title: Transcriptomic Profiling of L-Proline Induced Ferroptosis Reveals PPARγ-Mediated Regulatory Networks in HFpEF Progression

status: Public on Sep 17 2025

first: Kai

last: Huang

address: 168 Changhai Road Shanghai

institute: Changhai hospital

summary: This study investigates the molecular mechanisms by which L-proline contributes to diabetic heart failure with preserved ejection fraction (HFpEF) through the induction of ferroptotic stress under metabolic conditions. We found that L-proline exacerbates ferroptosis-related oxidative and lipid peroxidation stress in cardiac tissue within a metabolically driven HFpEF context. Mechanistically, L-proline markedly suppressed PPARγ signaling, a key regulator of lipid metabolism, redox homeostasis, and ferroptosis resistance. Downregulation of PPARγ was accompanied by upregulation of pro-ferroptotic mediators, including ACSL4 and TFR1, indicating enhanced iron-dependent lipid peroxidation and ferroptotic susceptibility. These findings support a mechanistic link between amino acid metabolic remodeling and fibroblast-centered cardiac vulnerability in diabetic HFpEF, highlighting the role of the proline–PPARγ–ferroptosis axis in promoting myocardial fibrosis and diastolic dysfunction under chronic metabolic stress.

overall_design: A metabolically driven HFpEF model was established in mice through high-fat diet–associated metabolic stress. Animals were randomly assigned to Control and L-proline–treated groups. Following the experimental intervention period, left ventricular tissues were collected for total RNA extraction and transcriptomic profiling. RNA sequencing was performed on the Illumina NovaSeq 6000 platform to identify differentially expressed genes related to L-proline–associated ferroptotic signaling and PPARγ pathway modulation. Subsequent bioinformatic analyses included differential expression analysis, pathway enrichment analysis, and functional annotation to delineate molecular signatures underlying proline-mediated metabolic remodeling and ferroptosis in HFpEF.

first: Lin

last: Han


title: KLF7 is a general inducer of human pluripotency

status: Public on Sep 19 2025

city: Padua

first: Elena

last: Carbognin

state: --- Select One ---

address: via Ugo Bassi 58b

department: Biology

country: Italy

institute: University of Padua

type: Expression profiling by high throughput sequencing

summary: Pluripotency is the capacity to give rise to all differentiated cells of the body and the germ line and is governed by a self-reinforcing network of transcription factors. The forced expression of only some of these factors enables the reprogramming of somatic cells to pluripotency. In murine cells, several kruppel-like factors (KLFs) have been identified as stabilisers and inducers of pluripotency. Human somatic cells are routinely reprogrammed by expression of KLF4 in combination with OCT4, SOX2 and cMYC (OSKM). An extensive transcriptome analysis revealed, however, that KLF4 is barely expressed in conventional human pluripotent stem cells (PSCs). Here we show that KLF7 is robustly expressed in conventional human PSCs and it allows transcription factor-mediated somatic reprogramming. Moreover, we find that KLF7 is highly expressed in naive PSCs and its forced expression in conventional hPSCs induces upregulation of naive markers and boosts efficiency of chemical resetting to naive PSCs, overall suggesting that KLF7 is a general human pluripotency factor and an inducer of pluripotency.

overall_design: Transcriptional analysis of human fibroblasts reprogrammed to iPSCs with OSKM or OSK7M reprogramming cocktails (samples 1-22) and transcriptional analysis of human iPSC expressing KLF7 or an EMPTY control (KiPS KLF7 and KiPS EMPTY) subjected to chemical resetting to naive PSCs (samples 23-47). Samples analysed for reprogramming: 3 replicates of BJ human fibroblasts (fibroblasts controls), 3 replicates of H9 hESCs (conventional PSCs controls), 4 replicates of OSKM P4 (iPSCs obtained with OSKM reprogramming cocktail and stabilised in colture for 4 passages), 4 replicates of OSKM P7 (iPSCs obtained with OSKM reprogramming cocktail and stabilised in colture for 7 passages), 4 replicates of OSK7M P4 (iPSCs obtained with OSK7M reprogramming cocktail and stabilised in colture for 4 passages), OSK7M P7 (iPSCs obtained with OSK7M reprogramming cocktail and stabilised in colture for 7 passages). Samples analysed for chemical resetting: 3 replicates of HPD00 primed-iPSCs (primed controls), 3 replicates of HPD01 naive-iPSCs (naïve controls), 3 replicates of HPD06 naive-iPSCs (naïve controls), 4 replicates of KiPS EMPTY, 4 replicates of niPSC EMPTY (KiPS EMPTY post-chemical resetting), 4 replicates of KiPS KLF7, 4 replicates of niPSC KLF7 (KiPS KLF7 post-chemical resetting).

first: Mattia

last: Arboit

first: Irene

last: Zorzan

first: Paolo

last: Martini

first: Graziano

last: Martello


title: Genetic, Hormonal, and Transcriptomic Analyses Highlight the Crucial Role of Phytohormones in First Branch Angle (FBA) Regulation in Pepper

status: Public on Sep 18 2025

city: Nanchang

first: Xinjie

last: Yuan

state: Jiangxi

address: No. 602, Nanlian Road

department: Institute of Vegetables and Flowers

country: China

institute: Jiangxi Academy of Agricultural Sciences

summary:
Background The first branch angle (FBA) is a critical trait influencing plant architecture, yield, and mechanized harvesting efficiency in pepper (Capsicum annuum L.). However, the genes and regulatory processes involved remain largely unclear.
Results The phenotypic evaluation of 220 pepper accessions revealed significant genetic variation in FBA, with a broad-sense heritability of 93.26%, indicating a strong genetic foundation and making it a stable trait for selection. A genome-wide association study (GWAS) with mixed linear model and FarmCPU detected 25 significant SNPs related to FBA. Several candidate genes were identified, encompassing components of brassinosteroid signaling, gibberellin signaling, serine/threonine-protein kinase signaling, and cell wall modification. To functionally contextualize these genetic findings, two accessions with divergent FBAs (compact B010 and loose B003) were selected for cytological and hormonal analyses. The paraffin sections stained with Periodic Acid-Schiff showed that the compact B010 exhibits more starch granules in endodermal amyloplasts, while the loose B003 has larger cell size on the adaxial side. Hormonal analysis based on HPLC-MS/MS revealed higher auxin levels in the compact B010 and higher gibberellin, cytokinin, brassinosteroid, and strigolactone levels in the loose B003. These results suggest a mechanism whereby brassinosteroid/gibberellin-mediated cell expansion, potentially through the action of cell wall modification genes, drives the loose architecture of B003. Furthermore, RNA-Seq and qRT-PCR confirmed the coordinated regulation of the key phytohormone pathways (auxin signaling; cytokinin, gibberellin, and brassinosteroid biosynthesis) and serine/threonine-protein kinase signaling. Therefore, our work integrates multi-layered analyses to propose a regulatory framework for FBA in pepper: genetic loci associate with alterations in phytohormone regulation, kinase activity, and cellular traits, which orchestrate the transcriptomic, hormonal, and cytological changes that collectively determine branch architecture.

overall_design: At the early flowering stage, the first branch sites of B010 and B003 were sampled for RNA sequencing, with three biological replicates for each accession.


title: Immunogenomic Diversity of Triple-Negative Breast Cancers in Obese and Non-obese Black and White Women

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

country: USA

institute: LSUHSC

summary: Racial disparities in incidence and outcomes of triple-negative breast cancer (TNBC) have been attributed to ancestry, socioeconomic factors and/or obesity. We studied 253 TNBCs from 128 Black and 125 White women. Arms were balanced for age, AJCC stage, histological grade and molecular subtypes, and differed significantly in BMI distribution, obesity, and Area Deprivation Index. We examined survival rates, whole-transcriptome RNASeq and genetic ancestry. In our sample, Black race or obesity were not intrinsically predictive of poor outcomes. TNBC molecular portraits varied with stage and biological aggressiveness, irrespective of race.  We identified a novel group of TNBCs with a distinctive luminal-like and stem-cell-like transcriptional profile that were equally distributed among Blacks and Whites. Genetic ancestry was highly admixed. Immune deconvolution showed a higher abundance of several immune cell populations in tumors from Blacks, which may have precision therapeutic significance, warranting further investigation of potential drivers of tumor immunity.

overall_design: Retrospective, two-arm observational study. The final sample set included  253 TNBCs - from 128 Black and 125 White women. The two arms were balanced with respect to age, AJCC stage, histological grade and molecular subtype. They differed significantly in BMI distribution, obesity rates and Area Deprivation Index. RNAseq was used to determine gene expression profiles associated with TNBC in African American (AA) and European American (EA), with and without obesity, from Louisiana. Gene profiles were used to determine associations with race/ethnicity, obesity stage, tumor stage, prediction of immune infiltration and survival

first: Fokhrul

last: Hossain

first: Denise

last: Danos

first: Xiao-Cheng

last: Wu

first: Luis

last: Del Valle

first: Chindo

last: Hicks

first: Jiande

first: Jerneja

last: Tomsic

first: Susan

last: Neuhausen

first: Yuan

middle: C

last: Ding

first: Kavitha

last: Mukund

first: Zahra

last: Mesrizadeh

first: Shankar

last: Subramaniam

first: Victoria

last: Seewaldt

first: Augusto

last: Ochoa

first: Lucio

last: Miele


title: Profiling linkage-specific ubiquitin chain functions reveals a key role of K29-linked ubiquitylation in epigenome integrity

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Linkage-specific ubiquitin (Ub) chains dictate the functional outcome of many critical Ub-dependent signaling processes. However, the functions and targets of several poly-Ub topologies remain poorly understood due to a lack of tools for their specific detection and manipulation. To remedy this knowledge gap, we applied a cell-based Ub replacement strategy enabling specific, conditional abrogation of each of the seven lysine-based Ub chain types in human cells to comprehensively profile global ubiquitylation changes resulting from disabling formation of individual Ub chain types. Focusing on K29-linked ubiquitylation, we found that this linkage type is enriched among chromatin-associated proteins, and that the H3K9me3 methyltransferase SUV39H1 is a prominent cellular target of this modification. We demonstrate that K29-linked ubiquitylation is essential for the proteasomal degradation of SUV39H1 despite its extensive modification by K48-linked ubiquitylation, and that K29-linked ubiquitylation of SUV39H1 is catalyzed and reversed by TRIP12 and TRABID, respectively. Importantly, preventing K29-linked ubiquitylation of SUV39H1 markedly increases H3K9me3 levels, but not other histone marks. Collectively, our Ub replacement cell line panel and datasets provide valuable resources for illuminating cellular functions of linkage-specific ubiquitylation processes and reveal a key role for K29-linked ubiquitylation in epigenome integrity.

overall_design: Quantitative chrommatin immunoprecipitation DNA- sequencing (qChIP-seq) for H3K9me3

first: Javier

last: Arroyo-Gómez

first: Nazaret

last: Reverón-Gómez


title: Toxoplasma gondii chromatin remodeler SWI/SNF controls parasite division and stage specific gene expression

city: Nanning

first: Dandan

last: Hu

state: China

address: Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.

institute: Guangxi University

summary: The SWI/SNF complex is evolutionarily conserved across species, initially identified in yeast, and later associated with various human cancers. In research on Toxoplasma gondii, this complex specifically creates nucleosome-free regions (NFRs) at the promoters of male gamete-specific genes, thereby activating their expression. Disruption of this complex results in the loss of male gametes. Although the SWI/SNF complex is relatively conserved across species, its specific role in T. gondii remains unclear. In this study, we first catalogued the core ATPase subunits of chromatin remodeling complexes and characterized the function of the SWI/SNF ATPase subunits TgSNF2a and TgSNF2b. We found that deletion of these two subunits severely impaired tachyzoite growth and altered the mode of division from endodyogeny to endopolygeny. Disruption of the complex led to a reduction in chromatin accessibility, suppressed stage-specific gene expression during the tachyzoite stage, and indirectly upregulated early endodyogeny stage (EES) genes by downregulating transcriptional repressors such as AP2XII-2 and AP2XII-5, and disrupting interactions with the MORC complex. Consequently, the knockout strains exhibited a shift in gene transcription toward the EES stage. These results provide new insights into the epigenetic regulation of sexual reproduction in T. gondii, offering potential strategies for controlling toxoplasmosis.

overall_design:
To assess the functions of TgSNF2a and TgSNF2b in T. gondii, an indole-3-acetic acid (IAA) degradation (mAID) system was used to generate inducible knockdown (iKD) of TgSNF2a and TgSNF2b parasites. Double knockdown parasites were also pruduced by using mAID system. Potentially regulated genes of TgSNF2a and TgSNF2b were investigated by RNA-seq using iKD parasites with or without IAA treatment for 24 or 72 hours.  Two or three biological replicates were employed.
To further characterize the genome occupancy of TgSNF2a and TgSNF2b, CUT&Tag experiments were performed using the endogenously 3xHA tagged parasite and ME49 strain.

first: Xuan

last: Li

first: Jiayi

last: Huang

first: Xueqin

last: Zou

first: Hongbin

last: Si

first: Xun

last: Suo

first: Xingju

last: Song


title: scRNAseq timecourse from wildtype C. elegans larvae sampled from 18 to 24 hours at 25oC, with FACS sorting cells using ubiquitous markers.

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: We collected a timecourse scRNA-seq dataset from wildtype C. elegans larvae, using ubiquitous flurophores to FACS sort cells in order to collect as many tissues as possible. The data deposited were collected from one single experiment with pools A,B,C representing different 10X runs for a given sample. The overall goal of the experiment was to identify the tissues in which oscillating gene expression occurs, and to understand tissue-specific differences in oscillatory output. We were able to identify 18 different tissues, 7 of which show clear oscillatory expression patterns.

overall_design: HW3125 worms, expressing transgenes for ubiquitous GFP and mCherry expression, were synchrnoized as hatched L1 larvae. 200,000 worms per plate were seeded onto 16 peptone-rich XL plates coated with 10x concentrated OP50 and grown at 25oC. 600,000 worms (3 XL plates) were collected at each timepoint, 18h, 20h, 22h and 24h after seeding. At each timepoint, worms were immediately processed to isolate cells, FACS sort, and perform 10x scRNA-seq protocol. To dissociate single cells, we followed the protocol of Cao et al., 2017, Science) with minor adjustments. To remove animal debry, cells were then sorted on a BD FACSAria using the GFP and mCherry markers. Following sorting, cells were diluted and libraries prepared using the 10x Genomics protocol with the Chromium Controller (10x 3'RNAv3). Sequencing was then performed using NextSeq HIGH-OUT 75 cycle paired-end sequencing.

first: Gaidatzis

last: Dimos

first: Graf-Landua

last: Maike

first: Methot

last: Stephen P.

first: Brancati

last: Giovanna

first: Braun

last: Kathrin

first: Aluri

last: Sirisha

first: Kohler

last: Hubertus

first: Smallwood

last: Sebastien

first: Großhans

last: Helge


title: RNA-seq analysis of human iPSC derived hepatocyte and stellate cell surround organoids (iHSOs)

city: bunkyo-ku

first: Masato

last: Miyoshi

address: yushima

department: Gastroenterology

country: Japan

institute: Tokyo Medical and Dental University

summary: To investigate the interaction between hepatocytes and hepatic stellate cells in iHSOs, we established contact co-culture organoids using iPSC-derived HSCs and hepatocytes; termed iPSC-derived hepatocyte-stellate cell surround organoids (iHSOs). Sorting based on fluorescent labeling (GFP/tdTomato) of the iPSCs used in iHSOs allowed analysis of each cell type. A comprehensive RNA-seq analysis was conducted.

overall_design: In addition to preparing RNA-seq samples from hepatocytes and HSCs sorted from iHSOs using FACS (CoSp-SortHep, n=3; CoSp-SortHSC, n=3), we also prepared RNA-seq samples from iPSCs (n=1), iPS-Heps (n=2), iPS-HSCs (n=2), iPS-Hep mono-spheroids (iPS-Hep-Sph, n=2), and iPS-HSC mono-spheroids (iPS-HSC-Sph, n=2).

first: Tomohiro

last: Mochida

first: Sei

last: Kakinuma


title: ATAC-seq time course (in parallel to mRNA-seq time course), of control or GRH-1 depleted C. elegans larvae sampled at 20oC

summary: The goal of these experiments were to evaluate how dynamic changes to gene expression (mRNA-seq) and chromatin accessibility (ATAC-seq) were affected by the acute depletion of the transcription factor GRH-1. To do so, we employed a strain that incorporated an auxin-inducible degron at the endogenous grh-1 locus (Meeuse et al., 2023, EMBO J). We can thereby acutely deplete GRH-1 in growing larvae. Based on linear modeling incorporating ATAC-seq dynamics and ChIP-seq data, we hypothesized that GRH-1 depletion should affect accessibility at a specific set of chromatin regions and expression of a specific set of genes.

overall_design: ATAC-seq was performed on nuclei isolated from larval C. elegans (HW2434 strain - grh-1::degron::3xFLAG), treated with either EtOH or 250 uM Auxin, and collected in a time course spanning 12-13 hours of development. Synchronized L1 animals were grown at a density of 1 animal/uL in liquid culture (S-Basal + OP50 at OD600=2.8) for 20-21 hours before splitting the culture to treat half the animals with EtOH, and the other half with 250 uM Auxin. Every hour following treatment, 14000 animals were collected for ATAC-seq. Nuclei were prepared from frozen animal pellets by douncing similar to a previosuly established protocol (Daugherty et al., 2017, Genome Res.). Library was sequenced using NovaSeq S1 2x50bp Paired-end reads.

first: Maike

last: Graf-Landua

first: Stephen P

last: Methot

first: Michaela

last: Woelk

first: A Alexander T

last: Smith

first: Helge

last: Großhans


title: Whole-organism C. elegans L2/L3 NHR-23 ChIP-seq [NHR23_ChIPseq]

first: Dimos

last: Gaidatzis

summary: We performed ChIP-seq to determine chromatin regions bound by transcription factor NHR-23, and thereby potential binding motifs and sites, in C. elegans (larval stage 2) whole organisms

overall_design: One sample was used as "input", ie non-specific pulldown.  Two NHR-23-specific samples were generated by collecting after 20 hrs at 25°C to cover the L2-L3 stage.

first: Woelk

last: Michaela

first: van der Does

last: Marit

first: Gaidatzis

last: Dimos


title: ATAC-seq time course (in parallel to mRNA-seq time course), of wildtype C. elegans larvae sampled from 14h to 30h at 25oC [ATACseq_N2]

summary: We collected timecourse samples for ATAC-seq, in parallel to mRNA-seq, in order to have matching samples for comparisson. The overall goal was to link oscillating gene expression (RNA-seq) to oscillating changes in chromatin accessibility (ATAC-seq), in order to identify enhancer elements that are critical to oscillatory regulation.

overall_design:
ATAC-seq was performed on nuclei isolated from larval C. elegans (N2 strain) in a time course spanning 16 hours of development. Synchronized L1 animals were seeded (2000 animals per plate) on multiple 10 cm NG 2% plates coated with OP50 bacteria, and then 7 plates per timepoint (14000 animals) were harvested every hour starting 14 hours after seeding. Nuclei were prepared from frozen animal pellets by douncing similar to a previosuly established protocol (Daugherty et al., 2017, Genome Res.). Library was sequenced using the NextSeq HIGH-OUT 75 Cycle Paired-end protocol.
In these experiments, samples were collected in parallel for mRNA-seq and ATAC-seq. And two independent experimental replicates were performed.

first: Graf-Landua

last: Maike

first: Methot

last: Stephen P


title: Quantifying HLA transcripts by genotype in chimeric mixtures at single-cell resolution [scrHLAtyping]

city: Seattle

first: Sami

middle: B

last: Kanaan

address: 1100 FAIRVIEW AVE N

department: TST

institute: FRED HUTCHINSON CANCER CENTER

summary: Gene products from the highly variable major histocompatibility locus, including HLA, are essential for self-recognition and immune surveillance of malignancy. Following allogeneic hematopoietic cell transplantation (alloHCT), genetic and epigenetic alterations in HLA can drive  disease recurrence, making precise HLA assessment critical for determination of future therapy. However, current methods lack the sensitivity to quantify HLA transcripts at the single cell level, limiting their clinical utility. We introduce scrHLA-typing, a novel method that accurately identifies and quantifies HLA transcripts in single cells using hybridization capture and long-read sequencing. When applied to samples from patients with post-transplant relapse, scrHLA-typing successfully detected allele-specific expression of MHC gene products at clinically actionable levels. By characterizing allele expression in residual leukemia cells, our assay identified differences in expression patterns among patients. This capability highlights scrHLA-typing’s potential to improve risk stratification and guide the selection of appropriate salvage therapies, enhancing personalized treatment strategies after post-transplant relapse.

overall_design: Mononuclear cells from bone marrow aspirates from patients with relapsing AML post-alloHCT were density-gradient collected and magnetically enriched for cells expressing on their surface the CD34 progenitor marker (in one patient, the CD117 marker was used instead). From both unsorted and enriched cells, full transcriptome single-cell libraries (10x Genomics) were generated using 5-prime chemistry capture (by default, unless otherwise indicated, i.e., prefix '3p' tagged to the sample name) and short-read sequenced to quantify global RNA expression. For most patients, cells were also stained prior to droplet capture with oligonucleotide-barcoded antibodies specific to cell surface/principal lineage antigens, and antibody-derived tags (ADT) were short-read sequenced and quantified. From the leftover transcriptomes, single-cell barcoded HLA full transcripts were magnetically enriched with biotinylated hybridization probes HLA-specific and streptavidin magnetic beads, afterwhich they were PCR-amplified and long-read sequenced. The HLA probe design incorporated all known HLA alleles available from the IMGT/HLA reference. In a few cases, long-read sequencing of HLA transcripts was augmented using ‘multiplexed arrays isoform sequencing’ (MAS-seq). The molecular method was supplemented with a computational pipeline we designed to iteratively align reads, predict genotypes, filter errors, and summarize HLA counts. Short-read and long-read sequencing were conducted on Illumina and PacBio platforms, respectively.


title: A Scheduler for Rhythmic Gene Expression

summary: Genetic oscillators drive precisely timed gene expression, crucial for development and physiology. Using the C. elegans molting clock as a model, we investigate how oscillators can schedule the orderly expression of thousands of genes. Single cell RNA sequencing reveals a broad peak phase dispersion in individual issues, mirrored by rhythmic changes in chromatin accessibility at thousands of regulatory elements identified by time-resolved ATAC-seq. We develop a linear model to predict chromatin dynamics based on the binding of >200 transcription factors. This identifies nine key regulators acting additively to determine the peak phase and amplitude of each regulatory element. Strikingly, these factors can also generate constitutive, non-rhythmic activity through destructive interference. The model accurately predicts the impact of GRH-1/Grainyhead perturbation on both chromatin and transcript dynamics, validating its power. This work provides a powerful framework for understanding how combinatorial, non-cooperative transcription factor binding schedules complex gene expression patterns in development and other dynamic biological processes.

overall_design: Refer to individual Series


title: CAR-T cells shape the immunological potential of the tumor microenvironment

city: Boston

first: Julia

last: Frede

address: 450 Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: CAR-T cells lose effectiveness over time and subsequent lines of immunotherapy become increasingly less potent. Investigating patients from two independent clinical trials at single cell resolution, we demonstrate that CAR-T cell treatment drives bystander CD8+ T lymphocytes along the differentiation path, which initially supports a clonal anti-tumor immune response, but ultimately results in terminal exhaustion, reduced potential for self-renewal and sustained depletion of the tumor-reactive T cell repertoire. The immune environment changes orchestrated by CAR-T cells result in reduced immune capacity, which could potentially diminish responses to other immunotherapies, such as response to checkpoint blockade. We describe the transcriptional modules that regulate plasticity of the T lymphocytic compartment and identify Tim3/Gal9 and CD27/CD70 as two crucial interactions of the cell-cell communication network that regulates immune capacity. The ability of the CAR-T cells to shape a regulatory immune microenvironment may explain why repeated immunotherapies become increasingly less successful, even when targeting distinct antigens. Our studies provide a framework for assessing and manipulating the ‘mileage’ of the immune system as a predictive marker and a therapeutic opportunity.

overall_design:
Single cell expression profiles of 4 patients with relapsed/refractory multiple myeloma (RRMM) treated with BCMA-directed CAR-T cells profiled with 10X Genomics technology (5' expression profiling) and single cell expression profiles of T cells and CAR-T cells isolated from RRMM 24 patients treated with BCMA-directed CAR-T cells profiled with plate-based scRNA-Seq (Smartseq2).
Submitter declares that the raw data is not provided due to patient privacy concerns.

last: Poller

first: Kayleen

last: Shi

first: Hannah

last: Stuart

first: Noori

last: Sotudeh

first: Claire

last: Havig

first: Klothilda

last: Lim

first: Caroline

middle: R

last: Wiggers

first: Eugene

middle: Y

last: Cho

first: Tushara

last: Vijaykumar

first: Johannes

middle: M

last: Waldschmidt

first: Monica

middle: S

last: Nair

first: Praveen

last: Anand

first: Valeriya

last: Dimitrova

first: Anna

last: Montanaro

first: Nikhil

last: Munshi

first: Kenneth

last: Anderson

first: Nathan

last: Martin

first: Shari

last: Kaiser

first: Marc-Steffen

last: Raab

first: Noopur

last: Raje

first: Birgit

last: Knoechel

first: Jens

middle: G

last: Lohr


title: Quantifying HLA transcripts by genotype in chimeric mixtures at single-cell resolution [scrHLAtyping_MAS-seq]

first: Sami

last: Kanaan


title: Quantifying HLA transcripts by genotype in chimeric mixtures at single-cell resolution [10x_RNA_ADT-seq]


title: An siRMSD parameter of structural distortion induced by chemical modification is predictive of the off-target effect of siRNA_(2/2)

status: Public on Sep 16 2025

city: Bunkyo-ku

first: Seongjin

last: An

state: Tokyo

department: Graduate School of Frontier Science

institute: The University of Tokyo

summary: To investigate effects of siRNA with various 2'- modifications on genome-wide off-target effect, we analyzed gene expression profile of HeLa cells transfected by their siRNAs.

overall_design: Total RNAs were extracted from HeLa cells transfected by mock, unmodified, 2'-deoxy-2'-fluoro, or 2'-O-methyl modified siRNA and performed microarray analysis.

first: Kumiko

last: Ui-Tei


title: mRNA-seq of wildtype C. elegans L3 larvae sampled at molt entry and molt exit [RNAseq_MoltEntry-MoltExit_N2]

first: Dimos

last: Gaidatzis

summary: In order to determine the gene expression profile of worms at molt entry and exit in more detail, we collected animals specifically at these points based on signal from a luciferase-based developmental assay (Olmedo et al., 2015, Genetics). This approach allowed us to pool sufficient animals to perform mRNA sequencing in order to specifically determine the transcriptome of animals at these developmental stages. Using these transcriptome profiles,we can re-align time course RNA-seq datasets to the beginning of a larval stage (molt exit).

overall_design: Synchronized L1 animals, expressing luciferase, were grown while measuring developmental trajectories using a luminometer. Assay was stopped when the majority of animals were at L3 molt entry and L3 molt exit respectively. Based on luciferase traces, individual animals of the appropriate developmental timepoint were collected from their wells and pooled for RNA isolation and library preparation.

first: Nahar

last: Smita

first: Hauser

last: Yannick

first: Meeuse

last: Milou

first: Gaidatzis

last: Dimos

first: Großhans

last: Helge


title: An siRMSD parameter of structural distortion induced by chemical modification is predictive of the off-target effect of siRNA_(1/2)

summary: To investigate effects of siRNA with various 2'-ribose modifications on genome-wide off-target effect, we analyzed gene expression profile of HeLa cells transfected by their siRNAs.

overall_design: Total RNAs were extracted from HeLa cells transfected by mock, unmodified, 2'-formamido, 2'-deoxy, or 2'-O-methoxyethyl modified siRNA and performed microarray analysis.


title: Tyk2 controls immunosurveillance of colorectal cancer liver metastasis

city: Vienna

first: Katharina

last: Schwertner

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University Vienna

summary: Colorectal cancer liver metastasis (CRLM) is a major clinical problem. However, little is known about immunosurveillance of CRLM. The Janus kinase Tyk2 is involved in several immune processes, but its role in CRLM is unclear. We have developed a murine colorectal cancer (CRC) organoid-based transplantation model to investigate the functions of Tyk2 in CRLM. Organoids with mutations in Apc, Kras, and p53 were injected into the spleen or portal vein of host mice with Tyk2 deletion in different subsets of immune cells as well as into wild-type host mice treated with the Tyk2 inhibitor deucravacitinib. In addition, cancer cell-intrinsic effects on CRLM were investigated using organoids with CRISPR/Cas9-mediated deletion of Tyk2. Our data show that Tyk2 is a key factor controlling CRLM. We found that Tyk2 is not required in cancer cells, macrophages, NK cells, T cells, and Kupffer cells, but controls CRLM via a dendritic cell-dependent mechanism that relies on MHC-I-dependent cross presentation of antigens to CD8+ T cells. Analysis of a scRNA-seq dataset for primary CRC and CRLM revealed that Tyk2 is predominantly expressed in a specific dendritic cell population that is destined to present antigens in tumor-draining lymph nodes. Although our data cannot prove a role for Tyk2 in immune surveillance of CRLM in humans, they should be considered when treating patients with Tyk2 inhibitors.

overall_design: Organoids with mutations in Apc, Kras, and p53 were injected into the spleen of Tyk2flox/flox and Tyk2Δhem mice to model colorectal cancer liver metastasis. After 7 weeks mice were sacrified and RNA was isolated from liver tissue, matastic tissue and liver tissue adjacent to metastases.

first: Dana

last: Krauß

first: Bernadette

last: Mödl

first: Daniela

last: Zwolanek

first: Robert

last: Eferl


title: mRNA-seq time course (in parallel to ATAC-seq time course), of wildtype C. elegans larvae sampled from 14h to 30h at 25oC [RNAseq_N2]

summary: We collected timecourse samples for RNA-seq, in parallel to ATAC-seq, in order to have matching samples for comparisson. The overall goal was to link oscillating gene expression (RNA-seq) to oscillating changes in chromatin accessibility (ATAC-seq), in order to identify enhancer elements that are critical to oscillatory regulation.

overall_design:
mRNA-seq of RNA isolated from larval C. elegans (N2 strain) in a time course spanning 16 hours of development. Synchronized L1 animals were seeded (2000 animals per plate) on multiple 10 cm NG 2% plates coated with OP50 bacteria, and then 1 plate per timepoint (2000 animals) was harvested every hour starting 14 hours after seeding. RNA was isolated with Trizol and the Direct-zol RNA microprep kit (R2062, Zymo Research) including DNase treatment. Libraries were prepared according to the TruSeq Illumina mRNA-seq (stranded - high input) protocol. Library was sequenced using Hiseq 50 Cycle Single-end reads.
In these experiments, samples were collected in parallel for mRNA-seq and ATAC-seq. And two independent experimental replicates were performed.

first: Graf-Landua

last: Maike

first: Methot

last: Stephen P


title: mRNA-seq time course (in parallel to ATAC-seq time course), of control or GRH-1 depleted C. elegans larvae sampled at 20oC [RNAseq_GRH1degron]

overall_design: mRNA-seq of RNA isolated from larval C. elegans (HW2434 strain - grh-1::degron::3xFLAG), treated with either EtOH or 250 uM Auxin, and collected in a time course spanning 12-13 hours of development. Synchronized L1 animals were grown at a density of 1 animal/uL in liquid culture (S-Basal + OP50 at OD600=2.8) for 20-21 hours before splitting the culture to treat half the animals with EtOH, and the other half with 250 uM Auxin. Every hour following treatment, 2000-5000 animals were collected for RNA prep. RNA was isolated with Trizol and the Direct-zol RNA microprep kit (R2062, Zymo Research) including DNase treatment. Libraries were prepared according to the Illumina Stranded mRNA-seq protocol. Library was sequenced using NovaSeq SP 2x56bp Paired-end reads.

first: Woelk

last: Michaela

first: Smith

last: A Alexander T.


title: Complete stranded RNA profiling during early mouse gonad development

city: Hong Kong

first: Wai-Yee

last: Chan

address: Rm 123, LKS integrated Biomedical Sciences Building

department: School of Biomedical Sciences

institute: The Chinese University of Hong Kong

summary: The sexual dimorphism in mouse gonads becomes evident at around E12.5 followed by initiation of germ cell development. Previous research has been focusing on protein-coding genes. Accumulating evidence has been showing the active involvement of various ncRNAs in development. However, we are still far from having a complete picture of the RNA regulatory networks in early gonadal development. In this study, we performed sequoia complete stranded RNA-Seq using pooled total RNAs from mouse male and female gonads at E11.5, E12.5, E13.5, and E14.5, respectively. By adding poly(A) tails and unique molecular identifiers (UMI) to all stranded RNAs, we were able to quantify short- and long-stranded RNAs with or without poly(A) tails in one preparation for each time point. This is the first profiling of complete stranded RNAs during early mouse gonad development, specifically emcompassing critical stages such as sex determination and initiation of germ cell development. with this advanced sequencing technique, we aim to gain a comprehensive understanding of RNA landscape and regulatory networks involved in these critical developmental processes.

overall_design: Embryos were collected from pregnant C57BL/6J wild-type mice at E11.5, E12.5, E13.5 and E14.5. The XX and XY gonads were dissected and pooled together in equal numbers for total RNA extraction with Trizol reagent, followed by SEQuoia Complete Stranded RNA-Seq. Each time point contained at least 6 embryos. Long RNA and small RNA expression profiles were compared across the four-time points.

first: Fanghong

last: OU

first: Zhangting

last: WANG

first: See

middle: W

last: CHAN

first: Kai

middle: K

last: MIU

first: Jinyue

last: LIAO

first: Hoi

last: SUN


title: Gene expression profile at single cell level of immune cells following spinal cord injury

city: Nanjing

first: Ziyang

last: Zheng

address: Longmian Avenue NO.101

institute: The first affiliated hospital of nanjing medaical university

summary: Immune cells infiltrate extensively into the lesion area after spinal cord injury and persist chronically, playing a crucial role in the inflammation and recovery of spinal cord injury. Here we investigated gene expression levels at single cell level of immune cells which distribute in the uninjured spinal cord and the lesion area at 1, 3, 7, 14, and 28 days after spinal cord injury. Heterogeneity analysis was performed to reveal the immune response after injury and how it is altered over time.

overall_design: Immune cells were collected from spinal cord tissues of uninjured mice (8- to 10-weeks-old C57BL/6) and mice with spinal cord injury on days 1, 3, 7, 14, and 28. Single-cell RNA sequencing was used to profile immune cells in the spinal cord.

first: Siming

last: Dai

first: Xuan

last: Zhao

first: Chenxi

last: Zhang

first: Jian

last: Chen

first: Shujie

first: Guoyong

last: Yin


title: Effect of knockdown of IGF2BP3 on gene expression of H1299 lung cancer cells

status: Public on Sep 15 2025

city: Guangzhou

first: Jingwei

last: Li

address: Guangzhou University Town, Panyu District

institute: Sun Yat-sen University

summary: Brain metastases represent a significant cause of morbidity and mortality in non-small cell lung cancer (NSCLC), with limited therapeutic options. The unique brain microenvironment, characterized by low lipid availability, may drive metastatic NSCLC cells to adapt through lipid metabolic reprogramming. In this study, we identify a novel mechanism in NSCLC brain colonization mediated by IGF2BP3-driven lipid metabolism. Elevated IGF2BP3 expression in NSCLC brain colonization correlates with poor prognosis and promotes cancer cell migration, invasion, and brain colonization by activating the lipogenesis pathway. Our findings highlight the critical role of IGF2BP3 in lipid metabolism and propose that targeting IGF2BP3 may provide a promising therapeutic strategy for NSCLC brain metastases.

overall_design: Conparative gene expression profiling analysis of RNA-seq data for H1299 lung cancer cells and its KD dericative (shIGF2BP3).

first: Shumin

last: Ouyang

first: Ziyou

last: Lin


title: Mitochondrial Complex II Orchestrates Divergent Effects in CD4+ and CD8+ T Cells

city: Houston

first: Pavan

last: Reddy

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

summary: Mitochondrial metabolism orchestrates T-cell functions, yet the role of specific mitochondrial components in distinct T-cell subsets remains poorly understood. Here, we explored the role of mitochondrial complex II (MC II), the only complex from the electron transport chain (ETC) that plays a role in both ETC and metabolism, in regulating T-cell functions. Surprisingly, MC II exerts divergent effects on CD4+ and CD8+ T cell activation and function. Using T cell-specific MC II subunit, succinate dehydrogenase A (SDHA), deficient mice, we integrated single-cell RNA sequencing and metabolic profiling, with in vitro and in vivo T-cell functional assays to illuminate these differences. SDHA deficiency induced metabolic changes and remodeled gene expression exclusively in activated T-cells. In CD4+ T-cells, SDHA loss dampened both oxidative phosphorylation (OXPHOS) and glycolysis, impaired cytokine production, proliferation, and reduced CD4+ T cell-mediated graft-versus-host disease after allogeneic stem cell transplantation (SCT). In contrast, SDHA deficiency in CD8+ T-cells reduced OXPHOS, but paradoxically upregulated glycolysis and demonstrated enhanced cytotoxic functions in vitro and in vivo. This metabolic reprogramming endowed SDHA KO CD8+ T-cells with superior in vivo antitumor efficacy after immune checkpoint inhibitor therapy and allogeneic SCT. These findings reveal MC II as a bifurcation point for metabolic and functional specialization in CD4+ and CD8+ T-cells.

overall_design: Purified T cells were from WT and SDHA KO mice were stimulated for 48h. Stimulated and unstimulated WT and SDHA KO T cells were analyzed using scRNAseq.

first: Keisuke

last: Seike

first: Shih-Chun

middle: A

last: Chu

first: Yuichi

last: Sumii

first: Takashi

last: Ikeda

first: Meng-Chih

last: Wu

first: Laure

last: Maneix

first: Dongchang

first: Yaping

last: Sun

first: Marcin

last: Cieslik


title: SETD1A Regulates Psychiatric Gene Networks Involved in Genomic Stability and Synaptic Function in Rare and Sporadic Schizophrenia

city: Baltimore

first: Tomoyo

last: Sawada

state: MD

address: 855 N Wolfe St

department: Molecular Neurogenetics

institute: Lieber Institute for Brain Development

summary: Rare loss-of-function (LoF) mutations in SETD1A are associated with schizophrenia (SCZ). However, how SETD1A haploinsufficiency leads to SCZ-associated phenotypes and its relevance to patients without these rare mutations is unknown. Here, we identify SETD1A bound loci and regulated genes in human prenatal cortex and isogenic pluripotent stem cell-derived neuronal models engineered with SETD1A LoF variants, including the most common patient mutation. SETD1A preferentially binds the promoters of SCZ and Bipolar risk loci that regulate chromatin remodeling, DNA repair, and synaptic function. Additionally, SETD1A binds to DNA damage prone sites in neural progenitor cells and postmitotic neurons. SETD1A haploinsufficiency causes accelerated neurogenesis, reduced neuronal complexity, and DNA damage accumulation in postmitotic neurons that is rescued by inhibiting the H3K4me2/3 demethylase KDM5. In postmortem SCZ cortical tissue, individuals who lack SETD1A mutations exhibit reduced SETD1A expression, associated with downregulation of SETD1A-regulated genes, implicating SETD1A-H3K4me dysfunction in sporadic SCZ cases. Therefore, restoring the SETD1A-H3K4me epigenetic imbalance may benefit individuals with SETD1A haploinsufficiency as well as a broader psychiatric population without SETD1A mutations.

overall_design: Single Cell RNA-seq profiling of human Cerebral Organoids engineered with SETD1A LoF variants.

first: Sawada

last: Tomoyo

first: Feltrin

last: Arthur

first: Erwin

last: Jennifer


title: Rescue of imprinted genes by epigenome editing in human cellular models of Prader-Willi syndrome

city: Shinjuku-ku

first: Akisa

last: Nemoto

address: 35 Shinanomachi

institute: Keio University School of Medicine

summary: Single cell gene expression profiling of PWS iPSC-derived hypothalamic organoids with and without epigenome editing. Raw data were not uploaded due to patient privacy concerns.

overall_design: Hypothalamic organoids at day 63-66 from epigenome-edited PWS iPSCs and unedited PWS iPSCs.

first: Kent

last: Imaizumi

first: Hirosato

last: Ideno

first: Hironobu

last: Okuno

first: Hideyuki

last: Okano


title: SETD1A Regulates Psychiatric Gene Networks Involved in Genomic Stability and Synaptic Function in Rare and Sporadic Schizophrenia [bulk RNA-seq]

overall_design: Bulk RNA-seq profiling of isogenic pluripotent stem cell-derived neuronal models engineered with SETD1A LoF variants.


title: Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo [scRNA-Seq]

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

summary: The colorectal epithelium is a rapidly renewing tissue, with a remarkable capacity to regenerate following injury. In colorectal cancer (CRC), this regenerative capacity can be co-opted to drive epithelial plasticity. Activation of oncogenic MAPK signalling in CRC is common, with mutations frequently found in both KRAS (40-50%) and BRAF (10%), alongside other mechanisms of EGFR pathway upregulation. Nonetheless, inhibition of this pathway is often linked to rapid therapeutic resistance in patients. Given the recent development of KRAS inhibitors and the licensing of BRAF+EGFR inhibitor combinations we have investigated mechanisms of resistance to these agents in complex mouse models of CRC. Here we show that MAPK signalling supports the regenerative/revival stem cell phenotype in vivo, while its inhibition leads to rapid remodelling of both Kras and Braf mutant mouse models to a high Wnt activity canonical stem cell phenotype marked by expression of Lgr5. This results in acute therapeutic resistance in Kras driven, and delayed resistance in Braf driven models. Importantly, where therapeutic MAPK targeting is applied in the presence of a single regenerative epithelial population, such as early metastatic disease, or where plasticity is restrained, for example through Wnt pathway restriction, a marked impact on tumourigenesis is observed. Modelling of an BRAF and RNF43-mutant patient population, clinically super-responders to BRAF/EGFR inhibitor therapy, demonstrates excellent response to therapy due to restricted epithelial plasticity, highlighting the criticality of cellular plasticity in therapeutic response. Together, our data provide clear insight into the mechanisms underpinning resistance to targeting oncogenic MAPK signalling in CRC. Moreover, we demonstrate that strategies that aim to restrict epithelial plasticity or corral into or intervene when tumours are in a regenerative cell fate may improve efficacy of MAPK targeting agents in CRC.

overall_design:
Mice were induced with a single 70uL injection of 100uM 4-OH tamoxifen into the colonic submucosa. When an established tumour was identified on colonoscope (beginning weekly two weeks post injection), mice were placed on a treatment regime. Mice were treated twice daily with MRTX1133 IP AM and PM (MRTX1133 100uL 7.5mg/kg) or vehicle (100uL10% hydroxpropyl beta cyclodextrin in 50mM citrate buffer ph5) for 4 days and sampled two hours post AM dose on the fourth day.

Single cell RNAseq data from colon and SI tumours (submitted previously in GSE280631 & GSE293737 as detailed in GSE307774_reanalysis_samples.xlsx), from mice expressing mutations in combinations of Apc, Braf, Kras, p53 and Rnf43. Genetic alterations were induced with intraperitoneal tamoxifen and tumours were homogenised and digested for sequencing using a Mcllwain Tissue Chopper and the GentleMACS Octo Dissociator in combination with the mouse tumour dissociation kit. Sequencing libraries were prepared using reagents from the 10x Chromium Single-Cell 3′ v3 Gel Bead Kit and Library (10x Genomics) according to the manufacturer’s protocol and then sequenced on an Illumina Novaseq 6000. Sequence alignment of single-cell data to the mm10 genome was performed using the count tool from the Cell Ranger package version 6.1.2 according to the developer’s instructions, generating barcodes, features and matrix output files for each sample.

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

last: White

first: Megan

middle: L

last: Mills

first: Laura

last: Millett

first: Andrew

middle: D

last: Campbell

first: Owen

middle: J

last: Sansom


title: SETD1A Regulates Psychiatric Gene Networks Involved in Genomic Stability and Synaptic Function in Rare and Sporadic Schizophrenia [CUT&Tag]

overall_design: CUT&TAG profiling from human prenatal frontal lobes and from isogenic pluripotent stem cell-derived neuronal models engineered with SETD1A LoF variants.


title: OVEREXPRESSION OF TEMPRANILLO-LIKE PROTEINS PROMOTES DORMANCY RELEASE IN POPLAR

status: Public on Sep 14 2025

city: Madrid

first: Daniela

last: Gomez Soto

address: Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38

country: Spain

institute: CBGP

summary: We investigated the effect of Populus TEML1 and TEML2 on the dormancy transcriptome through RNAseq experiments. We suggest these two genes play a role during poplar annual cycle, most specifically during dormancy based on their expression analysis. For this reason, we collected apical buds and generated bulk RNAseq libraries of overexpressing plants and their controls. We evaluated pathways which were altered in the transgenic lines and their role during the annual cycle.

overall_design: In vitro-cultivated hybrid poplars of TEML1ox, TEML2ox and WT were transfered to pots containing peat, and grown under LD and 22ºC conditions for 6 weeks. After this time, plants were moved to a short-day chamber for 8 weeks, where they ceased growth and set buds. After the 8 weeks of treatment, we collected the apical buds, grouping 3 buds per replicate, and 2 biological replicates. The remaining plants were subjected to a two-weeks of cold treatment and after this time, apical buds were collected following the short-day experimental design. RNA extraction was performed by adding to grinded frozen buds tissue CTAB extraction buffer with 2% β-mercaptoethanol, following by 3 washes with chloroform. After that, 7.5 M LiCl2:50mM EDTA was added, and samples were precipitated overnight at 4ºC. Next day, RNA was then purified according to the manufacturer’s instructions of NZY RNA purification kit (NZYTech, Lisboa, Portugal). A total of 100 ng of extracted RNA was used to generate the RNA-seq libraries. Libraries were generated from cDNA samples using the TruSeq Stranded mRNA Library Prep Kit (Nat Rev Genet. 2011 Sep 7;12(10):671-82) and they were sequenced on the Illumina platform (MACROGEN, Seúl, South Korea).

last: Gómez-Soto

first: Paolo Maria

last: Triozzi

first: Daniel

last: Conde

first: Cristina

last: del Barrio

first: Isabel

last: Allona

first: Mariano

last: Perales


title: Loss of cell-autonomously secreted laminin-α2 drives muscle stem cell dysfunction in LAMA2-related muscular dystrophy

city: Krakow

first: Krzysztof

last: Szade

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

summary: The extracellular matrix protein laminin-α2 is essential for preserving the integrity of skeletal muscle fibers during contraction. Its importance is reflected by the severe, congenital LAMA2-related muscular dystrophy (LAMA2 MD) caused by loss-of-function mutations in the LAMA2 gene. While laminin-α2 has an established role in structurally supporting muscle fibers, it remains unclear whether it exerts additional functions that contribute to the maintenance of skeletal muscle integrity. Submitted transcriptomic data represents  gene expression profile of control and LAMA2-deficient human myogenic precursor cells derived from induced pluripotent stem cells which was analyzed to better understand the role of laminin-α2 in human cells.

overall_design: Human induced pluripotent stem cells (hiPSCs) from a healthy donor in which exon 3 of the LAMA2 gene was deleted using CRISPR/Cas9 method, together with the isogenic control counterparts, were subjected to myogenic differention using Skeletal Muscle Differentiation Kit (Amsbio). RNA was isolated from four independent differentiations at the stage of myogenic precursors and subjected to next generation RNA-sequencing..

first: Józef

last: Dulak

first: Jacek

last: Stępniewski

first: Timothy

last: McGowan

first: Markus

last: Rüegg


title: In vitro Derivation of Midbrain Dopaminergic Neurons from Porcine Embryonic Stem Cells in Multi-dimensional Conditions [bulkRNA-seq]

status: Public on Sep 12 2025

city: Cheongju

first: Sang-Hwan

last: Hyun

state: Please select your state

address: 1 Chungdae-ro, Seowon-gu

department: Veterinary Medical Center and College of Veterinary Medicine

country: South Korea

institute: Chungbuk national university

summary: The generation of human-relevant dopaminergic (DA) neurons in large-animal models holds significant promises for translational neuroscience and regenerative medicine. Here, we establish a robust protocol to induce caudal ventral midbrain (VM) fate and generate functional midbrain DA (mDA) neurons and porcine midbrain-like organoids (pMLOs) from porcine embryonic stem cells (pESCs). Optimization of GSK3 inhibition and SHH signaling revealed species-specific requirements for inducing porcine VM progenitors, including a higher sensitivity threshold compared to human cells. Single-cell and bulk transcriptomic analyses demonstrated progressive lineage specification and functional maturation of mDA neurons, with IVF-derived pESCs showing superior differentiation potential over PA-derived cells. Moreover, 3D differentiation led to the formation of uniform neuroepithelial structures and enhanced electrophysiological activity and dopamine release. Notably, dopaminergic markers emerged across multiple neuronal clusters, reflecting a continuum of identity acquisition captured by high-resolution single-cell RNA sequencing. Compared to in vivo transgenic pig models, this platform enables rapid, scalable, and ethically favorable investigation of midbrain development and DA neuron biology. These findings position pig-derived organoids as a powerful tool for modeling human neurodevelopment and disease in a large-animal context.

overall_design: To investigate temporal gene expression dynamics during the differentiation of midbrain dopaminergic (mDA) neurons, bulk RNA sequencing was conducted using two porcine embryonic stem cell (pESC) lines derived from different embryonic origins: in vitro fertilization (IVF) and parthenogenetic activation (PA). Cells from both lines were collected at four representative time points during differentiation: day 0 (undifferentiated), day 16 (early neuronal specification), day 28 (synaptic maturation), and day 45 (late-stage differentiation). Each time point included biological duplicates, resulting in a total of 16 samples.  The experimental design aimed to capture transcriptomic changes over time and to compare differentiation patterns between IVF- and PA-derived mDA neurons. Correlation and gene ontology analyses were performed to assess temporal progression and functional enrichment. The dataset enables evaluation of key gene expression programs involved in neurogenesis, synaptogenesis, cellular responses, and lineage-specific differentiation during in vitro mDA neuron development.

first: Hyerin

last: Choi

first: Dongjin

last: Oh

first: Ali

last: Jawad

first: Jaehyung

last: Ham


title: Cell-cycle dynamics of nascent transcription and mature RNA accumulation are concordant in normal fibroblasts [RNA-seq]

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Dynamic changes of gene expression is fundamental to cell cycle control. A prevailing hypothesis states that cell-cycle gene expression dynamics is driven by a widespread transcription-to-maturation lag, in which nascent transcription occurs in a cell-cycle phase preceding the phase with mature RNA accumulation, based on a study in cancer cells. Here, we test this paradigm in non-transformed human fibroblasts. We define mature RNAs and nascent transcription during the cell cycle using FUCCI reporters. The two dynamics are strongly concordant without a lag. Our data suggest a widespread transcription-to-maturation lag may be a feature of some cancer cells, but not of normal cells.

overall_design: To investigate cell-cycle dynamics of gene expression in cycling non-transformed cells, we introduced the Fucci4 cell-cycle fluorescent reporters to the hTERT-immortalized human fibroblast cell line BJ-5ta (BJ-Fucci). We sorted BJ-Fucci cells into early G1 (mKO2–Clover–mTurquoise2–), G1 (mKO2+Clover–), early-S (mKO2+Clover+mTurquois+), and late-S/G2/M (mKO2–Clover+) phases using FACS. We sequenced poly A-selected RNAs using RNA-seq in these sorted populations. To define the nascent transcriptional dynamics, we sorted early G1, G1, and late-S/G2/M BJ-Fucci cells and performed GRO-seq, which quantifies nascent transcripts produced during a short incubation of permeabilized cells with bromouridine (BrU) by sequencing of BrU-incorporated RNAs.


title: Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis stem cells [scRNA-seq]

last: Ringwalt

address: 3400N Charles St

institute: Johns Hopkins University

summary: Stem cells have the unique ability to self-renew and differentiate into specialized cell types. Among the many factors influencing cell fate, epigenetic mechanisms, like histones, play a crucial role in regulating genomic programs like gene transcription and DNA replication, which are integral to a cell’s identity. However, the transcriptional, chromatin, and DNA replication timing profiles of stem cells within in vivo tissues remain poorly understood. The Drosophila testis serves as an excellent in vivo model for studying stem cells, as it contains two stem cell populations: the germline stem cells (GSC) and somatic cyst stem cells (CySC). Despite this, a comprehensive understanding of genome regulation in these cell types has been limited by the small number of stem cells and heterogeneity of the testis. In this study, we developed cell-specific genomic techniques to analyze the transcriptome, histone modification patterns, and replication timing profiles of GSCs and CySCs. Our single cell RNA-sequencing validated previous cell-biological and genetic studies on the role of intercellular communication between GSCs and CySCs while revealing high expression of chromatin regulators in GSCs. To characterize chromatin landscapes, we developed a cell-specific chromatin profiling assay to map H3K4me3, H3K27me3, and H3K9me3. These posttranslational modifications define euchromatic, facultative heterochromatic, and constitutive heterochromatic domains, respectively. Finally, we determined the cell-specific replication timing profiles of GSCs and CySCs, integrating our in vivo datasets with published in vitro data. Our results reveal that the replication program of GSCs is distinct from somatic lineages and that these differences align with variations in chromatin patterns. Collectively, our integrated genomic datasets build a framework for understanding genome-wide regulatory differences in two in vivo stem cell populations, demonstrating the power of combining transcriptomic, chromatin, and replication datasets to uncover cell-specific features of genome regulation.

overall_design: Drosophila melanogaster testis tumors were produced by overexpressing the Unpaired (Upd) ligand via two genetic strategies. Upd was either overexpressed using the germline-specific nanos promoter or cyst cell-specific traffic jam promoter. From each genetic strategy, approximately 18-20 testis pairs were dissected and dissociated to create a single cell suspension. Two replicates of each genetic type (four samples total) were proccessed for single cell RNA-sequencing using the 10X Genomics platform.

first: Jennifer

last: Urban

first: John

first: Wingel

last: Xue

first: Ryan

last: Gleason

first: Keji

last: Zhao

first: Xin

last: Chen


title: Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis stem cells [ChIC-ChIP]

first: Daniel

overall_design: Drosophila melanogaster testis tumors were produced by overexpressing the Unpaired (Upd) ligand via two genetic strategies. Upd was either overexpressed using the germline-specific nanos promoter or cyst cell-specific traffic jam promoter. From each genetic strategy, approximately 18-20 testis pairs were dissected and dissociated to create a single cell suspension. Replicates of each genetic type (combined samples of Input and Immunoprecipitation per histone modification) were proccessed for cell-specific sequential Chromatin Immunocleavage - Chromatin Immunoprecipitation (ChIC-ChIP).


title: mop1 reshapes maize recombination landscape by modulating DNA methylation at MITEs with open chromatin

city: Gainesville

first: Meixia

state: FL

address: 1355 Museum Drive

department: Microbiology and Cell Science

institute: University of Florida

summary: Meiotic recombination ensures genetic diversity and proper chromosome segregation, but its regulation remains not yet completely understood in many species. Here, we investigate the role of Mediator of paramutation1 (Mop1), a key component of the RNA-directed DNA methylation pathway, in reshaping the recombination landscape in maize. Using high-resolution crossover (CO) mapping, we show that mop1 mutants exhibit sex-specific effects on recombination, with CO numbers significantly reduced in male meiosis but unchanged in females. Sequence analysis of CO-associated motifs reveals increased enrichment of A/T polymer motifs in female mop1 and decreased enrichment of C/G motifs in male mop1 mutants, suggesting a transition to open chromatin states at these regions. Furthermore, we demonstrate that mop1 preferentially introduces new CO sites in females within regions of higher genetic diversity, particularly near miniature inverted-repeat transposable elements (MITEs). Epigenomic profiling reveals that mop1 significantly reduces CHH methylation at MITEs near genes. MITEs that overlap with differentially methylated regions (DMRs) and CO sites exhibit higher levels of histone marks associated with open chromatin, such as H2A.Z and histone acetylation, compared to MITEs outside DMRs or COs. However, the removal of CHH methylation in mop1 at MITEs that introduce COs does not alter the expression of flanking genes. Together, these results highlight the critical role of MOP1 in regulating meiotic recombination by modulating DNA methylation and chromatin states at transposable elements, providing new insights into the epigenetic regulation of meiotic recombination.

overall_design: Transcriptomic analysis of immature anthers undergoing meiosis I from mop1 plants (Mo17/B73;mop1/mop1) and their sibling controls (Mo17/B73;+/+) to identify expression changes associated with crossovers in mop1

first: Hasan

last: Moahmmad Mahmood

first: Zhao

last: Meixia


title: beta-catenin-1 localization and transcriptomic profiling provide insights into the early development of planarians

city: Barcelona

first: Josep

middle: F

last: ABRIL

state: Catalonia

address: Av Diagonal, 643, edifici Prevosti, planta -1, sala IBUB

department: Genetics, Microbiology & Statistics

institute: Universitat de Barcelona

summary: Background: The development of planarians is unique among Spiralians. Instead of the stereotypical spiral cleavage, planarians exhibit a disperse cleavage. There is no apparent gastrulation, and the morphogenesis of the yolk-feeding embryo remains a mystery. In this study, we examine the subcellular localization of βcatenin-1 and the transcriptomic profile during the early embryonic development of Schmidtea polychroa to shed light on these early events. Results: We find that the first nuclearization of βcatenin-1 occurs in yolk cells surrounding the embryonic syncytium. By 24 hours post deposition, βcatenin-1 starts to be nuclearized in blastomeres, coinciding with the activation of signaling and cell motility genes. During morphogenesis of the yolk-feeding embryo, βcatenin-1 is first nuclearized at one pole (gut and pharynx progenitors) and in epidermal progenitors, and afterwards in the embryonic pharynx. At this stage, genes involved in a first morphogenetic event are turned on. Following the yolk ingestion by the embryo, a dramatic transcriptomic shift occurs that coincides with the activation of genes related to cell proliferation. Finally, between 5-7 days post deposition βcatenin-1 is massively nuclearized, and genes involved in the morphogenesis and patterning of the adult tissues get activated. Conclusions: Our findings provide new insights into the early developmental events of Schmidtea polychroa, including cleavage, the involvement of βcatenin-1 in the formation of the embryonic tissues and the morphogenesis of two distinct body plans. These findings are significant to understand the evolution of the peculiar mode of planarian development.

overall_design: RNA-seq time course differential gene expression analysis of Schmidtea polychroa embryonic development from samples at 4, 24, 32, 48, 72, 96, 120, and 168 hours post cocoon deposition, taking 4h as reference time (t_x vs t_4h) or comparisons with previous time points (t_x vs t_(x-1)). The Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GLGS00000000. The version described in this paper is the first version, GLGS01000000.

first: Pablo

last: Coronel-Córdoba

first: Miquel

last: Sureda-Gómez

first: Jose Maria

last: Martín-Durán

first: Francisco

last: Monjo

first: Emili

last: Saló

last: Abril

first: Teresa

last: Adell


title: Cell-cycle dynamics of nascent transcription and mature RNA accumulation are concordant in normal fibroblasts [GRO-seq]

first: Kohta

last: Ikegami


title: Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens [snRNA-seq]

status: Public on Sep 10 2025

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

summary: The nucleus accumbens (NAc) is a key component of the mesolimbic dopamine system that critically regulates many behaviors related to reward and motivation. The NAc is implicated in several neuropsychiatric disorders, including major depressive disorder, schizophrenia, and substance use disorder. Rodent studies have identified spatial organization of heterogeneous medium spiny neuron (MSN) subtypes across the NAc core and shell, but the extent to which this cellular diversity and spatial organization is conserved in the human brain remains unclear. Here, we generated a spatiomolecular atlas of NAc cell types and spatial domains by integrating spatial transcriptomics and single-nucleus RNA sequencing data from postmortem NAc tissue from 10 neurotypical adult donors. We identified 20 transcriptionally unique cell populations and 8 spatial domains, including specialized D1 islands composed of distinct dopamine receptor 1 (DRD1) MSN subtypes, which were enriched for OPRM1. In contrast to a discrete core vs. shell division, we observed continuous spatial gradients of gene expression across MSN domains, suggesting a more complex organization of DRD1 and DRD2 MSNs. Cross-species comparisons demonstrated conservation of MSN subtypes and spatial features between human, rodent, and nonhuman primate NAc. Genetic enrichment analysis with stratified linkage disequilibrium score regression revealed specific spatial domains associated with risk for psychiatric and addiction-related traits. To investigate this further, we spatially mapped ligand-receptor interactions involving neuropsychiatric risk genes. Finally, we leveraged existing rodent NAc data to identify drug-responsive transcriptional programs and predict their spatial distribution in the human NAc. Collectively, we provide a spatiomolecular framework for understanding the human NAc and its relevance to neuropsychiatric disease.

overall_design: Ten neurotypical control postmortem human brain donors were selected for the single-nucleus and spatial transcriptomic study of the nucleus accumbens (NAc). We generated an integrated atlas with the two datasets of the human postmortem NAc to better understand the anatomical organization of heterogeneous medium spiny neuron (MSN) cell types. We identified multiple transcriptionally-distinct populations of MSNs that were organized in continuous gradients across the NAc.

first: Prashanthi

last: Ravichandran

first: Svitlana

middle: V

last: Bach

first: Robert

last: Phillips III

first: Madeline

last: Valentine

first: Nicholas

last: Eagles

first: Yufeng

last: Du

first: Ishbel

last: del Rosario

last: Miller

first: Heena

last: Divecha

first: Madhavi

last: Tippani

first: Kelsey

last: Montgomery

first: Joel

middle: E

last: Kleinman

first: Stephanie

last: Page

first: Thomas

last: Hyde

first: Leonardo

last: Collado-Torres

first: Alexis

last: Battle

last: Hicks

first: Kristen

last: Maynard


title: Cell-cycle dynamics of nascent transcription and mature RNA accumulation are concordant in normal fibroblasts

first: Kohta

last: Ikegami

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

overall_design: Refer to individual Series


title: Inflammation and lymphocyte activation during longitudinal progression to rheumatoid arthritis in at-risk individuals

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: Rheumatoid Arthritis is a chronic immune-mediated disease characterized by joint inflammation, autoantibodies, and systemic inflammatory features. Autoantibodies, including anti-citrullinated protein antibodies are highly predictive biomarkers that pre-date clinical disease and can be used to identify individuals “at-risk” for RA. We performed a prospective, longitudinal multi omic study of at-risk individuals at multiple timepoints to characterize their immune state. One-third of patients progressed to clinically active RA during the study. We show that at-risk RA subjects have systemic inflammation with features like those observed in active RA despite having no clinical disease. Progression to active disease was especially apparent in the T and B cells compartments, with pro-pathogenic features recognized in naive cells. We identify key molecular and cellular alterations in innate and adaptive immunity that accompany this inflammatory state.

overall_design:
A prospective, longitudinal study of individuals at-risk for RA was performed to define molecular and cellular changes that contribute to the development and onset of rheumatoid arthritis (RA). We enrolled 45 subjects with elevated anti-citrullinated protein antibodies (ACPA) but no clinical signs of arthritis and followed them up to 3 years post-enrollment. Peripheral blood and metadata were collected 2-3 times per year and at the time of onset of clinical RA. During the study, 16 subjects progressed to clinical RA and were diagnosed with inflammatory arthritis (IA) by a rheumatologist . For comparison, 38 site-matched ACPA- healthy controls (CON1) and 11 site-matched ACPA+ early RA patients (ERA), within 1 year of clinical diagnosis and naive to biological and targeted synthetic disease modifying anti-rheumatic drugs (DMARDs), were enrolled.

*_ARI: At Risk Individual Sample
*_LONG: Longitudinal At Risk Sample
*_ERA: Early RA Sample
*_CON1: ACPA -ve Control Sample
*_CON2: Healthy Controls

***Submitters state that raw data is subject to controlled access and thus will be submitted to dbGaP***

first: Adam

last: Savage

first: Alexander

middle: T

last: Heubeck

first: Ananda

last: Goldrath

first: Blessing

last: Musgrove

first: Cara

last: Lord

first: Charles

last: Roll

first: Christian

last: LaFrance

first: Christy

last: Bennett

first: Claire

last: Gustafson

first: Cole

last: Phalen

first: Elisabeth

last: Dornisch

first: Elliott

last: Swanson

first: Emma

last: Kuan

first: Erin

last: Kawelo

first: Jessica

last: Garber

first: Julian

last: Reading

first: Kevin

last: Lee

first: Lauren

last: Okada

first: Lucas

last: Graybuck

first: Lynne

last: Becker

first: Mark

last: Gillespie

first: Marla

last: Glass

first: Morgan

last: Weiss

first: Nhung

last: Tran

first: Padmapriyadarshini

last: Ravisankar

first: Palak

last: Genge

first: Peter

last: Skene

first: Pravina

last: Venkatesan

first: Qiuyu

last: Gong

first: Regina

last: Mettey

first: Samir

last: Zaim

first: Tao

last: Peng

last: Bumol

first: Troy


title: In vitro Derivation of Midbrain Dopaminergic Neurons from Porcine Embryonic Stem Cells in Multi-dimensional Conditions [scRNA-seq]

first: Sang-Hwan

last: Hyun

overall_design: Single-cell RNA sequencing was performed on pigMLOs at days 11, 28, and 45 of differentiation to characterize temporal changes in cellular composition and transcriptional dynamics. After alignment to the Sus scrofa Sscrofa11.1 genome and downstream processing, 103,310 high-quality cells were obtained and visualized via UMAP.

first: Hyerin

last: Choi

first: Dongjin

last: Oh

first: Ali

last: Jawad

first: Jaehyung

last: Ham


title: The SPN-4 Rbfox RNA-binding protein selects maternal mRNAs for CCR4-NOT-dependent clearance in C. elegans embryos

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: The elimination of many maternal mRNAs is an essential feature of the maternal-to-zygotic transition. We report an essential pathway that clears many maternal transcripts from early C. elegans embryos using the RbFox-related SPN-4 RNA-binding protein as a specificity factor and the CCR4-NOT deadenylase complex as an effector. We biochemically identified SPN-4-associated mRNAs from late-stage oocytes and found that the set of SPN-4-associated transcripts is enriched for maternal mRNAs that undergo early decay. Single-molecule fluorescence in situ hybridization experiments established that many SPN-4-associated mRNAs fail to be eliminated in the absence of SPN-4. In the 3’UTRs of two target mRNAs, we identified RbFox motifs that bind SPN-4 in vitro and are required for SPN-4-dependent clearance in vivo. In a genetic screen to identify factors that work with SPN-4, we isolated alleles of CCR4-NOT components. Auxin-induced degradation of the LET-711/NOT1 scaffold and the CCF-1 deadenylase disrupted clearance of two SPN-4-associated transcripts. Our results support a model in which SPN-4 initiates expression in late-stage oocytes, associates with maternal mRNA targets through RNA sequences in their 3’UTRs and promotes CCR4-NOT-mediated decay during early embryogenesis.

overall_design: Transcripts present in cell lysates and immunoprecipitates from SPN-4, LIN-41, and OMA-1 ribonuclear protein complexes were profiled by RNA sequencing. An amplification method was utilized for low input RNA because of the restricted distribution of SPN-4 in the adult C. elegans gonad.

first: Tsukamoto

last: Tatsuya

first: Gearhart

last: Micah

first: Greenstein

last: David

first: Osborne Nishimura

last: Erin


title: Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens [Spatial Transcriptomics]

first: Keri

last: Martinowich

first: Prashanthi

last: Ravichandran

first: Svitlana

last: Bach

first: Robert

last: Phillips III

first: Madeline

last: Valentine

first: Nicholas

last: Eagles

first: Yufeng

last: Du

first: Ishbel

last: del Rosario

first: Ryan

last: Miller

first: Heena

last: Divecha

first: Madhavi

last: Tippani

first: Kelsey

last: Montgomery

first: Joel

last: Kleinman

first: Stephanie

middle: C

last: Page

first: Thomas

last: Hyde

first: Leonardo

last: Collado-Torres

first: Alexis

last: Battle

last: Hicks

first: Kristen

last: Maynard


title: Mitochondrial iron transport via MFRN1 is required for erythroid cell cycle progression

city: Pittsburgh

first: Yvette

last: Yien

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

summary: The goal of the scRNAseq study was to identify developmental defects and differential gene expression in MFRN1 mutant d3 zebrafish embryos

overall_design: 10 Tg(lcr:GFP) and Tg(lcr:GFP); MFRN1 mutant 3 dpf zebrafish embryos of the AB strain were homogenized and subjected to scRNAseq anlysis.  GFP is under the control of the globin promoter and its expression is restricted to the erythroid lineage. The goal was to identify lineage defects (erythroid and other) that resulted from MFRN1 deficiency, as well as identify differnetially expressed genes.


title: Total RNA Sequencing in HCC Patients

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

institute: ETH ZURICH / University of Zurich

summary: Total RNA Sequencing in HCC Patients

overall_design: Liver resection was performed on HCC patients. Samples were carefully disected to separate tumor tissues from the adjacent CLD tissues. Normal liver tissue was obtained from healthy donors or liver resections resulted from other medical conditions. All samples were examined and verified by experienced pathologists. Total RNAseq was performed to compare the changes in their transcriptomic signatures.

first: Marc

last: Healy

first: Peter

last: Leary

first: Lap Kwan

last: Chan

first: Achim

last: Weber


title: Vaccination against Onchocerca volvulus induces IgG-mediated protective immunity dependent on neutrophils and complement

city: Philadelphia

first: Nathan

last: Ryan

institute: Thomas Jefferson University

summary: Onchocerciasis remains a significant cause of morbidity and economic loss in sub-Saharan Africa. Despite the existence of effective therapeutics, a prophylactic vaccine targeting the etiologic agent, Onchocerca volvulus, is needed to control ongoing disease and transmission. Mice were vaccinated against O. volvulus with a fusion of the recombinant antigens Ov-103 and Ov-RAL-2 (Ov-FUS-1) with Advax-CpG adjuvant. Immunized mice developed protective immunity with the killing of third-stage larvae (L3) within 36 hours of challenge infection. IgG from immunized mice passively transferred protective immunity to naïve mice, indicating that antigen-specific IgG mediated parasite elimination. Neutrophils were the most abundant subset of immune cells recruited to the parasite microenvironment in vivo, and their depletion resulted in the total loss of immune-mediated larval killing. Analysis of neutrophil gene expression revealed that both vaccination and the presence of O. volvulus larvae were capable of modulating neutrophil transcriptional activity. The mechanism by which antigen-specific IgG and neutrophils collaborated to kill L3 was independent of Fcγ receptors. However, the elimination of complement component C3 prevented vaccine-induced protection, which suggests these components may interact through the complement system. This study describes a vaccine-induced mechanism of protective immunity against O. volvulus L3 dependent on IgG, neutrophils, and complement, highlighting an effective collaboration between the innate and adaptive arms of the immune system to control O. volvulus infection.

overall_design: Samples were 95-99% pure neutrophil populations collected from diffusion chambers that were implanted subcutaneously into either immunized or control mice. Samples were collected 18 or 36 hours post implantation. Diffusion chambers were implanted either with or without O. volvulus L3.

first: Jessica

last: Hess

first: Mohini

last: Nakhale

first: Annabel

last: Ferguson

first: Darrick

last: Carter

first: Sara

last: Lustigman

first: David

last: Abraham


title: Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis stem cells [Repli-seq]

first: Daniel

last: Ringwalt

department: Biology

overall_design: Drosophila melanogaster testis tumors were produced by overexpressing the Unpaired (Upd) ligand via two genetic strategies. Upd was either co-expressed with GFP-tagged H3 histone using the germline-specific nanos promoter or cyst cell-specific traffic jam promoter. From each genetic strategy, 100-200 testis pairs were dissected and nuclei extracted. GFP-positive nucei were collected on a MoFlo XDP cell sorter. The nuclei were further sorted by DNA content, separating into one of four S-phase fractions (early, early-mid, late-mid, and late replicating). For each (stem cell-type) biological replicate, the replicating DNA from each of the four S-phase fractions was enriched and prepared for next generation sequencing (Repli-seq).

first: Jennifer

last: Urban

first: John

first: Wingel

last: Xue

first: Ryan

last: Gleason

first: Keji

last: Zhao

first: Xin

last: Chen


title: Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis stem cells


title: Androgen deprivation-mediated activation of AKT is enhanced in prostate cancer with TMPRSS2:ERG fusion [RNA-Seq]

city: Boston

first: Steven

last: Balk

state: MA

address: 3 Blackfan circle

institute: BIDMC

summary: The TMPRSS2:ERG gene fusion (T:E fusion) in prostate adenocarcinoma (PCa) puts ERG under the androgen receptor (AR) regulated expression of TMPRSS2. The T:E fusion is frequently associated with PTEN loss, and is highly correlated with decreased expression of INPP4B, both of which may compensate for ERG-mediated suppression of PI3K/AKT signaling. We confirmed in PCa cells and a mouse PCa model that ERG suppresses AKT activation, and that one potential mechanism is through downregulation of IRS2. In contrast, ERG knockdown did not increase INPP4B, suggesting its decreased expression is indirect and reflects selective pressure to suppress INPP4B function. Notably, INPP4B expression is similarly decreased in PTEN-intact and PTEN-deficient T:E fusion tumors, suggesting selection for a function distinct from regulation of PI3K activity. As ERG expression in T:E fusion tumors is AR regulated, we further assessed the extent to which AR inhibition increased AKT activity in T:E fusion tumors. T:E fusion positive versus negative PDXs had greater increases in AKT activity after castration. Moreover, in a neoadjuvant trial of AR inhibition prior to radical prostatectomy we similarly found greater increases in AKT activation in the T:E fusion tumors. Together these findings indicate that AKT activation may mitigate the efficacy of AR targeted therapy in T:E fusion PCa, and that these patients may most benefit from combination therapy targeting AR and AKT.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A model with doxycycline (DOX) regulated expression of ERG in mouse prostate, driven by a tetracycline operon regulated ERG (pTET-ERG) combined with a probasin promoter regulated reverse tetracycline transactivator (Pb-rTta), was generated to assess the functions of ERG in driving prostate adenocarcinoma (PRAD) in vivo. When crossed onto a Pten-/+ background and treated with doxycycline for ~1 year, these mice developed PRAD.  To identify ERG-regulated genes that may be contributing to PRAD development in this model, we carried out time course experiments with both short-term ERG induction and long term induction plus short term DOX withdrawal. For the short-term induction, previously untreated mice were treated with DOX or vehicle for 3 or 6 days. Ventral prostate epithelium was then laser capture microdissected and transcriptome profiles were obtained using Affymetrix Mouse Gene 1.0 ST arrays. Another cohort of mice with DOX regulated ERG on the Pten-/+ background were treated with DOX for ~1 year to generate PRAD. DOX was then discontinued in one set of mice and prostates were harvested after 1-2 weeks and analyzed by RNA-seq using the Illumina TruSeq stranded mRNA kit. To identify ERG regulated genes in VCaP cells (expressing the TMPRSS2:ERG fusion), cells were treated with ERG or nontargeted siRNA and assessed by RNA-seq.

first: Sen

first: Carla

last: Calagua

first: Seiji

last: Arai

first: Fang

last: Xie

first: Olga

last: Voznesensky

first: Larysa

last: Poluben

first: Eva

last: Corey

first: Changmeng

last: Cai

first: Yuzhuo

last: Wang

last: Einstein

first: Mary-Ellen

last: Taplin

first: Huihui

last: Ye

first: Adam

last: Sowalsky

first: Joshua

last: Russo

last: Yua

middle: P


title: Activation of mtDNA transcription by mitochondrial RNA polymerase overexpression enhances stress-induced exercise capacity

status: Public on Sep 11 2025

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

summary: POLRMT is the sole RNA polymerase in human mitochondria, where it generates primers for mitochondrial DNA (mtDNA) replication and transcribes the mtDNA to express genes encoding essential components of the oxidative phosphorylation (OXPHOS) system. Elevated POLRMT levels are found in several cancers and in mouse models with severe mitochondrial dysfunction. Here, we generated and characterized mice over-expressing Polrmt to investigate the physiological and molecular consequences of elevated POLRMT levels. Increasing POLRMT levels did not result in any pathological phenotype but led to increased exercise performance in male mice under stress conditions. Polrmt overexpression increased de novo transcription initiation, resulting in higher steady-state levels of the promoter-proximal L-strand transcript 7S RNA. Surprisingly, the abundance of mature mitochondrial RNAs was not affected by the elevated POLRMT levels. Furthermore, ubiquitous simultaneous overexpression of Polrmt and Lrpprc, which stabilizes mitochondrial messenger RNAs, did not increase steady-state levels of mitochondrial transcripts in the mouse. Our data show that POLRMT levels regulate transcription initiation, but additional regulatory steps downstream of transcription initiation and transcript stability limit OXPHOS biogenesis.

overall_design: RNA-Seq profiling of Polrmt overexpressor, Lrpprc overexpressor and double Polrmt/Lrpprc overexpressor mice against wild type

first: Maria

last: Miranda

first: Andrea

last: Mesaros

first: Nathalie

last: Scrima

first: Louise

last: Pérard

first: Irina

last: Kuznetsova

first: Martin

last: Purrio

first: Ilian

last: Atanassov

first: Aleksandra

last: Filipovska

first: Arnaud

last: Mourier

first: Nils-Goran

last: Larsson

first: Inge

last: Kühl


title: Gene expression in tissues of root tips from Pinus pinaster seedlings under nitrate nutrition

status: Public on Sep 09 2025

city: Malaga

first: Rafael

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

summary: In the present study, the gene expression changes in four different tissues of root tips from maritime pine were analyzed. The roots were under two nutritional conditions (3 mM KCl or 3 mM NO3K) and harvested after 2 hours of the treatment. This work was funded by Ministerio de Ciencia e Innovación, grant number PID2021-122641NB-C21, MICINN, FEDER, UE.

overall_design: Pine seedlings were subdivided into two groups. The control group was irrigated with 80 mL of 3 mM KCl (C), the second group was supplied with 80 mL of 3 mM NO3K. Root samples were collected 2 hours after the irrigation. Seedling’s root tips were cut and tissue pieces of 5 - 6 mm were imbibed in a specimen holder with Tissue‐Tek optimal cutting temperature embedding medium (Sakura Finetek, Alphen aan den Rijn, The Netherlands) and immediately frozen in liquid nitrogen for cryostat sectioning. The 24 samples were sequenced on an Illumina NovaSeq 6000 as paired-end reads of 150 bp length.

first: José

last: Valderrama-Martín

first: David

last: Salas-Vázquez

first: Francisco

middle: R

last: Cantón


title: Single-nucleus transcriptome profiling provides insights into the pathophysiology of OSA-related renal injury

city: Zhangzhou

first: Li-Da

last: Chen

address: No 59, Shenglixiroad, Xiangcheng district

institute: Zhangzhou Affiliated Hospital of Fujian Medical University

summary: Obstructive sleep apnea (OSA) has been demonstrated to be associated with renal injury. However, the cellular and molecular mechanisms by which chronic intermittent hypoxia (CIH), a hallmark of OSA, contributes to renal injury remain poorly understood. Twelve male Sprague-Dawley rats were randomized into normoxic control (NC) and CIH groups (n = 6 each), with CIH exposure for 12 weeks. Renal injury was evaluated by Hematoxylin and Eosin staining and a modified Jablonski score. Single-nucleus RNA sequencing (snRNA-seq) was performed. Data analysis included clustering of cells, differential gene expression analysis, and functional enrichment through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Histopathological analysis revealed renal injury with renal tubular epithelial cell edema, necrosis in the CIH group compared to NC. A total of 42,581 cells (19,655 cells from NC group and 22,926 cells from CIH group) were retained after quality control, with 13 distinct renal cell populations identified. CIH exposure resulted in an increased proportion of podocytes, while mesangial cells were reduced compared to the NC group. CIH exposure altered the transcriptomic landscape, with differentially expressed genes (DEGs) observed across multiple cell types. Functional enrichment analysis indicated that CIH-induced DEGs were associated with suppressed metabolic and signaling pathways in proximal tubule and loop of Henle epithelial cells, activation of apoptotic and sodium reabsorption pathways in distal convoluted tubule cells, and enhanced inflammatory and phagocytic signaling in mononuclear phagocytes. Our study provides a high-resolution atlas of CIH-induced transcriptional changes in the rat kidney. The findings reveal cell type-specific responses and pathways potentially contributing to OSA-associated renal injury, offering novel insights into pathogenesis and potential therapeutic targets for preventing renal damage in OSA patients.

overall_design: Twelve male Sprague-Dawley rats were randomized into normoxic control (NC) and CIH groups (n = 6 each), with CIH exposure for 12 weeks.3 renal tissue samples were randomly selected from each group and then subjected for single-nucleus transcriptome  sequencing.


title: Deiodinase type-3 establishes the period of circannual interval timing in mammals

first: Calum

last: Stewart

address: Jarrett Building, University of Glasgow

institute: University of Glasgow

summary: Animals respond to environmental cues to time phenological events, but the intrinsic mechanism of circannual timing remains elusive. We used advanced transcriptomic sequencing and high frequency resolution during the initiation, maintenance and recovery of circannual timing for Siberian hamster energy balance to delineate the molecular architecture of a neuroendocrine seasonal clock. Three distinct phases of transcript changes were identified, and deiodinase type-3 (Dio3) expression was activated during the initiation phase. Targeted mutation of Dio3 resulted in a shortening of the circannual interval timer period. Hamsters that exhibit a form of naturally occurring disruption in Dio3 eliminated circannual interval timing. Our work demonstrates that the evolutionary conserved changes in hypothalamic tanycytes expression of Dio3 is critical for timing seasonal life history traits in chordates.

overall_design: To investigate molecular changes occuring in the distinct regions of the hypothalamus. Siberian hamsters were held in long days (LD) or short days (SD) for up to 32-weeks. At 4-week intervals, animals were sacrificed and the piutiary and hpyothalamic nuclei were dissected. Microdissections were homogenised and RNA was extracted using the RNEasy plus mini kit. following this transcript abundance was assesed using the cDNA-PCR sequencing kit (SQK-PCB109, Oxford Nanopore).

first: Callum

first: Tyler

last: Stevenson


title: SPANXA2-OT1 promotes macrophage chemotaxis

first: Masanori

last: Aikawa

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB741

institute: Brigham and Women's Hospital

summary: Coronary artery disease (CAD) remains the leading global cause of death, with macrophages playing a central role in driving inflammation through cytokines, chemokines, and other mediators. Using gene expression meta-analysis and weighted gene co-expression network analysis (WGCNA) of human CAD datasets, we identified 26 lncRNA–mRNA modules and prioritized SPANXA2-OT1 as a key inflammation regulator. Conservation analysis revealed SPANXA2-OT1 to be primate-specific, necessitating human macrophage models derived from PBMCs. IL-1β stimulation induced cytoplasmic SPANXA2-OT1, and antisense oligonucleotide-mediated silencing reduced chemotaxis signatures, validated by RNA-seq and proteomics. Mechanistically, SPANXA2-OT1 directly bound miR-338, as shown by luciferase assays, thereby regulating IL-8 and related chemokines critical for monocyte recruitment. CRISPR/Cas9 deletion of exon 3 further confirmed reduced IL-8 expression and impaired macrophage chemotaxis. Collectively, these findings establish SPANXA2-OT1 as a human-specific regulator of macrophage-driven inflammation in CAD and highlight its promise as a translational biomarker and therapeutic target.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBMC derived human primary macrophages stimulated by IL-1beta and treated with negative control antisense oligos (NC_ASO) and SPANXA2-OT1 antisense oligos (SPAN_ASO).

first: Prabhash

last: Kumar Jha

first: Chelvanambi

last: Sarvesh

first: Nakamura

last: Yuto

first: Yuji Umesaki Itto

last: Lucas

first: Vijay

last: Aatira

first: Lupieri

last: Adrien

first: Cantadori Barbeiro

last: Miguel

first: Thanh

last: Dat Le

first: Borges Nascimento

last: Caio

first: Kasai

last: Taku

first: Whelan

last: Mary

first: Hosokawa

last: Daiki

first: Becker-Greene

last: Dakota

first: Sasha

last: Singh

first: Elena

first: Uchida

last: Shizuka


title: Three-dimensional Co-culturing Reveals Human Stem Cell-Derived Somatostatin Interneurons with Subclass Expression

city: Lund

first: Daniella

last: Rylander Ottosson

address: Sölvegatan 19, BMC A11.

department: Exp Med Science Department

country: Sweden

institute: Lund University

summary: Cortical interneuron deficiencies, particularly involving the somatostatin (SST) subtypes, contribute to neurological and neuropsychiatric disorders. These interneurons are difficult to derive in vitro from human embryonic stem cells (hESCs) due to their late embryonic development and dependence on glial interaction. To this end, we developed a three-dimensional co-culture model of hESC-derived neurons, enabling long-term development, functional maturity, and neuron-glial interaction. Under these conditions, hESCs successfully differentiated into functional GABAergic interneurons expressing the SST gene and protein within 50 days. Single-nuclei RNA sequencing revealed transcripts for SST subclasses, including Martinotti, non-Martinotti, and long-projecting neurons, that have not yet been described for hESC cultures. Upon injection into forebrain organoids, the interneuron progenitors spread and functionally matured while retaining their SST subclass identities, suggesting cell-intrinsic fate specification. Our in vitro model provides a robust platform for studying human SST interneurons, offering new avenues for investigating their role in health and disease.

overall_design:
RNA-seq analysis of hESC-derived interneurons in 3D co-cultures with glial cells at 100 DIV and transplanted hESC-derived interneurons in forebrain organoids at 100 DIV

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


title: Loss-of-function variants in ciliary genes confer high risk for Tetralogy of Fallot

city: Nanjing

first: Jimiao

last: Gao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

summary: Tetralogy of Fallot (TOF), the most common severe cyanotic congenital heart disease, has poorly understood genetic causes. Through next-generation sequencing in 131 nonsyndromic TOF patients, we identified an increased burden of rare deleterious variants in ciliary genes and cilium pathway, and observed a multigenic inheritance pattern, with an OR of 1.672 for more than two deleterious variants and a cumulative OR of 3.158 for six variants. Functional validation in single- and double-heterozygous mouse models carrying these variants recapitulated TOF-like phenotypes and impaired normal cilia structure and function, particularly disrupting Hedgehog signaling in cardiomyocytes, downregulating key transcription factors Gata4 and Nkx2-5.

overall_design: scRNA-Seq analysis of mice E10.5 cardiac OFTs from wild-type and ciliary gene knockout/mutant littermates of each strain.

first: Yayun

last: Gu

first: Yuan

last: Lin

first: Zhibin

last: Hu