title: RNA sequencing of human brain organoids to evaluate sex-specific and opto-FGFR-mediated responses to Simplified 5 Ion GCR Simulation

first: Gabsang

last: Lee

address: 733 N. Broadway

institute: Johns Hopkins School of Medicine

summary: This study aims to characterize transcriptomic responses to Simplified 5 Ion GCR Simulation  (simGCRsim) in human brain organoids derived from hiPSCs. Two independent RNA-seq experiments were conducted. The first set compared male- and female-derived organoids to evaluate sex-specific transcriptional responses to GCR. The second set assessed organoids derived from i) male hiPSCs expressing optogenetically-controlled FGFR (opto-FGFR) or mock constructs to explore FGFR signaling as a potential countermeasure and ii) one female hiPSC line (SC2131), with or without GCR exposure. Together, these datasets provide insight into both intrinsic sex differences and FGFR-dependent protective mechanisms in human neural tissues in the context of space radiation exposure.

overall_design: Human brain organoids were generated from hiPSCs and subjected to two independent RNA sequencing experiments. Experiment 1: Organoids were derived from 6 male and 2 female hiPSC lines and matured for 60 days. Organoids from each line were either untreated (control) or exposed to 50 cGy of simGCRsim. RNA was extracted for sequencing to investigate sex-specific transcriptional responses to radiation. Experiment 2: Male hiPSC lines were engineered to express either opto-FGFR or a mock construct, or one female hiPSC line (SC2131), followed by brain organoid differentiation and 60-day maturation. Organoids were then either left untreated or exposed to 50cGy of simGCRsim. RNA was sequenced to assess FGFR-mediated modulation of radiation response or responses of female-derived brain organoids against GCR radiation. Each condition was represented by three biological replicates. Differential gene expression analyses were performed to identify radiation-induced transcriptomic alterations and FGFR-dependent protective mechanisms.

first: Eun

last: Ra

first: Han Byeol

last: Kim

first: Wonjin

last: Yun

first: Anjalika

last: Bandaru

first: Micheal

last: Anderson

first: Min Seong

first: Hyesoo

first: Yohan

last: Oh


title: Macrophages are specialised at MR1 antigen presentation to MAIT cells [RNA-seq]

status: Public on Dec 08 2025

city: Melbourne

first: Lachlan

last: Dryburgh

state: Victoria

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

country: Australia

institute: The Peter Doherty Institute for Infection and Immunity

type: Expression profiling by high throughput sequencing

summary: Mucosal associated invariant T (MAIT) cells are lymphocytes that mediate tissue homeostasis and antimicrobial immunity. MAIT cells recognize microbial vitamin B-derived antigens (VitBAg) presented by MHC class I-related protein 1 (MR1). The cells that express MR1 and present VitBAg to MAIT cells remain unknown. We found that MR1 expression varies across tissues and cell types. Expression is regulated transcriptionally and induced by the tissue environment and microbiota. Depletion of MR1 in macrophages, dendritic cells and monocytes changed the composition of the microbiota and impaired MAIT cell responses against bacteria infection. Macrophages expressed the highest levels of MR1 and were the most efficient at capturing and presenting VitBAg to MAIT cells. We conclude that macrophages are key players in MR1 antigen presentation and MAIT cell immunity.

overall_design: Peritoneal macrophages were isolated from C57BL/6J mice that were maintained in either Specific Pathogen Free or Germ Free conditions. RNA was isolated, libraries prepared then sequenced to understand the full impact of the microbiome of specific pathogen free mice on macrophage gene transcription.

first: Jieru

last: Deng

first: Jose

last: Villadangos

first: Hamish

last: McWilliam


title: Differentially expressed miRNAs in the temporal cortex of Alzheimer’s disease patients and their association to tau pathology.

city: Brussels

first: Siranjeevi

last: Nagaraj

address: Route de Lennik 808 B-1070 Bruxelles

country: Belgium

institute: Université Libre de Bruxelles, Brussels, Belgium

type: Non-coding RNA profiling by high throughput sequencing

summary: Alzheimer's disease (AD) is a major contributor to dementia in the elderly, characterized by progressive impairments in memory and behaviour. AD is marked by pathological hallmarks: amyloid plaques and neurofibrillary tangles (NFTs). Despite extensive efforts to understand these hallmarks, there is still a lack of efficient therapeutic approaches due to limited knowledge of the fundamental cellular mechanisms underlying the disease. One potential avenue of research involves the investigation of the roles of non-coding RNAs, particularly, microRNAs (miRNAs), which bind to the 3' UTRs of target mRNAs to suppress expression. In our study, we analysed the temporal superior T1 isocortex of control and AD patients, identifying differentially expressed miRNAs using next-generation sequencing (NGS). To validate these findings, we utilized an additional technique, RT-qPCR. Overall, our study confirms the previous findings  on the dysregulation of miR-129-5p, miR-132-3p, and miR-146b-5p, while also providing novel insights into the dysregulation of miR-151a-5p and miR-1-3p. Importantly, the expression levels of miR-129-5p, miR-146b-5p, miR-132-3p, and miR-151a-5p were significantly correlated with the neuropathological Braak stages and with biochemically quantified tau phosphorylation levels in brain homogenates. Additionally, we found that miR-146b-5p and miR-151a-5p significantly modulated tau seeding in tau biosensor cell model, highlighting their potential roles in tau pathology.

overall_design: microRNA sequencing profile of postmortem brain samples (temporal superior T1 isocortex) from control and Alzheimer's diseases patients

first: Karelle

last: Leroy

first: Carolina Quintanilla

last: Sanchez

first: Kunie

last: Ando

first: Lidia Lopez

last: Gutierrez

first: Yannick

last: Gansemans

first: Emilie

last: Doeraene

first: Andreea-Claudia

last: Kosa

first: Emmanuel

last: Aydin

first: Filip

last: Van Nieuwerburgh

first: Jean-Pierre

last: Brion


title: Macrophages are specialised at MR1 antigen presentation to MAIT cells [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Different cell types were isolated from C57BL/6J mice that were maintained in either Specific Pathogen Free or Germ Free conditions. These included B cells, alveolar macrophages and peritoneal macrophages that have a range of MR1 expression. Then ATAC-seq was performed to understand if the accessibility of the Mr1 gene correlated with its expression.


title: Temporal multi-omics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation [Ribo-seq]

city: New York

first: Marko

last: Jovanovic

state: NY

address: 1212 Amsterdam Avenue

department: Biological Sciences

country: USA

institute: Columbia University

summary: Human embryonic stem cells (hESCs) provide a powerful in vitro model to study lineage specification and the regulatory programs underlying early human development. Here, we present a high-resolution, temporal multi-omics dataset tracking mRNA, translation, and protein expression dynamics during hESC differentiation into definitive endoderm and subsequent polyhormonal (PH) cells, a key pancreatic lineage. RNA-seq, ribosome profiling, and quantitative mass spectrometry-based proteomics were performed on matched samples collected at ten time points in biological duplicates, allowing detailed characterization of transcriptional, translational, and protein abundance changes over the differentiation timeline. The dataset exhibits high technical quality, with strong reproducibility between replicates and rigorous quality control metrics across all omics platforms. This extensive dataset provides critical insights into the complex regulatory mechanisms driving polyhormonal cell differentiation and serves as a valuable resource for the research community, enabling deeper exploration of mammalian development, endodermal lineage specification, and gene regulation.

overall_design: To comprehensively investigate the gene regulatory mechanisms underlying human embryonic development, we performed genome-wide measurements of mRNA, translation, and protein levels during hESC differentiation. Our experimental design encompassed the generation of all three embryonic germ layers—endoderm, mesoderm, and ectoderm—followed by their directed differentiation into polyhormonal cells, cardiomyocytes, and motor neurons, respectively. In the present study, we focus on the endoderm-to-polyhormonal cell differentiation trajectory. Samples were collected at ten distinct time points, enabling high-resolution tracking of gene expression dynamics over the course of differentiation. Matched samples were measured for mRNA levels by mRNA sequencing (mRNA-seq), for translation level proxies by ribosome profiling (Ribo-seq), and for protein levels by quantitative mass spectrometry-based proteomics. All differentiations and measurements were performed in biological duplicates.

first: Abdurrahman

last: Keskin

first: Hani

middle: J

last: Shayya

first: Achchhe

last: Patel

first: Dario

last: Sirabella

first: Barbara

last: Corneo


title: Kar4 acts as a Ste12 regulator in Saccharomyces cerevisiae, promoting Ste12 binding to a specific DNA motif genome-wide [ChIP-exo]

city: Bethesda

first: Hernan

middle: A

last: Lorenzi

state: Maryland

address: 8 Center Dr, Bldg 8A

department: National Institutes of Diabetes and Digestive and Kidney Diseas

institute: National Institutes of Health

summary: Kar4 is a putative transcription factor essential for mating in the budding yeast Saccharomyces cerevisiae. Kar4 has been shown to function with Ste12, the master transcriptional regulator of the yeast mating pheromone response, to promote the transcription of a subset of Ste12 targets required for efficient mating. However, the mechanism by which Kar4 modulates Ste12 activity has remained uncertain. Here, we examine the effect of Kar4 on the mating pheromone response via ChIP-exo

overall_design: ChIP-exo of Ste12-TAP in WT and kar4D cells and Kar4-TAP. All groups done in at least biological replicate, with and without pheromone (alpha-factor) treatment

first: Jason

last: Rogers

first: Amanda

last: Yeo

first: Val

last: Meleshkevich

first: Mark

last: Rose

first: Orna

last: Cohen-Fix


title: Temporal multi-omics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation [RNA-seq]


title: Kar4 acts as a Ste12 regulator in Saccharomyces cerevisiae, promoting Ste12 binding to a specific DNA motif genome-wide [RNA-seq]

summary: Kar4 is a putative transcription factor essential for mating in the budding yeast Saccharomyces cerevisiae. Kar4 has been shown to function with Ste12, the master transcriptional regulator of the yeast mating pheromone response, to promote the transcription of a subset of Ste12 targets required for efficient mating. However, the mechanism by which Kar4 modulates Ste12 activity has remained uncertain. Here, we examine the effect of Kar4 on the mating pheromone response at the levels of transcription (RNA-seq)

overall_design: RNA-seq samples were prepared from synchronized cell cultures of the VM05 MATa strain carrying deletions in either KAR4 (ACY01) or STE12 (ACY02). Generally, each strain was pelleted for total RNA extraction after synchronization (time point = 0 hours) or treated with alpha-factor for 60 minutes before RNA sample preparation, except for the "VM" samples, where the control was a timepoint of 60 minutes (without alpha factor)


title: Histone H3K4 methylation regulation and three-dimensional aggregating distribution of a subset of genomic loci mediated by CHD3 homolog PKL in Arabidopsis [Hi-C]

city: Beijing

first: Mengfei

last: Song

state: Beijing

address: 北京市海淀区颐和园路5号

country: China

institute: Peking university

summary: Arabidopsis PICKLE (PKL) is a putative CHD3-type chromatin remodeling factor. Despite its importance in environmental stimulus responses and plant development, how PKL is recruited to target gene loci and its detailed regulatory role in controlling target gene chromatin states is not fully understood. Here, we report genome-wide evidence for the recruitment of PKL by specific transcription factors, establish the molecular connection between PKL and H3K4me2/3, and demonstrate PKL is essential for the space-clustering distribution of its target genes. We captured the genome-wide binding sites of PKL by ChIP-seq using endogenous antibody. Further analyses gave evidence that plant-specific transcriptional factors containing TCPs, PIFs, and HY5, play dominant role in recruiting PKL to its target gene loci in Arabidopsis thaliana. The chromatin of PKL target genes showed significantly enriched depositions of H3K4me2 and H3K4me3. PKL directly interacted with the COMPASS complex scaffold protein WDR5A. It seems that PKL acts through WDR5A to stabilize the highly accumulated levels of H3K4me2 at specific euchromatic loci. Strikingly, PKL-bound genes distributed space-contiguously, the manner of which is dependent on PKL and PKL-interacted TFs. Moreover, the working model of PKL we proposed in this study is likely conserved in liverwort and rice. PKL associates with specific gene loci by interacting with specific transcription factors and promotes H3K4me2 depositions locally. Meanwhile, PKL acts as a hub mediating its target gene loci spatial-aggregation. PKL and its homologs in rice and liverwort might display similar molecular functions

overall_design: Three biological replicates of each genotype were used for high-throughput sequencing analysis. All experiments wer conducted using  9-day-old seedlings grown in continuous white light.

first: Yuqiu

last: Wang

first: XingWang

last: Deng

first: Danmeng

last: Zhu


title: Histone H3K4 methylation regulation and three-dimensional aggregating distribution of a subset of genomic loci mediated by CHD3 homolog PKL in Arabidopsis [9-day-old seedlings, RNA-Seq]

address: 北京市海淀区颐和园路5号


title: The single cell landscape of the human vein after arteriovenous fistula creation and implications for maturation failure.

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: We performed single-cell RNA sequencing of venous samples from 20 patients, including 6 pre-access veins, 2 early AVF resections, and 12 second-stage AVFs that matured (6) or failed (6).

overall_design: Vessels were collected in cold cell culture media and enzymatically digested to generate single-cell suspensions. Samples were run using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics) with a target capture of 10,000 cells. Libraries were sequenced on the Illumina NovaSeq 6000/X Plus. FASTQ files were generated with Cell Ranger's mkfastq pipeline (version 6.0.2). The Cell Ranger's count pipeline (version 6.0.2) was used to generate raw gene-barcode matrices from alignment to the 10X Genomics pre-built Cell Ranger human reference package (version 2020-A), from GRCh38 Ensembl build 98/GENCODE v32 gene annotations.

first: Laisel

last: Martinez

first: Roberto

middle: I

last: Vazquez-Padron


title: Histone H3K4 methylation regulation and three-dimensional aggregating distribution of a subset of genomic loci mediated by CHD3 homolog PKL in Arabidopsis [RNA-Seq]

address: 北京市海淀区颐和园路5号

overall_design: Three biological replicates of each genotype were used for high-throughput sequencing analysis. All experiments wer conducted using  14-day-old seedlings grown in at 25°C (12h light/12h dark).


title: Histone H3K4 methylation regulation and three-dimensional aggregating distribution of a subset of genomic loci mediated by CHD3 homolog PKL in Arabidopsis [ChIP-Seq]

address: 北京市海淀区颐和园路5号


title: Genetic alterations of SENP6 disrupt DNA repair and proteostasis conferring sensitivity to proteasome inhibition in multiple myeloma

city: Berlin

first: Uta

middle: Margareta

last: Demel

address: Hindenburgdamm 30

department: Hematology and Oncology

country: Germany

institute: Charité - CBF

summary: Targeting of the ubiquitin-proteasome system (UPS) remains a mainstay in the treatment of multiple myeloma (MM). Hyperactivation of the closely related SUMO pathway is implicated in disease progression and associated with poor prognosis. Here we investigated the functional imbalance of aberrant SUMOylation in MM by analyzing the large CoMMpass dataset for molecular alterations associated with SUMO pathway regulation. SENP6 and SENP7, key SUMO proteases, were significantly downregulated in patients with high SUMO pathway signatures. Recurrent loss of SENP6, a negative regulator of SUMOylation, was directly linked to adverse prognosis across all disease stages. SENP6 reconstitution markedly reduced cellular growth kinetics in SENP6-deficient MM, indicating a functional role for SENP6 as a tumor suppressor. Mechanistically, SENP6 loss resulted in the accumulation of DNA damage and misfolded proteins, thereby activating the unfolded protein response, increasing reliance on proteasomal degradation, and driving synthetic lethality to therapeutic proteasome inhibition. Together, we establish SENP6 as a biologically relevant biomarker and provide a mechanistic rationale for the clinical efficacy of proteasome inhibitors in the prognostically unfavorable subgroup of SENP6-deficient MM patients.

overall_design: RNA-seq profiling of NCI-H929 and OPM-2 multiple myeloma cell lines with and without CRISPR-Cas9-mediated SENP6 knockdown.

first: Frederik

last: Herzberg

first: Michael

last: Korenkov

first: Konstandina

last: Isaakidis

first: Chuanbing

last: Zang

first: Matthias

last: Wirth

first: Stefan

last: Müller

first: Ulrich

last: Keller

middle: M


title: High resolution spatial trancrioptomics combined with deep learning-based image segmentation enables single-cell spatial profiling of archival FFPE kidney tissue from patients with idiopathic nephrotic syndrome

city: Bergen

first: Øystein

last: Eikrem

state: Vestland

address: Jonas Lies vei 91B

department: Department of Clinical Medicine

country: Norway

institute: University of Bergen

summary: We have perfomed Visium HD spatial transcriptomics on archival FFPE kidney biopsies from patients with different manifistations of nephrotic syndrome, i.e., steriod sensitive, frequent relapsing and/or steroid dependent, and focal segmental glomerulosclerosis. Using a pre-trained deep learning model from StarDist to segment nuclei, we reconstructed single-nucleus level spatial trancriptomic datasets through custom binning of subcellular capture areas. We integrated the datasets from the different patients and indentified conserved cell types. Moreover, we identified patient specific transcriptomic differences in the podocyte cell population. This article demonstrates the usefullness of this approach to future studies of pathophysilogical mechanisms in idiopathic nephrotic syndrome.

overall_design:
Archival FFPE kidney biopsies from three patients with different manfistations of idiopathic nephrotic syndrome (SSNS, FR/SDNS, FSGS) were prepared for Visium HD WT Panel Gene Expression. Deep lerning-based image segmentation of nuclei and custom binning was used to reconstruct single-nucleus level spatial datasets.
** Raw data not provided due to patient privacy concerns**

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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: Simen

middle: F

last: Pettersen

first: Eleni

last: Skandalou

first: Jessica

last: Furriol

first: Tarig

last: Osman

first: Hans-Peter

last: Marti

middle: S


title: The placental effects of trisomy for human chromosome 21 orthologs in four mouse models of Down syndrome

first: Laura

middle: L

last: Baxter

state: MD

address: 35A Convent Drive

department: NHGRI

institute: NIH

summary:
Down syndrome (DS) is caused by trisomy for human chromosome 21 (Hsa21) and is associated with atypical neurodevelopment that begins prenatally. The developing human fetus receives nutritional support and gas exchange from the placenta, and normal placental function is essential for proper development. Placentas that sustain fetuses with trisomy 21 contain trisomic cells, but little is known about which trisomic genes are overexpressed in the placenta or their downstream molecular, cellular, and functional effects. Mouse models of DS are useful in vivo systems for studying the prenatal effects of trisomy.
This study examined the placental transcriptome in four mouse models of DS: Dp(16)1/Yey, Ts65Dn, Ts66Yah, and Ts1Cje. Despite modest overlap of trisomy-associated gene dysregulation among these four models, pathway enrichment analyses identified alterations in extracellular matrix pathways in all four models and notable upregulation of immune system pathways in Dp(16)1/Yey and Ts66Yah.

overall_design: Total RNA was isolated from the placentas supporting E18.5 embryos using the NuceloMag® RNA/DNA high throughput extraction kit following the manufacturer’s instructions (Macherey-Nagel, Bethlehem, PA). RNA was processed and hybridized using Clariom S high throughput arrays. Total samples for all four mouse models of DS = 140: Sample numbers for each model were: Dp16 = 20 trisomic, 20 euploid; Ts65Dn = 19 trisomic, 17 euploid; Ts66Yah = 9 trisomic, 14 euploid; Ts1Cje = 24 trisomic, 17 euploid.

first: Taisuke

last: Sato

first: April

middle: D

last: Adams

first: Lauren

last: Bishop

first: Faycal

last: Guedj

first: Diana

middle: W

last: Bianchi


title: Role of SRP/dGATAb in the response of Drosophila S2 Schneider cells to 20-hydroxyecdysone

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: Background: The tissue-specific response to steroid hormones remains unclear even in model organisms. The mechanism is proposed to be based on the selective binding of nuclear hormone receptors to regulatory sites that are primed by tissue-specific factors. But studies directly describing the cooperative work of nuclear receptors with tissue-specific transcription factors remain sparse. Earlier, GATA family factor SRP/dGATAb was proposed to prime regulatory sites in S2 Schneider cells for their activation by 20-hydroxyecdysone (20E), the main steroid hormone of the Drosophila development. Highly specific expression of SRP/dGATAb in Drosophila tissues makes it a suitable candidate for a factor enabling tissue-specific response to 20E. Results: The role of SRP/dGATAb in the response of S2 Schneider cells to 20E was determined using SRP/dGATAb depletion via RNA interference. Combination RNA-Seq with ChIP-Seq analysis helped identify the primary targets of SRP/dGATAb whose transcription is induced in response to 20E treatment and whose loci contain EcR and SRP/dGATAb binding sites. SRP/dGATAb depletion was found to alter transcription of different 20E-induced genes in opposite ways. For 20E-activated genes whose transcription was decreased upon depletion, SRP/dGATAb was found to control active regulatory sites marked by the H3K27Ac and enriched with SRP/dGATAb motifs. In this group SRP/dGATAb depletion reduced EcR binding level at sites co-bound with EcR and SRP/dGATAb, demonstrating a priming role for GATA family protein. In contrast, for 20E-activated SRP/dGATAb-suppressed genes whose transcription was increased upon SRP/dGATAb depletion, SRP/dGATAb and EcR co-bound sites showed unchanged H3K27Ac levels and EcR binding. The overall level of H3K27 acetylation at the loci of the second group of genes showed increase upon SRP/dGATAb depletion. Conclusions: Obtained data showed a positive role of SRP/dGATAb in 20E-inducible transcription in S2 Schneider cells for some genes. SRP/dGATAb worked as a priming transcriptional factor for 20E-inducible regulatory sites controlling EcR recruitment and chromatin acetylation. But for another group of 20E-inducible genes, SRP/dGATAb had negative impact on transcription. Its recruitment through the protein-protein interactions restrained activity of the regulatory sites.

overall_design: RNA-Seq, FAIRE-Seq, ChIP-Seq experiments were performed on Drosophila S2 Schneider cells treated with 20-hydroxyecdysone for 1 h or sham-treated (DMSO) under SRP/dGATAb-depleted or control conditions (SKi).

first: Aleksandra

last: Evdokimova


title: Single nuclei RNAseq of skin sensory neurons during psoriasis

city: San Diego

first: Eduardo

last: Ansaldo

address: 15550 Torrey Pines Rd

department: IMM

institute: Scripps Research

summary: The peripheral nervous system plays important roles in orchestrating tissue function in health and disease. In this work, we perform single nuclei RNAseq of skin sensory neuron DRGs in a mouse model of psoriasis to interrogate the impact of skin inflammation on the function and transcriptome of skin sensory neurons.

overall_design: 10000 nuclei per lane isolated from dorsal root ganglion of mice (total of 6 lanes, 3 Control and 3 S. aureus IMQ) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the nuclei into droplets. The gene expression (GEX) library was prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq2000 platform

first: Jeremie

last: Delaleu

first: Eduard

first: Michel

last: Enamorado


title: Single Cell and Spatial Transcriptomics Implicate Vascular Cell Orchestration of Inflammatory Changes After Ultraviolet Light Exposure [Spatial Transcriptomics]

city: Seattle

first: Jie

last: An

state: WA

address: 750 Republican Street

institute: University of Washington

summary: To elucidate the complex effects of acute UV radiation (UVR) on the skin, we exposed shaved mouse skin to UVB and performed transcriptomic profiling of the epidermis, deep dermis and adipose tissue. Spatial transcriptomic analysis revealed the most pronounced gene expression changes in the epidermis, peaking at 24 hours post-irradiation. While CD45⁺ immune cells showed differential expression of chemokines, cytokines, and acute-phase proteins, cytokeratin⁺ epidermal cells upregulated genes related to cellular stress and damage (e.g., Usp19, Adam25), as well as structural remodeling and apoptosis (e.g., Krt18, Phlda1). Single-cell RNA sequencing (scRNA-seq) conducted 12 hours after UVR exposure identified 4,849 differentially expressed genes (DEGs), with the epidermis and endothelial cells showing the highest DEG counts. Pathway analysis of upregulated genes in the epidermis revealed enrichment in VEGF, HIPPO, complement, IL-6, and apoptosis signaling pathways. In endothelial cells, UVR induced expression of multiple chemokines and cytokines. Notably, receptor-ligand analysis highlighted endothelial cells as key targets of CXCL chemokines and complement component C3. In fibroblasts, UVR triggered upregulation of inflammatory activation markers (Osmr, Cux1) alongside genes associated with glucose metabolism (Hif1a, Pkm). Cross-species comparison of UVR-responsive DEGs between mice and humans revealed strong concordance, particularly in TGF-β and TNF-associated pathways.

overall_design: Mice used in this study were 12-16 week old C57BL/6 (B6, wild type) females. Mice were anesthetized with isoflurane and a single dose of UVB (500 mJ/cm2) was delivered to the shaved whole back using FS40T12/UVB bulbs (National Biological Corporation) as described previously (Skopelja-Gardner et al., 2021). The narrow band UVB light energy (290-320 nm) at the dorsal surface was measured with Photolight IL1400A radiometer with a SEL240/UVB detector (International Light Technologies). Biopsies were taken at times 0, 6, and 24 hours after UVB exposure (n=3 per group) for spatial transcriptome analysis.

first: Rachael

last: Bogle

first: Rayan

last: Najjar

first: Lam

middle: C

last: Tsoi

first: Michelle

last: Kahlenberg

first: Ksenia

last: Anufrieva

first: Erin

last: Theisen

first: Kevin

last: Wei

first: Johann

last: Gudjonsson

first: Keith

last: Elkon


title: Single Cell and Spatial Transcriptomics Implicate Vascular Cell Orchestration of Inflammatory Changes After Ultraviolet Light Exposure [scRNA-seq]

overall_design: Mice used in this study were 12-16 week old C57BL/6 (B6, wild type) females. Mice were anesthetized with isoflurane and a single dose of UVB (500 mJ/cm2) was delivered to the shaved whole back using FS40T12/UVB bulbs (National Biological Corporation) as described previously (Skopelja-Gardner et al., 2021). The narrow band UVB light energy (290-320 nm) at the dorsal surface was measured with Photolight IL1400A radiometer with a SEL240/UVB detector (International Light Technologies). Biopsies were taken at times 0 and 12 hrs (snRNAseq) or at 0, 6, and 24 hours after UVB exposure (n=3 per group) for spatial transcriptome analysis.


title: A novel human blood-brain barrier model reveals pericytes as critical regulators of viral neuroinvasion

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

summary: The blood-brain barrier (BBB) plays a vital role in regulating the passage of biomolecules between the bloodstream and the central nervous system (CNS) while also protecting the CNS from pathogens. Pericytes reside at the interface between the endothelial cells that form the vessel walls and the brain parenchyma. These cells are critical for maintaining BBB integrity and regulate vessel permeability, blood flow, and immune cell migration. In this study, we developed a novel serum-free protocol to generate neural crest cell-derived pericytes (NCC-PCs) from human pluripotent stem cells (hPSCs). These NCC-PCs enhance BMEC barrier function and can be co-cultured with hPSC-derived brain microvascular endothelial cells (BMECs) in a co-culture BBB model that recapitulates the in vivo cellular interactions at the BBB. We used this model to evaluate the pathological consequences of BBB exposure to highly neuroinvasive flaviviruses. Our results identify a previously undescribed role for NCC-PCs in maintaining BMEC barrier integrity during infection and reducing the spread of viral infection to the CNS.

overall_design: Human brain microvascular endothelial cells (BMECs), pericytes (PCs), and astrocytes were differentiated from human pluripotent stem cells (hPSCs).  Cells were infected with neuroinvasive flaviviruses including West Nile virus, Poweassan virus, and Japanese encephalitis virus.  In addition, hPSC-derived BMECs and PCs were plated in a transwell co-culture system and then exposed to West Nile virus. The transcriptional response of both BMECs and PCs to West Nile virus was examined at both early (8 hours post infection) and late (48 hours post infection) time points.  The hPSC-derived pereicytes were made using a novel serum-free protocol, for cell characterization experiments the transciptional profile was compared to both primary brain pericytes as well as hPSCs, hPSC-derived neural crest cells, and hPSC-derived PCs generated from previously published protocols.

first: Alexsia

last: Richards


title: Rete ridges form via evolutionarily distinct mechanisms in mammalian skin

city: Pullman

first: Sean

last: Thompson

address: BLS 240

department: School of Molecular Biosciences

institute: Washington State University

summary: The loss of fur during human evolution has long mystified scientists and the public. Reduced hair density coincides with the acquisition of epidermal rete ridges, whose developmental timing and molecular mechanisms are poorly understood despite their prominence in humans. Examination of human and pig skin development revealed that rete ridges form through an independent mechanism from hair follicles and sweat glands by establishing interconnected epidermal invaginations. We documented rete ridge occurrence across Mammalia, including in grizzly bears and dolphins, and showed that neonatal pig wounds can regenerate them de novo. Multi-species spatiotemporal transcriptomics identified significant signaling interactions between epidermal and dermal cells during rete ridge morphogenesis, particularly through BMP. We also demonstrated that murine fingerpad skin forms rete ridges and functionally requires epidermal BMP signaling. We propose that evolution of rete ridges in mammalian skin involved replacement of the molecular program for formation of discrete microscopic appendages, including hair follicles and sweat glands, with a distinct program for the interconnected appendage network. Broad epidermal activation of BMP is required for the development of rete ridge networks organized around underlying dermal pockets. Understanding rete ridge mechanisms may enable the development of therapeutic approaches to regenerate epidermal appendages lost during wounding or disease in humans.

sample_organism:
Homo sapiens
Sus scrofa
Mus musculus

overall_design:
Skin from a E90 fetal pig, P3 neonatal pig, P10 neonatal pig, and 6-month old adult pig was collected under approved protocols and processed to generate a single-cell suspension from the epidermis and dermis in 1:1 ratios for 10x Genomics scRNA-seq. Additionally, we re-analyzed previously published scRNA-seq datasets from Glover et al., 2023; Cheng et al., 2018; Solé-Boldo et al., 2020; Liu et al., 2022 based on their published sequencing files. Finally, skin from P3, P10, and 6mo pigs were processed to generate spatial transcriptomics datasets using Complete Genomics Stereo-seq.

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

last: Phan

first: Iwona

last: Driskell

first: Ryan

middle: R


title: Ythdc1-p300-Klf5 complex-mediated Golgi dysfunction promotes aortic aneurysm

city: Shijiazhuang

first: siming

last: Bu

state: CHINA

address: Zhongshan East Road

institute: Hebei Medical university

summary: Klf5 and Golph3l-mediated regulation of Golgi morphology has been implicated in the development of apoptosis induced by diverse stress stimuli, and the loss of VSMCs caused by VSMCs apoptosis is a major factor leading to aortic wall thinning and aneurysm development. However, the molecular link between Klf5, Golph3l, and Golgi morphology alteration in the context of the aortic aneurysm is unclear. Here, we show that apoptosis-induced proliferation (AIP) in VSMCs occurs in AD and AAA tissues of humans and mice. The upregulation of Golph3l by Klf5 facilitates TNF-α and TNFSF12 secretion from AngII-stimulated VSMCs by inducing the compaction of the Golgi, which is essential for AIP and aneurysm development. Mechanistic studies reveal that AngII-induced elevation of global m6A RNA level, especially m6A-Gm40097, is responsible for Golph3l upregulation and AIP in VSMCs. Further, m6A-Gm40097 mediates Klf5 interaction with Ythdc1 and p300 to form a transcription complex on the Golph3l promoter, unveiling a novel lncRNA m6A modification-dependent regulatory mechanism of chromatin remodeling and transcription activation.

overall_design: ApoE−/− mice, Tgln-cre mice, and Golph3l-flox mice containing loxP sites flanking exons 2 and 3 were purchased from Suzhou Cyagen Biotechnology Co., Ltd. Smooth muscle cell–specific Golph3l knockout (smcGolph3l−/− mice) by crossing Golph3l-flox mice and Tgln-cre mice (Golph3l-flox mice served as controls). Mice were kept under a 12-hour light/dark cycle at 23℃ with ad libitum access to food and water.

first: Wenli

last: Wang

first: Zhixue

last: Song

first: Siming

first: Dong

last: Ma


title: The DLX2-LAP2α axis licenses ectomesenchymal specification by unlocking chromatin barriers for craniofacial regeneration [RNA-seq]

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

summary: The ectomesenchyme generates much of the craniofacial skeleton, sutures, and diverse connective tissues in the mammalian head, yet its derivation from embryonic stem cells (ESCs) and the underlying molecular drivers remain poorly defined. Here, we identified Dlx2 as a key regulator that efficiently directed murine ESCs towards Msx1+ ectomesenchyme, recapitulating the developmental trajectory. These Msx1+ progenitors expressed classical craniofacial markers and retained robust osteochondral bipotency in vitro and in vivo. Mechanistically, DLX2 utilized a lamina-associated polypeptide 2 (LAP2)-dependent nuclear chaperoning system, engaging LAP2α via a 38-amino-acid homeodomain motif to interact with nucleosomes, thereby opening chromatin and activating a craniofacial ectomesenchymal gene network. Disrupting DLX2-LAP2α interaction or silencing Dlx2 targets largely diminished ectomesenchymal differentiation. Our findings established DLX2 as a pioneer factor in ectomesenchyme specification, offering insights into craniofacial development and stem cell engineering.

overall_design: Total RNAs were extracted from mESCs, day-2 Dlx2-OE embryoid bodies (EBs), and day-2 GFP-OE EBs to compare the effects of Dlx2 overexpression on ES cell differentiation toward ectomesenchymal lineages at the early stage (day 2), as well as from day-8  Msx1+ and Msx1-  cells and day-16 Msx1+ and Msx1- cells to evaluate the differences between Msx1 positive and negative populations at two distinct differentiation timepoints (day 8 and day 16).

first: Ziwei

last: Zhang

first: Zhiheng

last: Xu

first: Hong

last: Hu

first: Yao

first: Youmei

last: Jin

first: Yi

last: Zhong

first: Yunqiu

first: Yike

last: Yin

first: Jing

last: Chen

first: Yufeng

last: Duan

last: Hao


title: The DLX2-LAP2α axis licenses ectomesenchymal specification by unlocking chromatin barriers for craniofacial regeneration [scRNA-seq]

overall_design: To investigate if Dlx2-induced ectomesenchymal differentiation would follow the known developmental principles, we harvested EBs at day-2, -8, -12, and -16 for single cell sequencing (scRNA-seq)


title: The DLX2-LAP2α axis licenses ectomesenchymal specification by unlocking chromatin barriers for craniofacial regeneration [CUT&Tag]

overall_design: CUT&Tag profiling was performed for LAP2 and the histone modifications H3K9me3 and H3K27ac in day-2 Dlx2-OE EBs, as well as for DLX2 (FLAG) in day-2 EBs with or without Dox treatment.


title: Lysosomal RNA profiling reveals targeting of specific types of RNAs for degradation

first: Graham

middle: Jordan

last: Ray

address: 77 Massachusetts Ave

department: Biology

institute: Massachusetts Institute of Technology

summary: Autophagy targets a wide variety of substrates for degradation within lysosomes. Although lysosomes are known to possess RNase activity, the role of lysosomal RNA degradation in post-transcriptional gene regulation is not well understood. We defined RNASET2, PLD3, and both endogenous and exogenous RNase A family members as lysosomal RNases. Cells lacking these RNases accumulated large amounts of lysosomal RNA. Quantitative RNA sequencing of lysosomal contents revealed that although all RNA types can enter lysosomes, the SRP RNAs, Y RNAs, 5′ TOP mRNAs, long-lived mRNAs, and mRNAs encoding membrane and secreted proteins were specifically enriched. This specificity was due to autophagy, and lysosomally degraded transcripts had autophagy-dependent changes in stability. To explore the basis of this specificity, we identified sequence motifs of SRP RNAs and 5′ TOP mRNAs that are necessary and sufficient for enhanced lysosomal targeting. Our results establish lysosomes as selective modulators of cellular RNA content.

overall_design: RNA sequencing of whole cell and lysosomal samples as well as RNA stability measurements using 5EU.

first: David

last: Sabatini

last: Bartel


title: Drp1 regulates mitochondrial health and controls skeletal muscle mass through the Erk1/2-Nur77 pathway

city: Los Angeles

first: Zhenqi

last: Zhou

state: CA

address: 650 Charles E Young Dr. S

department: Medicine

institute: University of California Los Angeles

summary: The maintenance of skeletal muscle mass is critically dependent upon mitochondrial quality control, including balanced mitochondrial dynamics and mitophagy. Dynamin-related protein 1 (Drp1), a key mediator of mitochondrial fission, plays an important role in these processes. However, the precise mechanisms by which Drp1 regulates mitochondrial integrity and muscle mass remain inadequately understood. Here, we show that acute Drp1 deletion from skeletal muscle impairs mitochondrial activity, increases Parkin-mediated mitophagy, progressively reduces mitochondrial DNA (mtDNA) content, and ultimately causes severe muscle atrophy. Interestingly, dual deletion of Drp1 and Parkin from skeletal muscle restored mtDNA content, but did not prevent muscle loss. Mechanistically, Drp1 deletion disrupted mitochondrial respiratory chain activity, which suppressed extracellular signal-regulated kinase 1/2 (Erk1/2) signaling and downregulated the nuclear receptor subfamily 4 group member 1 (Nur77), a regulator of muscle quality. Finally, clenbuterol, a β2-adrenergic receptor agonist, activated Erk1/2 signaling, restored Nur77 expression, and rescued muscle atrophy. Collectively, our findings identify a Drp1-Erk1/2-Nur77 signaling axis that connects mitochondrial integrity to the preservation of skeletal muscle mass and represents a potential therapeutic avenue for muscle degeneration in mitochondrial and metabolic disorders.

overall_design: We studied the role of acute Drp1 deletion on skeletal muscle mass

first: Alice

first: Peter

middle: H

last: Tran

first: Nicole

last: Yang

first: Hirotaka

last: Iwasaki

first: Andrea

last: Hevener


title: Melatonin primes mesenchymal stem cells via glutathione dynamics to enhance therapeutic efficacy in asthma

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

summary: Mesenchymal stem cells (MSCs) offer therapeutic potential for inflammatory diseases, but their efficacy is often compromised during in vitro expansion. Here, we identified melatonin (MT) as a safe and effective priming agent that enhances MSC functionality by reinforcing intracellular glutathione (GSH) dynamics. Using FreSHtracer, a live-cell GSH-sensitive imaging probe, we established a high-throughput screening platform and developed a set of quantitative GSH indices to assess redox capacity. Screening over 50 flavonoids and vitamins, we identified MT as a clinically relevant compound that robustly activates the CREB1–NRF2 pathway, leading to improved antioxidant defense. MT-primed MSCs (MT-MSCs) exhibited enhanced clonogenicity, migration, angiogenesis, and immunosuppressive properties via JAK–STAT3–PD-L1 signaling. Transcriptomic analysis revealed molecular signatures associated with immune modulation and tissue regeneration. In a murine model of allergic asthma, MT-MSCs significantly alleviated Th2-mediated inflammation and improved lung engraftment. Additionally, we implemented a deep learning-based convolutional neural network for automated bronchoalveolar lavage fluid analysis, enabling objective and efficient inflammatory cell profiling. This study introduces MT as a pharmacopeia-compliant priming molecule and presents an integrated approach combining functional priming and AI-assisted diagnostics to advance the development of high-quality MSC-based therapies for asthma and other inflammatory diseases

overall_design: RNA-seq data of naïve hES-MMSC cells and hES-MMSC primed with melatonin (200 µM) for 24 hours.

first: Hyun Jun

last: Im

first: Seok Woo

last: Ha

first: Keunhong

last: Jeong

first: Sang-Yeob

last: Kim

first: Eui Man

first: Dong-Myung

last: Shin


title: Kar4 acts as a Ste12 regulator in Saccharomyces cerevisiae, promoting Ste12 binding to a specific DNA motif genome-wide

first: Hernan

last: Lorenzi

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

overall_design: Refer to individual Series


title: A BRCT Domain-Containing Protein Induced in Early Phagocytosis Plays a Crucial Role in Mucorales Pathogenesis

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

summary: Mucormycosis, caused by Mucoralean fungi, is among the most lethal fungal diseases, and a deeper understanding of its pathogenesis is urgently needed. In this study, we examined the early stages of fungal interaction with host macrophages using Mucor lusitanicus and Rhizopus microsporus as model organisms. Transcriptomic profiling of virulent (WT) and an RNAi-deficient strain (r3b2Δ) of M. lusitanicus strains during phagocytosis uncovered thousands of differentially expressed genes (DEGs), highlighting early metabolic activation as a key survival strategy inside the phagosome. Enriched pathways included amino acid transport, nucleotide metabolism, and translation, reflecting an adaptive fungal response to nutrient deprivation and host immune stress. Integrative analyses of mRNA and sRNA profiles also revealed a critical role of the RNAi pathways in modulating gene expression during infection. Building on these observations, we identified four chromatin- and transcription-related candidate virulence genes—brca1, box, hist1, and hda10—which were strongly upregulated during phagocytosis and regulated by RNAi. Functional validation through gene deletion in M. lusitanicus and disruption in R. microsporus revealed that while loss of these genes in M. lusitanicus did not significantly affect virulence, R. microsporus mutants for brca1, hist1, and hda10 showed attenuated virulence in a murine model. Our findings suggest that although M. lusitanicus remains a valuable tool for genetic manipulation, species-specific differences must be considered when studying virulence. The study also underscores the importance of using multiple Mucorales models to uncover conserved and divergent strategies employed by pathogenic fungi. These insights contribute to a broader understanding of fungal adaptation, immune evasion, and the identification of novel targets for antifungal intervention.

overall_design: Transcriptomic analysis using RNA-seq to study the impact of R3B2 gene deletion on gene expression at both messenger RNA (mRNA) and small RNA (sRNA) levels in Mucor lusitanicus. Wild-type strain MU636 and r3b2Δ mutant MU412 were used. Total RNA was extracted from samples collected after 1 hour of interaction with macrophages and after 1 hour of saprophytic growth as a control condition. Three biological replicates were performed for each condition.

first: Ghizlane

last: Tahiri

first: Ulrike

last: Binder

first: Jakob

last: Scheler

first: Eusebio

last: Navarro

first: Francisco E

last: Nicolás

first: Victoriano

last: Garre


title: NFAT Mediates Pro-Tumorigenic Inflammation in Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma [mouse model]

city: Stanford

first: Chuner

last: Guo

address: 257 Campus Dr

department: Surgery

institute: Stanford University

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense stroma, low immunogenicity, and resistance to therapy. Cancer-associated fibroblasts (CAFs) are key stromal cells within the tumor microenvironment (TME) that drive tumor progression. Interleukin-1 (IL-1) promotes fibrosis, pathogenic inflammation, and poor prognosis in PDAC. Using a novel single-cell multiomic approach, we investigate the IL-1 signaling axis in human and mouse models of PDAC, identifying nuclear factor of activated T cells (NFAT) transcription factors as key mediators. IL1R1+ CAFs activate an inflammatory phenotype associated with elevated NFAT motif activity and gene expression. In vivo, NFAT inhibition in a mouse model of PDAC significantly reduces tumor weight and fibrosis, supporting its pro-tumorigenic role. Our findings suggest that NFAT mediates IL-1-induced inflammation in PDAC, highlighting its potential as a therapeutic target. This study demonstrates the power of multiomic analyses to uncover therapeutic targets within the complex tumor microenvironment.

overall_design: To study IL-1 signaling in a mouse model of PDAC, we developed an orthotopic allograft model via pancreatic inoculation of KPC cells following suture ligation at the mid-pancreas. The suture ligation occludes the pancreatic duct and induces pancreatitis, which helps generate an inflammatory response conducive to PDAC induction while preserving adequate blood supply to the distal pancreas via the short gastric and left gastroepiploic vessels. To model IL-1 signaling inhibition, we chose AF12198, a small peptide antagonist of IL1R1. To study the effects of IL-1 inhibition in vivo, KPC cells were injected into the suture-ligated pancreas, followed by weekly intraperitoneal injections of saline or AF12198. Tissues from normal pancreas, suture ligated pancreas, control KPC tumors, and KPC tumors treated with intraperitoneal injections of AF12198 were harvested and analyzed at 4 weeks.

first: Michelle

last: Griffin

first: Annah

middle: G

last: Morgan

first: Michael

middle: T

last: Longaker

first: Jeffrey

last: Norton


title: NFAT Mediates Pro-Tumorigenic Inflammation in Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma [human multiome]

overall_design: Human PDAC specimens were obtained from patients undergoing surgery at Stanford Hospital under a Stanford University approved IRB protocol (#45051). The patients were counseled in the pre-operative area by one of the manuscript authors. The aims of the study were discussed with the patient. Participation was entirely voluntary. Written, informed consent was obtained from all the patients included in this study prior to surgery. Tissue specimens were collected by one of the authors from the pathologist once the PDAC tumor specimen had been inked (from a non-critical part of the tumor), placed directly into sterile saline, and kept on ice for transport. Tumor specimens were dissociated into single nuclei and profiled for gene expression and chromatin accessibility simultaneously from the same nucleus.


title: Fluorescence tracking Treg movement identifies anti-CCR8 and radiation as a therapeutic combination

city: Portland

first: Wesley

last: Rosales

state: OR

address: 4805 NE Glisan St

institute: Earle A. Chiles Research Institute

summary: Using 10X Genomics single-cell RNA sequencing, we investigated the migration of regulatory T cells (Tregs) following radiation therapy (RT). Employing the Kaede photoconvertible mouse model, we tracked Tregs migrating from the tumor-draining lymph node (TdLN) to the tumor within the post-RT tumor microenvironment. This study serves to identify how RT influences the migrating Treg phenotypes change within the tumor in order to better inform and improve thearaputic strategies for targeting Tregs in combination with RT.

overall_design: MC38 tumors established in Kaede mice. On day 14 post tumor innoculation, TdLNs were photoconverted followed by immediate treatment with 12Gy of radiation. Mice were also injected intraperitoneally with FTY720 on day 15. Tumors were harvested on either 24 hours (day 15) or 72 hours (day 17) post-RT. Tumors were processed into single cell suspensions, magnetically enriched for CD8/CD4 TIL, and stained for with viability dye, CD90.2-Alexa Fluor 700, and Totalseq hashtag antibodies. Kaede green or red live CD90.2+ cells were sorted using a Symphony S6 cell sorter. Each experimental condition had 2 replicates each containing 4 tumors pooled from 4 mice. Samples were immediately processed and libraries were constructed using the Chromium GEM-X Single Cell 5’ Reagent v3 protocol. Libraries were sequenced using the Illumina NovaSeq 6000 with the NovaSeq 6000 S1 Reagent Kit (v1.5). All cDNA pools and resulting libraries were measured using the Agilent Fragment Analyzer with the DNF-474 HS NGS Fragment Kit and Qubit High Sensitivity assays.

first: David

middle: J

last: Friedman

first: Sina

last: Ramin

first: Tiffany

last: Blair

first: Gwen

last: Kramer

first: Shelly

last: Bambina

first: Alejandro

last: Alice

first: Jason

last: Baird

first: Terry

last: Medler

first: Kristina

last: Young

first: Marka

last: Crittenden

last: Gough


title: Whole blood transcriptomics characterize molecular phenotypes of pulmonary Mycobacterium avium complex disease

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

country: Japan

institute: Tsukuba university

summary: Pulmonary Mycobacterium avium complex (MAC) disease shows a range of clinical phenotypes and responses to treatment. While Th1 immunity and neutrophils have been implicated in its pathogenesis, the precise mechanisms remain unclear. Furthermore, comprehensive gene expression analysis in this context are scarce.  This study aimed to elucidate the heterogeneity of pulmonary MAC disease by gene expression profiling of whole blood cells. Unsupervised cluster analysis was performed on whole blood gene expression data at 0M. In addition, we also evaluated the variation in gene expression profiles of whole blood cells before (0M) and after starting treatment (1M) with guideline based therapy (GBT; azithromycin [AZM]/clarithromycin [CAM]+ethambutol [EB]+rifampicin [RFP]).

overall_design: We enrolled 100 patients with pulmonary MAC disease requiring treatment according to standard guidelines. Whole blood cells were collected for RNA-sequencing before (0M) and one month (1M) after the start of guideline based therapy (GBT; azithromycin [AZM]/clarithromycin [CAM]+ ethambutol [EB]+rifampicin [RFP]). Unsupervised cluster analysis was performed on whole blood gene expression data at 0M. In addition, gene expressions in whole blood cells was compared between before (0M) and after starting treatment (1M) with GBT.

first: Chio

last: Sakai

first: Masayuki

last: Nakajima

first: Mizu

last: Nonaka

first: Sosuke

last: Matsumura

first: Masafumi

last: Muratani

first: Nobuyuki

last: Hizawa


title: The cortical microenvironment drives early immune organization and controls early osteoclastogenesis in bone healing

first: Anne

last: Noom

address: Augustenburger Pl. 1

institute: Charité - Universitätsmedizin

summary: We employed single-cell RNA sequencing using the 10x Genomics platform to investigate the cellular dynamics and early immune-stromal interactions during fracture healing in young and aged mice. Tissue-resident and infiltrating cell populations were collected from spatially defined bone marrow and cortical compartments from intact femurs as well as day 3 adn day 7 post-osteotomy. In totall, over 178,000 cells were profiled without prior enrichment or cell sorting, capturing the full diversity of immune and stromal cells involved in early bone regeneration. This dataset provides a comprehensive, unbiased atlas of the early fracture healing response and offers novel insights into the spatial regulation of osteoclastogenesis and the alterations with age.

overall_design:
Young (12-week-old) and aged (52-week-old) C57BL/6J mice underwent standardized femoral osteotomy and were sacrificed at day 3 adn day 7 post-osteotomy. Cells were isolated separately from the bone marrow and cortex compartments of the injured femur, using marrow flushing and enzymatic digestion, respectively. Samples from intact contralateral femurs and age-matched uninjured mice served as additional controls. A total of 30 mice were used to collect tissues (n=5, per age and timepoint). Single-cell suspensions were processed during the 10x Genomics Chromium platform with 3' v3 chemistry. To enable sample multiplexing, cells were stained with hashtag oligonucleotide (HTO) antibodies prior to pooling and library generation.
Sample abbreviations: BM = Bone marrow, CB =  Cortical bone, H = Hematoma.

first: Hülya

last: Oktay

first: Duncan

last: Morgan

first: Sandy

last: Kroh

first: Agnes

last: Ellinghaus

first: Merle

last: Kochan

first: Olufemi

last: Bolaji

first: Ralf

last: Uecker

first: Robert

last: Günther

first: Christian

last: Bucher

first: Antigoni

last: Triantafyllopoulou

first: Simon

last: Haas

first: Katharina

last: Schmidt-Bleek

first: Anja

last: Hauser

first: Birgit

last: Sawitzki

first: Georg

last: Duda


title: t6A tRNA modification defines RIG-I mediated anti-tumour immune response [RNA-seq1]

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

institute: University of Liège

summary: The immune response in cancer, particularly in melanoma, is often hindered by tumour-induced immune evasion strategies, but the precise mechanisms for this remains unclear. Here, we reveal how the tRNA modification threonine-6-adenosine (t6A), mediated by O-sialoglycoprotein endopeptidase (OSGEP), maintains proteostasis in melanoma cells to prevent anti-tumour immune recognition. Cytoplasmic translation depends on the formation of t6A modification in position 37 of tRNANNU for efficient decoding of ANN codons. Defective protein homeostasis resulting from knockdown of OSGEP triggers accumulation of protein aggregates and the formation of stress granules. This disrupted codon-specific translation induces the activation of RIG-I and type I interferon response. Hence, t6A-deficient tumours prompt recruitment and activation of T-cells, affecting tumour growth. Finally, an OSGEP-driven gene signature in melanoma patients is predictive for T-cell infiltration and overall survival. Together, our results reveal t6A tRNA modification as a novel therapeutic target to fight melanoma.

overall_design: RNAseq of RNA on B16F10 murine cell line depleted for shCtr and shOSGEP

first: Cléa

last: Dziagwa

first: Pierre

last: Close


title: RNA-seq of Drosophila Glioma Model with Ca-α1T and Slo Knockdowns

city: LLEIDA

first: Judit

last: Herreros

address: Rovira Roure 80 (lab 2.11)

department: Basic Medical Sciences

institute: University of Lleida-IRBLleida

summary: This dataset presents transcriptomic profiles of Drosophila melanogaster glioma model to investigate the effects of Ca-α1T and Slo knockdowns on gene expression. The samples consist of dissected Drosophila heads. The glioma model used were based on the study by Read et al., 2009 (PLOS Genetics), which established a Drosophila model of glioma by co-overexpressing an activated form of dEGFR (dEGFRλ) and dp110 (dp110CAAX) in glial cells (Read et al., 2009). This work was supported by the research project 'Programa Generación de Conocimiento PID2022-138688OB-I00' funded by the Spanish Ministry of Science and Innovation.

overall_design: The dataset includes the following conditions: Control, Glioma, GliomaxCa-α1T-RNAi and GliomaxSlo-RNAi

first: Lía

last: Alza

first: Carles

last: Cantí

first: Sergio

last: Casas

first: Andreu

last: Casali


title: t6A tRNA modification defines RIG-I mediated anti-tumour [Ribo-seq] immune response

overall_design: Ribosome Sequencing on B16F10 murine cell line depleted for shCtr and shOSGEP


title: NFAT Mediates Pro-Tumorigenic Inflammation in Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma [mouse multiome]

first: Chuner

last: Guo

overall_design: To study IL-1 signaling in a mouse model of PDAC, we developed an orthotopic allograft model via pancreatic inoculation of KPC cells following suture ligation at the mid-pancreas. The suture ligation occludes the pancreatic duct and induces pancreatitis, which helps generate an inflammatory response conducive to PDAC induction while preserving adequate blood supply to the distal pancreas via the short gastric and left gastroepiploic vessels. To model IL-1 signaling inhibition, we chose AF12198, a small peptide antagonist of IL1R1. To counteract any potential immunosuppressive effects of IL-1 inhibition and enhance antitumor immunity, we included IL-12, a potent immune activator. We injected KPC cells into the suture-ligated pancreas, waited for 2 weeks to ensure tumor induction, then performed intratumoral injection with saline, AF12198, IL-12, or a combination of AF12198 plus IL-12. Tissues were harvested and analyzed 2 weeks following intratumoral injection

first: Michelle

last: Griffin

first: Annah

last: Morgan

first: Michael

last: Longaker

first: Jeffrey

middle: A

last: Norton


title: ELOVL5 Promotes the Progression of T-Cell Acute Lymphoblastic Leukemia

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Acute lymphoblastic leukemia (ALL) represents the most prevalent pediatric malignancy, with acute T-lymphoblastic leukemia (T-ALL) comprising 10-25% of ALL cases. Functional studies revealed that ELOVL5 knockdown inhibited T-ALL cell proliferation and enhanced apoptosis in vitro, while in vivo experiments demonstrated that ELOVL5 suppression resulted in reduced tumor burden and extended survival. RNA-seq analysis was conducted and the differently expressed genes were revealed in the ELOVL5-knockdown J.gamma1 cells in comparison to control group.

overall_design: mRNA profiles of J.gamma1 cells transfected with control shRNA (sh-NC) or sh-ELOVL5 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Shuqi

first: Jun

last: Lu

first: Jian

last: Pan


title: NFAT Mediates Pro-Tumorigenic Inflammation in Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma [mouse VIVIT]

overall_design: To test the effects of NFAT inhibition in vivo, we used the orthotopic allograft KPC PDAC model described previously. KPC cells were injected into the suture-ligated pancreas, followed by a 2-week interval to ensure tumor induction. Mice were then treated with intratumoral injections of saline or VIVIT, a small peptide inhibitor of NFAT. Tissues were harvested and analyzed 2 weeks following intratumoral injection


title: t6A tRNA modification defines RIG-I mediated anti-tumour immune response [RNA-seq2]

first: Arnaud

overall_design: RNAseq of RNA after immunoprecipitaition of the RIG-I/RNA complex. IP was performed on B16F10 murine cell line depleted for shCtr and shOSGEP


title: Human microphysiological systems of aging recreate the in vivo process expediting evaluation of anti-gerontic strategies

city: Berkeley

first: Yuchen

last: He

state: California

address:
344 Morgan Hall, University of California
 Berkeley

department: Department of Nutritional Science and Toxicology

institute: University of California Berkeley

summary: The search for biological mechanisms of human aging is stalled by a lack of suitable models and it remains unknown whether, and to what degree, rejuvenation reported in rodents translates to people. Here we report a hiPSC-derived microphysiological system modelling the white adipose tissue-liver axis in the presence of heterochronic human serum to study aging and rejuvenation in humans. We reveal changes in functional and molecular hallmarks of aging and rejuvenation, and we investigate unknown biomarkers and mechanisms of plasticity in human tissue aging as well as potential rejuvenation strategies. The microphysiological chip recapitulates, in 4 days, aging-associated hallmarks that occur after decades of aging in people, including gerontic shifts in gene expression and oxidative DNA damage.  We uncover unknown signaling networks in human aging, knock-on effects of aging in fat on liver, sexual polymorphisms of aging, tissue memory of age, and develop a custom machine learning model for biological age. Combining heterochronic human serum with the microphysiological system allows for rapidly establishing human tissue aging, discovering clinically relevant mechanisms, biomarkers, and testing of anti-gerontic approaches.

overall_design:
To investigate the effect of human serum from old and young donors on WAT-MPS, we performed RNA-seq using RNA extracted from WAT-MPS perfused with old circulatory milieu (OCM) and young circulatory milieu (YCM).
Then, inspired by heterochronic parabiosis, we examined whether switching from OCM to YCM can reverse experimental on-chip aging for WAT-MPS. RNA extracted from OY (old-to-young) and YO (young-to-old) serum treated WAT-MPS, as well as the OO and YY controls, were sequenced.

first: Lin

last: Qi

first: Xiaoyue

last: Mei

first: Alexandra

last: Sviercovich

first: Erzhen

last: Chen

first: Yihan

last: Xia

last: Conboy

first: Irina

first: Andreas

last: Stahl


title: Single-nucleus RNA sequencing revealed the impact of post-mortem interval on the cellular component and gene expression analysis of mouse brains

city: Nanjing

first: Hao

last: Huang

address: Dongnandaxue Road

department: Department of Bioinformatics

institute: Southeast University

summary: Accurate analysis of cell atlas and gene expression in biological tissues using single-nucleus RNA sequencing (snRNA-seq) is closely related to the quality of their RNA quality, and post-mortem interval (PMI) is one of the major origins of RNA variation. Although the use of RNA-degraded tissues in transcriptome analysis remains controversial, such samples are sometimes the sole means to address specific questions. Current studies on the impact of PMI on transcriptome data are limited to large-scale RNA-seq, which ignores cellular heterogeneity. Thus, deciphering the non-cell-autonomous effects caused by PMI is imperative for understanding the cellular and molecular disruption it elicits. Here, we investigated the impact of PMI on cellular components and gene expression using snRNA-seq data from mouse brain tissues of post-mortem. We collected samples that were allowed to decay for varying amounts of time at 25 ̊C prior to snRNA-seq, covering the entire range of RIN values. The different effects on the PMI to the degradation rate of mRNA and rRNA within nuclei, and the mRNA presented a more stable state. Multi-channel analysis revealed the preferential transient depletion oligodendrocytes and OPCs with increasing PMI. In addition, a rapid widespread overregulation of ribosomal transient recruitment to protein (RP) genes in various cells, and reached a plateau at PMI of 36 h. Although state depletion of neuronal cells was not detected, we reported significant upregulation of PMI-dependent RP genes in its subpopulations and their cell loss. Moreover, RP genes showed the greatest differential expression in the subpopulations with greater cell perturbation, and we speculated that aberrant expression of these genes might be associated with cell death. In this study, we systematically investigated the changes in the transcriptome profile of brain tissue induced by PMI at single-cell resolution, and revealed one of the important factors that might be responsible for the changes. In addition, our data complemented a possible explanation for the changes in the cellular state of brain tissue induced by postmortem hypoxia-ischemia, and provided a reference for transcriptome studies of RNA degradation samples.

overall_design: Eight-week-old male C57BL/6J mice were purchased from the Qing Long Shan Dong Wu Fan Zhi Chang, Nanjing, China The animals were anesthetized with 500 mg/kg tribromoethanol (Sigma, Saint Louis, MO, USA) and were killed by cervical dislocation. After the animals were sacrificed, brain tissues (hippocampus) were isolated, placed in 2 mL enzyme-free centrifuge tubes, and stored at 25 ̊C at constant temperature. Postmortem tissues were sampled at 0 h (snap frozen, H0), 24 h (H24), 36 h (H36), 48 h (H48), and 54 h (H54), followed by snap frozen in liquid nitrogen and stored at -80 ̊C until use. For the reliability of the data, we maintained the consistency of the environment for each sample and set up biological replicates of three mice per group.

first: Xiangwei

last: Zhao

first: Yunxia

first: Junjie

last: Ma


title: CD8αα+ intraepithelial lymphocytes recruited from peripheral CD4+ and CD8+ T cells represent functionally distinct lineages

city: Singapore

first: Lukasz

last: Wojciech

address: 5 Science Drive 2 Blk MD4

country: Singapore

institute: Nus

summary: The TCRαβ CD8αα+ intraepithelial lymphocytes (IELs) play a significant role in primary immune defence in the small intestine. The canonical model of their development distinguishes TCRαβ IELs into induced and natural (TCRαβ CD8αα+) types, each influenced by distinct developmental pathways and antigen encounters. It is believed that natural CD8αα+ IELs differentiate solely from triple positive (TP) CD4+CD8αβ+CD8αα+ thymic progenitors that recognized self MHC-peptide complexes with high affinity but avoided deletion during selection. Our investigation reveals that, in addition to this central commitment, the CD8αα+ IELs undergo in situ enrichment through recruitment from peripheral CD4+ and CD8αβ+ T cell populations. We found that the functional makeup of individual clones within the CD8αα+ IEL subset is dictated by their origin. We demonstrate that expression of Bmp7 or Ly49 (Ly49C, F, H, and I) serve as markers indicating the CD8αα+ IELs’ peripheral provenance: CD8αβ+ and CD4+ T lymphocytes, respectively.

overall_design: Rag2–/– animals were intravenously (i.v.) injected with ether conventional CD4+ T cells or CD8αβ+ T cell isolated from the LN of  Themis WT.  Each of the Rag2–/– recipients received minimum 2x106 T cells  in single i.v. injection. After one week from adoptive transfer of T cells, the mLN and small intestine tissues were collected for further investigation. The RNA was isolated from sorted TCRβ CD8αα+, TCRβ CD8αβ+ and TCRβ CD4+ IEL, expanded/developed in Rag2–/– host.

first: Nicholas

last: Gascoigne

first: Kandhadayar

last: Srinivasan


title: Inhibition of the cancer stem cell immune checkpoint SOAT1 suppresses regulatory T cell functions through a trans-cellular 20(S)-Hydroxycholesterol-GPR132 pathway in mice.

city: shanghai

first: wanqi

last: fang

address: jiangwan

institute: fudan

summary: SOAT1 (sterol O-acyltransferase 1) serves as a cancer stem cell-specific immune checkpoint that facilitates trans-cellular signaling through the release of 20-Hydroxycholesterol (20-OHC) and subsequent activation of GPR132 on regulatory T cells (Tregs). This pathway plays a crucial role in modulating the tumor immune microenvironment and can significantly influence the balance between immune activation and suppression. In the context of cancer, SOAT1 is instrumental in regulating the cholesterol metabolism of cancer stem cells. When SOAT1 is inhibited, there is an increase in the secretion of 20-OHC by tumor cells. This oxysterol not only functions as a signaling molecule but also acts as a ligand that binds to GPR132, a G protein-coupled receptor primarily expressed on immune cells, including Tregs. This binding triggers a cascade of intracellular signaling pathways that ultimately enhances the immunosuppressive functions of Tregs. Mechanistically, the activation of GPR132 by 20-OHC leads to downstream signaling events that may involve pathways such as JAK-STAT and PKC signaling, promoting the development and survival of Tregs while enabling them to exert their immunosuppressive effects within the tumor microenvironment. This results in the downregulation of effector T cell activities and impairs the maturation and activation of dendritic cells (DCs), which are pivotal for effective anti-tumor immune responses. The presence of Tregs, particularly in elevated frequencies within tumors, can contribute to an immunosuppressive environment that protects cancer cells from immune-mediated destruction. Thus, the SOAT1-20OHC-GPR132 axis represents a critical mechanism through which cancer cells can evade immune surveillance. By controlling cholesterol metabolism through SOAT1, tumors can manipulate the availability of 20-OHC, amplifying the immunosuppressive capacity of Tregs and facilitating an environment conducive to tumor growth and progression. Targeting SOAT1 and the associated 20-OHC signaling pathway may offer a promising therapeutic strategy to neutralize Treg-mediated immunosuppression. Inhibiting SOAT1 not only disrupts the tumor's ability to produce 20-OHC but also potentially reprograms the immune landscape, promoting a more activated and effective anti-tumor immune response. Overall, SOAT1's dual role as a cancer stem cell-specific immune checkpoint and its involvement in the trans-cellular signaling of 20-OHC make it a valuable target for innovative cancer immunotherapies aimed at enhancing immune recognition and attack on cancer cells.

overall_design: DMSO,scRNAseq;STK,scRNAseq

first: Yahui

last: Ding


title: Methylation analysis of adult patients with severe Obstructive Sleep Apnea before and after CPAP treatment.

city: Cincinnati

first: Bala S. C.

last: Koritala

state: Ohio

address: 3333 Burnet Avenue

department: Division of Pediatric Otolaryngology

institute: Cincinnati Children's Hospital Medical Center

type: Methylation profiling by genome tiling array

summary: Obstructive Sleep Apnea is a sleep-related breathing disorder. Differential methylation analysis was conducted to evaluate differentially methylated regions across the chromosomes in patients with severe OSA compared to healthy subjects. We further evaluated how these differentially methylated regions were altered with long-term (24 months) continuous positive airway pressure treatment.

overall_design: Methylation profiling of peripheral blood mononuclear cells (PBMCs) collected from blood from healthy subjects, patients with OSA, and the same patients following long-term CPAP treatment.

first: Laetitia

last: Gaspar

first: David

last: Smith

first: Ana

last: Álvaro

first: Bala


title: Cell-free transcriptome of Barrett’s Esophagus and Esophageal Cancer [Nanopore - long read]

city: Santa Cruz

first: Vikas

last: Peddu

email: vpeddu@ucsc.edu, dkim142@ucsc.edu

address: 1156 High Street

department: Biomolecular engineering

institute: University of California Santa Cruz

summary: Esophageal adenocarcinoma (EAD) benefits from a large improvement in five-year survival when detected in early stages, therefore, early detection strategies are paramount to mitigating disease. Those diagnosed with Barrett’s Esophagus (BE) are at higher risk for EAD, though there exists no routine screening for EAD. Recent advances in cell-free RNA sequencing aim to create minimally-invasive diagnostic modalities. We present short and long read data from plasma of BE, EAD, and Healthy patients for biomarker discovery.

overall_design: CfRNA samples were sequenced using both long and short reads. Long reads were used for transcript discovery, appended to repeat element and GENCODE transcript annotation files to create an extended transcriptome


title: BMP-Dependent Modulation of ROS Generation and Scavenging Controls Interdigital Cell Death [RNA-seq: Noggin]

city: Yokohama

first: Satomi

last: Ono

state: Kanagawa

address: B-17, 4259, Nagatsuta-cho, Midori-ku

institute: Institute of Science Tokyo

summary: Programmed cell death plays a vital role in shaping limb morphology in amniotes. BMP signaling has been shown to be essential for inducing interdigital cell death, but its relationship with reactive oxygen species (ROS) production, a known driver of this process, remains unclear. Here, we explore the molecular mechanisms by which BMP signaling regulates ROS production and cell death in the interdigital regions of chicken hindlimbs. To identify the ROS-producing cascade genes regulated by BMP signaling, we performed RNA-Seq of the interdigital region with PBS or Noggin bead implantation in chicken hindlimb buds. Subsequently, we performed RNA-seq of the interdigital region from stage 30 to stage 31 chicken hindlimb buds to analyze temporal expression changes of ROS-related genes during the normal progression of interdigital cell death in chicken hindlimbs. This study provides new insights into the ROS-mediated mechanisms of BMP-driven programmed cell death, highlighting the coordinated regulation of ROS generation and scavenging in limb morphogenesis.

overall_design: RNA sequencing of interdigital region 3 (ID3) tissue implanted beads soaked in Noggin (left or right) or PBS (right or left) for 12 hours.

first: Rikito

last: Furukawa

first: Ingrid

last: Cordeiro

first: Kaori

last: Kabashima

first: Kyohei

last: Yoshida

first: Taiki

last: Hatano

first: Koki

last: Hayafune

first: Makoto

last: Kashima

first: Akiha

last: Kagehira

first: Reiko

last: Yu

first: Toru

last: Kawanishi

first: Mikiko

last: Tanaka


title: BMP-Dependent Modulation of ROS Generation and Scavenging Controls Interdigital Cell Death [RNA-seq: Temporal]

overall_design: RNA sequencing of interdigital region 3 (ID3) tissue incubated for 7 days and 4 hours, 6 hours, 8 hours, or 11 hours.


title: Phosphorylated-Ser807 STAT6 protects macrophages from senescence

city: Beijing

first: Zhao

last: Zhou

address: No. 5 Yiheyuan road

institute: Peking University

summary: STAT6 play a key role in homeostasis of macrophages. We identified a new modification of STAT6 at Ser807, which may contribute to STAT6 function. Thus, we generated STAT6 point mutant mice (S807A and S807E). We sequenced the mRNA of macrophages from these mutant mice to rule out the function of the specific phosphorylation.

overall_design: Primary Thio-elicited peritoneal macrophages were isolated from WT and mutant mice. After short-term adherent, the PMs were collected for RNA extraction.

first: Yifu

last: Qiu


title: Cell-free transcriptome of Barrett’s Esophagus and Esophageal Cancer [Illumina - short read]


title: RNAseq of human primary lung adenocarcinoma and brain metastases

city: Pittsburgh

first: Laura

middle: P

last: Stabile

state: Pennsylvania

address: 5117 Centre Avenue

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh, PA, USA

summary: Non-small cell lung cancer (NSCLC) exhibits the highest rates of brain metastases (BM) among all solid tumors and presents a significant clinical challenge. The development of novel therapeutic strategies targeting BM is clearly needed.  We performed RNA sequencing on primary lung adenocarcinoma (LUAD) and matched brain metastases (BM) cases. Additionally, we performed RNA sequencing on MET amplified and non-MET amplified LUAD BM to evaluate transcriptomic differences in these molecular subsets.

overall_design: To investigate transcriptomic differences between primary LUAD and LUAD BM, we performed RNA sequencing (RNAseq) on 5 matched cases. We also sequenced MET amplified (N = 11) versus non-MET amplified (N = 23) LUAD BM.

first: Vinod

last: Kumar

first: Timothy

last: Burns


title: Position-independent emergence of neocortical neuron molecular identity, connectivity and function

city: Geneva

first: Sergi

last: ROIG-PUIGGROS

state: Geneva

address: 1 Rue Michel Servet

department: Fundamental Neuroscience

country: Switzerland

institute: University of Geneva

summary: Brain architectures vary widely across species, yet how neuronal positioning constrains the type of circuits that can be made, and their function, remains poorly understood. Here we examine how neuronal position affects molecular identity, connectivity and function by studying Eml1 knockout mice, which exhibit abnormally located (heterotopic) neurons beneath the cortex. Heterotopic neurons maintained their molecular signatures, formed appropriate long-range connections and exhibited normal electrophysiological properties. They organized into functional sensory-processing centers that mirrored their cortical counterparts, with preserved somatotopic mapping and responsiveness to sensory stimuli. Remarkably, cortical silencing did not impair sensory discrimination, revealing that heterotopic neurons were the main drivers of this function. Hence, equivalent circuits can emerge in different spatial configurations, allowing diverse brain architectures to converge on similar functional outcomes.

overall_design: Mouse single-nucleus RNA seq of FAC-sorted P23 SSp cells of Eml1lox/lox and Emx1:Cre; Eml1lox/lox


title: Escape from X inactivation is directly modulated by Xist non-coding RNA

city: Solna

first: Jasper

last: Panten

address: Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

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

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design: Refer to individual Series


title: RT-qPCR analysis of apoptosis related genes in regrown GOT1-tumors in Balb/c NM after single or fractionated treatment regime of Lu-177-octreotate

city: Gothenburg

first: Eva

last: Forssell-Aronsson

address: Gula Stråket 2B

institute: University of Gothenburg

summary: We recently demonstrated that therapy with hyperfractionated administration of 177Lu-octreotate gave a larger volume reduction of GOT1 tumors compared to single administration of the same amount of radiopharmaceutical. The molecular mechanisms behind this response need to be examined. Transcriptional response in apoptotic-related genes have been found both early and late after treatment with 177Lu-octreotate suggesting that apoptosis-related responses appear also in tumor regrowth stage after treatment. The aims of this work were to compare the expression of genes involved in apoptosis in GOT1 tumors during growth phase from mice treated with 177Lu-octreotate and from untreated mice, and to compare gene expression in regrown GOT1 tumors from mice treated with single injection and hyperfractionated injections. The study was performed on tumor samples previously collected and analyzed by other methods. BALB/c mice, bearing the small-intestine neuroendocrine tumor GOT1, were divided into groups and treated i.v. with 2x15 MBq or 1x30; 2x30 or 1x60 MBq; 3x40, 2x60, or 1x120 MBq177Lu-octreotate. Controls were given saline. After tumor volume reduction and regrowth, the mice were euthanized and tumors were collected, and one part was prepared for IHC analysis, RNA was extracted from the other tumor tissue sample and analyzed by PCR Array for expression of 84 genes involved in apoptosis. Expression of each gene was compared with that in controls. Pathway analysis was performed from genes exhibiting at least 1.5-fold change in expression. The highest regulated gene, compared to untreated controls, was RIPK2 in the group that received 3x40 MBq of 177Lu-octreotate. The most frequently regulated gene among the groups in the study was the pro-apoptotic TNFSF8. Most genes in the study were upregulated. The │FC│-values were all below 3.5. The study present similarities and differences in molecular response between the groups of different 177Lu-octreotate treatments. The results point to a complexity that these studies bring and may have impact on the optimization of therapy in the future.

overall_design: In total, 38 samples were included. Three to five biological replicated were included in each test group, and four biological replicates were included in corresponding controls. An equal amount of total RNA (40 µg) was extracted from all samples, and 200 ng of total RNA was reversed transcribed into cDNA per sample.

first: Mikael

last: Elvborn

first: Nishte

last: Rassol

first: Daniella

last: Pettersson

first: Emman

last: Shubbar

first: Johan

last: Spetz

first: Khalil

last: Helou


title: Effect of depletion of Hand1 and Foxf1 on gene expression during CM differentiation of E14 embryonic stem cells II

first: Jingjing

last: He

state: 2 Sipailou

address: 2 Sipailou

department: School of Life Science and Technology

summary:
To investigate the function of Hand1 and Foxf1 in the regulation of Cardiac differentiation, we established E14 cell lines in which each target gene has been knocked out by sgRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of these cell lines at different time points during the CM differentiation process.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E14 cells and its KO derivatives (Hand1, Foxf1 KO).

first: Chengqi

last: Lin


title: Gene expression profile at single nuclear level of E7.0 Ctrl and Hand1 CKO mouse embryos.

summary: We used single nuclear RNA sequencing (snRNA-seq)  to analyze E7.0 Ctrl and Hand1 CKO mouse embryo.

overall_design: E7.0 Ctrl and Hand1 CKO mouse embryos were digested into single cells using TrypLETM Express (Thermo) at 37°C and analyzed using snRNAseq.


title: Effect of depletion of Hand1 and Foxf1 on gene expression during CM differentiation of E14 embryonic stem cells I

summary: To investigate the function of Hand1 and Foxf1 in the regulation of Cardiac differentiation, we established E14 cell lines in which each target gene has been knocked out by sgRNA.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of these cell lines at different time points during the CM differentiation process.
Comparative gene expression profiling analysis of RNA-seq data for E14 cells and its KO derivatives (Hand1, Foxf1 KO).


title: Epigenetic delineation of the earliest cardiac lineage segregation by single cell multi-omics


title: ChIP-seq analysis of Hand1 and Foxf1 at different stages of directed cardiac differentiation of mouse embryonic stem cells

summary: ChIP-seq data for candidates identified from targeted screen for cardiac differentiation

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Hand1 and Foxf1 using HA antibody in Hand1-HA knock-in cell line and inducible Foxf1-HA OE cell line. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq)  using H3K27AC antibody in WT and Hand1 KO cell line .


title: Early life microbiota skew long-term gene expression and epigenome of bone marrow hematopoietic precursors

status: Public on Dec 07 2025

city: Vancouver

first: Misha

last: Bilenky

state: BC

address: 500 W Broadway

country: Canada

institute: BCGSC

summary: Asthma is the most prevalent chronic childhood disease in developed nations, yet its etiology remains incompletely understood. Emerging evidence suggest a crucial role for the gut microbiota in shaping immune development and future susceptibility to atopic disease. We previously demonstrated that short-chain fatty acids (SCFAs) as fermentation products of normal gut bacteria, regulate an innate type 2 immune axis that serves to dampen susceptibility to allergic lung inflammation. Here, we show that neonatal depletion of SCFA-producing gut bacteria via antibiotics robustly alters Lin⁻Sca-1⁺c-Kit⁺ (LSK) hematopoietic stem and progenitor cell (HSPC) output, resulting in a transplantable atopic immune phenotype:  bone marrow (BM) transplants from these mice generates recipients with increased lung B cell IgE expression, elevated serum levels of IgE, dowstream increased IgE bound to basophils and exacerbated allergic lung inflammation following papain challenge. Notably, neonatal depletion of SCFA bacteria also enhanced susceptibility to chemotherapy (5-fluorocuracil) -induced myelosuppression, marked by impaired neutrophil recovery and increased DNA damage in long-term HSCs. Importantly, these antibiotic effects were reversed by supplementation of antibiotic-treated mice with exogenous SCFA. Single-cell RNA sequencing (scRNA-seq) of LSK HSPCs revealed distinct shifts in gene expression following vancomycin treatment, including increased proliferation-associated signatures with stress-adaptive features. Epigenetic profiling further revealed differential histone acetylation in HSPCs, consistent with an SCFA-mediated epigenetic regulatory mechanism. Collectively, these findings establish an epigenetic link between gut microbiota composition, hematopoiesis, and long-term immune function, providing a mechanistic basis for microbiota-driven atopic disease susceptibility and hematopoietic dysfunction.

overall_design: ChIP-Seq for H3K27ac and H3K27me3 histone modifoications were perfomed on bone marrow derived mouse cells with progenitor potential; the corresponding DNA Input control was also seqeunced.

first: Ahmed

middle: K

last: Kabil

first: Alissa

last: Cait

first: Martin

last: Hirst

first: Wilder

last: Scott

first: Michael

last: Hughes

first: Kelly

last: McNagny


title: Transcriptional profiling of mesothelioma and mesothelial cell lines treated with brefeldin A

city: Nagoya

first: Tatsuhiro

last: Sato

state: Aichi

address: 1-1 Kanokoden

department: Division of Cancer Biology

institute: Aichi Cancer Center Research Institute

summary:
This study investigates the transcriptional response of mesothelioma cell lines to low-dose brefeldin A.
Gene expression profiles were compared to untreated controls to identify transcriptional signatures associated with selective cytotoxicity.

overall_design: Gene expression was analyzed in three mesothelioma cell lines (NCI-H2052, Y-MESO-27, NCI-H2452) and mesothelial MeT-5A cell line treated with brefeldin A or vehicle control. Total RNA was extracted after 48 hours of treatment.


title: Mechanisms of PM2.5 Exposure Impact on the Malignant Progression of Breast Cancer Subtype [MDA-MB-231 RNA-seq]

city: 南充市

first: ziru

last: zhou

state: 四川

address: 顺庆区涪江路234号

institute: 川北医学院

summary: As a major global health threat to women, breast cancer demonstrates significant molecular subtype-specific variations in response to PM2.5 exposure. While epidemiological evidence has confirmed the association between PM2.5 and breast cancer, the molecular mechanisms by which severe PM2.5 pollution drives subtype heterogeneity remain poorly understood and are difficult to characterize using conventional phenotypic approaches. To address this, we apply integrated transcriptomic sequencing and bioinformatics analysis to investigate molecular response mechanisms in three representative breast cancer cell lines—Luminal A (MCF-7), Luminal B (T-47D), and triple-negative (MDA-MB-231)—following severe PM2.5 exposure. Our results reveal that although all three subtypes share a common response to the stress of metal ions and inorganic substances, each exhibits distinct molecular alterations after PM2.5 exposure: the response mechanisms of MCF-7 cells are primarily involved in extracellular matrix remodeling, neuro-lik differentiation, and inflammatory signaling; T-47D cells show significant enrichment in the synaptic membrane, oxidoreductase metabolism, and ferroptosis pathway; and MDA-MB-231 cells exhibit a core response centered on cell cycle progression and mitosis. Furthermore, we identify subtype-specific hub genes and predict the corresponding targeted drugs: Niclosamide targeting BRCA1 in MCF-7, Menadione targeting NQO1 in T-47D, and PHA-793887 targeting CDK1 in MDA-MB-231. This study establishes a comprehensive research framework spanning environmental exposure, cellular response, clinical validation, and drug prediction. The findings provide important insights into the subtype-specific carcinogenic mechanisms of PM2.5 and support the development of individualized prevention strategies for breast cancer.

overall_design: RNA-seq profiling of MDA-MB-231 cells under control (CK1_231, CK2_231, CK3_231) and experimental treatment (CQ1_231, CQ2_231, CQ3_231) conditions. The study includes three biological replicates per condition to investigate transcriptomic changes in response to the experimental treatment.


title: Histone H3K4 methylation regulation and three-dimensional aggregating distribution of a subset of genomic loci mediated by CHD3 homolog PKL in Arabidopsis

first: Mengfei

last: Song

state: Beijing

address: 北京市海淀区颐和园路5号

institute: Peking university

summary: Arabidopsis PICKLE (PKL) is a putative CHD3-type chromatin remodeling factor. Despite its importance in environmental stimulus responses and plant development, how PKL is recruited to target gene loci and its detailed regulatory role in controlling target gene chromatin states is not fully understood. Here, we report genome-wide evidence for the recruitment of PKL by specific transcription factors, establish the molecular connection between PKL and H3K4me2/3, and demonstrate PKL is essential for the space-clustering distribution of its target genes. We captured the genome-wide binding sites of PKL by ChIP-seq using endogenous antibody. Further analyses gave evidence that plant-specific transcriptional factors containing TCPs, PIFs, and HY5, play dominant role in recruiting PKL to its target gene loci in Arabidopsis thaliana. The chromatin of PKL target genes showed significantly enriched depositions of H3K4me2 and H3K4me3. PKL directly interacted with the COMPASS complex scaffold protein WDR5A. It seems that PKL acts through WDR5A to stabilize the highly accumulated levels of H3K4me2 at specific euchromatic loci. Strikingly, PKL-bound genes distributed space-contiguously, the manner of which is dependent on PKL and PKL-interacted TFs. Moreover, the working model of PKL we proposed in this study is likely conserved in liverwort and rice. PKL associates with specific gene loci by interacting with specific transcription factors and promotes H3K4me2 depositions locally. Meanwhile, PKL acts as a hub mediating its target gene loci spatial-aggregation. PKL and its homologs in rice and liverwort might display similar molecular functions

overall_design: Three biological replicates of each genotype were used for high-throughput sequencing analysis. All experiments wer conducted using  9-day-old seedlings grown in continuous white light.

first: Yuqiu

last: Wang

first: Xing

last: Deng

first: Danmeng

last: Zhu


title: The G3BP Stress-Granule Proteins Reinforce the Translation Program of the Integrated Stress Response

city: Boston

first: Jarrett

last: Smith

state: MA

address: 455 Main st, Room 627

institute: Whitehead Institute

summary: When mammalian cells are exposed to extracellular stress, they coordinate the condensation of stress granules (SGs) through the action of key nucleating proteins G3BP1 and G3BP2 (G3BPs) and, simultaneously, undergo a massive reduction in translation. Although SGs and G3BPs have been linked to this translation response, their overall impact has been unclear. Here, we investigate the longstanding question of how, and indeed whether, G3BPs and SGs shape the stress translation response. We find that SGs are enriched for mRNAs that are resistant to the stress-induced translation shutdown. Although the accurate recruitment of these stress-resistant mRNAs does require the context of stress, a combination of optogenetic tools and spike-normalized ribosome profiling demonstrates that G3BPs and SGs are necessary and sufficient to both help prioritize the translation of their enriched mRNAs and help suppress cytosolic translation. Together these results support a model in which G3BPs and SGs reinforce the stress translation program by prioritizing the translation of their resident mRNAs.

overall_design: Ribo-seq and RNA-seq were performed on replicate samples from HCT116 cells treated with 500 uM sodium arsenite for 1 hour, heat shocked at 45C for 25 min, depleted of their endogenous G3BPs using Auxin induced degrons, or that had  SGs, OGs, or SOGs, purified from them and were subsequently sequeneced.

first: David

last: Bartel


title: A bifunctional optical reporter for tracking estrogen response dynamics in neurons

city: Los Angeles

first: J Edward

last: van Veen

address: 610 Charles E Young Dr

department: IBP

institute: University of California, Los Angeles

summary: Estrogens are inherently dynamic signaling molecules whose fluctuations induce profound shifts in physiology and behavior. However, methods for tracking the dynamics of estrogen action in vivo are limited and not tissue-specific, making it difficult to directly relate dynamics to ongoing physiological, behavioral, and neural changes. Traditionally, estrogen sensitive cells have been identified by metrics such as receptor expression or radioactive ligand binding, but these measures do not capture the dynamic nature of hormone response. In addition, current methods for assessing the dynamics of estrogens in an individual, including microdialysis and vaginal cytology, lack temporal and spatial resolution.To address this need we developed a bifunctional reporter called neuro-seeER (neuronal see Estrogen Response) that can be used to track changes in exogenous and endogenous estrogen dynamics in vitro and in vivo, including longitudinally in behaving animals. We confirmed that the fluorescent response requires estrogen receptor expression, is specific to activation with estradiol, and is consistent with the timescale of transcriptional induction.  Neuro-seeER expression in the hypothalamus of Esr1-Cre mice revealed dynamic labeling of estrogen-responsive cells following treatment with exogenous estradiol, and fluorescence-aided cell sorting followed by RNA-sequencing confirmed that high neuro-seeER response is associated with enriched expression of genes associated with endogenous estrogen responses. Using a novel “snapshot” photometry method to track the dynamics longitudinally in vivo, we demonstrate that we can robustly detect exogenous estrogen response across multiple hypothalamic sites simultaneously.  Finally, we demonstrate that this tool is uniquely suited to capturing endogenous estrogen response dynamics in vivo across the long timescale of the estrous cycle, revealing individual differences in neural estrogen dynamics. Together, these findings reveal unexpected cellular and temporal heterogeneity of the transcriptional response and demonstrate the feasibility of tracking the dynamics of hormonal response alongside additional neural, cell signalling, or behavioral measures.

overall_design: Esr1-Cre mice were stereotaxically transduced with neuro-seeER, a reporter that marks Cre+ neurons in FusionRed and reports estrogen action in EGFP. Hypothalami were rough dissected and dissociated into single cell suspensions before being gated for FusionRed positivity and then divided into high and low EGFP fractions. These fractions were processed for RNA sequencing. Thus all samples are predicted to contain Esr1+ neuons. High-gfp samples are predicted to be comprised of neurons actively responding to estrogens, whereas low gfp samples are not responding to estrogen.

first: Ally

last: Cara

first: Stephanie

last: Correa