title: DeCAF redefines fibroblast states uncovering multidimensional tumor-stroma relationships driving clinical tumor progression and immunotherapy response [RNA-Seq]

summary: Cancer-associated fibroblast (CAF) heterogeneity within pancreatic ductal adenocarcinoma (PDAC) has been previously assessed through single-cell RNA sequencing (scRNAseq) to discover distinct CAF populations such as myCAFs and iCAFs. While useful as a biological framework, no studies have conclusively and robustly demonstrated a correlation of CAF subpopulations with clinical prognosis or therapy response. We define restraining (rest) and promoting (pro) CAFs in patient samples that are both prognostic and predictive of therapy response in disparate tumor types. Using a single sample classifier, DeCAF, we uncover distinct clinical and spatial interactions between pro- and restCAF subtypes and basal-like and classical tumor subtypes that support tumor stroma crosstalk where basal-like tumors are enriched in proCAFs and classical tumors are enriched in restCAFs. Finally, we find striking differences in the immune contexture of pro- and restCAF tumors where restCAF dominant tumors are enriched in patients who respond to immune checkpoint inhibition (ICI) in two large clinical trials, and proCAF dominant tumors are enriched in patients who respond to myeloid inhibition. This work is the first to define CAF subtypes that are clinically robust, prognostic, predictive of immunotherapy response, and associate with tumor molecular subtype.

overall_design:
129 de-identified primary PDAC patient samples were collected from the IRB-approved University of North Carolina Lineberger Comprehensive Cancer Center Tissue Procurement Core Facility and were flash frozen in liquid nitrogen.  FFPE samples were prepared, hematoxylin and eosin stained.

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

first: Xianlu

last: Peng

first: Ian

middle: C

last: McCabe


title: Positional Interpretation of Cis-Regulatory Code and Nucleosome Organization with Deep Learning Models

status: Public on Dec 12 2025

city: Kansas City

first: Melanie

last: Weilert

state: MO

country: USA

institute: Stowers Institute for Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Sequence-to-function neural networks learn cis-regulatory sequence rules driving many types of genomic data. Interpreting these models to relate the sequence rules to underlying biological processes remains challenging, especially for complex genomic readouts such as MNase-seq, which maps nucleosome occupancy but is confounded by experimental bias. We introduce pairwise influence by sequence attribution (PISA), an interpretation tool that combinatorially decodes which bases contributed to the readout at a specific genomic coordinate. PISA visualizes the effects of transcription factor motifs, detects undiscovered motifs with complex contribution patterns, and reveals experimental biases. By learning the bias for MNase-seq, PISA enables unprecedented nucleosome prediction models, allowing the \emph{de novo} discovery of nucleosome-positioning motifs and their long-range chromatin effects, as well as the design of sequences with altered nucleosome configurations. These results show that PISA is a versatile tool that expands our ability to train and interpret sequence-to-function neural networks on genomics data and understand the underlying cis-regulatory code.

overall_design: Micrococcal nuclease digestion with deep sequencing (MNase-seq) experiments were conducted in Saccharomyces cerevisiae BY4741 strains across a wildtype set and a CRISPR mutant (3 point-mutations upstream of Pho5) set of replicates.

first: Charles

last: McAnany

first: Grishma

last: Mehta

first: Fahad

last: Kamulegeya

first: Jennifer

last: Gardner

first: Schreiber

last: Jacob

first: Anshul

last: Kundaje

first: Julia

last: Zeitlinger


title: Erucamide regulates retinal neurovascular crosstalk

status: Public on Dec 16 2025

city: La Jolla

first: Guoqin

last: Wei

state: CA

address: 10550 North Torrey Pines Rd, MB216

institute: The Scripps research institute

type: Expression profiling by high throughput sequencing

summary: Neurovasculoglial crosstalk is critical in establishing and maintaining a functional neurovascular unit. Breakdown in the unit is central to many neurodegenerative disorders of the CNS of which the retina is a component. A growing literature indicated that primary fatty acid amides (PFAMs) can regulate this crosstalk between vasculature and neuronal tissues. In this study we describe a central role for erucamide, a 22:1 mono-unsaturated omega-9 fatty acid amide, in degenerating retinal tissues. Using high-resolution global mass spectrometry-based metabolomics, we cataloged metabolites in murine models of retinal degeneration and show that while PFAMs, in general, are highly dysregulated, erucamide is the one most significantly diminished during photoreceptor atrophy. Using rodent models of retinal degeneration and novel organosilane-modified porous silicon nanoparticles (pSiNPs) for the in vivo delivery of erucamide, we demonstrate that erucamide activates CD11b+ myeloid cells, leading to the upregulation of angiogenic and neurotrophic cytokines that stabilize retinal degeneration. We identified TMEM19 as a novel binding protein for erucamide that is crucial for human iPSC-derived macrophage precursor cells activation and subsequent neurotrophic and angiogenic factor production. These findings reveal a previously unknown PFAM pathway that is modulated during retinal degenerative diseases, demonstrating that erucamide or functional analogues and their action through TMEM19 may be useful as a therapeutic alternative to neuroprotective and stem cell-based approaches for the treatment of retinal degenerative diseases.

overall_design: To investigate the function of erucamide in myeloid cells and signaling pathways mediated by erucamide through TMEM19, we conducted a bulk RNA sequencing experiment. iPSC-MPCs cells were treated with a combination of erucamide (Eru-C18-pSi) or not (C18-pSi), with (using scrambled siRNA) or without (using siTMEM19) TMEM19. Differential expression analysis was performed to compare the treatment combinations.

first: Shreyosree

last: Chatterjee

first: Qinglin

last: Yang

first: Daisuke

last: Ogasawara

first: Sarah

last: Giles

first: Peter

last: Westenskow

first: Junhua

last: Wang

first: Ruhan

last: Fan

first: Helena

last: Pham

first: Edith

last: Aguilar

first: Jacob

last: Robinson

first: Ayumi

last: Usui-Ouchi

first: Roberto

last: Bonelli

first: Kevin

last: Eade

first: Gary

last: Siuzdak

first: Benjamin

last: Cravatt

first: Michael

last: Sailor

first: Dale

last: Boger

first: Martin

last: Friedlander


title: Disambiguating Transcriptional Effects from Post-Transcriptional Effects of Genetic Variants with an Inferred Stability Optimized Massively Parallel Reporter Assay (ISOMPRA).

city: St. Louis

first: Joseph

middle: D

last: Dougherty

address: 4370 Duncan Ave

department: Genetics

institute: Washington University in St. Louis

summary: Some widely used methods to study functional effects of DNA sequence on transcription cannot readily disambiguate these from post-transcriptional impacts of the same element on RNA. Therefore, we developed an approach enabling assessment of DNA/RNA regulatory elements in parallel: Inferred Stability Optimized Massively Parallel Reporter Assay (ISOMPRA). ISOMPRA quantifies pre-spliced RNA to more directly assess transcription rate, and spliced RNA, corrected for transcription rate, to correctly identify RNA stability-altering 3’ UTR elements. We benchmark ISOMPRA with both predicted enhancers and 3’ UTR elements, selected regions containing autism patient mutations. We identify numerous functional enhancers/UTRs, and discover a subset with high impact mutations. We further show failing to consider both potential transcriptional and post transcriptional effects results in numerous false-positives and false-negatives. Finally, we adapt ISOMPRA for in vivo analysis of element effects via AAV transduction. Combined with Cre-dependent priming sites, this permits analyses of both transcriptional and post-transcriptional effects within specific cell types of the brain, and further enables measurement of regulatory impacts of in vivo traits, such as sex.

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus
Adeno-associated virus 9

overall_design: RNA sequencing libraries prepared from mouse RNA and HEK293 cell RNA alongside plasmid and AAV sequenced DNA

first: Anthony

last: Fischer

first: Din

last: Selmanovic

first: Colin

last: Florian

first: Tomas

last: Lagunas

first: Stephen

last: Plassmeyer

first: Lily

last: Meyer


title: Profiling of terminating ribosomes reveals translational control at stop codons

status: Public on Dec 11 2025

city: Ithaca

first: Saori

last: Uematsu

address: 526 Campus Road, Cornell University

department: Division of Nutritional Sciences

institute: Cornell University

summary: Accurate termination of protein synthesis is paramount for the integrity of cellular proteome. Here we establish profiling of terminating ribosomes in mammalian cells and report a wide range of ribosome pausing at individual stop codons. We identify a sequence motif upstream of stop codons that contributes to termination pausing, which was confirmed by massively paralleled reporter assays. Lack of termination pausing increases the chance of stop codon slippage, generating proteins with mixed C-terminal extensions. We demonstrate that the sequence- dependent termination pausing is a result of post-decoding mRNA scanning by the 3’ end of 18S rRNA. We further uncover tissue-specific termination pausing that correlates with the stoichiometry of Rps26, which constrains mRNA:rRNA interaction. Termination pausing represents a translational signature associated with translational control at stop codons.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Ribo-seq under 18S rRNA mutation, RPS26 knockdown, and RPS26 overexpression; Ribo-seq from mouse liver, testis, kidney, brain, and heart.


title: Cardiac Fibrosis in Dilated Cardiomyopathy: Transcriptomics Insights, Histological Correlations, and Organoid Model Verifications

status: Public on Dec 09 2025

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

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

overall_design: Refer to individual Series


title: Single-cell transciptional profiling of thymic hAPCs in perinatal mice

status: Public on Dec 05 2025

city: Nashville

first: Qi

last: Liu

state: Tennessee

address: 2525 WEST END AVE

institute: Vanderbilt University Medical Center

summary: This study carried out single-cell transcriptional profiling of FACS purified thymic hematopoietic antigen presenting  cells (hAPCs) to determine changes in cellular composition and gene signatures in neonatal to perinatal (P00, P03, P07, P10, and P14)  mice.

overall_design: CD45+ MHC-II lo to + hematopoietic APCs (HAPCs) were FACS-isolated from C57BL6/J (WT) mice at postnatal ages P00, P03, P07, P10, and P14 mice to identify transcriptional heterogeneity of hAPCs throughout perinatal stages of thymus growth.

first: Lauren

last: Ehrlich

first: Jayashree

last: Srinivasan

first: Aparna

last: Calindi

last: Moore

first: Ken

last: Lau

first: Bryan

last: Helm


title: Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane

status: Public on Dec 04 2025

summary: Cells tightly control the homeostatic levels and subcellular localizations of membrane phospholipids through the regulation of the activities of numerous lipid-metabolizing enzymes and lipid transfer proteins. Yet, the mechanisms by which lipid imbalances are sensed and corrected to establish and maintain homeostasis are, in many cases, unknown. Here we present an expanded view of plasma membrane phosphoinositide metabolism by revealing an unexpected metabolic connection between two key anionic lipids in this membrane, phosphatidylinositol 4-phosphate (PI4P) and phosphatidic acid (PA). Plasma membrane pools of PI4P are generated by PI 4-kinase Type IIIα (PI4KIIIα/PI4KA), an essential enzyme whose partial dysfunction leads to numerous hereditary human diseases. We find that depletion of PI4P by pharmacological inhibition of PI4KA increases the activity of phospholipase Ds (PLDs) and the levels of their lipid product, PA. Guided by RNA-seq analysis and proximity labeling proteomics, we elucidate how cells connect this PI4P decrease to a compensatory increase in PA levels. Loss of plasma membrane PI4P induces a concomitant decrease of phosphatidylserine (PS) levels, and this metabolic rewiring activates a reciprocal relationship between PS synthesis and PLD-mediated PA generation. These metabolic changes lead to transcriptional and translational upregulation of the small GTPase RhoB, which enhances PLD-mediated PA synthesis and subsequent actin cytoskeletal remodeling. Our study reveals how disease-relevant perturbation of phosphoinositide synthesis induces an integrated response that ultimately boosts levels of a key anionic lipid and metabolic intermediate in phosphoinositide resynthesis.

overall_design: Ribo-seq and mRNA-seq from HEK293T cells treated with GSK-A1 at different timepoints (0, 60, and 360 min).


title: Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer

status: Public on Dec 08 2025

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah


title: Single-nucleus RNA sequencing of male and female brain in a tau P301L transgenic zebrafish

status: Public on Dec 10 2025

city: Esch-Sur-Alzette

first: Mohamed

last: Soudy

address: 2 Avenue de l'Universite

country: Luxembourg

institute: University of Luxembourg

summary: The microtubule-associated protein tau forms pathological aggregates in Alzheimer’s disease and related tauopathies, and animal models are widely used to dissect the cellular processes involved. Transgenic zebrafish expressing human mutant tau provide a vertebrate system in which neuronal tau pathology can be examined, yet single-cell-resolution transcriptomic resources for such models remain scarce. Here we describe a single-nucleus RNA sequencing dataset generated from whole-brain tissue of six-month-old transgenic zebrafish expressing human tau carrying the P301L mutation under a neuron-specific promoter, alongside wild-type controls. Both sexes were profiled, with two replicate libraries per sex and genotype, giving eight libraries in total. Nuclei were isolated from pooled brains, processed with a droplet-based 3′ assay, and sequenced to generate transcriptome-wide expression profiles across the major brain cell types. We provide the raw sequencing reads, processed gene-by-nucleus count matrices, and cell-type annotations. This resource can be reused to study cell-type-specific and sex-resolved transcriptional features of the model and to support comparative analyses with mammalian datasets.

overall_design: We used the Tg(TauP301L-dsRed) transgenic zebrafish line, which expresses human mutant tau (P301L) under the control of the HuC/D promoter, ensuring neuron-specific expression. This model recapitulates key features of human tauopathy, including tau hyperphosphorylation, neurofibrillary tangle formation, and progressive neurodegeneration. Wild-type AB zebrafish served as controls. We used two biological replicates for each condition (transgenic and wildtype control), with two technical replicates for each biological replicate. All zebrafish procedures were conducted under authorization from Luxembourg's Grand-Ducal Decrees (20 January 2016 and 26 January 2023) and adhered to European regulations (Directive 2010/63/EU). Wild-type AB and Tg(TauP301L-dsRed) zebrafish were maintained under standard conditions at 28.5 ± 0.5°C with a 14h light/10h dark cycle. Adult fish (6 months old) were housed at 4-6 fish per liter in 3.5L tanks with controlled water parameters (pH 7.5, conductivity 700-900 μS/cm). Fish were euthanized using buffered tricaine methanesulfonate (MS-222; 250 mg/L) for 15 minutes, and brains were dissected under stereomicroscopic guidance using sterilized tools, immediately flash-frozen in liquid nitrogen, and stored at -80°C until processing. Nuclei isolation was performed using the Minute Single Nucleus Isolation Kit (BN-020, Invent Biotechnologies) with modifications including addition of Protector RNase Inhibitor (3335399001, Roche) at 0.4U/μl before homogenization. Isolated nuclei from three zebrafish brains were pooled per condition, resuspended in PBS with 4% BSA and 0.2U/μl RNase inhibitor, filtered through 20μm filters (04-004-2335, CellTrics), centrifuged, and resuspended in PBS with 2% BSA and 0.2U/μl RNase inhibitor to achieve 1300-1700 nuclei/μl. Single-nuclei RNA sequencing libraries were prepared using the Chromium GEM-X Single Cell 3' Kit v4 (1000686, 10X Genomics) following the manufacturer's protocols with approximately 17,000 nuclei loaded per sample for GEM generation. Libraries were quantified using Qubit Fluorometer 4.0 (ThermoFisher Scientific), size distribution was assessed on Fragment Analyzer 5200 (Agilent), and equimolar pooled libraries were sequenced on NextSeq2000 (Illumina) in the Luxembourg Centre for Systems Biomedicine (LCSB) Genomics platform (RRID: SCR_021931).

first: Varsha

middle: V

last: Murthy

first: Maria

middle: L

last: Cordero-Maldonado

first: Rashi

last: Halder

first: Enrico

last: Glaab


title: Modeling Liver Cancer Molecular and Histological Features by CRISPR Editing of Primary Porcine Hepatocytes

status: Public on Dec 01 2025

city: Chicago

first: Lobna

last: Elkhadragy

state: Illinois

address: 2201 W Campbell Park Dr,

department: Radiology

institute: University of Illinois at Chicago

summary: Preclinical models are essential for advancing therapeutic strategies in hepatocellular carcinoma (HCC), an aggressive disease with poor survival outcomes. Here, we established genetically defined HCC models by ex vivo CRISPR editing of porcine hepatocytes. Hepatocytes were isolated from Yucatan minipigs and subjected to combinations of 2-4 gene alterations, including CRISPR-mediated knockout of tumor suppressor genes (TP53, PTEN, CDKN2A, AXIN1), with or without c-myc overexpression. Edited hepatocytes were expanded in culture, and those harboring at least three gene alterations formed tumors in SCID mice that recapitulated human HCC histologically. Clonal derivatives from the cell pools generated mouse xenograft tumors with distinct liver cancer histological features. Transcriptomic profiling of the cell models and xenograft tumors revealed activation of cell cycle pathways and similarity with human HCC. Further, autologous intrahepatic implantation of edited hepatocytes into pigs produced tumors with prominent immune infiltration, establishing an immune-competent large-animal model of HCC. Collectively, this HCC modeling platform provides insights into cooperative gene alterations underlying HCC pathogenesis and enables preclinical testing of systemic and locoregional therapies in a clinically relevant large-animal context.

overall_design: RNA-seq profiling of primary porcine hepatocytes, cell lines developed by subjecting the hepatocytes to gene alterations, xenograft tumors developed in SCID mice, intrahepatic pig tumors, normal pig liver tissues.

first: Olayinka

middle: G

last: David

first: Caitlyn

last: Castillo

first: Luke

middle: N

last: Redlon

middle: R

last: Jordan

first: Kyle

middle: M

last: Schachtschneider

first: Ron

last: Gaba


title: RNA-Seq of ADAMTS4 knockout mice and WT mice

status: Public on Nov 28 2025

city: Chengdu

first: Ming

last: Chen

state: Sichuan

address: No. 37, GuoXue Xiang, Chengdu, China

country: China

institute: West China Hospital of Sichuan University

summary: RNA-Seq was performed on ADAMTS4 knockout mice and WT mice after 7 days of DSS treatment.

first: Chengwei

last: Tang

first: Zhiyin

last: Huang


title: Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Prediction in Pediatric AML

status: Public on Nov 26 2025

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine


title: Integrating multi-omics data with genome scale metabolic modeling for the analysis of Pseudomonas aeruginosa persister cells

city: Charlottesville

last: Papin

state: Virginia

address: 415 Lane Road Room 2041

department: Biomedical Engineering

institute: University of Virginia

summary: Pseudomonas aeruginosa is a gram-negative bacterial pathogen, capable of forming antimicrobial-tolerant subpopulations known as persister cells. These cells are transient phenotypic variants that can tolerate antimicrobial treatment, and have been associated with chronic infections and the development of antibiotic- resistance. While persister cells are classically associated with reduced metabolic activity, the characteristics of their metabolism are not well understood, especially in the context of biocides. In this work, we performed an experimental and computational systems-level analysis to characterize the metabolic state of biocide persister cells. To accomplish this, we conducted in-depth profiling ofdeeply profiled both wild-type and persister samples of P. aeruginosa with transcriptomic sequencing and metabolomic analyses. These analyses revealed a distinct metabolic repertoire in biocide persister cells, marked by an upregulation in genes associated with activity in central metabolism. Integration of both the transcriptomic datasetdata set with a P. aeruginosa genome-scale metabolic network reconstruction (GENRE) provided condition-specific models, which were used to identify metabolic reactions and genes that differentiated the persister phenotype from the untreated. Experimental testing of model predictions revealed metabolic functions, such as pyrimidine synthesis and methionine recycling, which could serve as potential targets for inhibiting persister cell formation.

overall_design: RNA was extracted from untreated and persister Pseudomonas aeruginosa (PA14) cells immediately before exposure, 5 and 24 hours after exposure to 10X MIC conditions.

first: Anna

middle: S

last: Blazier

first: Glynis

last: Kolling

first: Joseph

last: Ficarrotta


title: Mutant p53 binds RNA to drive mitochondrial dysfunction [CLIP-seq]

status: Public on Nov 25 2025

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

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

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

overall_design: CLIP-seq of p53 bound RNA from HEK cells stably expressing wild-type or mutant p53 constructs. Materials were collected in biological duplicates. HEK cells stably expressing wild-type p53 served as the control.

first: Alice

last: Long

first: Cameron

middle: J

last: Douglas

first: Dalila

last: Gallegos

first: James

last: Burke

first: David

last: MacMillan

first: Ezgi

last: Hacisuleyman

first: Ciaran

middle: P

last: Seath


title: Single-cell RNA sequencing of MCF-7 cells treated with 17-β estradiol or fulvestrant, and fulvestrant resistant derivatives of MCF-7 cells

status: Public on Nov 24 2025

city: Darlinghurst

first: Leila

last: Eshraghi

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: Single-cell RNA sequencing (scRNA-seq) on MCF-7 breast cancer cells treated with fulvestrant or 17-β estradiol, and MCF-7 cell line derivatives made resistant to fulvestrant.

overall_design: High throughput single cell RNA sequencing (RNA-seq) using the Drop-seq method was used to analyse single cell transcriptomes of MCF-7 cells that are treated with fulvestrant, and then released from fulvestrant arrest by the addition of 17-β estradiol. Fulvestrant resistant cell lines were also examined.

first: Catherine

middle: E

last: Caldon


title: RNA-seq for T-REX of NCBP1 (WT)

city: Lausanne

first: Dalu

last: CHANG

state: Not US or Canada

address: EPFL SB ISIC LEAGO, CH A2 397,Station 6

country: Switzerland

institute: EPFL,

summary: In the current project, we aim to study transcriptomics changes coupled to RNA-seq would give us a borad idea of changes in mRNA abundance and splicing events triggered as a result of spatiotemporally controlled NCBP1-specific hydroxynonenylation.

overall_design: T-REX of NCBP1 (WT) was performed in human cell lines, eliciting spatiotemporally controlled NCBP1-specific hydroxynonenylation and three technical negative controls. Each set was performed over four independent biological replicates. RNA was isolated at three time points, 3hrs, 6hrs, or 12 hrs after reaction or controls.

last: Chang

first: Yimon

last: Aye


title: The contribution of Arpc5 for gene expression in intestinal macrophages

status: Public on Nov 20 2025

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

country: United Kingdom

institute: Francis Crick

summary: Patients with loss-of-function mutations in the ARPC5 subunit of the Arp2/3 complex develop inflammation and immunodeficiency after birth, leading to early mortality.  However, the mechanistic basis for these phenotypes remains obscure.  Our work demonstrate that loss of Arpc5 in the murine hematopoietic system causes early-onset intestinal inflammation.  This condition is initiated by microbiota breaching the ileal mucosa, leading to local and systemic inflammation.  Macrophage infiltrate into the ileum, but in the absence of Arpc5 fail to restrict microbial invasion.  So, we wanted to investigate the Arpc5 contribution for intestinal macrophages expression.

overall_design: intestinal content from control and mutant mice was extracted, FACS sorted and sequenced for analysis. The intestines were divided in small intestine and colon. Small intestines were subdivided in intraepithelial and lamina propria phases.

first: Michael

last: Way

first: Luiz

last: Vasconcellos

first: Shaina

last: Huang

first: Emanuele

last: Libertini


title: Neferine improves cardiac remodeling induced by hypertension by modulating multiple signaling pathways --heart

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to compare the differently expressed genes in heart tissue of WKY and SHR with or withoutneferine treatment. The SHRs were randomly divided into 2 groups: SHR, and SHR +neferine (10mg/kg/d) groups . WKY rats  were set as control. Rats in WKY and SHR groups were  intragastrically with double distilled water (dd H2O), while rats in  SHR + neferine (10mg/kg/d) group were intragastrically with 10 mg/kg/d of neferine for 10 weeks.  Then the  heart tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with heart tissue of rats in 3 groups: WKY, SHR, SHR +neferine (10mg/kg/d) treated  to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Meizhu

last: Wu

first: Zhi

last: Guo


title: A RiboCancer cell line panel reveals that CLL-associated Rps15 mutations translationally rewire transcription through codon-specific tRNA accommodation defects

status: Public on Nov 18 2025

city: Leuven

first: Marino

last: Caruso

address: Herestraat 49

department: Oncology

country: Belgium

institute: KULeuven

summary: Various somatic deletions and point mutations targeting ribosomal proteins (RPs) have been identified in cancer. To assess how these affect ribosomal translation, we applied genomewide translatome analysis (proteome, Ribo-seq and total RNA-seq) on an isogenic cell line library modeling the most recurrent RP defects (Rpl5+/-, Rpl11+/- , Rpl22+/- , Rpl22-/-, Rpl10 R98S, Rps15 P131S and Rps15 H137Y). We detected little translational changes in the RP knock-out models. In contrast, RP point mutations were associated with a significant number of translation efficiency changes, reaching up to 10% of expressed genes in Rps15 mutants associated with Chronic Lymphocytic Leukemia (CLL). Further cryo-electron microscopy and biochemical analyses revealed that these Rps15 mutations alter the stability of the C-terminal Rps15 domain, affecting the translation elongation cycle dynamics of these mutant ribosomes, and deregulating accommodation of aminoacylated tRNAs at the ribosomal A-site. Using Ribo-seq and translation reporter assays, we show that this accommodation defect shows codon specificity, explaining the reduced translation efficiency of genes enriched for these codons in Rps15 mutant cells, such as histones. Finally, the genes presenting reduced translation efficiency in Rps15 mutants are enriched for transcriptional regulators such as transcription factor Runx3, resulting in downregulation of Runx3 target genes involved in immune regulation. Overall, this study compares the translational rewiring imposed by the most frequent somatic RP mutations. We provide unprecedented mechanistic insights in the translation defects induced by CLL-associated Rps15 mutations, and reveal an unappreciated cross-talk between translational and transcriptional dysregulation in these RP mutant cells.

overall_design: RNA-seq and RIBO-seq profiling of a RiboCancer cell line panel including CRISPR-CAS9 clones of ribosomal protein defects (WT, Rpl5+/-, Rpl11+/- , Rpl22+/- , Rpl22-/-, Rpl10 R98S, Rps15 P131S and Rps15 H137Y) generated from Ba/F3 mouse cell line.

first: Anaïs

last: Astier

first: Stijn

last: Vereecke

first: Coralie

last: Capron

first: Steven

last: Verbruggen

first: Gerben

last: Menschaert

first: Pierre

last: Close

first: Francesca

last: Rapino

first: Célia

last: Plisson-Chastang

first: Kim

last: De Keersmaecker


title: Sex-specific molecular and cellular phenotypes during resolution of neuropathic pain in dorsal root ganglia

status: Public on Nov 14 2025

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

country: Germany

institute: University Hospital Würzburg

summary: Neuropathic pain, affecting 10% of the general population, poses a significant socioeconomic burden that current treatment options cannot sufficiently cover. While pain naturally resolves in some patients, the mechanisms driving this process remain elusive. we hypothesized that pain resolution modulates multicellular interactions of neurons, satellite glial cells (SGCs), and local macrophages within the dorsal root ganglia (DRGs). Therefore, we aimed to identify molecular and cellular processes that characterize ongoing pain resolution. With behavioral tests, we determined a 50% improvement of the pain phenotype to capture ongoing mechanisms of pain resolution. We expect to see dysregulated signaling mediators in the DRG, as well as channels and components influencing hypersensitivity, as well as regulation of an immune and inflammatory phenotype. Comparing the ipsilateral sides during hypersensitvity and pain resolution, we aim to elucidate pathways that characterize the resolution phase. Based on prior knowledge and imaging data, we expected to initially see a strong immune phenotype, with differences between male and female rats during pain resolution, potentially reflecting a difference in pain prevalence between sexes in the clinic. Pathway analysis of the bulk RNA data confirmed an ongoing immune phenotype in female rats as opposed to males. Top regulated factors after CCI, include many mediators such as NPY, VIP, Gal, IL24 and IL6. Biological processes associated with pain resolution included G-protein coupled receptor signaling, synaptic transmission and regulation of the membrane potential.

overall_design: We analyzed L4 rat DRG, that were harvested and snap frozen in liquid nitrogen after chronic constriction injury (CCI). Experimental groups were male and female rats at 1 week or 5 weeks after CCI, with investigation of both the injured, ipsilateral side and the contralateral side as control.

first: Felicitas

last: Schlott

first: Thorsten

last: Bischler


title: Bruceine A protects nuclear receptor 4A1 from ubiquitin-degradation to alleviate mesangial proliferative glomerulonephritis

status: Public on Oct 30 2025

city: Taipa

first: Huating

last: Hu

address: Avenida WaiLong

institute: Macau University of Science and Technology

summary: The nuclear receptor 4A1(NR4A1) plays a crucial role in maintaining cellular homeostasis and is involved in various disease processes; however, its functional role and pharmacological potential in mesangial proliferative glomerulonephritis (MsPGN) remain unexplored. In this study, we found that downregulation of NR4A1 promotes the pathogenesis of MsPGN by regulating inflammatory and proliferative responses in mesangial cells (MCs), whereas overexpression of NR4A1 reverses these processes. Bruceine A (BA) binds to NR4A1 at residues D481/Q568 and exhibits NR4A1-dependent anti-inflammatory and anti-proliferative effects both in vitro and in vivo. Notably, adeno-associated virus serotype 9 (AAV9)-mediated overexpression of NR4A1 alleviates glomerular injury and inflammatory cascades, while knockout of NR4A1 impairs the renoprotective effects of BA. BA binds to the ligand-binding domain (LBD) of NR4A1 and further sterically blocks K48-linked polyubiquitination at K558, thereby stabilizing NR4A1 protein levels. This stabilization enables NR4A1 to auto-activate its own promoter, amplifying the transcriptional repression of nuclear factor kappa-B (NF-κB) signaling phosphorylation, which ultimately attenuates inflammatory cascades and mesangial proliferation to confer renal protection. This study provides a promising therapeutic avenue for the development of next-generation therapies against MsPGN.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for healthy control group, anti-Thy1 nephritis model group  and its treatment groups (Bruceine A and Olmesartan).

first: Hudan

last: Pan

first: Runze

last: Li

first: Kancheng

last: He

first: Ruimin

last: Tian

first: Chuanghai

last: Zhang

first: Rongrong


title: Gene expression-based, profiles characterizing recurrence sites in surgically treated pancreatic cancer patients

status: Public on Nov 01 2025

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Gene expression characteristics associated with different recurrence patterns were successfully identified through expression profiling of a total of 8,644 genes in 16 pancreatic cancer cases, which had been consecutively operated on within a defiend short period of time

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 16 pancreatic cancer cases, followed up more than two years, was used to acquire expression profiles of a total of 8,644 unique genes, leading to the successful construction of supervised models

first: S

last: Miyahara

first: Y

last: Tomimaru

first: H

last: Takahashi

last: Eguchi


title: Gene expression profile at single cell level of immune cells from ileum of ArpC5 mutant and control mice

status: Public on Nov 13 2025

first: Probir

last: Chakravarty

summary: ArpC5 mutant mice develop spontaneous enteritis. We sought to investigate the gene expression profile in the single cell level to have insight into the pathology observed comparing to control conuterparts.

overall_design: immune cells from small intestine lamina propria (ileum) were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Luiz

last: Ricardo C. Vasconcellos

first: Michael

last: Way


title: A human-specific microRNA controls the timing of excitatory synaptogenesis (time course smallRNA)

city: Zurich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: HEST

institute: ETH Zürich

type: Non-coding RNA profiling by high throughput sequencing

summary: Neural circuit development in the human cortex is considerably prolonged in comparison to non-human primates, a trait that contributes to the remarkable cognitive capacity of modern humans. Here, we explore the regulatory role of non-coding RNAs, which dramatically expanded during brain evolution, in synapse development of human-induced pluripotent stem-cell derived neurons. We found that inhibition of a human-specific microRNA, miR-1229-3p, alters the trajectory of human neuronal maturation and enhances excitatory synaptic transmission. Transcriptome analysis following miR-1229 knockdown revealed a downregulation of mitochondrial DNA (mtDNA) encoded genes. We further show that miR-1229 regulates mitochondrial morphology, mtDNA abundance as well as mitophagy, and that stimulation of mitochondrial metabolism rescues decreased calcium buffering in miR-1229-3p depleted neurons. Accordingly, miR-1229 directly targets an entire network of genes involved in mitochondrial function and ER-associated protein homeostasis. Our findings reveal an important function of human-specific miR-1229-3p in developmental timing of human synaptogenesis and generally implicate non-coding RNAs in the control of human connectivity and cognition.

overall_design: To investigate gene expression during human neuronal differentiation, we differentiated hiPSC into human neurons following an optimized protocol ("igNeurons"). RNA from these differentiations was extracted at seven time points (Day 0, Day 9, Day 15, Day 21, Day 27, Day 33 & Day 40) and sent for "Ribosomal Depletion"- as well as "SmallRNA"- sequencing.

last: Soutschek


title: A human-specific microRNA controls the timing of excitatory synaptogenesis

summary:
Neural circuit development in the human cortex is considerably prolonged in comparison to non-human primates, a trait that contributes to the remarkable cognitive capacity of modern humans. Here, we explore the regulatory role of non-coding RNAs, which dramatically expanded during brain evolution, in synapse development of human-induced pluripotent stem-cell derived neurons. We found that inhibition of a human-specific microRNA, miR-1229-3p, alters the trajectory of human neuronal maturation and enhances excitatory synaptic transmission. Transcriptome analysis following miR-1229 knockdown revealed a downregulation of mitochondrial DNA (mtDNA) encoded genes. We further show that miR-1229 regulates mitochondrial morphology, mtDNA abundance as well as mitophagy, and that stimulation of mitochondrial metabolism rescues decreased calcium buffering in miR-1229-3p depleted neurons. Accordingly, miR-1229 directly targets an entire network of genes involved in mitochondrial function and ER-associated protein homeostasis. Our findings reveal an important function of human-specific miR-1229-3p in developmental timing of human synaptogenesis and generally implicate non-coding RNAs in the control of human connectivity and cognition.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: A human-specific microRNA controls the timing of excitatory synaptogenesis (pLNA dataset)

overall_design: To explore gene expression regulation of candidate microRNAs in human neurons, we differentiated hiPSC into human neurons following an optimized protocol ("igNeurons") for 21 days and inhibited those microRNAs (namely miR-181c-5p, miR-1229-3p and miR-3943) from day 9 on. RNA was extracted from 4 independent differentiations and sent for polyA-RNA sequencing. Neurons treated with a control inhibitor (pLNA-Ctrl) as well as untreated neurons ("Empty") were used as control.


title: DNGR-1 signalling limits dendritic cell activation for optimal antigen cross-presentation

status: Public on Oct 28 2025

summary: Innate immune receptors often induce activation of conventional dendritic cells (cDCs) and enhance antigen (cross-)presentation, favouring immune responses. DNGR-1 (CLEC9A), a receptor expressed by type 1 cDCs (cDC1s) and implicated in immune responses to viruses and cancer, recognises F-actin exposed on dead cell remnants and promotes cross-presentation of associated antigens. Here, we show that recruitment of phosphatase SHIP1, a process governed by a single amino acid residue adjacent to the signalling motif of the receptor, partly explains how DNGR-1 fails to trigger cDC1 activation in vitro. Substituting this residue converts DNGR-1 into an activating receptor but decreases induction of cross-presentation of dead cell-associated antigens. Introducing the reverse mutation into the related receptor Dectin-1 impairs its activation capacity while enhancing its ability to promote cross-presentation. These findings reveal a functional trade-off in receptor signalling and suggest that DNGR-1 has evolved to prioritise antigen cross-presentation over cellular activation, possibly to minimise inflammatory responses to dead cells.

overall_design: DNGR-1 or mutant DNGR-1 expressing MuTuDCs were treated with 12.5 nM DNGR-1 ligand for 6 hours

last: Buck

first: Caetano

last: ReiseSousa


title: A human-specific microRNA controls the timing of excitatory synaptogenesis (time course ribozero)


title: Cellular and molecular mediators of thymic dendritic cell homeostasis

city: Nashville

first: Qi

last: Liu

address: 2525 WEST END AVE

institute: Vanderbilt University Medical Center

summary: To determine changes in cellular composition and gene signatures of hematopoietic antigen-presenting cells (APCs) in thymi harvested from mice where T-cell development is blocked at different maturation stages.

overall_design: 1) CD45+ MHC-II lo to + hematopoietic APCs were FACS-isolated from WT (C57BL6/J), Rag2-/-, B2m-/- and MHC-II-/- mice to determine the role of thymocytes in regulating DC homeostasis and activation (N=2 experimental repeats per genotype). We used scRNA-seq to determine the transcriptional heterogeneity of DCs across the four genotypes. 2) To determine if our flow-validated DC subsets correlate with transcriptional DC clusters, we FACS-isolated 7 DC subsets and labeled each DC subset with a unique TotalSeqBTM hashtag antibody (BioLegend), prior to pooling all subsets for scRNA-seq and hashtag-derived oligonucleotide (HTO) amplification.

first: Ehrlich

last: Lauren

first: Srinivisan

last: Jayashree

first: Liu

last: Qi

first: Lau

last: Ken

first: Helm

last: Bryan


title: DDX5 alleviates osteoarthritic temporomandibular joint by maintaining homeostasis of cartilage metabolism

status: Public on Oct 24 2025

city: 南京

first: liang qingqing

middle: liang qingqing

last: liang qingqing

address: 栖霞区仙林大道163号南京大学仙林校区

institute: 南京市口腔医院

summary: Temporomandibular joint osteoarthritis (TMJOA) is a prevalent musculoskeletal disease without effective therapeutic measure. DDX5 regulated the progression of cancer，immune disease, as well as skin inflammation by activating a series of signal transduction pathways. However, the role of DDX5 in TMJOA has not been reported yet. The distribution of DDX5 in human cartilage was performed by HE, Safranin O and Masson staining. Moreover, the expression of DDX5 was unveiled by immunofluorescent analyses. The role of DDX5 in TMJOA was verified by UAC-induced TMJOA mice and Aggrecan-CreERT; DDX5flox/flox mice. The downstream protein expression profile of DDX5 were examined by RNA-Seq analysis. The DDX5 expression remarkably decreased in the condylar cartilage of patients with TMJOA. DDX5 decreased with cartilage degradation in UAC-Induced TMJOA mice. Cartilage specific DDX5 knockout induced cartilage degeneration. Mechanistically, the inhibition expression of DDX5 accelerates cartilage degeneration by activating NF-κB Signaling. Additionally, DDX5 overexpression alleviated the progression of TMJOA under excessive mechanical stress.

first: Qingqing

last: Liang

first: Ji

last: Jun


title: Single-Cell Transcriptomic Analysis of Periodontal Granulation Tissue from Surgical Patients

status: Public on Oct 23 2025

city: Solna

first: Wentao

last: Zhu

address: 17177 Solna

country: Sweden

institute: Karolinska Institutet

summary: This study profiles single-cell transcriptomes derived from human periodontal granulation tissue collected during routine periodontal surgery at Guy’s Hospital, King’s College London. Tissue was harvested following step 1 and step 2 periodontal treatment. Following dissociation and quality control, libraries were prepared using the 10x Genomics Chromium Single Cell 3’ kit and sequenced on an Nextseq 2000. The study aimed to elucidate cellular heterogeneity in periodontal lesions in otherwise healthy individuals.

overall_design: This study profiles single-cell transcriptomes derived from human periodontal granulation tissue collected during routine periodontal surgery at Guy’s Hospital, King’s College London. Tissue was harvested following step 1 and step 2 periodontal treatment. Following dissociation and quality control, libraries were prepared using the 10x Genomics Chromium Single Cell 3’ kit and sequenced on an Illumina Nextseq 2000. The study aimed to elucidate cellular heterogeneity in periodontal lesions in otherwise healthy individuals.


title: Spatial transcriptomics analysis of normal lung tissues, precursor lung lesions and invasive lung adenocarcinomas

status: Public on Oct 11 2025

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Understanding cellular processes underlying early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies. Here, we performed spatial trancriptomics analysis of human treatment-naive lungs comprising various stages in the sequence of pathogenesis of LUAD including normal lung tissues, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA) and LUAD.

overall_design:
Spatial transcriptomics analysis of samples was done using the Visium CytAssist platform from 10x Genomics. All tissues were surgically resected and formalin-fixed paraffin embedded.

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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: Fuduan

last: Peng

first: Ansam

last: Sinjab


title: Single-nucleus RNA-sequencing (snRNA-seq) analysis of normal lung tissues, precursor lung lesions and invasive lung adenocarcinomas

summary: Understanding cellular processes underlying early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies. Here, we performed snRNA-seq analysis of human treatment-naive lungs comprising various stages in the sequence of pathogenesis of LUAD including normal lung tissues, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA) and LUAD.

overall_design:
snRNA-seq was performed on isolated nuclei from tissue scrolls of formalin-fixed parafin embedded tissues using the 10x Genomics Chromium Fixed RNA protocol.

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

first: Sujuan

last: Yang


title: Whole-exome sequencing of normal lung tissues, precursor lesions and invasive lung adenocarcinomas

type: Genome variation profiling by high throughput sequencing

summary: Understanding cellular processes underlying early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies. Here, we performed whole exome sequencing (WES) of human treatment-naive lungs comprising various stages in the sequence of pathogenesis of LUAD including normal lung tissues, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA) and LUAD.

overall_design:
WES of tissues was performed on DNA isolated from formalin-fixed paraffin embedded tissues using the TWIST-WES protocol. Sequencing was done on the NovaSeq 6000 platform from Illumina.

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


title: Single-cell and spatial transcriptomics analysis of tobacco-associated lung adenocarcinoma development, and in response to targeting inflammation alone or in combination with immune checkpoint blockade in precancerous phase [Spatial transcriptomics]

summary: Understanding cellular processes underlying early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies. Here, we performed single-cell RNA sequencing (scRNA-seq) of mouse lungs from Gprc5a−/− mice during lung tumor development and also following therapeutic targeting of inflammation (IL-1𝛽) alone and in combination with immune checkpoint blockade in precancerous stages. We coupled scRNA-seq analysis with spatial transcriptomics of mouse lungs under different conditions.

overall_design: Gene expression profiling by high throughput single-cell sequencing and spatial transcriptomics


title: Single-cell and spatial transcriptomics analysis of tobacco-associated lung adenocarcinoma development, and in response to targeting inflammation alone or in combination with immune checkpoint blockade in precancerous phase [scRNA-seq]


title: Dual role of Oct4 and Sox2 in controlling the developmental capacity and timing of tissue morphogenesis in the embryonic lineage

status: Public on Oct 10 2025

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

institute: Max Planck Institute for Molecular Biomedicine

summary: Here, we molecularly defined Sox2 KO at single-cell resolution, revealing hidden transcriptional dynamics that govern epithelial morphogenesis via tight junction assembly and organisation of actomysin, cadherin and integrin-mediated binding.

overall_design: Approximately 13 blastocysts from each replicate – one replicate of control and an two replicates of Sox2 MZ KO embryos from E4.5 were collected and analyzed using sc-RNA seq.

first: Deepthi

last: Chandramohan

first: Katja

last: Mueller

first: Rongge

last: Yan

first: Ivan

last: Bedzhov


title: Catch and release of sialoglycoRNAs enables sequencing-based profiling across cellular and extracellular material

status: Public on Oct 05 2025

city: Boston

first: Ryan

middle: A.

last: Flynn

state: MA

address: 1 Blackfan Circle

department: Department of Pediatrics

institute: Boston Children's Hospital

summary: Glycosylated RNAs (glycoRNAs) represent a recently discovered class of small RNAs, but their systematic characterization has been limited by reliance on metabolic chemical reporters and high RNA input requirements. Here we present rPAL sequencing (rPAL-seq), a sensitive and selective platform for de novo discovery of sialoglycoRNAs. rPAL-seq combines enhanced periodate oxidation of sialic acids with a capture–release workflow and optimized library construction using poly(A) extension coupled with template-switching reverse transcription. The method enabled reproducible profiling from less than 100 ng of input RNA, corresponding to less than 2% of the material required by previous approaches. When applied across 13 human cell lines, rPAL-seq identified lineage-associated glycoRNA patterns alongside a conserved core dominated by uridine-rich snRNAs and snoRNAs, with modification signatures implicating glycosylation on acp³U or related uridine-based modifications. Extending to extracellular fractions, rPAL-seq revealed secreted glycoRNA profiles distinct from those of the cellular fraction. rPAL-seq provides a robust, scalable strategy for glycoRNA profiling, opening new avenues for studying this emerging biopolymer.

sample_organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

overall_design: This study aimed to profile sialoglycoRNA from diverse human and animal cell lines using rPAL-seq, a sequencing method first introduced in this study that combines enhanced reductive periodate–aminoxy labeling with sialidase-specific elution. Cells (including HeLa, A549, 293T, Huh7, LPS853, LN308, OCI-AML2, OCI-AML3, Molm13, Jurkat, Jeko1, Nalm6,  DiFi, MDCK, and EMT6) were cultured under standard conditions. Extracellular vesicles (EVs) and non-vesicular extracellular nanoparticles (NVEPs) were isolated from conditioned medium of DiFi and MDCK using previously established protocols. For each biological sample, sialoglycoRNA was captured and processed in 3 parallel groups: IP (VC sialidase–eluted), Control (mock elution with heat-inactivated enzyme), and Input (1% reserved prior to elution). Libraries were prepared using the rPAL-seq workflow and sequenced on an Illumina NovaSeq X platform with single-end 100 bp reads.

first: Ruiqi

last: Ge

first: Dennis

middle: K

last: Jeppesen

first: Sandeep

last: Rai

first: Robert

last: Coffey

middle: A


title: Programmable mRNA translation initiation by trans-RNA

status: Public on Oct 02 2025

city: Ithaca

first: Saori

last: Uematsu

address: 526 Campus Road, Cornell University

institute: Cornell University

summary: The ability to modulate specific gene expression is crucial for interrogating, perturbing, and engineering cellular systems. A wide range of approaches have been developed for gene silencing, but few tools are available to activate individual mRNAs for translation inside cells. 16Guiding ribosomes to specific start codons without altering the original sequence remains a formidable task. Here we design capped trans-RNAs capable of engaging ribosomes to specific initiation sites on individual mRNAs. By positioning the trans-cap near the target start codon, the 19anti-parallel trans-RNA enables the ribosome to select nearby start codons in a simple, specific, robust, and tunable manner. Structural and biochemical data suggest that the capped trans-RNA facilitates ribosome loading and scanning on the target mRNA via a synergistic mechanism. The trans-RNA also acts independently of the original cap, enabling translation of circular RNAs lacking internal ribosome entry sites. We demonstrate that trans-RNAs can be applied in vivo to 24achieve programmable alternative translation of endogenous genes in mouse liver. Finally, we discover the existence of naturally occurring trans-RNAs that differ from antisense RNAs by activating translation of endogenous mRNAs. The discovery and the application of trans-RNAs in programmable mRNA translation holds great potential in advancing fundamental and applied biology.

overall_design: Ribo-seq of HEK293 cells transfected with trans-RNAs targeting the main ORF of ATF4; Total and capped small RNA-seq of HEK293 cells; RNA-seq of mouse liver


title: Single Cell Transcriptional Perturbome in Pluripotent Stem Cell Models

status: Public on Sep 30 2025

city: Torino

first: Elisa

last: Balmas

address: via Nizza 52

country: Italy

institute: University of Torino

summary: Functional genomics screens in human induced pluripotent stem cell (hiPSC) models offer immense potential yet remain challenging. We developed iPS2-seq: iPS-optimized inducible Postranscriptional Silencing in pool deconvoluted by single cell sequencing. This method allows phenotype-agnostic screens in hPSCs and their derivatives through loss-of-function perturbations that are mRNA-depleting (bypassing genotoxicity), clonally traced (controlling genetic and epigenetic variability), single cell aware (accounting for asyncronous and heterogeneous differentiation), isogenic engineered (preventing silencing), inducible and reversible (enabling stage-specific studies and robust control-treatment paired analyses). iPS2-seq is compatible with both commercial microfluidics and homebrew split-pool scRNA-seq protocols, enabling screens with different scales, costs, and input materials. A dedicated bioinformatics pipeline, catcheR, supports iPS2-seq design and analysis. We demonstrate this by studying congenital heart disease-associated genes in hiPSC-derived monolayer cardiomyocytes and cardiac organoids, identifying a key role for SMAD2 in cardiomyogenesis. iPS2-seq strengthens and democratizes access to functional single cell genomics in and beyond hiPSC-derived organoids.

overall_design: Proof of principle and testing experiments on sci-RNAseq iPS2-seq have been performed on two batches of hPSC-derived cardiomyocytes at day 21 and 25, respectively. Cells have been treated with Tetracycline throughout differentiation. For this experiment it was used a 2-level of indexing sci-RNAseq protocol (Cao J. et. al, Science 2017). During RT and PCR indexing steps, additional primers have been used to enrich for UCI and shRNA barcodes for the iPS-2 seq pipeline. Sequencing has been performed on a NextSeq 500 with a High Output kit 75 cycles. Read1, 18 cycles; Index1, 10 cycles; Index2, 10 cycles, Read2, 52 cycles.

first: Maria

last: Ratto

first: Alessandro

last: Bertero

first: Kirsten

last: Snijders


title: Transcriptomic profile and validation of the protective role of celecoxib on cirrhotic splenomegaly

status: Public on Sep 28 2025

city: Chengdu

first: Shihang

last: Tang

address: GUOXUE 37

institute: West China hospital

summary:
Splenomegaly can exacerbate liver cirrhosis and portal hypertension. We have previously demonstrated that cyclooxygenase-2 (COX-2) inhibitor can attenuate cirrhotic splenomegaly. However, the mechanism of cirrhotic splenomegaly remains unclear and is the focus of this study.
Material and methods: Intraperitoneal injection of thioacetamide (TAA) was used to induce cirrhotic splenomegaly. Thirty rats were randomized into the control group. TAA and TAA+Celecoxib groups. Splenic gene profiling was analyzed by high-throughput RNA sequencing. Histological analysis of spleen tissue was evaluated by H&E, Sirius red, Prussian blue staining, and transmission electron microscopy. The splenic mRNA levels of collagen III and α-SMA and splenic contents of Ki-67, VEGF, IL-6, and TNF- were quantified.
Results: A total of 1461 differentially expressed genes (DEGs) were identified in the spleens of the TAA group compared to the control group. The immune response and immune cell activation might be the major signaling pathways involved in the pathogenesis of cirrhotic splenomegaly. With its immunoregulatory effect, celecoxib can ameliorate cirrhotic splenomegaly and liver cirrhosis. Furthermore, 304 coexisting DEGs were obtained between TAA vs. control and TAA+celecoxib vs. TAA. According to GO and KEGG analyses, celecoxib may attenuate cirrhotic splenomegaly by suppressing splenic immune cell proliferation, inflammation, immune regulation, and fibrogenesis. The impacts of celecoxib on splenic immune cell proliferation, inflammation, immune regulation, and extracellular matrix were then validated by the decreased splenic Ki-67-positive cells, macrophages, fibrotic areas, and mRNA levels of collagen III and α-SMA.
Conclusions: Celecoxib attenuates cirrhotic splenomegaly by inhibiting splenic immune cell proliferation, inflammation, and fibrogenesis. The current study sheds light on the therapeutic strategy of liver cirrhosis by targeting splenic abnormalities and provides COX-2 inhibitors as a novel medical treatment for cirrhotic splenomegaly.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for spleens from control group, TAA group and TAA+Celecoxib group

first: Yanting

last: Ye

first: Yang

last: Tai

first: Chong

last: Zhao

first: Zhiyin

last: Huang

first: Chengwei

first: Jinhang

last: Gao


title: snRNA-seq dataset for "Morphine regulates astrocyte transcriptional dynamics by stimulation of glucocorticoid signaling"

status: Public on Sep 22 2025

city: Birmingham

first: Jeremy

last: Day

state: Alabama

address: 1825 University Blvd SHEL 910

department: Neurobiology

institute: University of Alabama at Birmingham

summary: This dataset contains single-nucleus RNA-seq results from rat ventral tegmental area brain tissue in a chronic pain model with morphine administration.

overall_design: This experiment contains 28 biological samples, which represent four experimental groups of rats. To assess neuropathic pain response, Complete Freund’s Adjuvant (CFA) or saline vehicle (100 µl) was injected into the plantar surface of one hind paw of male and female rats (n = 3-4/sex/treatment group). Mechanical sensitivity was then evaluated 48 hours and 7 days after the injection using the Von Frey assay. 7 days after CFA injection, rats received either morphine (10mg/kg) or saline injections I.P., generating a 2x2 experimental design (Veh-Sal, Veh-Mor, CFA-Sal, CFA-Mor). One hour after injections, animals were euthanized prior to rapid decapitation. Brains were blocked in 1mm sections, and VTA tissue was obtained and flash frozen, and stored at -80°C prior to nuclei isolation. Following FACS-assisted nuclei isolation and quantification, a total of 8,000 nuclei pooled from two rats (4,000 male nuclei/4,000 female nuclei from the same treatment group) and were loaded into individual wells of the Chromium NextGem Single Cell Chip (10x Genomics, catalog no. 10000121) and processed on the 10X Genomics Chromium Controller. Libraries were constructed according to manufacturer’s instructions for Chromium Next GEM single cell 3’ library and gel bead kit (10x Genomics, v3.1 single index, catalog no. 10000121, version 3 chemistry). Libraries were sequenced on an Illumina NovaSeq6000 (S2 flow cell)  to an average read depth of ~42,000 read pairs per nuclei. Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.

first: Jennifer

last: Tuscher

last: Phillips III

first: Catherine

last: Newman

first: Guy

last: Twa

first: Lara

last: Ianov

last: Sorge


title: Identification of a shared drug-tolerant persister program in triple-negactive breast cancer across treatments and patients [scRNA-Seq]

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

summary: Acquisition of resistance to anti-cancer therapies is a multistep process, which initiates with the survival of drug tolerant persister cells. Understanding the mechanisms driving the emergence of drug tolerant persister cells remains challenging, primarily because of their limited accessibility in patients. Here, using multiple patient-derived models to isolate persister cells, we show these cells are transcriptionally plastic in vivo and return to a common treatment-naïve like state upon relapse, regardless of the treatment they have been exposed to. We reveal hallmarks of the persister state in TNBC across treatment modalities: high expression of basal keratins together with activation of a stress response and inflammation pathways. HER2+ breast and lunger cancer cells also activate these hallmarks of drug tolerance in response to targeted therapies. Leveraging gene regulatory networks, we identify AP-1, NFKB and IRF/STAT as the key drivers of this hallmark persister state. As a proof of concept, we show that FOSL1 - an AP-1 member - is sufficient to drive cells to the persister state by binding enhancers and reprogramming the transcriptome of cancer cells. On the contrary, cancer cells without FOSL1 have a decreased ability to reach the persister state. By defining hallmarks of drug persistence to multiple therapies of the standard of care in TNBC, our study provides a resource to design novel combination therapeutic strategies to limit resistance. All datasets produced for this study are available and deposited on GEO at : GSE280454, GSE280455, GSE303200, GSE303201 & GSE303203

overall_design:
scRNAseq of HBCx39, HBCx95, HBCx172, HBCx221 and HBCx218 Patient Derived Xenograft (PDX) of Triple Negative Breast Cancer (TNBC) in response to chemotherapies (Capecitabine and Anthracyclines

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Raw FASTQ files are not publicly available due to patient data privacy considerations.
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first: Léa

last: Baudre

first: Grégoire

last: Jouault

first: Elisabetta

last: Marangoni

first: Justine

last: Marsolier


title: Identification of a shared drug-tolerant persister program in triple-negactive breast cancer across treatments and patients [array]

overall_design: Gene expression data (Affymetrix) of HBCx10 and HBCx33 Patient Derived Xenograft (PDX) of Triple Negative Breast Cancer (TNBC) in response to chemotherapies (Capecitabine, Cisplatin and Anthracyclines)   >>> Raw data not provided due to patient privacy concerns <<<


title: Identification of a shared drug-tolerant persister program in triple-negactive breast cancer across treatments and patients [RNA-Seq]

overall_design:
RNAseq of HBCx14 Patient Derived Xenograft (PDX) of Triple Negative Breast Cancer (TNBC) in response to chemotherapies (Cisplatin, Carboplatin and Anthracyclines)

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Raw FASTQ files are not publicly available due to patient data privacy considerations.
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title: Identification of a shared drug-tolerant persister program in triple-negative breast cancer across treatments and patients [CUT&Tag]

overall_design: CUT&Tag was performed on a pool of samples of MDA-MB-468, WT or GOF (HA and VPR), treated with DMSO or 5-FU, for H3K27ac and FOSL1.


title: Transcriptomic analysis of budding yeast with re-engineering acetyl coenzyme A metabolic pathways that prevent senescence

status: Public on Sep 19 2025

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

summary: mRNA sequencing was performed on young and 48h aged MEP yeast in wild type, acc1S1157A, PGPD-SAK1, acc1S1157A PGPD-SAK1, and ALD6 deletion cells, asa well as wildtype with oleic acid

overall_design: MEP cells were collected at log or aged (48h) before being collected, ethanol fixed, and purified using the MEP protocol.

first: Hanane

last: Hadj-Moussa

first: Megan

last: Ulusan

first: Dorottya

last: Horkai

first: Jonathan

last: Houseley


title: Deep longitudinal immune profiling reveals reprogramming of memory T cells that links to B cell dysregulation with age.

status: Public on Sep 12 2025

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: Immune aging is a dynamic process shaped by time and external perturbation. Here, we sought to untangle the complexity of the healthy human immunity across age using deep molecular profiling. Applying our new Healthy Immune Cell Atlas, we profiled the transcriptional dynamics of peripheral immune cells in a longitudinal cohort of ~100 healthy young and older adults followed over 2 years, both under homeostasis and perturbation induced by vaccination, building a scRNA-seq dataset of more than 13.5 million PBMCs. From these data, we revealed that T cells exhibit substantially more age-related changes in transcription at homeostasis than other immune cell subsets, which persist both over time and across age and are distinct from those associated with biological sex or CMV infection status. B cells, which demonstrated few age-related differences at homeostasis, had numerous and persistent changes in vaccine-induced responses with age linked to an age- and GATA3-related transcriptional skewing in the central memory CD4 T cell compartment of older adults. Our study collectively highlights that gradual, age-related alterations in the homeostatic transcriptional networks in immune cells leads to shifts in the landscape of immune responsiveness as we age. This rich resource is further provided with data exploration tools at https://explore.allenimmunology.org/.

overall_design: A cohort of healthy participants aged 40-89+ was recruited for this study in the greater Palo Alto, CA area. A subset of 235 donors was selected from a larger pool of 800+ donors to represent our confirmatory cohort. This sample subset comprises 136 female and 98 male donors spanning ages 40-89+. The ethnicities of the donors include 132 Caucasians, 49 Asians, 12 African Americans, 4 American Indians, 2 Pacific Islanders, and 35 others. The population distribution was selected to be representative of Palo Alto, CA. Blood was collected from all participants at a single time point and PBMCs were isolated. PBMCs were assayed using the 10x flex scRNA-seq chemistry.

first: Qiuyu

last: Gong

first: Emma

last: Kuan

first: Mehul

last: Sharma

first: Marla

last: Glass

first: Aishwarya

last: Chander

first: Mansi

last: Singh

first: Lucas

middle: T

last: Graybuck

first: Zachary

last: Thomson

first: Christian

last: LaFrance

first: Samir

last: Zaim

first: Tao

last: Peng

first: Lauren

middle: Y

last: Okada

first: Palak

last: Genge

first: Cate

last: Speake

first: Thomas

middle: F

last: Bumol

first: Ananda

middle: W

last: Goldrath

first: Troy

last: Torgerson

first: Xiao-jun

last: Li

first: Peter

last: Skene

first: Jane

middle: H

last: Buckner

first: Claire

last: Gustafson


title: Identification of a shared drug-tolerant persister program in triple-negative breast cancer across treatments and patients [CITE-seq]

first: Céline

last: Vallot

overall_design: CITE-seq was performed on a pool of 5 samples MDA-MB-468 (GOF VPR control, VPR FOSL1 gRNA2, VPR FOSL1 gRNA3, HA control and HA FOSL1)

first: Léa

last: Baudre

first: Grégoire

last: Jouault

first: Justine

last: Marsolier


title: Pre-Treatment peripheral Immune composition can accurately predict CAR-T outcomes in patients with Large B-Cell Lymphoma

status: Public on Sep 14 2025

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Chimeric Antigen Receptor (CAR)-T cell therapy has revolutionized the treatment landscape for relapsed/refractory B-cell malignancies. Despite its success, approximately 60% of patients experience treatment failure, underscoring the need to better understand the determinants of response and resistance. We performed single-cell RNA-sequencing of pre-treatment peripheral blood samples and anti-CD19 CAR-T products from 57 diffuse large B-cell lymphomas (DLBCL), correlating molecular and cellular features with clinical outcomes. At the time of leukapheresis, responders presented elevated levels of CD16+ monocytes and CD4+ effector memory T cells. In contrast, non-responders showed an inflammation-driven gene expression signature across T-cell and myeloid compartments, marked by upregulation of TNF-α response signaling pathways. Notably, the presence of malignant or healthy B cells (13 of 57 patients) was strongly associated with a favorable response. These findings shed light on the immune landscape conducive to successful CAR-T therapy and offer a molecular framework for developing personalized tools to improve patient selection, stratification, and the design of next-generation CAR-T treatments.

overall_design:
We performed single-cell RNA sequencing of CD45+ sorted PBMC samples collected at the time of leukapheresis from 57 Diffuse Large B Cell patients, and their matching infusion product, receiving anti CD19 CAR-T products axicbtagene ciloleucel (axi-cel), tisagenlecleucel (tisa-cel) , and a Point-of-Care CD28 -costimulation based product, and correlated their molecular and cellular features with treatment outcome.
Please note that the Bulk_* samples were only used as a reference genome to demultiplex the cells from the 10x sequencing.
Code supporting the analyses performed in this paper is available at https://github.com/AmitLab/CAR_T.

first: Gurevich-Shapiro

last: Anna

first: Zwicky

last: Pascale

first: Winter

last: Eithan

first: Zada

last: Mor

first: Shapira

last: Noam

first: Barboy

last: Oren

first: Chalan

last: Paulina

first: Sharet-Eshed

last: Reut

first: Kedmi

last: Merav

first: Florian

last: Ingelfinger

first: Truong-San

last: Phan

first: David

last: Eyal

first: R

last: Shouval

first: D

last: Luan

last: Sandeep

first: M

last: Shapiro

first: O

last: Itzhaki

first: Accav N

last: Golan

first: A

last: Avigdor

first: Avivi

last: Irit

first: Weiner

last: Assaf

first: Ram

last: Ron

first: Amit

last: Ido


title: Transcriptomic profiling of right ventricular remodeling in MCT rat model treated with CM5480

status: Public on Sep 16 2025

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary: To better understand the molecular mechanisms of CM5480 treatment in MCT rats, a RNA sequencing analysis was performed in right ventricles (RV) tissues collected from 5 control-vehicle, 5 control-CM5480, 5 MCT-vehicle, 5 MCT-CM5480 rats.

overall_design: mRNA profiles of RV tissues from control and MCT rats treated with vehicle or CM5480

first: Fabrice

last: Antigny

first: Anaïs

last: Saint-Martin-Willer

first: Grégoire

last: Ruffenach


title: C5a-C5AR1 axis as a potential trigger of the rupture of intracranial aneurysms

status: Public on Sep 08 2025

city: Nishi-Shinbashi, Minato-ku

first: Tomohiro

last: Aoki

state: Tokyo

department: Pharmacology

institute: Jikei University School of Medicine

summary: Subarachnoid hemorrhage due to rupture of intracranial aneurysm (IA) still has poor prognosis once after the onset in spite of modern technical advancement in medical care. The development of the novel therapeutic strategy based on molecular machineries regulating the rupture is thus mandatory for social health. Here, recent studies have clarified the potential role of neutrophil-mediated inflammatory responses in the process leading to rupture. Thereby, factors mediating the recruitment of neutrophils in situ could be the therapeutic targets to prevent rupture of IAs. In the present study, complement C5a receptor 1 (C5AR1) was picked up as the candidates from comprehensive gene expression profile data. The induction of C5AR1 in IA lesions exclusively in rupture-prone or ruptured lesions was then confirmed in immunohistochemistry. The ligand of C5AR1, C5a, was induced through the enzymatic digestion by tissue-type Plasminogen Activator and, intriguingly, forms the auto-amplification in C5a-C5AR1 axis to exacerbate neutrophil infiltration and resultant neutrophil-mediated inflammation in situ, which triggers rupture of IAs. In conclusion, we have, in the present study, examined potential factors mediating the infiltration of neutrophils into IA lesions and then identified C5a-C5AR1 axis. This cascade could become the therapeutic target to prevent rupture of IAs.

overall_design: To investigate the difference of gene expression patterns between intracranial aneurysms and normal intracranial arteries in rats

first: Kampei

last: Shimizu


title: Effects of Gestational and Lactational Exposure to Perfluorohexanoic Acid on the cerebellar transcriptome

status: Public on Sep 03 2025

city: Rochester

first: Ania

last: Majewska

state: NY

address: 601 Elmwood Ave.

department: Neuroscience

institute: University of Rochester

summary: Legacy per- and polyfluoroalkyl substances (PFAS) have been associated with immune, endocrine, and neurotoxicity following gestational exposures. As a result, industries have effectively replaced them with next generation PFAS, including perfluorohexanoic acid (PFHxA). PFHxA is increasingly found in the serum of pregnant women and in breast milk, and adult human post-mortem studies indicate that PFHxA is found in the brain, with highest concentrations in the cerebellum and hypothalamus. Despite evidence of gestational, lactational, and nervous system exposure to PFHxA, developmental neurotoxicity (DNT) testing in mammals has not been conducted. For DNT evaluation, we exposed pregnant C57Bl/6J mice daily from gestational day 0 through postnatal day (P) 21 to two PFHxA exposure levels (a lower (0.32 mg/kg of body weight (bw)), or higher (50 mg/kg of bw) dose of PFHxA) or ddH20 using treat based administration. Given the high PFHxA levels in cerebellum and protracted developmental window, acute transcriptional dysregulation and cellular morphology of the cerebellum was assessed on the last day of exposure at P21. Using bulk-RNA sequencing, overall PFHxA showed subtle effects in transcripts related to neurons and glia, with females having a greater number of dysregulated transcripts than males. Using immunohistochemistry, we found that Purkinje cell linear frequency was increased in specific lobules in the higher exposure group and that microglial morphology underwent subtle changes in specific cerebellar layers in the lower exposure group in both sexes. Together these data suggest that PFHxA exposure may have lobule specific impacts on the development of both neurons and glia in the cerebellum, highlighting the importance of studying the neurotoxicity of PFHxA in both sexes.

overall_design: C57Bl6J pregnant mice were exposed to control, 0.32 mg/kg of bw (lower), or 50 mg/kg of bw (higher) exposures of PFHxA from gestational day (GD) 0 through postnatal day (P) 21 resulting in in utero and lactational exposure to PFHxA. On P21, offspring were euthanized and whole cerebella were dissected and prepared for bulk-RNA sequencing.

first: Elizabeth

middle: C

last: Plunk

first: Linh

last: Le

first: Marissa

last: Sobolewski


title: Gene Expression Data from the Hippocampus of Mice Subjected to Tail Suspension Test

status: Public on Sep 01 2025

city: Tsukuba

first: Hisako

last: Iwahashi

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary:
This study investigates the functional effects of pine needle (PN) extract on depressive-like behavior in a tail suspension test model.
Gene expression profiling was conducted in the hippocampus of control, LPS-induced, and LPS plus PN-treated mice to explore the potential neuroprotective effects of PN.

overall_design: Total RNA was extracted from the hippocampus using an ISOGEN (Nippon Gene Co. Ltd., Tokyo, Japan) following the manufacturer's instructions. Total RNA concentration was determined using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA).Microarray analysis was performed on RNA samples extracted from the hippocampus of mice subjected to the TST, control (water treatment), LPS groups and 50 mg/kg PN administration groups. The Clariom S assay Mouse system (Thermo Fisher Scientific K.K., Tokyo, Japan) was used for triplicate RNA samples from each group. According to the user manual, cDNA for microarray analysis was generated using a GeneChip WT Plus Reagent kit (Thermo Fisher Scientific K.K.). The samples were hybridized using a Clariom S GeneChip Microarray Kit for mouse (Thermo Fisher Scientific K.K.). After washing and staining, images were captured, and raw intensity data were generated using a GeneChip Scanner 3000 (Thermo Fisher Scientific K.K.).Raw image data processing and normalization were performed using Transcriptome Analysis Console (TAC) software version 4.0.2 (Thermo Fisher Scientific, MA, USA) following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. The gene-level analysis was then performed employing the Limma Bioconductor package included with TAC 4.0.2. A one-way ANOVA was applied to identify the differentially expressed genes (DEGs), followed by an empirical Bayes correction to enhance the statistical reliability of the results.A detected above background (DABG) cutoff of 0.05 was set to refine the analysis further to eliminate non-significant signals. Additionally, the positive vs. negative area under the curve (AUC) value was conservatively set at greater than or equal to 0.7 to focus on genes with strong discriminatory potential.The final selection of DEGs was based on stringent filter criteria, requiring a p-value of less than 0.05 (calculated using one-way between-subject ANOVA). −1.2 > linear fold change > 1.2.

first: Farhana

last: Ferdousi

first: Shinji

last: Kondo


title: Intestinal and mesenteric artery formation by intestine-derived prearterial endothelial cells

status: Public on Aug 29 2025

first: Kai

last: Kruse

summary: The cellular and molecular mechanisms mediating arterial development remain little understood for most organs. Here, we show that a small subpopulation of endothelial cells inside the intestinal villi of the embryonic mouse, characterized by the expression of endothelial cell-specific molecule 1 (Esm1/endocan), serves as an arterial progenitor population. The specification of arterial progenitors is initiated inside the villus capillary network and contributes to the formation of intestinal and mesenteric arteries during development.

overall_design: E18.0 embryos were collected following Esm1-CreERT2-mediated lineage tracing for 24 hours. Unsorted total intestinal cells and unsorted total mesenteric cells were isolated from 3 pooled embryos and CD31+GFP+ and CD31+GFP- FACS-sorted intestinal blood ECs were isolated from 13 pooled embryos. Single cell RNA isolation was performed utilizing BD rhapsody.

first: Esther

last: Bovay

first: Emma

last: Watson

first: Vishal

last: Mohanakrishnan

first: Mark

middle: L

last: Kahn

first: Ralf

last: Adams


title: Endothelial plasticity in atrial fibrosis by integrating single-cell sequencing and genetic lineage tracing

status: Public on Aug 27 2025

city: Beijing

first: Xiaoyi

last: Wang

address: No.167, Beilishi Road, Xicheng District, 100037

department: Department of Cardiovascular Surgery, Fuwai Hospital

institute: Fuwai Hospital, National Center for Cardiovascular Diseases

summary:
Background and aims: Atrial fibrosis represents a critical determinant in atrial fibrillation (AF) pathogenesis. Although endothelial dysfunction is a hallmark feature of AF, the precise mechanisms by which endothelial cells (ECs) contribute to atrial fibrosis remain incompletely understood.

Methods: This study employed single-cell RNA sequencing (scRNA-seq) to analyze intercellular communication networks in atrial tissues from both sinus rhythm (SR) and AF patients. Cdh5-CreERT2;RFP mice were generated to track endothelial plasticity following transverse aortic constriction (TAC). Cell-cell interactions were investigated using isolated human primary atrial ECs and fibroblasts (FBs) in vitro. To elucidate the regulatory role of endothelial-derived TGF-β1 on FB function, endothelial-specific Tgf-β1 knockout (Tgf-β1ECKO) mice were generated.

Results: scRNA-seq analysis identified ECs as predominant signal-sending cells with extensive FB connectivity in both SR and AF atrial tissues. During fibrosis progression, ECs displayed significant mesenchymal activation at the transcriptional level. However, immunofluorescence and high-content screening revealed minimal complete endothelial-to-FB transition. Cell-cell communication analysis and in vitro studies identified TGF-β1 as the key mediator through which mesenchymal-activated ECs (EndoMA) promoted FB proliferation and collagen production. Notably, endothelial-specific Tgf-β1 deletion attenuated TAC-induced atrial fibrosis and reduced AF susceptibility.

Conclusions: Our findings demonstrate that EndoMA-derived TGF-β1 critically regulates FB function and drives atrial fibrosis progression. Targeting endothelial-specific pathways represents a promising therapeutic strategy for attenuating atrial fibrosis in AF pathogenesis.

overall_design:
Human: Single cell sequencing from heart donors with sinus rhythm and patients with atrial fibrillation;  Mice: Single cell sequencing from C57BL/6 J Cdh5-CreERT2/RFP  mice performed transverse aortic constriction or sham surgery.

***Raw data for human samples will be submitted to the Genome Sequence Archive for Human due to patient privacy concerns***

UPDATE
[Jun-24-2026] The associations between the GSM records and the processed data files were corrected.

first: Zhiwei

last: Zeng

first: Jianqiu

last: Pei

first: Peng

first: Jun

last: Li

first: Fangzhou

first: Juncheng

first: Yan

last: Zhao

first: Chunyu

last: Yu

first: Hanning

last: Liu

first: Zhe

last: Zheng


title: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7) [I36]

status: Public on Aug 19 2025

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: This study is part of the immgenT Open Source Project, specifically from IGT36, which focuses on a pan-organ and time course analysis of T cells in acute LCMV (Armstrong) infection at day 7 post-infection. The dataset includes T cells isolated from multiple organs: spleen, prostate, submandibular gland, bone marrow, mesenteric lymph node, small intestine epithelium, small intestine lamina propria, lung, and mediastinal lymph node. 7-week-old male C57BL/6J mice infected intraperitoneally with 2×10^5 PFU LCMV Armstrong, and T cells were analyzed at 60 days post-infection (dpi). The study includes both endogenous T cells and adoptively transferred P14 and SMARTA TCR transgenic T cells. Mice received IV 100,000 SMARTA (CD45.1.2) and 50,000 P14 (CD45.1) T cells one day before infection.

overall_design: T cells were isolated from individual organs using mechanical dissociation, enzymatic digestion (collagenase I or DTE), and anti-CD45 intravenous labeling to distinguish tissue-resident from circulating cells. Sorted CD3e+ or IV- CD3e+ were profiled using single-cell RNA sequencing (10x Genomics), combined with CITE-seq (TotalSeq C) and paired TCR α/β sequencing. Samples were pooled using hashtags.

first: Giovanni

last: Galletti

first: Sara

last: Quon

first: Nicole

last: Scharping

first: Kennidy

last: Takehara

first: Amir

last: Ferry

first: Ananda

last: Goldrath

first: Ian

last: Magill

first: David

last: Zemmour

first: Christophe

last: Benoist


title: Bronchoalveolar lavage of healthy human adults after LPS exposure

status: Public on Aug 14 2025

city: Denver

first: Elizabeth

last: Wynn

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

summary: Rationale: Macrophages are both drivers of dysregulated inflammation and essential for healthy repair following acute lung injury. Distinct subsets of human macrophages have been associated with lung pathology but whether unique cellular programs are causally linked to disease or merely represent a conserved response to tissue damage is unknown. Objectives: We sought to identify the transcriptional heterogeneity and cellular programing of airspace macrophages (AM) during normal lung repair in a human model of self-resolving acute lung injury. Methods: Fifteen subjects underwent bronchoscopic lavage before and at a pre-assigned time point after endobronchial exposure to bacterial endotoxin. Cells from lavage were subjected to single-cell RNA sequencing and a longitudinal assessment of AM programing during resolution of inflammation and lung repair was performed. Measurements and Main Results:  We identify transcriptionally distinct subsets of AM present at all time points, in all subjects.  We focus on two populations that increase following inflammation, one which aligns closely with classical circulating monocytes (MoAM) and one with interstitial macrophages (IMAM). Comparison of subset-specific markers to those identified in disease states reveals that IMAM express many so-called “pathogenic” macrophage markers during both health and inflammation.  Conclusions: By applying a uniform inflammatory stimulus to healthy adults and examining BAL cells obtained at precise time points following inflammation, we construct a time-resolved kinetic of AM transcriptional programing during inflammation and normal lung repair. Our data suggest that IMAM are similar to cells identified at increased frequency in disease states and may reflect a conserved cellular response to tissue injury.

overall_design:
scRNA-seq was performed on bronchoaelveolar lavage samples collected from healthy adults following lipopolysaccharide (LPS) exposure. Samples were collected 1-5 days post-exposure with 2-4 replicates per timepoint (total n=15) Each sample was collected from a participant with a corresponding baseline BAL sample available under GEO accesssion GSE151928

UPDATE
[Jun-04-2026] GSM9072562 was removed due to incorrect data.
[Jun-10-2026] GSM9802606 has been added as a replacement for GSM9072562.

first: Camille

last: Moore

first: Shannon

last: McManus

first: Jazalle

last: McClendon

first: William

last: Janssen

first: Kara

last: Mould


title: Targeting Liver Epsins Ameliorates Dyslipidemia in Atherosclerosis through Inhibition of Proprotein Convertase Subtilisin/Kexin Type 9-Mediated Low-density Lipoprotein Receptor Degradation

status: Public on Sep 04 2025

first: Krishan

last: Gupta

state: MASSACHUSETTS

address: 300 Longwood Avenu, Boston children's Hospital

institute: Boston Children's Hospital/Harvard Medical School

summary:
Background: The low-density lipoprotein receptor (LDLR) in the liver plays a crucial role in clearing low-density lipoprotein cholesterol (LDL-C) from the bloodstream. This process takes place mainly in the liver. Under atherogenic conditions, Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9), secreted by the liver, binds to LDLR on hepatocytes, preventing its recycling and enhancing its lysosomal degradation. This process reduces LDL-C clearance, promoting hypercholesterolemia. Epsins, a family of ubiquitin-binding endocytic adaptors, are key regulators of atherogenesis in lesional cells, including endothelial cells and macrophages. Given epsins' canonical role in regulating endocytosis of cell-surface receptors, we aimed to determine whether and how liver epsins contribute to PCSK9-mediated LDLR endocytosis and degradation, thereby impairing LDL-C clearance and accelerating atherosclerosis.
Methods: Liver-specific epsin knockout (Liver-DKO) atherosclerotic models were generated in ApoE-/- and PCSK9-AAV8-induced atheroprone mice fed on a Western diet. We utilized single-cell RNA sequencing, along with molecular, cellular, and biochemical analyses, to investigate the physiological role of liver epsins in PCSK9-mediated LDLR degradation. Additionally, we explored the therapeutic potential of nanoparticle-encapsulated siRNAs targeting epsins 1 and 2 in ApoE-/- mice with established atherosclerosis.
Results: Western diet (WD)-induced atherosclerosis was significantly attenuated in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls, as well as in PCSK9-AAV8-induced Liver-DKO mice compared with PCSK9-AAV8-induced wild-type (WT) mice, accompanied by reductions in blood cholesterol and triglyceride levels. Mechanistically, single-cell RNA sequencing of hepatocytes and aortas isolated from atherosclerotic ApoE-/- and ApoE-/-/Liver-DKO mice revealed epsin-deficient Ldlrhi hepatocytes with diminished lipogenic potential. Notably, pathway analysis of hepatocytes revealed increased LDL particle clearance and enhanced LDLR-cholesterol interactions under WD treatment in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls, which correlated with decreased plasma LDL-C levels. Furthermore, pathway analysis of the aortas showed attenuated inflammation and endothelial activation, coupled with reduced lipid uptake, and enhanced cholesterol efflux under WD treatment in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls. Moreover, the absence of liver epsins led to an upregulation of LDLR protein expression in hepatocytes. We further demonstrated that epsins bind LDLR via the ubiquitin-interacting motif (UIM), enabling PCSK9-mediated LDLR degradation. Depleting epsins abolished this degradation, thereby preventing atheroma progression. Lastly, targeting liver epsins with nanoparticle-encapsulated epsins siRNAs effectively ameliorates dyslipidemia and inhibits atherosclerosis progression. These results are consistent with findings showing increased expression of epsin1 and epsin2 in patients with atherosclerotic cardiovascular disease.
Conclusions: Liver epsins drive atherogenesis by promoting PCSK9-mediated LDLR degradation, thereby elevating circulating LDL-C levels and heightening lesional inflammation. As such, targeting epsins in the liver represents a promising therapeutic strategy to mitigate atherosclerosis by preserving LDLR and enhancing LDL-C clearance.

overall_design: In this study, all animal procedures were performed in compliance with institutional guidelines and mouse protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of Boston Children’s Hospital, MA, USA.

first: Gupta

last: Krishan

first: Zhu

last: Bo

first: Chen

last: Hong

last: Kaifu


title: The transcription factors TCF1 and LEF1 promote B-1a cell homeostasis and regulatory function

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

institute: Francis Crick

summary: B-1 cells are innate-like immune cells found abundantly in serosal cavities and their secreted antibodies are enriched for bacterial recognition1–5. The subset known as “B-1a” repress inflammation by production of regulatory molecules including IL-10 6–8. Unlike conventional B cells, which are produced daily in the bone marrow, B-1a cells are primarily generated from foetal precursors and maintained through self-renewal 9. The mechanisms regulating B-1a homeostasis and function are incompletely understood. Here we demonstrate that serosal cavity mouse and human B-1 cells as well as chronic lymphocytic leukaemia (CLL) B cells express the transcription factors TCF1 and LEF1, and circulating TCF1+LEF1+ B-1 cells increase significantly in patients with bacterial pleural infection. LEF1 is expressed from foetal B-1 progenitors, while TCF1 expression is higher in peripheral B-1a cells. TCF1 and LEF1 deficiency significantly reduces B-1a cells in mice. These transcription factors support B-1a turn-over regulating Myc targets and metabolic pathways. Upon B-1 cell activation, TCF1/LEF1 induce formation of a stem-like population, partly through IL-10 production. TCF/LEF1-deficient B-1 cells proliferate excessively, acquire an exhausted/senescent phenotype, express reduced IL-10 and PD-L1, and fail to suppress brain inflammation. These findings reveal a transcriptional program that links stemness and regulatory potential in B-1a cells.

overall_design: B-1 progenitors from fetal liver and bone marrow, B-1 cells from peritoneal cavity and spleen of  TCF1WTLEF1WT mice were isolated by Fluorescence-activated cell sorting (FACS) followed by hashtage with Cite-seq antibodies. B-1 cells from peritoneal cavity of TCF1ΔLEF1Δ mice  were isolated by Fluorescence-activated cell sorting (FACS).

first: Qian

last: Shen

first: Carola

last: Vinuesa


title: The transcription factors TCF1 and LEF1 promote B-1a cell homeostasis and regulatory function.

summary: B cells are innate-like immune cells found abundantly in serosal cavities and their secreted antibodies are enriched for bacterial recognition1–5. The subset known as “B-1a” repress inflammation by production of regulatory molecules including IL-10 6–8. Unlike conventional B cells, which are produced daily in the bone marrow, B-1a cells are primarily generated from foetal precursors and maintained through self-renewal 9. The mechanisms regulating B-1a homeostasis and function are incompletely understood. Here we demonstrate that serosal cavity mouse and human B-1 cells as well as chronic lymphocytic leukaemia (CLL) B cells express the transcription factors TCF1 and LEF1, and circulating TCF1+LEF1+ B-1 cells increase significantly in patients with bacterial pleural infection. LEF1 is expressed from foetal B-1 progenitors, while TCF1 expression is higher in peripheral B-1a cells. TCF1 and LEF1 deficiency significantly reduces B-1a cells in mice. These transcription factors support B-1a turn-over regulating Myc targets and metabolic pathways. Upon B-1 cell activation, TCF1/LEF1 induce formation of a stem-like population, partly through IL-10 production. TCF/LEF1-deficient B-1 cells proliferate excessively, acquire an exhausted/senescent phenotype, express reduced IL-10 and PD-L1, and fail to suppress brain inflammation. These findings reveal a transcriptional program that links stemness and regulatory potential in B-1a cells.

overall_design: Total B cells (CD19+CD3-) from peritoneal cavity of  TCF1WTLEF1WT and TCF1ΔLEF1Δwere isolated by Fluorescence-activated cell sorting (FACS).