (read counts) and associated metadata are provided in this submission, providing a resource for studying SIT1-dependent transcriptional regulation in human T cells

overall_design:
CRISPR-Cas9 KOs of SIT1 were generated from PBMCs of three healthy donors using two guide RNA (sgRNA), separately. Control samples were electroporated with AAVS1 sgRNA complexes. Assays were performed seven days post-electroporation. Cells were stimulated with 200 ng/ml anti-CD3 (Hit3a, Thermofisher) or left unstimulated for 2 hours before proceeding to RNA extraction using a total RNA purification kit (Norgen Biotek Corp).

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Due to privacy regulations and participant consent,raw sequencing data cannot be deposited in public repositories. Data access is restricted to ensure compliance with consent for studying rare immunological/hematological diseases. Qualified researchers may request the raw data by submitting a formal application demonstrating compliance with these conditions. Direct requests to: j.s.saarela@ncmbm.uio.no.
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first: Janna

last: Saarela


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

city: Shenzhen

first: Qin

last: Peng

address: Gaoke Innovation Center

institute: Shenzhen Bay Laboratory

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

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

first: Liping

last: Guo

first: Yanjing

last: Zhao


title: Mouse heart RNA-seq in isoproterenol (ISO) injury model with or without polystyrene nanoplastics co-exposure

city: Beijing

first: Yilin

last: Pan

address: Anzhen Road #2, Chaoyang District

institute: Beijing Anzhen Hospital

summary: Male C57BL/6 mice were assigned to three groups (n=6 per group): ISO, ISO+100 nm polystyrene nanoplastics (PS), and ISO+1 µm PS. Hearts were collected at the study endpoint and profiled by bulk mRNA-seq to identify transcriptional signatures associated with PS size in the setting of ISO-induced myocardial injury. Libraries were prepared and sequenced in two batches (Batch 1 by Novogene; Batch 2 by Majorbio Bio-Pharm Technology).

overall_design: Bulk RNA-seq was performed on mouse heart tissue (n=18). Differential expression analyses compared ISO+PS groups versus ISO, accounting for sequencing batch. Raw sequencing reads (FASTQ) and processed gene-level count are provided.

first: Linqi

last: Liu

first: Jiyuan

last: Luo

first: Xiaozheng

last: Zhou

first: Kun

last: Hua

first: Hanqing

first: Xiubin

last: Yang


title: Human left atrial appendage RNA-seq in cardiac surgery patients with high versus low micro(nano)plastic burden

summary: Micro(nano)plastics (MNPs) were quantified in left atrial appendage tissue collected intraoperatively from adult cardiac surgery patients at Beijing Anzhen Hospital. Samples were stratified into high (H1–H9) versus low (L1–L9) NP burden groups and profiled by bulk mRNA-seq to identify transcriptional signatures and pathways associated with tissue NP burden.

overall_design: Bulk RNA-seq was performed on human left atrial appendage tissue (n=18). Differential expression and pathway analyses compared high versus low NP burden groups. Raw sequencing reads (FASTQ) and processed gene-level count matrices are provided.


title: Loss of Gαq reshapes fibroblast traits and drives tumor-stroma remodeling in oral cancer progression

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

summary: Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy with limited therapeutic options and poor outcomes due to metastasis.  A major driver of tumor progression is the tumor microenvironment, particularly cancer-associated fibroblasts (CAFs), which remodel the extracellular matrix and secrete pro-tumorigenic signals. Emerging evidence suggests that autophagy and vesicle trafficking pathways regulate these secretory functions, though their role in HNSCC remains unclear. Building on our discovery of Gαq as a central autophagy regulator, we investigated how its absence reshapes fibroblast behavior and modulates crosstalk with oral HNSCC cells. Our findings demonstrate that loss of Gαq reprograms murine fibroblasts into a CAF-like phenotype, in part through deregulated intracellular trafficking and increased ceramide accumulation. Gαq-deficient fibroblasts display increased collagen I deposition, ECM remodeling, and a shift toward secretory activity. Their exosomes, enriched in tumor-promoting growth factor receptors, suppress Caveolin 1 expression in tumor cells and induce an EMT-like phenotype that fuels aberrant HNSCC growth. In co-culture and in vivo, Gαq-silenced fibroblasts assemble into “railroad-track” structures that guide cancer cell migration and invasion. Reduced Gαq expression in human fibroblasts recapitulate these features underscoring a conserved mechanism of stromal activation. Overall, Gαq emerges as a key regulator of fibroblast plasticity and tumor-stroma interactions in HNSCC progression.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data obtained from WT and GαqKO mouse embrionary fibroblasts (3 biological replicates each genotype)

first: Inmaculada

last: Navarro-Lérida

first: Raquel

last: Huertas-Lárez

first: Ramón

last: García-Escudero

first: Federico

last: Mayor Jr

first: Catalina

last: Ribas


title: Integrative single cell RNA-sequencing and spatial transcriptomics uncovers distinct macrophage-fibroblast cross-talk in human hip synovium between patients with femoroacetabular impingement and osteoarthritis

city: Rochester

first: Gulzada

last: Kulzhanova

state: NY

address: 310 University Park

department: Biomedical Engineering

institute: University of Rochester

summary: Femoroacetabular impingement (FAI) and synovitis have been recognized as essential factors for developing osteoarthritis (OA) in the hip joints. However, little is known about altered synovial cellular compositions, their associated transcriptomic profiles, and cell-cell interactions between patients with FAI and hip OA. In the current study, by using integrative single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (Spatial-seq), we identified the molecular mechanisms by which synovial cells promote hip OA pathogenesis from FAI. Compared to FAI synovium, epiregulin (EREG)-enriched lining fibroblast-like synoviocytes (FLS) were significantly increased in the hip OA synovium. These EREG+ FLS are pro-inflammatory due to their high expression of CXCL1, IL8 (CXCL8), and MMPs. Furthermore, pseudotime analysis predicts that EREG+ FLS are potentially derived from DPP4+PI16+ sublining FLS. Importantly, analysis of cell-cell interactions indicates that fibroblast growth factor 2 (FGF2) secreted from COL1A1+IGFBP5+ fibrotic macrophages may signal through syndecan 4 (SDC4) expressed by EREG+ lining FLS, inducing the expression of IL6, IL8, MMP1, and PTGS2. The GO term analysis of activated genes downstream of FGF2-SDC4 signaling revealed that biological processes associated with inflammation and angiogenesis were upregulated in hip OA, while mechanical stimulus and skeletal muscle differentiation were dominant in FAI. Moreover, we also found that EREG+CCL20+MMP3hi lining FLS as well as most macrophage and monocyte populations are unique to hip OA patients when compared to knee OA and RA patients. The findings of this study offer a groundwork in tailoring novel targets and therapies for FAI and hip OA patients.

overall_design: Single cell RNA-sequnecing and Spatial transcriptomics of the human hip synovium samples from patients with femoroacetabular impingement and osteoarthritis

first: Chia-Lung

last: Wu


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

status: Public on Mar 27 2026

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

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

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

first: Pauline

last: Bardet

first: Lize

last: Allonsius

first: Eva

last: Hadadi

first: Damya

last: Laoui


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

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

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

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

first: Aya

last: Sasaki

first: Kimberly

last: Kelly

first: Lindsay

last: Michalovicz

first: David

last: Ashbrook

first: Sanoji

last: Wijenayake

first: James

last: O'Callaghan

middle: O


title: Dormancy exit correlates with CREB1 reactivation that is a potential target to overcome endocrine therapy resistance in ER+ breast cancer cells.

city: Chicago

first: Lei

last: Duan

state: IL

address: 1653 W Congress Pkwy

department: Anatomy and Cell Biology

institute: Rush University Medical Center

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

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

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

last: O'Hara

first: Carl

last: Maki


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

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

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


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

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

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

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

first: Mathilde

last: Bizou

first: Joel

last: Howard

first: Alexandre

last: Dubrac


title: Fibroblast orchestration of inflammaging via NF-kB activation

city: San Francisco

first: Lucile

middle: P A

last: Neyton

state: CA

address: 505 Parnassus Ave

institute: UCSF

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

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

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

middle: C

last: Allen

first: Carolyn

last: Calfee


title: Age-related gene expression alteration responding to mechanical force and TGFβ signaling [ATAC-seq]

city: Villigen

last: Shivashankar

state: Aargau

address: Forschungsstrasse 111

department: LNB

institute: Paul Scherrer Institute

summary: The aging process significantly alters the biomechanical properties of fibroblasts, impacting their cytoskeletal and chromatin organization. These changes are pivotal in modulating cellular responses to mechanical and biochemical stimuli. This study investigates the hypothesis that aging leads to fibroblasts’ divergent adaptation mechanisms to external stimuli. Herein, fibroblasts from young and old cohorts were embedded in 3D collagen gels and subjected to tension and Transforming Growth Factor beta (TGFb) stimulation. The study revealed that mechanical forces and aging exert profound effects on chromatin architecture. Young cells adapted more rapidly to mechanical stress and showed a heightened responsiveness to TGFβ compared to older cells. The identification of key transcription factors implicated in age-dependent responses was further examined, assessing their potential in cellular rejuvenation.

overall_design: ATAC-seq profiling of primary dermal fibroblasts from two age groups (old: 75 years old; young: 10 years old) seeded in 3D collagen gel exposed to tension force and TGFβ stimulation

first: Yawen

last: Liao

first: Luezhen

last: Yuan

first: Trinadha

last: Sornapudi

first: G

middle: V


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

first: Patrick

last: McGowan

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

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

first: Aya

last: Sasaki

first: Kimberly

last: Kelly

first: Lindsay

last: Michalovicz

first: David

last: Ashbrook


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

city: Lausanne

first: Raphael

last: Gottardo

state: Vaud

address: Rue du Bugnon 21

department: Biomedical Data Science Center

institute: Lausanne University Hospital

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

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

first: Krisztian

last: Homicsko


title: Evolutionary transcriptomic and cellular specializations within the mammalian striatum

city: Los Angeles

first: Genevieve

last: Konopka

address: 650 Charles Young Drive South, 73-214 CHS

department: Neurobiology

institute: UCLA David Geffen School of Medicine

summary: In this study we generated and analyzed single-nucleus RNA sequencing (snRNA-seq) of human, chimpanzee, rhesus macaque (this study and GSE167920), marmoset (GSE151761 and GSE165578), bat caudate (CN) and putamen (Pu) separately, ferret caudate (GSE151761), and mouse caudoputamen (C-Pu)(GSE151761) spanning 94 million years of evolution. We identified novel interneuron cell types in bat Pu while uncovering fundamental cellular compositional and transcriptomic differences between primate and non-primate striata.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens
Phyllostomus discolor

overall_design: Generated single nuclear RNA profiles of human, chimpanzee, rhesus macaque, and bat striatal regions, caudate nucleus and putamen.

first: Gozde

last: Buyukkahraman

first: Emre

last: Caglayan

first: Yaqiang

last: Zhang

first: Stephen

last: Hoerpel

first: Carlos

last: Orozco

first: Amber

last: Main

first: Chet

last: Sherwood

first: William

last: Hopkins

first: Todd

last: Roberts

first: Sonja

last: Vernes


title: Single-cell RNA sequencing identifies a unique population of macrophages in the Aristolochic acid I (AAI)-induced AKI-to-CKD transition murine model

city: Shanghai

first: Xiangchen

last: Gu

address: 110 Ganhe Rd, Hongkou  Distrcit

department: Department of Nephrology

institute: Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine

summary: Acute Kidney Injury (AKI) often progresses to Chronic Kidney Disease (CKD), resulting in significant morbidity and mortality. The transition from AKI to CKD is driven by complex cellular mechanisms that are not yet fully understood. In this study, we used an Aristolochic Acid I (AAI)-induced murine model to investigate these mechanisms, performing single-cell RNA sequencing (scRNA-seq) to comprehensively profile kidney immune cells during the AKI to CKD transition. Our analysis revealed significant changes in immune cell populations, particularly macrophages and T lymphocytes. We identified a novel subpopulation of macrophages characterized by the expression of Ctsk, Mmp9, and Acp5, which emerged during the CKD phase. These macrophages were found to interact with T cells, injured proximal tubules, and fibroblasts, suggesting their involvement in chronic inflammation and fibrosis. Targeting this specific macrophage subpopulation may represent a potential therapeutic approach to prevent CKD progression. Additionally, T lymphocytes underwent a transition from effector to exhausted phenotypes, indicating chronic immune activation and sustained inflammation in CKD. Our findings provide new insights into the immune landscape of kidney injury and highlight potential targets for therapeutic intervention in preventing the progression from AKI to CKD.

overall_design: Male C57BL/6 mice, aged 8 to 10 weeks, were used in this study; acute kidney injury (AKI) was induced by intraperitoneal injections of aristolochic acid I (AAI) at a dose of 3 mg/kg administered every three days over a two-week period, followed by a two-week cessation to allow for chronic kidney disease (CKD) development; control mice received equivalent volumes of vehicle solution; all animal procedures were approved by the Institutional Animal Care and Use Committee (IACUC) and conducted following institutional guidelines. The sample sizes were as follows: control group (n=1), AKI phase (n=2), CKD phase (n=2).

first: Chenxi

last: Wang

first: Lin

last: Xie

first: Yaodong

first: Min

last: Chen


title: Directed evolution of a genetically encoded photocatalyst for temporally resolved proximity labeling of subcellular RNAs and proteins

first: Yuxin

last: Fang

state: Beijing

address: Yiheyuan Road No.5

institute: Peking University

summary: In eukaryotic cells, the precise spatial localization of RNAs and proteins is essential for proper cellular function. Genetically encoded photocatalytic proximity labeling techniques have expanded our ability to map subcellular proteomes and transcriptomes, but their temporal resolution remains limited. Here, we introduce Lantern, an engineered flavoprotein optimized via directed evolution, which enables sub‑minute, spatially resolved labeling of cellular biomolecules. Lantern is targetable to diverse subcellular compartments, including the endoplasmic reticulum, mitochondria, and stress granules (SGs), to map local transcriptomes (CAP-seq) and proteomes (CAP-MS). Using Lantern, we observed that m6A‑enriched RNAs are recruited to SGs within five minutes of stress induction, while ER‑proximal RNAs associate with the SG scaffold protein G3BP1 during early SG assembly. Additionally, Lantern was adapted for cell-surface tagging (CAP-CELL), enabling spatially resolved cell typing and the analysis of cell-cell interactions. Collectively, this study establishes Lantern as a powerful tool that offers unprecedented temporal resolution for investigating the dynamic organization of subcellular molecular networks.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: RNA-seq profiling of the endoplasmic reticulum membrane (ERM)-proximal transcriptome, outmer mitochondrial membrane (OMM)-proximal transcriptome and G3BP1-proximal transcriptome in HEK293T cells. RNA-seq profiling of the G3BP1-proximal transcriptome in rat cortical neurons. RNA-seq profiling of migrating MC38 cells. Profiling m6A sites via GLORI2 in HEK293T cells treated with or without 0.5 mM sodium arsenite for 1 h.

first: Ziqi

last: Ren

first: Fu

last: Zheng

first: Ruixiang

first: Songrui

last: Zhao

first: Wentao

first: Peng

last: Zou


title: Mutual Antagonism Between PRC1 Condensates and SWI/SNF in Chromatin Regulation

city: Boston

first: Philipp

last: Schneider

state: Massachusetts

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Opposing activities of conserved chromatin regulatory complexes, such as the Polycomb Repressive Complex 1 (PRC1) and the activating chromatin remodeler SWI/SNF play critical roles in regulating gene expression. However, the mechanisms by which these complexes compete to regulate chromatin states remain poorly understood. Here, we demonstrate that the condensate-forming properties of PRC1 play an important role in excluding SWI/SNF from chromatin. Consistently, PRC1 compositions with a higher propensity for condensate formation are more effective in preventing SWI/SNF binding. Conversely, SWI/SNF-bound chromatin significantly reduces PRC1 binding and subsequent condensate formation. Notably, SWI/SNF can suppress PRC1 condensate formation in an ATP-hydrolysis independent manner, suggesting a mechanism driven by competitive binding and steric hindrance rather than active remodeling. Our findings reveal a mutual antagonism between PRC1 condensates and SWI/SNF chromatin remodeling, highlighting the importance of PRC1 composition and condensate formation in regulating gene repression.

overall_design: RNA-Seq and CUT&RUN experiments using antibodies: BAF155, EZH2, EED, H3K27ac, H3K27me3, IgG, PHC2, PHC3, RING1B, SMARCA1

first: Stefan

last: Niekamp

first: Sharon

last: Marr

first: Rebecca

last: Sanon

first: Radhika

last: Subramanian

first: Robert

last: Kingston


title: H2O2-induced astrocytic collagen triggers neuronal death in ischemic stroke [ATAC-seq]

city: Daejeon

first: C. Justin

last: Lee

address: 55 Expo-ro

institute: Institute for Basic Science

summary: Ischemic stroke is a brain injury caused by the occlusion of blood vessels, leading to reduced blood flow, excessive oxidative stress, and the cascade of events, including the formation of the glial barrier, fibrotic scar, neuronal death, and motor impairment. Despite extensive research into stroke etiology, the specific initiation trigger for neuronal death is mainly unknown, severely limiting the development of effective treatments. Here, we demonstrate that excessive H2O2 generation is the initiating factor of ischemic stroke in the photo-thrombosis (PT) mouse and non-human primate (NHP) models, with H2O2-induced astrocytic type I collagen (COL1) playing a crucial role in the cascade of stroke pathology. Treatment with KDS12025, an H2O2-decomposing peroxidase enhancer, significantly alleviates these effects by reducing H2O2-induced COL1 in extremely low doses in mouse and NHP stroke models. In cultured astrocytes, H2O2 stimulates the production of astrocytic COL1 through post-transcriptional up-regulation of Col1 mRNA by decreasing microRNA29, leading to the death of neighboring neurons. Using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), we observe profound alterations in N-glycan profiles, particularly fucosylated N-glycans, which reverted to normal levels in both the KDS12025 treatment and astrocytic Col1 gene-silencing groups. The gene-silencing of astrocytic Col1 or Fut8, a key enzyme responsible for core fucosylation necessary for COL1 secretion, prevents neuronal death and motor impairment. Our findings reveal that H2O2-induced astrocytic COL1 production is critical to ischemic stroke. These findings propose that targeting H2O2, astrocytic COL1, and FUT8 could be effective therapeutic strategies for ischemic stroke, offering new avenues for treatment.

overall_design: ATAC-sequencing of primary mouse cortical astrocyte isolated from p4 pub. The astrocytes are treated with H2O2 for 3 hours and then harvested after 1 day.

first: In

middle: Y

last: Hwang

first: Jae

middle: H

first: C

middle: J


title: Bulk RNA Sequencing of Chimera-Derived Monocyte-Derived Macrophages Targeted for Mitochondrial ROS During Peak Experimental Autoimmune Encephalomyelitis

city: Zürich

first: Juan

last: Villar Vesga

address: Winterthurerstrasse 190

institute: University of Zurich

summary: Reactive oxygen species (ROS) produced by mononuclear phagocytes (MPs) are widely believed to drive tissue damage in multiple sclerosis (MS), yet the distinct roles of central nervous system (CNS)-resident versus CNS-invading MPs remain unclear. Here, we combined single-cell profiling and conditional gene targeting to map and modulate ROS production across CNS MPs in a preclinical mouse model of MS. We show that monocyte-derived macrophages (MdMs) exhibit a higher oxidative stress gene signature and produce more ROS than Mglia. Challenging previous assumptions, our findings reveal that phagocytic NADPH oxidase 2 is dispensable for neuroinflammation. In contrast, quenching mitochondrial ROS (mtROS) through mitochondria-targeted catalase (mCAT) expression in MdMs, but not in Mglia, ameliorated disease severity in acute neuroinflammation. While core phagocyte functions were unaltered in mCAT-expressing MdMs, our results demonstrate a direct neurotoxic role of mtROS. Together, we identify MdMs as the primary driver of ROS-mediated oxidative neurological tissue damage.

overall_design: Bulk RNA sequencing of CNS-infiltrating monocyte-derived macrophages (MdMs) isolated from central nervous system with targeted modulation of mitochondrial ROS pathways during peak experimental autoimmune encephalomyelitis (EAE). The dataset contains sorted MdMs from donor wt (CD45.1) and donor mitochondrial catalase(CD45.2) targeted mice.

last: Villar-Vesga

first: Donatella

last: De Feo

first: Pauline

last: Clément

first: Viola

last: Bugada

first: Elèni

last: Meuffels

first: Sarah

last: Mundt


title: H2O2-induced astrocytic collagen triggers neuronal death in ischemic stroke [RNA-seq]

overall_design: RNA-sequencing of primary mouse cortical astrocyte isolated from p4 pup. The astrocytes are treated with H2O2 for 3 hours and then harvested after 1 day and 3 days.


title: Transcriptome of napM-deleted strain in Mycobacterium smegmatis mc2 155

city: Wrocław

first: Kornel

last: Milcarz

address: Fryderyka Joliot-curie 14a

department: Faculty of Biotechnology

country: Poland

institute: University of Wrocław

summary: RNA-Seq results for M. smegmatis wild type and napM-deleted strain, deprived of one of the nucleoid-associated proteins - NapM.

overall_design: Three replicates of wild type and napM deleted strains of M. smegmatis mc2 155 were grown in 7H9 + 10%ADC + 0,05% Tween 80 medium in 37 degrees, to logarythmic phase.


title: An optimized protocol for efficient derivation of pancreatic islets from multiple human pluripotent stem cell lines

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

summary: Future success of cell therapy for type 1 diabetes (T1D) relies on robust protocols for the differentiation of stem cells to pancreatic islets. However, currently established protocols generate stem cell-derived pancreatic islets (SC-islets) which contain non-endocrine cell populations and have immature functionality. Herein we report the development of a new protocol for the generation of potent SC-islets enriched in functional endocrine cells from multiple human pluripotent stem cell (hPSC) lines. We show that laminin-521 efficiently supports monolayer differentiation of 8 testes hPSC lines to endocrine progenitor (EP)  stage. The efficiency was further improved by reducing the pancreatic progenitor (PP) stage. Importantly, we find that aggregation of EP reduces unwanted non-endocrine and proliferative cells. Subsequent suspension cultures generate SC-islets with  strong in vitro glucose responsiveness, similar to human islets. Upon transplantation of 300 SC-islets into the anterior chamber of the eye of a diabetic mouse model, the SC-islets undergo further maturation in vivo and re-establish normal glycemic control. The SC-islets before and after transplantation are to a major extent free of non-endocrine cell populations. In conclusion, our robust differentiation protocol results in endocrine enriched and highly functional SC-islets that should be well suited for transplantation into patients with T1D.

overall_design: In vitro differentiation of human pluripotent stem cells into pancreatic islets followed by thier transplantation into the anterior chamber of the eye of diabetic mice

first: Siqin

last: Wu

first: Galyna

last: Bryzgalova

first: Shivam

last: Chandel

first: Paschalis

last: Efstathopoulos

first: Kelly

last: Blust

first: Anna

last: Voznesenskaya

last: Falk

first: My

last: Hedhammar

first: Per-Olof

last: Berggren

first: Fredrik

last: Lanner


title: A molecular atlas of brain neurovascular interactions reveals a spatiotemporal requirement of TGFβ signaling in brain angiogenesis

first: Gael

last: Cagnone

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

overall_design: Refer to individual Series


title: A molecular atlas of brain neurovascular interactions reveals a spatiotemporal requirement of TGFβ signaling in brain angiogenesis [scRNA-seq]

overall_design: Endothelial cell enriched scRNA-seq profiles of the mouse brain in healthy and Alk5iEKO P12 mice

first: Alexandre

last: Dubrac


title: A molecular atlas of brain neurovascular interactions reveals a spatiotemporal requirement of TGFβ signaling in brain angiogenesis [Visium]

overall_design: Spatial transcriptomics of the developing mouse brain - duplicate of coronal sections from P6, P12 and P60 mouse brain.

first: Mathilde

last: Bizou

first: Joel

last: Howard


title: Single-cell transcriptome atlas of human embryos after gastrulation

status: Public on Mar 26 2026

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: The comprehensive spatiotemporal atlas of gene expression during early human embryonic development is critical for insights into embryogenesis, organogenesis, and disease origins. Leveraging Stereo-seq technology, we generated spatial transcriptomic profiles across 77 sagittal sections of 13 whole human embryos ranging from Carnegie stage 12 to 23, integrated with single-nucleus RNA-seq to elucidate gene expression patterns within defined cellular contexts, revealing the cellular heterogeneity that drives organ-specific differentiation. Our study has established a regulatory profile for the development of 50 organs and 198 substructures, and identified potential tissue-identity regulators. Notably, it uncovered previously uncharacterized gene functions in cardiac and brain development. The atlas not only substantiates and refines current understanding of human organ development but also highlights key organs susceptible to viral infections and genetic disorders. Furthermore, we characterized the allelic gene expression within specific organs at different developmental stages. This work presents a groundbreaking compilation of genome-wide gene expression profiles for each spatially defined cell population, which can be visualized as a spatial display of the embryonic transcriptional landscape. These results offer the most thorough delineation to data of the spatiotemporal transcriptomic dynamics of human organogenesis.

first: Jiexue

last: Pan

first: Yuejiao

last: Li

first: Zhongliang

last: Lin

first: Qing

last: Lan

first: Ying

last: Zhang

first: Huixi

last: Chen

first: Shengwei

last: Sui

first: Man

last: Zhai

first: Lijian

first: Hongbo

last: Yang

first: Ya

last: Gao

first: Guolian

last: Ding

first: Xun

last: Xu

first: Hefeng

last: Huang


title: DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A (RNA-seq)

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

summary: Loss of DNA methylation is a hallmark of cancer that is proposed to promote carcinogenesis through gene expression alterations, retrotransposon activation and induction of genomic instability. Cancer-associated hypomethylation does not occur across the whole genome but leads to the formation of partially methylated domains (PMDs). However, the mechanisms underpinning PMD formation remain unclear. PMDs replicate late in S-phase leading to the proposal that they become hypomethylated due to incomplete re-methylation by the maintenance methyltransferase DNMT1 during cell division. Here we investigate the role of DNMT1 in the formation of PMDs in cancer by conducting whole genome bisulfite sequencing (WGBS), repli-seq and ChIP-seq on DNMT1 knockout HCT116 colorectal cancer cells (DNMT1 KO cells). We find that DNMT1 loss leads to preferential hypomethylation in late replicating, heterochromatic PMDs marked by the constitutive heterochromatic mark H3K9me3 or the facultative heterochromatic mark H3K27me3. However, we also observe that a subset of H3K9me3-marked PMDs gain methylation in DNMT1 KO cells. We find that, in DNMT1 KO cells, these hypermethylated PMDs remain late replicating but gain DNMT3A localisation. This is accompanied by loss of heterochromatic H3K9me3 and specific gain of euchromatic H3K36me2. Our observations suggest that hypermethylated PMDs lose their heterochromatic state, enabling their methylation by DNMT3A and the establishment of a hypermethylated, non-PMD state, despite their late replication timing. More generally, our findings suggest that the de novo DNMTs play a key role in establishing domain level DNA methylation patterns in cancer cells.

overall_design: This series contains RNA-seq from human cancer cell lines. HCT116 cells and derivatives lacking DNMT1 were grown before RNA was harvested before being quantified by RNA-seq. Includes new samples as well as re-processing of existing GEO samples using the same approach as for the new samples (GSM7818564, GSM7818565, GSM7818566 - all from GSE244518)


title: Effect of AAV-mediated non-fibrogenic TBX18 expression in mouse hearts

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: Gene therapy-based biological pacemakers have been proposed as an alternative to their hardware-based counterparts. In this context, short-term ectopic expression of the T-box transcription factor 18 (TBX18) in the ventricle reportedly generated potent short-term pacemaker function in various animal models. Here, we investigated the effect of adeno-associated virus (AAV)-mediated long-term expression of TBX18 in mouse hearts. Mice were injected with AAV vectors containing GFP-labeled Nanoluciferase or GFP-labbeled TBX18 at the left ventricular apex. Left ventricular tissues were harvest 2 weeks later. The results suggest that at non-fibrogenic level, TBX18 expression suppress working myocardial genes but does not induce pacemaker phenotype.

overall_design: RNA-seq profiling of mouse left ventricular tissues transduced with AAV-Nluc and AAV-TBX18 vectors.

first: Jianan

last: Wang

first: Karel

last: van Duijvenboden

first: Gerard

last: Boink


title: RNA Seq of rhabdomyosarcoma cells with sgRNA targeting oncofusion interacting proteins

city: Durham

first: Seth

last: Zimmerman

state: NC

address: 308 Research Dr.

institute: Duke University

summary: We identified the common protein interactome of rhabdomyosarcoma interacting proteins. Here we selected a subset of interactors, targeted them with sgRNA, and performed RNAseq is RH4-flag cells.

overall_design: Cells were transduced in triplicate with each sgRNA, selected for a week and the RNA from resultant cells were sequenced.

first: Christopher

middle: M

last: Counter


title: Cleavage Under Targets & Release Using Nuclease (CUT&RUN) of monosomy 7 compared to normal karyotype control

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale G. Menghini, 9

institute: University of Perugia

summary: Monosomy 7 is one of the most frequent aneuploidies in myeloid malignancies, associated to heterogeneous phenotypes. Its poor prognosis differentiates it from  aberrations leading to partial/complete loss of 7q region.  Underlying pathogenic mechanisms are still undetermined. We performed a comprehensive epi-genomic study of karyotypically isolated monosomy 7 in adult Myelodysplastic Syndromes/Acute Myeloid Leukemias.

overall_design: CUT&RUN was performed in one mon7 case and one nkMN to identify IKZF1 and PAX8 transcription factors binding sites across the genome, starting from 280,000 cells per reaction. The CUT&RUN Assay kit was used following manufacturer’s instruction (Cell Signaling Technology, Danvers, MA, USA), with Ikaros (D6N9Y, 1:100), PAX8 (D2S2I, 1:50), negative control rabbit IgG (DA1E, 1:20), and positive control H3K4me3 (C42D8, 1:50) antibodies (Cell Signaling Technology).

first: Anair

middle: G

last: Lema Fernandez

first: Carlotta

last: Nardelli


title: Interactome CRISPR screen for rhabdomyosarcoma cells driven by four oncofusions

summary: We identified and interactome for seven diffent rhabdomyosarcoma oncofusions. The proliferative effects of the loss of these proteins was tested by a CRISPR loss of function library screen in four rhabdomyosarcoma cell lines engineered to be driven by 4 different oncofusions.

overall_design: RH4-flag cells expressing a PAX3::FOXO1 targeted shRNA and one of four oncofusions (PAX3::FOXO1, PAX3::NCOA1, PAX3::INO80D, PAX3::MAML3) were transduced with a CRISPR library and CAS9 in triplicate. Initial time points were taken after selection. Final time points were taken after 2 weeks of proliferation.


title: Kinome CRISPR screen for Rhabdomyosarcoma cells in combination with pralatrexate

summary: We found that pralatrexate causes temporary tumor regression in RH4 cell xenograft model. In order to identify possible therapeutic targets that could be targeted in combination with pralatrexate, we performed a whole Kinome CRISPR loss of function screen in cells dosed with pralatrexate.

overall_design: RH4 cells were infected with lentivirus encoding the Brunello kinome library at 1,000x coverage.  48 hours later, cells were selected with 0.25 µg/ml puromycin for 72 hours.  A portion of the cells were harvested at this point for baseline measurements.  The remaining cells were allowed to recover for 72 hours, and then treated with 1.5 nM pralatrexate or vehicle control and passaged at 4 day intervals for 10 days.  On day 10, 5 x 106 cells were harvested and genomic DNA isolated using an ammonium acetate precipitation method.  The sgRNA sequences from each sample were PCR amplified using primers with Illumina adaptors and indexes for multiplexing as described.  Samples were pooled and sequenced at the Duke Genome Sequencing Core Facility, to an average sequencing depth of 1,200 reads per sgRNA.

first: So Young

last: Kim


title: Obesity supersizes the immune response to stroke

city: Palo Alto

first: Karen

last: Bradshaw

address: 1201 Welch Road

institute: Stanford University

summary:
Please cite: Bradshaw K,  Holsten J, Hahn O, Foltz A, Zera KA, Zhu L, Haarslev C, Wyss-Coray T, Peterson TC, Buckwalter M (in press). Obesity supersizes macrophage and neutrophil activation after stroke while lipid droplets play a protective role. Journal of Neuroinflammation.

Obesity is a key risk factor for stroke and by 72 hours after stroke, obese mice have exacerbated stroke sizes, increased neuroinflammation, and motor deficits. To understand how obesity worsens outcomes, we performed single-cell RNA sequencing (scRNASeq) of immune cells in the blood (peripheral blood mononuclear cells, PBMCs) and brain (cortex) 72 hours after stroke or sham surgery in control or diet-induced obese mice. In the blood of obese mice compared to normal diet mice, myeloid cells exhibit the most transcriptional change in both sham and stroke mice. This includes two distinct chemotaxis neutrophil subtypes (enriched with neutrophil chemokine ligand Cxcl2 and receptor Cxcr2, respectively), interferon signaling neutrophils, and two macrophage subtypes enriched in the lipid droplet gene perilipin-2 (Plin2) with and without the foamy macrophage marker Cd36. In the brain, obesity did not induce major transcriptional changes in immune cells in sham mice, but after stroke there were dramatic changes in infiltrating Plin2+ and Plin2- macrophages, interferon-signaling dendritic cells, and 1 chemotaxis neutrophil subtypes. The immune changes induced by stroke in obese mice in brain macrophages and dendritic cells mirrored obesity-induced changes in blood macrophages, including amplification of lipid-related, interferon, and protein degradation genes and downregulation of protein synthesis genes. In neutrophils, obesity amplified interferon and TNF signaling in the blood while in addition enhancing oxidative stress, complement, and a robust pro-thrombotic transcriptional signature in brain neutrophils. Co-expression analysis revealed that Plin2 expression correlates with lipid-related, immune, stress, and coagulation genes, suggesting that lipid droplet accumulation, inflammation, oxidative stress, and coagulation are processes that amplify each other and are attractive candidates for therapies to ameliorate obesity-exacerbated stroke outcomes.

overall_design: Single cell RNA sequencing of the infarct core and surrounding cortex or corresponding region in stroke or sham 24-week old male mice, respectively, fed a 6-week high fat diet or control diet. 10x genomics was used.

first: John

last: Holsten

first: Oliver

last: Hahn

first: Aulden

last: Foltz

first: Kristy

last: Zera

first: Li

last: Zhu

first: Christine

last: Haarslev

first: Tony

last: Wyss-Coray

first: Todd

last: Peterson

first: Marion

last: Buckwalter