title: JAK/STAT inhibition restores disease tolerance in malaria-infected glucocorticoid receptor knockout mice.

city: Leuven

first: Philippe

last: Van den Steen

address: Herestraat 49 Box 1044

country: Belgium

institute: KU Leuven

summary: Disease tolerance is a defense strategy, whereby the host limits tissue damage, without affecting the pathogen load. In malaria, the disease tolerance mechanisms by which many infected individuals are protected against severe disease, are still incompletely understood. In this study, we show that endogenous glucocorticoids are integral components of disease tolerance in malaria, as genetic deletion of the glucocorticoid receptor in mice resulted in the development of lethal hypoglycemia during Plasmodium chabaudi AS infection. This was paralleled by altered metabolism in liver and spleen, marked by increased glucose uptake, a predominant glycolytic transcriptome, reduced gluconeogenic gene expression and depletion of glycogen stores. Hypoglycemia was highly associated with activation of the JAK/STAT pathway in the liver and spleen. Treatment with ruxolitinib, a JAK1/2 inhibitor, ensured survival by protecting against lethal hypoglycemia. These findings highlight the pivotal role of endogenous glucocorticoids in disease tolerance, and suggest a potential therapeutic role for ruxolitinib in managing malaria-induced hypoglycemia.

overall_design: To investigate the transcriptional regulation of the glucocorticoid receptor in liver tissue during PcAS infection, we collected liver tissue from uninfected and PcAS-infected wildtype (WT) and tamoxifen-inducible glucocorticoid receptor knockout (GRiKO) mice, at day 10 post infection. We then performed differential gene expression analysis using data obtained from bulk RNA-seq on RNA extracted from liver tissue (4-6 mice per group).

first: Fran

last: Prenen

first: Leen

last: Vandermosten

first: Sofie

last: Knoops

first: Emilie

last: Pollenus

first: Hendrik

last: Possemiers

first: Pauline

last: Dagneau de Richecour

first: Giorgio

last: Caratti

first: Christopher

last: Cawthorne

first: Sabine

last: Vettorazzi

first: Uwe

last: Himmelreich

first: Jan

last: Tuckermann

middle: E

last: van den Steen


title: Transcriptome analysis of Aspergillus oryzae RIB40 under chemical stress reveals mechanisms of adaptation to fungistatic compounds of lignocellulosic side streams

status: Public on Jun 18 2025

city: Espoo

first: Miika-Erik

last: Korpioja

address: Tekniikantie 21

country: Finland

institute: VTT Technical Research Centre of Finland

type: Expression profiling by high throughput sequencing

summary: Industrial lignocellulolytic side streams are considered an attractive carbon source for the cultivation of biotechnologically important fungi, although the presence of toxic pretreatment by-products is a major challenge yet to be overcome. Aspergillus oryzae is a filamentous fungus with a large secretion capacity, high tolerance for toxins, and a wide substrate variety, making it a promising candidate for side stream utilization. In the present study, the cellular detoxification of furfural, 5-hydroxymethylfurfural (HMF), levulinic acid, ferulic acid and vanillin was studied at the transcriptome level. A. oryzae RIB40 was grown in the presence of different inhibitors commonly found in the lignocellulolytic side streams and RNA sequencing was utilized to investigate the different transcriptomic changes in response to the inhibitors. The main cause of the transcriptomic response in all conditions was the xenobiotic-induced formation of reactive oxygen species (ROS). Apart from levulinic acid, all conditions showed strong initial suppression of metabolic pathways relating to cell proliferation, ribosomal functions and protein folding and sorting in the endoplasmic reticulum. Genes associated with cellular detoxification, namely NAD(P)H-dependent oxidoreductases and efflux transporters, such as the ATP-Binding Cassette (ABC) transporters and major facilitator superfamily (MFS) transporters showed strong upregulation upon exposure to xenobiotics. The results obtained provide important insights into the stress response of A. oryzae to the xenobiotic compounds and their cellular detoxification. Aldehydic inhibitors, especially HMF, caused stronger and more severe stress response in A. oryzae RIB40. Additionally, we identified several promising target genes for future strain engineering.

overall_design: Strain RIB40 was grown overnight at about 28°C with 220 rpm in shake flasks containing 250 mL Czapek-Dox with 2 % D-fructose. Mycelia was harvested on Miracloth and washed with Czapek-Dox. Equal portions of mycelia were transferred to flasks containing 50 mL Czapek-Dox with 2 % D-fructose and with or without a defined IC50 concentration of furfural, 5-hydroxymethylfurfural, vanillin, ferulic acid or levulinic acid. The cultures were incubated in rotary shakers for 24 h at 220 rpm. Total RNA of three biological replicates (quadruple for the control) was extracted at five different time points, 0 h, 1 h, 3 h, 5 h, and 24 h. The sample quality of 3 h and 5 h samples of ferulic acid and levulinic acid was not sufficient and those samples were excluded from the data set.

first: Adiphol

last: Dilokpimol

first: Andriy

last: Kovalchuk


title: A singular cockroach insulin-like peptide specific for a male reproductive gland

status: Public on Jun 17 2025

city: Barcelona

first: Jose Luis

last: Maestro

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37-49

department: Complexity of Life

country: Spain

institute: Institute of Evolutionary Biology

summary: The insulin-IGF-signalling (IIS) pathway plays crucial roles in animal physiology. In insects, this pathway works using multiple ligands, insulin-like peptides (ILPs), and a lower number of insulin receptors (InRs). Consequently, much of the regulation of IIS pathway activity is driven by the expression of ILPs, its timing, tissue, and mode of action: endocrine, paracrine, or autocrine. In the adult male of the cockroach Blattella germanica, tissue expression and the regulation in relation to food restriction of the BgILP1-7 genes is similar to that observed in females. However, we identified the expression of BgILP8, an ILP absent in females, in the conglobate gland of males, and only in this organ. BgILP8 expression in the conglobate gland is high during the initial days of adulthood and is reduced under starvation. The conglobate gland is a male sexual accessory gland specific to cockroaches, involved in spermatophore formation. It is composed of twisted tubules that ramify into different branches and converge in a general collecting tubule that opens into the ejaculatory duct. The tubules are lined with a single layer of secretory cells, each of the cells crossed by a small ductule formed by cuticle and actin fibres through which the secretory products will be released. Decreasing BgILP8 levels through RNAi (dsILP8) resulted in a reduction in the size of secretory cells, although the total protein extracted remained unaffected. A comparison of the transcriptomes of control and dsILP8 glands revealed only small differences. Further, comparing genes expressed in the conglobate gland to those expressed in adult females provided a list of putative conglobate gland-specific genes. Our results suggest that BgILP8 plays a role in the development of the conglobate gland. However, a potential function in other male organs or its possible transfer to the female in the copulation cannot be ruled out.

overall_design: Two micrograms of dsRNA (dsILP8 or dsMock) were injected into the abdomen of Blattella germanica males on the day 7 of the sixth instar nymph. Dissections were performed at adult day 7.

first: Viviana

last: Pagone

first: David

last: Pujal

first: José

middle: L


title: Unique nigral and cortical pathways implicated by epigenomic and transcriptional analyses in a rotenone rat model of Parkinson’s disease [ChIP-Seq]

city: London

first: Maria

last: Tsalenchuk

address: Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Road

country: United Kingdom

institute: King's College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pesticide exposure is increasingly recognised as a potential environmental factor contributing to the onset of idiopathic Parkinson’s disease, yet the molecular mechanisms underlying this connection remain unclear. This study aims to explore how pesticide exposure disrupts key brain regions involved in Parkinson’s disease pathology by reshaping gene expression and epigenetic landscapes. Using the  well established rotenone rat model of the disease, we used H3K27ac ChIP-sequencing and RNA-sequencing to profile active regulatory elements and transcriptional activity in the substantia nigra and cortex. We identified widespread transcriptomic and epigenetic differences which are consistent across the assays. Our results indicate there is a strong immune response to rotenone localised to the substantia nigra and highlight an enrichment of immune-related motifs in this brain region, suggesting that the immune response is at least partially driven by gene regulatory mechanisms. We also noted an increase in C1q complement pathway activity in the substantia nigra. In contrast, we identified widespread dysregulation of synaptic function at the gene regulatory level in the cortex of these same rats. Our results highlight a role for gene regulatory mechanisms potentially mediating the effects of pesticide exposure, driving region-specific functional responses in the brain that may contribute to the pathology of Parkinson’s disease.

overall_design: To profile gene regulatory variation in the SN and cortex of rats exposed to rotenone compared to vehicle controls, we used RNA sequencing (RNA-seq) and H3K27ac chromatin immunoprecipitation (ChIP)-seq

first: Kyle

last: Farmer

first: Sandra

last: Castro

first: Abigail

last: Scherier

first: Yuqian

last: Ye

first: Timothy

last: Greenamyre

first: Emily

last: Rocha

first: Sarah

last: Marzi


title: Pseudomonas aeruginosa Raw sequence reads

status: Public on Jun 16 2025

city: Guangzhou

first: Jiayu

last: Gu

address: Xingangxi street

country: China

institute: SCSIO

summary: To study the changes and differences in gene expression levels during biofilm formation of two Pseudomonas aeruginosa sublines.

overall_design: RNA-seq profiling of wildtype MPAO1 and PAO1 cells at Day0 (planktonic) and Day6 (biofilm).


title: Novel Single-Cell Multiomics Approach to Analyze Replication Timing and Gene Expression in Mouse Preimplantation Embryos

city: Minneapolis

first: Micah

last: Gearhart

state: MN

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

department: Genetics, Cell Biology and Development

country: USA

institute: University of Minnesota

summary: Analysis of a cell’s replication timing (RT) provides insight into how genes replicate, early or late, during the S-phase of the cell cycle. RT is cell-type specific, inheritable, and has been correlated to gene expression in normal and diseased states. However, most studies have been limited to somatic cells. Very little is known about RT in early mouse embryos, and how it correlates with the start of transcription during zygote gene activation (ZGA), at the 2-cell stage. In this study, we used a novel in-house single-cell multiomics approach to simultaneously analyze RT and gene expression in individual cells of the mouse 1-cell, 2-cell, and 4-cell embryos. We demonstrated that RT was established at the 1-cell stage prior to ZGA. Surprisingly, we observed RT and gene expression correlation trends that were different in early totipotent embryos, compared to previously published studies in somatic cells. Late replicating regions correlated with higher gene expression and open chromatin in the early developing embryos. Lastly, we performed an integrated pseudo time trajectory analysis combining RT and gene expression information per cell.

overall_design: Mouse zygotes at E0.5 were extracted from super ovulated C57/Bl6 mice. Zygotes were cultured in vitro until 2-cell and 4-cell stages. Zygotes/1-cell embryos were directly transferred into RLT buffer in 96-well plates with 1 zygote/ well. Single cells from 2-cell embryos were extracted 26-28 hours after zygote extraction. Single cells from 4-cell embryos were extracted 38-40 hours after zygote extraction. For 2-cell and 4-cell stages, first the zona pellucida was removed using the Tyrode Acid Solution, then the embryos were incubated in TrypLE: Accutase (1:3) solution for ~10 minutes until the embryos dissociated into single cells. Single cells were then mouth pipetted into individual wells of a 96-well plate containing RLT buffer. The wells were spun down and stored at -20C until further processing.

first: Anala

middle: V

last: Shetty

first: Clifford

middle: J

last: Steer

first: Walter

middle: C

last: Low


title: Macromolecular interactions dictate Polycomb-mediated epigenetic repression [ChIP-seq]

city: New York

first: Yicheng

last: Long

state: New York

address: 413 East 69th Street

department: Biochemistry, CVRI

institute: Weill Cornell Medicine

summary: Dynamic regulation of epigenetic states relies on complex macromolecular interactions such as at the protein-protein and protein-DNA level. It remains an unsolved question how H3K27me3, the hallmark histone modification for facultative heterochromatin, and its writer Polycomb repressive complex 2 (PRC2) are spatiotemporally regulated during development. Here we engineered separation-of-function mutants to surgically dissect the roles of individual macromolecular interactions required for PRC2 function. We show that Polycomb-mediated silencing is precisely regulated by the dynamic interactions among the PRC2 core complex, its accessory proteins, DNA sequences, and other histone modifications. Combining CRISPR-mediated engineering of separation-of-function mutants, human stem cell differentiation models, next-generation sequencing approaches, and reconstituted biochemical assays, we identified distinct regulatory functions of these macromolecular interactions on epigenetic repression in human pluripotent stem cells and cardiac differentiation. Disruption of key interactions led to distinct and opposing effects on cardiomyocyte differentiation, suggesting their highly specified roles in cell fate determination. Together, these results reveal the importance of individual macromolecular interactions at the center of PRC2 controlling epigenetic repression.

overall_design: Two independent CRSIPR clones of each of the two edited cell lines (WT or mutant) were analyzed. For ChIP-seq, hiPSCs at 70–80% confluency were collected by Accutase treatment and crosslinked with 1% formaldehyde in PBS at room temperature for 10 min. The crosslinking reaction was quenched by adding one volume of 1.25 M glycine to 10 volumes of PBS for 2 min. Cells were washed in ice-cold PBS and cell pellets stored at -80°C. Aliquots of 10 million cells were lysed in 1 mL ChIP lysis buffer (800 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.5% sodium deoxycholate, 1X protease inhibitor cocktail) on ice for 30 min. Lysates were sonicated in MilliTubes (Covaris, 520135) with the Covaris S220 focused-ultrasonicator at 4°C for 10 min at a PIP of 140 W, a duty factor of 5%, and 200 cycles/burst. Lysate was cleared by centrifugation at 16,000xg for 10 min at 4°C, and supernatant was collected. For each IP, 1 mL chromatin dilution buffer (25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 1X protease inhibitor cocktail) together with 20 ng spike-in chromatin from Drosophila melanogaster S2 cells (Active Motif, 53083) was added to the cleared lysate from 2.5-5.0 million cells. Chromatin samples were incubated with 2-4 μg of anti-CBX7 (4 μL), anti-FLAG (2 μL), anti-H2AK119ub (5 μL), anti-H3K27me3 (6 μL), anti-H3K36me3 (3 μL), anti-H3K4me3 (4 μL), anti-JARID2 (4 μL), anti-MTF2 (5 μL), anti-RING1B (7 μL), or anti-SUZ12 (4 μL) antibody at 4°C overnight. A spike-in antibody against the Drosophila-specific histone variant H2Av was added to all chromatin samples. Then, 25 μl of washed Pierce Protein A/G Magnetic Beads (Thermo Fisher, 88803) were added to the IP solution to incubate at room temperature for 2 h. Beads were washed twice with 1 mL of LSB buffer (20 mM Tris pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, 1% Triton X-100), HSB buffer (20 mM Tris pH 8.0, 2 mM EDTA, 500 mM NaCl, 0.1% SDS, 1% Triton X-100), LiCl buffer (10 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% sodium deoxycholate, 1% Igepal), and TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Chromatin was then eluted by incubating the beads with 120 μl of elution buffer (100 mM sodium bicarbonate, 1% SDS) for 20 min at room temperature. Formaldehyde crosslinking was reversed by adding 5 μL of 5 M NaCl and incubating at 65°C for 3 h. Protein and RNA were removed by adding 14 μL of 1M Tris pH 8, 3 μL of 500 mM EDTA, 3 μL of proteinase K (Thermo Fisher, 25530049), and 1 μL of 1 mg/mL RNase A (Thermo Fisher, EN0531) and incubating at 37°C for 1 h. DNA was extracted by phenol–chloroform–isoamyl extraction followed by ethanol precipitation. DNA samples were resuspended in 30 μl of 10 mM Tris pH 8.0 and quantified using a Qubit fluorometer (Invitrogen). Between 2 ng and 100 ng of each sample was used for library preparation using the KAPA HyperPlus Kit according to the manufacturer’s instructions, except for skipping the fragmentation step. DNA libraries were pooled and sequenced on a NovaSeq 6000 or NovaSeq X Plus using a 150-cycle kit (paired end, 2 x 150 bp). ChIP-seq analysis was performed similar to what was described previously.14 Adapter sequences were trimmed from the read pairs using Cutadapt (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT). Trimmed reads were aligned to the human reference genome (hg38) using BWA (MEM). Properly paired read alignments with mapping scores greater than 30 were used for downstream analysis. PCR duplicates were removed using Picard MarkDuplicates (https://broadinstitute.github.io/picard/). Peak calling was performed with MACS215 with the options of ‘macs2 callpeak -g hs -f BAMPE --keep-dup all --bdg’. Bigwig files were generated using bedGraphToBigWig tool. Peak metaplots and heatmaps were generated on pooled replicates using deepTools. Gene-specific ChIP enrichment analysis was performed by comparing the number of reads mapped to gene bodies (defined by the featureCounts tool using the GENCODE v42 annotation) in mutant versus WT cell lines. For each biological replicate (individual clone), the read counts of input and pulldown were normalized by total number of aligned reads for the genes whose counts were great than one. Similar to what was previously described,14 a generalized linear model was constructed to estimate log2Foldchange of the normalized read counts in pulldown relative to input while adjusting for cell line variability. Shrunken fold change was estimated using the R package DESeq2. The statistical significance of the log2Foldchange was calculated empirically by the R package fdrtool, with the input of Wald statistics calculated using DESeq2. The differential ChIP enrichment between the mutant and WT lines was calculated with an interaction term of cell line (mutant versus WT) and library (pulldown versus input) in a regression model. Plots were generated using ggplot2 and Tableau software. Gene ontology analysis was performed using ShinyGO.

first: Christian

last: Much

first: Sandy

middle: M

last: Rajkumar

first: Liming

last: Chen


title: Targeting SUMOylation triggers interferon-beta-dependent activation of patient and allogenic Natural Killer cells in preclinical models of Acute Myeloid Leukemia [ATAC-seq I]

city: Montpellier

first: Denis

last: Tempé

address: 1919 route de Mende

country: France

institute: CNRS

summary: Natural Killer (NK) cells are critical actors of the anti-tumoral immune response. However, NK cells are often dysfunctional in cancer patients, particularly in hematological malignancies like Acute Myeloid Leukemias (AML), where patients typically exhibit low NK cells numbers and activity. In addition, there is increasing interest in using allogenic NK cells transplantation as cancer immunotherapy. New strategies are however required to both reactivate NK cells in cancer patients and enhance the anti-tumor activity of transplanted NK cells. Here, we demonstrate that targeting SUMOylation, a protein post-translational modification, activates NK cells from both healthy donors and AML patients. Subasumstat (TAK-981), a first-in-class inhibitor of SUMOylation used in phase I/II clinical trials, enhances NK cells degranulation, secretion of inflammatory cytokines (IFN-γ, TNF-α, FasL) and cytotoxicity against AML cells. In vivo, TAK-981 improves the anti-leukemic efficacy of ex-vivo expanded cord-blood NK cells in leukemia-bearing mice. One early effect of TAK-981 is to specifically increase the accessibility and activation of cis-regulatory regions of interferon pathway genes and induce their transcription. TAK-981 induces the secretion of interferon-beta, mostly by NK cells and monocytes, which is required for NK cells activation. Surprisingly, IFNB1 induction is independent of MDA5, cGas, IRF-1, -3 and -7. Altogether, this suggests that targeting SUMOylation activates a non-canonical interferon pathway able to boost NK cells anti-leukemic potential.

overall_design: DNA from NK cells purified from 2 differents healthy donors and treated or not with TAK-981 for 6 h, were tagmented using Tagment DNA Enzyme 1 followed by sequencing.

first: Rawan

last: Hallal

first: Guillaume

last: Bossis


title: Spatial transcriptome profiling for nasopharyngeal carcinoma [GeoMx-DSP]

status: Public on Jun 14 2025

city: HK

first: Lai Shun Dittman

last: CHUNG

state: HK

address: 21 Sassoon Road, Pokfulam

department: Department of Clinical Oncology

country: Hong Kong

institute: the University of Hong Kong

summary: As the first human DNA tumour virus Epstein-Barr virus (EBV) is detectable in over 90% of nasopharyngeal carcinoma (NPC) patients in the endemic regions. Genome-wide analysis of 3D chromosome conformation revealed the virus-host chromatin interactions induce spatial reorganisation of loops and compartments, exhibiting “enhancer infestation” and “H3K27 bivalency” at EBV interaction regions (EBVIRs). Through this mechanism, EBV hijacks KDM5B, a genome stability gatekeeper, and its binding targets leading to aberrant activation of the EBVIRs-enhancer-KDM5B signature. The cancer cells with this signature had increased MYC activation, DNA damage responses, and epigenetic plasticity for epithelial-immune cell dual features with metastatic potential. Our multi-centre multi-omics study further confirmed that this signature was highly relevant to chromosome instability and could be utilised as a risk factor for distant metastasis. This study highlights a novel paradigm where latent viral episomes could alter host high-order epigenotype, promoting transcriptional rewiring and risk of metastasis in NPC.

overall_design: Spatial transcriptome data were generated from primary NPC patients. Patients with NPC who developed distant metastasis within three years after treatment were classified as metastatic NPC (MET-NPC), while those without early metastasis were designated as non-metastatic NPC (nonMET-NPC).

first: Wei

last: Dai

first: Yunfei

last: Xia


title: Macromolecular interactions dictate Polycomb-mediated epigenetic repression [RNA-seq]

overall_design: Two independent CRSIPR clones of each of the two edited cell lines (WT or mutant) were analyzed. RNA-seq libraries were prepared from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase according to the manufacturer’s instructions. Libraries were pooled and sequenced on a NovaSeq 6000 or NovaSeq X Plus using a 150-cycle kit (paired end, 2 x 150 bp). RNA-seq analysis was performed similar to what was described previously.14 Adapter sequences were trimmed from the read pairs using Cutadapt (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT). Trimmed reads were aligned to the human reference genome (hg38) using STAR with GENCODE basic gene annotation (v42). Read counts were calculated as transcripts per million (TPM) using uniquely mapped reads counted using featureCounts in a strand-specific way. Differential expression analysis between the mutant and WT lines was performed by modeling read counts in a generalized linear model accounting for cell lines. Fold change and p-values were calculated using DESeq2, in which two-sided Wald tests for regression coefficients of interest were performed. Differential expression heatmaps were generated using the R package pheatmap. Scatter plots were generated using the Tableau software. Gene ontology analysis was performed using ShinyGO.


title: Virus-Human Chromatin Interactions Reorganise 3D Genome and Hijack KDM5B for Promoting Metastasis in Nasopharyngeal Carcinoma [10X Visum Spatial Transcriptome]

overall_design: Visium spatial transcriptome sequencing was performed on frozen tissue sections obtained from one patients with primary and treatment-naïve NPC. Hematoxylin and eosin (H&E) staining was performed and imaged on each frozen section to determine the optimal sequencing location and used as a reference for the downstream spatial analysis.

first: Dittman Lai-Shun

last: Chung

first: Lanqi

last: Gong


title: Mapping and engineering RNA-driven architecture of the multiphase nucleolus

city: Gosselies

middle: LJ

last: Lafontaine

state: Hainaut

address: Av Profs Jeneer & Brachet, 12

institute: Universite libre de Bruxelles

summary: Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a multiphase liquid-like structure where ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps to form the small and large ribosomal subunits (SSU and LSU).  However, how rRNA processing is coupled to the layered nucleolar organization is poorly understood due to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here, we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. Furthermore, by generating synthetic nucleoli in cells through an engineered rDNA plasmid system, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.

overall_design: RiboMethSeq sequencing data from "control", "60" and "90" samples that refer to Extended Data Fig.1g

first: SA

last: Quinodoz

first: L

last: Jiang

first: AA

last: Abu-Alfa

first: TJ

last: Comi

first: H

last: Zhao

first: Q

last: Yu

first: LW

last: Wiesner

first: JF

last: Botello

first: A

last: Donlic

first: E

last: Soehalim

first: P

last: Bhat

first: C

last: Zorbas

last: Wacheul

last: Košmrlj

first: DLJ

first: S

last: Klinge

first: CP

last: Brangwynne


title: Vitamin D and Lipopolysaccharide jointly induce a distinct epigenetic and transcriptional program in Human Monocytes [ATAC-seq]

status: Public on Jun 13 2025

city: Olsztyn

first: Mariusz

last: Jankowski

address: Trylińskiego

country: Poland

institute: Institute of Animal Reproduction and Food Research

summary: Pathogen-associated molecular patterns such as lipopolysaccharide (LPS) mimic immune responses triggered by bacterial infections. The hormonally active form of vitamin D, 1α,25-dihydroxyvitamin D₃ [1,25(OH)₂D₃], supports innate immunity, but its molecular mechanisms remain incompletely understood. Here, we investigated epigenomic and transcriptomic changes in THP-1 monocytes exposed to 1,25(OH)₂D₃, LPS, or their combination over 24–48 hours. Epigenome profiling via ATAC-seq revealed that co-stimulation with 1,25(OH)₂D₃ and LPS induces substantially more chromatin accessibility changes than either treatment alone, with up to 81% of altered regions uniquely responsive to the combination. Motif enrichment analysis highlighted JUN/FOS transcription factors as key regulators of this synergistic response. Transcriptomic analysis via RNA-seq mirrored these findings, though fewer genes than chromatin regions were affected. Notably, under 1,25(OH)₂D₃-primed conditions, 333 genes exhibited synergistic expression changes upon co-treatment, meaning their responses significantly deviates from the additive effects of the individual stimulations. This includes 267 previously unrecognized as vitamin D targets. Functional annotation revealed these genes are primarily linked to monocyte and T cell differentiation, in contrast to classical vitamin D targets associated with inflammation. In conclusion, our findings uncover a distinct and cooperative regulatory program driven by vitamin D and LPS, advancing our understanding of how vitamin D shapes immune responses at the chromatin and transcriptional levels.

overall_design: ATAC-seq libraries of THP-1 cells treated with 1,25D, LPS and 1,25D+LPS over a 24-48 hour period

first: Carsten

last: Carlberg


title: Zea mays B73 seedlings incubated 2 hours in water, primary and seminal root tips (0-1mm), RNA-seq, cellular transcription data

city: Austin

first: Lorenzo

last: Concia

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

summary: These maize (Zea mays L.) B73 cellular RNA samples were prepared from seedlings treated in 2 h water and extracted cellular RNA directly from frozen 1-mm root tips. They are parallel experiment to compare to two other types of RNA extracted from isolated nuclei.

overall_design: To investigate the cellular transcriptomes of primary and seminal root root tips of maize B73 seedlings that have been incubated 2 hour in aerated water

first: Leigh

last: Mickelson-Young

first: Emily

last: Wear

first: Linda

last: Hanley-Bowdoin

first: William

middle: F

last: Thompson


title: USP17L promotes the 2-cell program through deubiquitination of H2AK119ub1 and ZSCAN4 [RNA-Seq]

city: Jinan

first: Xukun

last: Lu

address: No. 44 Wenhua West Road

institute: Shandong University

summary: Zygotic genome activation (ZGA) is the first transcription event after fertilization. A minor wave of ZGA (minor ZGA) precedes and is essential for the major wave of ZGA (major ZGA) in two-cell (2C) mouse embryos. A subset of minor ZGA genes (known as “2C” genes) are also activated in a rare population of embryonic stem cells (ESCs) (2C-like cells), which possess expanded developmental plasticity to both embryonic and extra-embryonic tissues, like 2-cell embryos. However, the functions of these 2C genes remain to be fully understood. Here, through knockdown, overexpression, and biochemical analyses, we find that one family of such 2C genes, Usp17l, plays essential roles in both transcriptional and post-translational regulation of the 2C program. Specifically, USP17LE, a member of the USP17L family, deubiquitinates H2AK119ub1 and promotes the expression of Dux and the downstream 2C genes, including Zscan4, Tcstv1, and retrotransposons such as MERVL, in ESCs. Moreover, USP17LE deubiquitinates and stabilizes ZSCAN4. In mouse pre-implantation embryos, Dux is marked by strong H2AK119ub1 at most stages except for the 1-cell and early 2-cell stages, and overexpression of Usp17le reduces H2AK119ub and further promotes the activation of Dux and 2C genes. Thus, our findings identify USP17L as a key regulator of the 2C program.

overall_design: To investigate the function of USP17L in mouse ZGA and early development, we conducted knockdown, overexpression combined with systematic molecular and bioinformatic analyses in mouse ESCs and pre-implantation embryos.  STAR ChIP-seq was used to examine H3K9me3 in control and Usp17l KD mESCs. Stacc-seq was used to examine H2AK119ub1 in mouse control, Usp17l KD and Usp17le OE late 2-cell embryos. CUT&RUN was used to examine H3K27me3 in mouse control, Usp17l KD and Usp17le OE late 2-cell embryos. Two replicates were involved for each sample.

first: Panpan

last: Shi

first: Wei

last: Xie

first: Lin

last: Liu


title: USP17L promotes the 2-cell program through deubiquitination of H2AK119ub1 and ZSCAN4 [ChIP-Seq]


city: Princeton

first: Sofia

middle: Agustina

last: Quinodoz

state: NJ

address: 25 William St

department: CBE

institute: Princeton University

summary: Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a multiphase liquid-like structure where ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps to form the small and large ribosomal subunits (SSU and LSU). However, how rRNA processing is coupled to the layered nucleolar organization is poorly understood due to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here, we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. By generating synthetic nucleoli in cells through an engineered rDNA plasmid system, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.

overall_design: RNA-seq was performed on 5eU pulse-chase labeled samples to monitor rRNA processing dynamics over time in response to various perturbations affecting ribosome biogenesis.

first: Lifei

last: Jiang

first: Troy

last: Comi

first: Clifford


title: Vitamin D and Lipopolysaccharide jointly induce a distinct epigenetic and transcriptional program in Human Monocytes [RNA-Seq]

overall_design: RNA-seq libraries of THP-1 cells treated with 1,25D, LPS and 1,25D+LPS over a 24-48 hour period


title: MALNC: A new mutant NPM1/IDH2R140 and PML-RARA-associated lncRNA with impact on AML cell proliferation, maturation and drug response

status: Public on Jun 12 2025

city: Stockholm

first: Sören

last: Lehmann

address: Blickagången 16

department: the Department of Medicine

country: Sweden

institute: Karolinska Institute

summary: As the non-coding genome remains poorly characterized in acute myeloid leukemia (AML), we aimed to identify and functionally characterize novel long non-coding RNAs (lncRNAs) relevant to AML biology and treatment. We first identified lncRNAs overexpressed in AML blasts and discovered a novel lncRNA, which we named myeloid and AML-associated intergenic long non-coding RNA (MALNC). MALNC is overexpressed in AML, particularly in cases with the PML-RARA fusion or IDH2R140/NPM1 co-mutations, and is associated with a distinct gene expression profile. Functional studies showed that MALNC knockout impairs AML cell proliferation and colony formation, enhances ATRA-induced differentiation, and sensitizes cells to arsenic trioxide. Transcriptomic analysis revealed that MALNC loss alters the expression of retinoic acid pathway genes, and chromatin binding studies showed that MALNC binds to genes related to the retinoic acid and Rho GTPase pathways. In conclusion, we have identified MALNC as a novel lncRNA that promotes leukemic cell proliferation, counteracts ATRA-induced differentiation, and modulates drug sensitivity in AML.

overall_design: CRISPR-Cas9 editing was used to generate several MALNC-knockout (KO) in NB4 cell lines by deleting various TSSs. In KOA, Ex1.1 and Ex1.2 were deleted, in KOB, Ex1.0 was deleted. Three NB4 KOA, three NB4 KOB and three NB4 WT clones were selected for RNA-seq analysis at basal level. Additionally, one NB4 KOB clone and one NB4 WT clone were  treated in three biological replicates with ATRA (1µM) for 72h and subject to RNA-seq.

first: Anne

last: Neddermeyer

first: Xiangfu

last: Zhong

first: Elisabetta

last: Cozzi


title: MALNC: A new mutant NPM1/IDH2R140 and PML-RARA-associated lncRNA with impact on AML cell proliferation, maturation and drug response [ChIRP-seq]

overall_design: NB4 cells were used to evaluate the DNA-binding sites of the long non-coding RNA MALNC through ChIRP-seq analysis.


title: Methionine metabolism regulates T cell fate by KCa3.1 activity (Cut&Run)

status: Public on Jun 11 2025

city: Memphis

first: Douglas

middle: R

last: Green

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St. Jude Children's Research Hospital

summary: We found that methionine availibility during T cell activation regulates rapid NFAT1 activation, thereby governing T cell fate. Further, acute methionine limitation didn't affect global histone methylation status stating the crucial role of methioinine during early TCR activation.

overall_design: Cut&Run analysis of 18 samples. NFAT1 binding sites along with Histone modification status of H3K27me3 and H3K4me3 were analyzed. Two conditions (0.1mM and 0.03mM methionine) were used with 2 replicates/condition were used for NFAT1 analysis and 3 replicates/condition were used for Histone modification analysis.

first: Piyush

last: Sharma

first: Ao

last: Guo

first: Poudel

last: Suresh

first: Mark

last: Chen


title: Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst [mouse_ERKi_scRNAseq]

city: Cambridge

first: Loke CTR

last: Bioinformatics

address: Downing Street

department: Physiology building

institute: Loke Centre for Trophoblast Research

summary: Studies in the mouse demonstrate the importance of fibroblast growth factor (FGF) and extra-cellular receptor tyrosine kinase (ERK) in specification of embryo-fated epiblast and yolk-sac-fated hypoblast cells from uncommitted inner cell mass (ICM) cells prior to implantation. Molecular mechanisms regulating specification of early lineages in human development are comparatively unclear. Here we show that exogenous FGF stimulation leads to expanded hypoblast molecular marker expression, at the expense of the epiblast. Conversely, we show that specifically inhibiting ERK activity leads to expansion of epiblast cells functionally capable of giving rise to naïve human pluripotent stem cells. Single-cell transcriptomic analysis indicates that these epiblast cells downregulate FGF signalling and maintain molecular markers of the epiblast. Our functional study demonstrates the molecular mechanisms governing ICM specification in human development, whereby segregation of the epiblast and hypoblast lineages occurs during maturation of the mammalian embryo in an ERK signal-dependent manner.

overall_design: Day 3.25 mouse embryos were treated for 24 hours with 5µM Ulixertinib or 0.1% DMSO and collected at day 4.25 for single-cell RNA sequencing using the SMART-seq protocol from Takara.

first: Kathy

last: Niakan

first: Claire

last: Simon

first: Martin

last: Proks

first: Naz

last: Salehin

first: Josh

last: Brickman


title: RNA sequencing analysis of the genes regulated by CueR in Vibrio parahaemolyticus.

city: Yangzhou

first: Chengkun

last: Zheng

address: No.48 East Wenhui Road

institute: Yangzhou university

summary: The transcriptome of the wild type strain and ΔcueR of Vibrio parahaemolyticus was compared by RNA sequencing analysis.

overall_design: The transcription profiles of the ΔcueR mutant grown in LB Broth supplemented with 1 mM CuSO4 were compared with that of the wild type strain. Each strain contains three biological replications.

first: Yimeng

last: Zhai


title: Sex differences in the rewiring of brainstem miRNA regulatory networks driving hypertension development

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

summary: In this study, we elucidated the role of miRNA dysregulation in brainstem autnomic circuits as hypertension develops. Female spontaneously hypertensive rats (SHR) and normotensive wistar kyoto rats were sacrified at 8, 10, 12, 16, and 24 weeks of age. 8 weeks is considered prior to the onset of hypertension while 10 and 12 weeks correspond to the age of onset. At 16 weeks hypertension has developed and at 24 weeks is considered chronic persistent hypertension. Three autonomic nuclei in the brainstem were collected, the nucleus of the solitary tract (NTS), the caudal ventrolateral medulla (CVLM), and rostral ventrolateral medulla (RVLM). NanoString rat miRNA panel was used to obtain miRNA expression profiles from all collected samples.

overall_design: miRNA expression was profiled in the nucleus of the solitary tract (NTS), caudal ventrolateral medulla (CVLM) and rostral ventrolateral medulla (RVLM) in the brainstems of spontaneously hypertensive rats (SHR) and normotensive wistar-kyoto (WKY) at 8, 10, 12, 16, and 24 weeks of age throughout the development of hypertension.

first: Alison

last: Moss

first: Ankita

last: Srivastava

first: James

middle: S

last: Schwaber


title: Methionine metabolism regulates T cell fate by KCa3.1 activity

first: Douglas

last: Green

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

overall_design: Refer to individual Series


title: Beyond chromatin: The role of histone variant H2A.B in modulating the genomic distribution of SWI/SNF in cancer

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

summary: The fact that the testis-specific H2A.B is ectopically expressed in Hodgkin lymphoma (HL) and its derived cell lines implicates H2A.B in having a role in oncogenesis (either as an oncogene or a tumour suppressor) similar to other epigenetic regulators of the testis. In order to understand the mechanism of H2A.B-mediated epigenetic regulation in Hodgkin lymphoa, the epigenomic profiles of pan-H2A.B and major H2A.B post-translational modificaitons were investigated using the CUT&RUN method.

overall_design: Epigenomic profiling of post-translationally modified H2A.B in L1236 and L428 cell lines.

first: Xuanzhao

last: Jiang

first: Tanya

last: Soboleva

first: David

last: Tremethick


title: Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst [RNA-seq II]

first: Loke CTR

last: Bioinformatics

summary: Studies in the mouse demonstrate the importance of fibroblast growth factor (FGF) and extra-cellular receptor tyrosine kinase (ERK) in specification of embryo-fated epiblast and yolk-sac-fated hypoblast cells from uncommitted inner cell mass (ICM) cells prior to implantation. Molecular mechanisms regulating specification of early lineages in human development are comparatively unclear. Here we show that exogenous FGF stimulation leads to expanded hypoblast molecular marker expression, at the expense of the epiblast. Conversely, we show that specifically inhibiting ERK activity leads to expansion of epiblast cells functionally capable of giving rise to naive human pluripotent stem cells. Single-cell transcriptomic analysis indicates that these epiblast cells downregulate FGF signalling and maintain molecular markers of the epiblast. Our functional study demonstrates the molecular mechanisms governing ICM specification in human development, whereby segregation of the epiblast and hypoblast lineages occurs during maturation of the mammalian embryo in an ERK signal-dependent manner.

overall_design: Naïve hESCs derived in PXGL or UXGL media following human embryo treatment with either Ulixertinib or DMSO. The embryo-derived naïve hESCs were transcriptionally profiled by bulk RNA-seq analysis.

first: Laura

last: Woods

first: Desi

last: Staneva


title: Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst [RNA-seq I]

summary: Studies in the mouse demonstrate the importance of fibroblast growth factor (FGF) and extra-cellular receptor tyrosine kinase (ERK) in specification of the epiblast and hypoblast in the inner cell mass (ICM). We recently demonstrated cross-talk of ERK and PI3K activity downstream of FGF and insulin growth factor signaling. We therefore hypothesized that ERK may have a conserved role in human hypoblast versus epiblast specification. Here we determined that FGF signaling is sufficient to specify hypoblast in human blastocysts. We describe ERK signaling during the blastocyst stage and demonstrate that blocking ERK activity, by small-molecule inhibition, is necessary for hypoblast specification in human blastocysts, and leads to expansion of the epiblast cells functionally capable of giving rise to naïve pluripotent embryonic stem cells. Transcriptomic analysis further reveals that these epiblast cells downregulate insulin growth factor and FGF signaling, while maintaining molecular markers of the epiblast. Moreover, we generate human naïve pluripotent stem cells following ERK inhibition. Our functional studies provide mechanistic insight into human blastocyst formation. We propose a unified model in which segregation of the epiblast and hypoblast lineages occurs during maturation of the mammalian blastocyst in an FGF/ERK signal-dependent manner.

overall_design: Human d6.5 blastocysts incubated with Ulixertinib to suppress ERK signalling or with DMSO as a control. Embryos were dissected by immunosurgery and single-cells collected for analysis by RNA-seq.

first: Claire

last: Simon

first: Kathy

last: Niakan


title: Methionine metabolism regulates T cell fate by KCa3.1 activity (RNA-Seq)

overall_design: RNA-Seq analysis of 8 samples. CD8+ Tumor infiltrating T cells were isolated at day 9 post T-cell transfer. Two groups 0.1mM Methionine and 0.03mM Methionine (n=4/group).

first: Piyush

last: Sharma

first: Ao

last: Guo

first: Poudel

last: Suresh

first: Mark

last: Chen


title: Methionine metabolism regulates T cell fate by KCa3.1 activity (ATAC-Seq)

overall_design: ATAC-Seq of 12 samples : 24 hrs activated OT-I CD8+ T cells in either 0.1mM methionine (control) or 0.03mM Methionine for 30 min, before methionine restoration in 0.03mM to control concentration (n=3/group) Other samples are KCa3.1 WT or mutant, activated for 24 hrs with SIINFEKL before processing (n=3/group).


title: AAV-mediated ARSA replacement for the treatment of Metachromatic Leukodystrophy

status: Public on Jun 10 2025

first: Michael

last: Tsabar

state: MA

address: 350 Water Street

institute: Sanofi

summary: Metachromatic leukodystrophy (MLD) is an autosomal recessive neurodegenerative disorder caused by mutations in the arylsulfatase A (ARSA) gene, resulting in lower sulfatase activity and the toxic accumulation of sulfatides in the central and peripheral nervous system. Children account for 70% of cases and become progressively disabled with death occurring within 10 years of disease onset. Gene therapy approaches to restore ARSA expression via adeno- associated viral vectors (AAV) have been promising but hampered by limited brain biodistribution. We report the development of a novel capsid AAV.GMU01, demonstrating superior biodistribution and transgene expression in the central nervous system of non-human primates (NHPs). Next, we show that AAV.GMU01-ARSA treated MLD mice exhibit persistent, normal levels of sulfatase activity and a concomitant reduction in toxic sulfatides. Treated mice also show a reduction in MLD-associated pathology and auditory dysfunction. Lastly, we demonstrate that treatment with AAV.GMU01-ARSA in NHPs is well-tolerated and results in potentially therapeutic ARSA expression in the brain. In summary, we propose AAV.GMU01-ARSA mediated gene replacement as a clinically viable approach to achieve broad andvtherapeutic levels of ARSA.

overall_design: snRNAseq of brains from 4 healthy mice trasnfected with AAV.GMU01-eGFP at a dose of 1.6e11 VG per mouse, and samples prepared from forebrain and hindbraind of each mouse.

first: Shyam

last: Ramachandran


title: Chemical reprogramming ameliorates cellular hallmarks of aging and extends lifespan

city: Lausanne

first: kevin

last: perez

address: rue du Bugnon 27

country: Switzerland

institute: University of Lausanne

summary: The dedifferentiation of somatic cells into a pluripotent state by cellular reprogramming coincides with a reversal of age-associated molecular hallmarks. Although transcription factor induced cellular reprogramming has been shown to ameliorate these aging phenotypes in human cells and extend health and lifespan in mice, translational applications of this approach are still limited. More recently, chemical reprogramming via small molecule cocktails have demonstrated a similar ability to induce pluripotency in vitro, however, its potential impact on aging is unknown. Here, we demonstrated that chemical-induced partial reprogramming can improve key drivers of aging including genomic instability and epigenetic alterations in aged human cells. Moreover, we identified an optimized combination of two reprogramming molecules sufficient to induce the amelioration of additional aging phenotypes including cellular senescence and oxidative stress. Importantly, in vivo application of this two-chemical combination significantly extended C. elegans lifespan and healthspan. Together, these data demonstrate that improvement of key drivers of aging and lifespan extension is possible via chemical-induced partial reprogramming, opening a path towards future translational applications.

overall_design: RNA-seq profiling of human dermal fibroblasts treated with 2c (N = 6), 7c (N = 6) and control (N = 12); sampled at day 6 and 14 after treatment.

first: Schoenfeldt

last: Lucas

first: Ocampo

last: Alejandro

first: Perez

last: Kevin


title: Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

overall_design: Day 5 human embryos were treated with 5µM Ulixertinib (Cambridge Bioscience); 0.1% DMSO for 36 hours and single-cell RNA sequencing was performed using the SMART-seq protocol from Takara.

middle: K

first: M

last: Proks

first: N

last: Salehin

last: Brickman


title: Gene expression profile at the single cell level of tumor endothelial cells from two orthotopic mouse models: KPC (pancreas) and PYMT (breast).

city: Palo Alto

first: Kevin

last: Brulois

state: CA

address: 3801 Miranda Ave

institute: Stanford University

summary: Single cell analyses have revealed unexpected diversity of endothelial cell subsets in various tissues. However, the expression provile and divsersity of EC in tumor tissue has remained less clear.

overall_design: PyMT or KPC tumor cells (100,000) were implanted in 6-week-old female C57BL6 mice. Ten days after implantation, tumors were digested as described below, and endothelial cells were sorted.

first: Yu

last: Zhu

first: Eugene C.

last: Butcher


title: Visfatin facilitates esophageal cancer migration by suppressing miR-3613-5p expression and promoting VEZF1/VCAN production

status: Public on Jun 09 2025

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Esophageal cancer, one of the most prevalent cancers worldwide, frequently exhibits distant metastases. The adipokine visfatin has been implicated in cancer progression and metastasis. However, the mechanisms by which visfatin regulates motility in esophageal cancer remain unclear. Here, we found that visfatin levels are higher in metastatic esophageal cancer patients than in primary esophageal cancer patients. Visfatin stimulation enhances migration and invasion in esophageal cancer cells. miRNA sequencing results revealed that miR-3613-5p controls visfatin-induced cell motility. Visfatin promotes esophageal cancer cell migration by reducing miR-3613-5p expression and subsequently increasing VEZF1/VCAN production. The visfatin/miR-3613-5p axis exhibits a promising target for inhibiting esophageal cancer metastasis.

overall_design: To identify miRNAs influenced by Visfatin, KYSE410 cells were incubated with Visfatin (30ng/ml) for 24 h before undergoing miRNA sequencing.

first: Shubham Suresh

last: Ghule


title: Effect of knockdown OFD1 on gene expression in pancreatic cancer cells

status: Public on Jun 08 2025

city: Shanghai

first: Peng

last: Li

address: Chongqing nanlu 280

department: Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education

institute: Shanghai JiaoTong University School of Medicine

summary: PARP inhibitors (PARPi) have demonstrated efficacy in treating human cancers with BRCA1 or BRCA2 gene mutations, which are present in only a small portion of breast, ovarian, prostate, and pancreatic cancers. In this study, we discovered that OFD1 is highly expressed in pancreatic cancer and is associated with a poor prognosis. Through screening an FDA-approved drug library, we found that OFD1 knockdown synergizes most effectively with PARPi for the treatment of pancreatic cancer cells. To explore the mechanism of OFD1 knockdown and PARP inhibitor-induced synthetic lethality, we knocked down OFD1 in three pancreatic cancer cell lines and performed RNA sequencing analysis of the whole genome to investigate the mechanisms underlying OFD1 inhibition and PARP inhibitor-induced synthetic lethality. In summary, our research will provide insights into the role of OFD1 in pancreatic cancer by revealing changes in the whole-genome expression profile and the underlying mechanisms.

overall_design: RNA sequencing analysis was performed on wild-type pancreatic cancer cell lines (MIA PaCa-2, PANC-1, PaTu 8988T) and their knockdown derivatives (shOFD1) at 0 and 3 days following doxycycline-induced knockdown

first: Junjie

last: Ye

first: Qian

last: Yang

first: Zaiming

first: Qing

last: Zhong


title: DDR1 regulates RUNX1-CBFβ to control breast stem cell differentiation

city: Boston

first: Charlotte

last: Kuperwasser

address: 150 Harrison Ave

department: Developmental, Molecular and Chemical Biology

institute: Tufts School of Medicine

summary: Understanding epithelial stem cell differentiation and morphogenesis during breast tissue development is essential, as disruption in these processes underlie breast cancer formation. Recent work has shown that epithelial stem and progenitor cells use the collagen receptor Discoidin Domain Receptor 1 (DDR1) for differentiation into both basal and luminal cell lineages, which together are necessary for complex ductal-lobular morphogenesis. Here, we used  a next-generation single cell derived organoid model that generates miniaturized breast tissue, to study how single stem cells can give rise to multiple cell types and compound tissue structures. We show that DDR1inhibition traps cells in a bipotent state, blocking alveolar morphogenesis and luminal cell expansion necessary for complex epithelium formation. Disrupting RUNX1 function produced nearly identical phenotypes, underscoring its critical role downstream of DDR1. Mechanistically, DDR1 affects the interaction and expression of RUNX1 and its cofactor CBFβ, thereby regulating its activity. Mutational analyses in breast cancer patients reveal frequent alterations in the DDR1-RUNX1 signaling axis, particularly co-occurring mutations. Together, these findings uncover DDR1-RUNX1 as a central signaling pathway driving breast epithelial differentiation, whose dysregulation may contribute fundamentally to breast cancer pathogenesis.

overall_design: Three primary patient samples were cultured in 3D hydrogels for 7 days bafore receiving chronic treatment (Vehicle, DDR1i, AI-10-104 (RUNXi) for an additional 14-21 days until control was fully developed. Bulk RNA-seq was performed on these samples, followed by gene expression analysis comparison of differential gene sets from RUNXi and DDR1i treated samples compared to the control.

first: Colin

last: Trepicchio


title: Expression data from uterine tissue of Egr1 knockout mice.

city: Seongnam-si

first: Gae Hoon

last: Jo

address: 64 Yatap-ro

country: South Korea

institute: CHA university

summary:
Microarrays have been widely used to study estrogen responses, as estrogen-induced transcriptome changes significantly impact the uterus. This study investigates the gene expression profiling of Egr1 knockout (KO) mice treated with estrogen. Our goal is to identify transcriptomic features that differ between estrogen-treated Egr1 knockout uteri and wild-type (WT) uteri.
We examined the gene expression patterns of 17 samples, consisting of Egr1 KO and WT uteri, at different time points: before estrogen treatment (0 h) and after treatment at 3 h, 6 h, and 24 h, using the MouseWG-6 V2 platform. Our findings indicate that Egr1 KO uteri exhibit dysregulation in reproductive and immune systems compared to WT uteri, and we observed altered insulin growth factor and PARylation activity related to uterine proliferation.

overall_design:
Microarrays were initially performed by using total uterine RNA. Uterine tissues were collected at 0, 3, 6, and 24 h after E2 treatment. The Illumina Mouse WG-6 V2 (48 K) array (Illumina, San Diego, CA, USA) was hybridized with appropriate cRNA probes at ISTECH (Goyang, South Korea). Expression values and detection calls were computed from the raw data.
<<< Submitter states that raw (non-normalized) data is unavailable for this submission due to circumstances beyond their control >>>

first: Gaehoon

first: Haengseok

last: Song


title: Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Xenium]

status: Public on Jun 07 2025

city: Saint Louis

first: Qiao

last: Xuanyuan

state: MO

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

summary: Spatial transcriptomics (ST) technologies enable the mapping of gene expression to specific regions within tissues. However, current ST platforms present inherent trade-offs between resolution and throughput, which cannot be entirely addressed by a single technology. To unravel the spatiotemporal landscape of gene expression and cellular interactions during kidney injury and repair, we employed an integrated approach combining Xenium's high-resolution in situ sequencing with Visium's whole-transcriptome spatial profiling.

overall_design: Bilateral ischemia-reperfusion injury (IRI) was induced on the kidneys of 8-10 week-old male mice (18 minutes), and control mice underwent sham surgery. Kidneys were harvested at various time points (Sham, 4 hours, 12 hours, 2 days, 14 days, and 42 days) and preserved as formalin-fixed paraffin-embedded (FFPE) tissue blocks. Serial tissue sections from these blocks were subjected to parallel Xenium in situ sequencing and Visium whole-transcriptome spatial profiling.

first: Benjamin

last: Humphreys

first: Haojia

last: Wu

first: Hemalatha

last: Sundaramoorthi

first: Pierre

last: Isnard

first: Changfeng

last: Chen

first: Waleed

last: Rahmani


title: LRP2 gene silencing expression by in vitro shRNA delivery on human iRPE cells

status: Public on Jun 06 2025

city: paris

first: kimberley

last: Delaunay

address: 15 rue de l'école de médecine

institute: Inserm

summary: To investigate the consequence of LRP2 loss-of-function in RPE cells in non-syndromic myopia, we differentiated IPS cells into iRPE in which the LRP2 gene was knocked out by shRNA.

overall_design: Comparative gene expression profile analysis of RNA-seq data for iRPE scrumble and shRNA LRP2 cells.

first: Kimberley

first: Alicia

last: Torriglia

first: Francine

last: Behar-Cohen


title: Virus-Human Chromatin Interactions Reorganise 3D Genome and Hijack KDM5B for Promoting Metastasis in Nasopharyngeal Carcinoma [ATAC-seq]

city: HK

first: Lai Shun Dittman

last: CHUNG

address: 21 Sassoon Road, Pokfulam

institute: the University of Hong Kong

summary: As the first human DNA tumour virus Epstein-Barr virus (EBV) is detectable in over 90% of nasopharyngeal carcinoma (NPC) patients in the endemic regions. Genome-wide analysis of 3D chromosome conformation revealed the virus-host chromatin interactions induce spatial reorganisation of loops and compartments, exhibiting “enhancer infestation” and “H3K27 bivalency” at EBV interaction regions (EBVIRs). Through this mechanism, EBV hijacks KDM5B, a genome stability gatekeeper, and its binding targets leading to aberrant activation of the EBVIRs-enhancer-KDM5B signature. The cancer cells with this signature had increased MYC activation, DNA damage responses, and epigenetic plasticity for epithelial-immune cell dual features with metastatic potential. Our multi-centre multi-omics study further confirmed that this signature was highly relevant to chromosome instability and could be utilised as a risk factor for distant metastasis. This study highlights a novel paradigm where latent viral episomes could alter host high-order epigenotype, promoting transcriptional rewiring and risk of metastasis in NPC.

overall_design: Two normal epithelial cells (NP69, NP460), three EBV+NPC cells (C17, C666, NPC43), three EBV-NPC cells (NPC53, NPC38 HK1) were conducted ATAC-seq to assess the chromatin accessibility. Each cell line has two replicates.

first: Dittman Lai-Shun

last: Chung

first: Wei

last: Dai


title: Cardiomyocyte Janus Kinase 1 (JAK1) Signaling is Required for Cardiac Homeostasis and Cytokine-Dependent Activation of STAT3

city: Ann Arbor

first: Matthew

middle: Jacob

last: Brody

state: MI

address: 1150 MEDICAL CENTER DR, 1240A MSRBIII

department: Department of Pharmacology

institute: University of Michigan

summary: Cytokine receptors respond to circulating inflammatory cytokines by signaling through Janus kinases (JAK) to ultimately elicit phosphorylation-dependent nuclear translocation and transcriptional activity of signal transducer and activator of transcription (STAT) proteins.  JAK1 is particularly important for STAT3-dependent cytokine production and macrophage recruitment by cardiomyocytes, however the role of basal JAK1 signaling in cardiac homeostasis remains unclear.  Downstream signaling through STAT3 promotes cardiac hypertrophy and remodeling in response to pressure overload or angiotensin-II but is protective during ischemic injury.  To assess the roles of JAK1 in cardiac physiology we generated mice with cardiomyocyte-specific deletion of JAK1 and evaluated cardiac structure and function, myocardial remodeling, and intracellular signal transduction.  Loss of JAK1 in cardiomyocytes results in dilated cardiomyopathy by 6 months of age, indicating cytokine receptor signaling through JAK1 is essential for cardiac physiology.  Cardiomyopathy in aged mice lacking cardiomyocyte JAK1 was characterized by substantial myocardial fibrosis.  Transcriptomics and gene expression analyses identified JAK1-dependent cytokine-inducible target genes in adult cardiomyocytes.  JAK1-deficient cardiomyocytes were resistant to phosphorylation and nuclear translocation of STAT3 and transcriptional reprogramming in response to the cytokine oncostatin M.  Collectively these data indicate cardiomyocyte JAK1 kinase activity is required for proper cardiac maturation and homeostasis and is indispensable for STAT3 activation by oncostatin M.

overall_design: RNAseq performed on isolated wild-type adult mouse cardiomyocytes treated with the cytokine oncostatin M or vehicle control. This experiment sought to determine the set of genes upregulated by activation of JAK1 through the oncostatin M receptor.

first: Michael

last: Young

first: Arasakumar

last: Subramani

first: Kobina

last: Essandoh

first: Francesca

last: Marino

first: James

last: Teuber

first: Kaye-Uwe

last: Wagner


title: Virus-Human Chromatin Interactions Reorganise 3D Genome and Hijack KDM5B for Promoting Metastasis in Nasopharyngeal Carcinoma [CUT&RUN-seq]

overall_design: Histone modifications, including H3K27ac and H3K4me3, were performed CUT&RUN-seq to profile at normal epithelial cells and EBV+NPC cells.


title: Virus-Human Chromatin Interactions Reorganise 3D Genome and Hijack KDM5B for Promoting Metastasis in Nasopharyngeal Carcinoma [Omni-C]

overall_design: In total, 16 samples were obtained for modified Hi-C analysis including normal immortalised nasopharyngeal epithelial cells (NPE) (NP69 and NP460), EBV+ NPC cell lines (EBV+ NPC) (C17, C666, NPC43, and HK1EBV), NPC cell lines with undetectable EBV copies (EBV- NPC) (NPC43noEBV, NPC53, NPC38, and HK1), EBV+ patient-derived xenografts (EBV+ PDXs) (C15, Xeno23, Xeno32, and NPC113), EBV+ gastric carcinoma (EBVaGC) (YCCEL1), and one EBV+ clinical NPC sample

first: Dittman


title: Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Visium]

first: Qiao

last: Xuanyuan

first: Benjamin

last: Humphreys

first: Haojia

last: Wu

first: Hemalatha

last: Sundaramoorthi

first: Pierre

first: Changfeng


title: Multimodal spatial transcriptomic characterization of mouse kidney injury and repair

overall_design: Refer to individual Series


first: Loke CTR

last: Bioinformatics

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Kathy

last: Niakan


title: Disulfiram inhibits bacterial growth by inducing zinc-dependent reactive oxygen species

status: Public on Jun 05 2025

city: Hangzhou

first: Qinyu

last: Luo

state: Zhejiang

address: Yuhangtang road #866

institute: zhejiang university

summary: With the growing threat posed by emerging drug-resistant bacteria, the discovery of new antibiotics and the exploration of additional antimicrobial mechanisms of medicines currently used in the clinic are urgent. In this study, we found that disulfiram, a drug used for the treatment of alcohol addiction, inhibited the growth of multiple bacteria and quickly inhibited the growth of E. coli. When combined with kanamycin or polymyxins in vitro, disulfiram could augment the bactericidal effect against E. coli or A. baumannii. When combined with colistin in vivo, disulfiram also protected against murine E. coli infection. Disulfiram inhibited the motility of E. coli but did not change its length morphologically. Transcriptomic analysis revealed that disulfiram-treated E. coli presented an oxidative stress pattern and zinc-related transcriptomic changes. Moreover, the bacteriostatic effect of disulfiram on E. coli and S. aureus could be fully prevented by the ROS scavenger NAC. In addition, zinc ions increased ROS levels and further suppressed bacterial growth, whereas zinc chelators suppressed ROS and restored the growth of both E. coli and S. aureus. This study reveals that disulfiram inhibits bacterial growth by inducing zinc-dependent intracellular reactive oxygen species (ROS). This bacteriostatic effect can be reversed by ROS scavengers or zinc chelators, highlighting a previously uncharacterized antimicrobial mechanism for disulfiram.

overall_design: E. coli cultures were grown in LB medium to mid-log phase and then divided into two groups: a treatment group and a control group. For the treatment group, E. coli was incubated with disulfiram at a final concentration of 64 μg/mL for 4 hours at 37°C with shaking. The control group received an equal volume of vehicle (DMSO) without disulfiram under identical conditions. Each condition was performed in three independent biological replicates (n = 3). Following treatment, cells were collected for downstream analysis.


title: Characterizing the Staphylococcus aureus fatty acid degradation operon

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

summary: Staphylococcus aureus can supplement its endogenous fatty acid synthesis pathway (FASII) with exogenous fatty acids it acquires from the environment through the fatty acid kinase (Fak) complex. While S. aureus has been thought to not degrade fatty acids, it does possess a potential fadXDEBA locus that contains all the genes necessary for -oxidation. Using mRNA analysis, we determined that the fadXDEBA operon can be found on one polycistronic mRNA. Moreover, we identified the fadX promoter and a putative binding site within this region that is consistent with negative regulation by the metabolism-responsive regulator, Carbon Catabolite Protein A (CcpA). Indeed, in the absence of glucose or CcpA, we saw the fadXDEBA operon was derepressed. S. aureus is annotated to lack the crotonase domain of FadB; however, new analysis indicates it is present. To test the functionality of the S. aureus FadB, we performed complementation assays with E. coli fad mutants using minimal media supplemented with single fatty acids. We were able to restore growth of E. coli fad mutants when providing safadBA genes on a plasmid and demonstrate that the SaFadB crotonase domain is required for complementation. Together, these data demonstrate the SaFadBA proteins are functional within a well characterized fatty acid degradation system and the fadXDEBA operon is under strong catabolite repression.

overall_design: Six samples in total, three biological replicates of both wild type Staphylococcus aureus and an isogenic fakA mutant.

first: Cindy

last: Menjivar

first: Zachary

last: DeMars

first: Richard

last: Wiemels

first: Jeffrey

last: Bose


title: Usp17l can regulate the expression of 2C gene through Dux in mouse embryonic stem cells

city: Tianjin

first: Pan

middle: Pan

last: Shi

address: No. 38 Tongyan Road

institute: Nankai University

summary: In order to study  Usp17l can regulate 2C gene expression through Dux, we overexpressed  Usp17le and knockdown Dux.Then we performed gene expression profiling  with the data obtained from the RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT,Usp17le OE, Usp17le OE-Dux KD, Dux KD, Dux KD-Usp17le OE groups.

first: panpan

last: shi

first: Xukun

last: Lu

first: Kairang

last: Jin

first: Linlin

last: Liu

first: Guoxing

last: Yin

first: Jiao

last: Yang

first: Wei

last: Xie

first: Lin


title: Immature monocytic cells within tumors differentiate into immunosuppressive cells in resistant tumors to immunotherapy

city: Kfar Sava

first: Sapir

last: Levin

address: Adam Yekutiel 7

country: Israel

institute: Technion

summary: Immune checkpoint inhibitors (ICIs) have improved outcomes in advanced cancers, yet resistance remains a major obsticle. Here, we investigated the role of myeloid cells in shaping the immunosuppressive tumor microenvironment that contributes to ICI resistance. Using mutagenized ICI-sensitive and resistant 4T1 breast cancer clones, we performed single-cell RNA sequencing to characterize immune cell populations post-ICI therapy. We identified monocytic dendritic progenitors (MDPs) and common monocytic progenitors (cMOPs) enriched in sensitive tumors, which may differentiate into immunosuppressive cells in resistant tumors. Analysis of public datasets confirmed the presence of MDP-cMOPs in tumors and blood of breast, lung, and colorectal cancer patients. We found high expression of CXCR4 and IL6R in MDP-cMOPs, and inhibiting these pathways blocked their recruitment and differentiation. Combined targeting of CXCR4 and IL6 pathway with ICI improved responses in resistant tumors, highlighting MDP-cMOPs as contributors to immunotherapy resistance and potential therapeutic targets.

overall_design: To investigate tumors responsive and resistant to immunotherapy, we used an experimental model of the 4T1 cell line, a triple negative breast carcinoma known for its resistance to immune checkpoint inhibitor (ICI) therapy. We exposed 4T1 cells to 1-methyl-3-nitro-1-nitrosoguanidine (MNNG) and generated polyclonal cells that would respond to anti-PD1 (referred to as 4T1m) as opposed to the resistant (parental) clone (referred to as 4T1p). The cells were then implanted into the mammary fat pad of mice and subsequently treated with anti-PD1 or IgG control. At the endpoint (following two weeks of treatment), both 4T1p and 4T1m tumor-bearing mice treated with anti-PD1, were harvested and processed into single-cell suspensions for further analysis. Evetually, we isolated cells from anti-PD1-treated 4T1p and 4T1m tumors based on the GR-1 marker.


title: Phosphoglycerate mutase regulates Treg differentiation through control of serine synthesis and one-carbon metabolism

city: Baltimore

first: Wesley

last: Godfrey

state: MD

address: 600 N Wolfe, Pathology 508, pathology 508

institute: Johns Hopkins University

summary: The differentiation and suppressive functions of regulatory CD4 T cells (Tregs) are supported by a broad array of metabolic changes, providing potential therapeutic targets for immune modulation. In this study, we focused on the regulatory role of glycolytic enzymes in Tregs and identified phosphoglycerate mutase (PGAM) as being differentially overexpressed in Tregs and associated with a highly suppressive phenotype. Pharmacologic or genetic inhibition of PGAM reduced Treg differentiation and suppressive function while reciprocally inducing markers of a pro-inflammatory, T helper 17 (Th17)-like state. The regulatory role of PGAM was dependent on the contribution of 3-phosphoglycerate (3PG), the PGAM substrate, to de novo serine synthesis. Blocking de novo serine synthesis from 3PG reversed the effect of PGAM inhibition on Treg polarization, while exogenous serine directly inhibited Treg polarization. Addi-tionally, altering serine levels in vivo with a serine/glycine-free diet increased peripheral Tregs and at-tenuated autoimmunity in a murine model of multiple sclerosis. Mechanistically, we found that serine limits Treg polarization by contributing to one-carbon metabolism and methylation of Treg-associated genes. Inhibiting one-carbon metabolism increased Treg polarization and suppressive function both in vitro and in vivo in a murine model of autoimmune colitis. Our study identifies a novel physiologic role for PGAM and highlights the metabolic interconnectivity between glycolysis, serine synthesis, one-car-bon metabolism, and epigenetic regulation of Treg differentiation and suppressive function

overall_design: Naïve CD4 T cells were cultured under Treg polarizing conditions with either scramble or anti-PGAM ASO for 3 days.


title: A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function

status: Public on Jun 04 2025

city: Toronto

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street, Room 1350

department: Terrence Donnelly Centre for Cellular and Biomolecular Research

country: Canada

institute: University of Toronto

summary: Although RNA-binding proteins (RBPs) are key regulators of gene expression, their RNA-binding specificities, i.e., motifs, have not been comprehensively determined. Here, we introduce EuPRI (Eukaryotic Protein-RNA Interactions), a freely available resource of RNA motifs for 34,746 RBPs from 690 eukaryotes. EuPRI includes in vitro binding data for 504 RBPs, including newly collected RNAcompete data for 174 RBPs, along with thousands of predicted motifs. We predict these motifs with a new algorithm, Joint Protein-Ligand Embedding (JPLE), which can detect distant homology relationships and map specificity-determining peptides. EuPRI quadruples the number of available RBP motifs, expanding the motif repertoire across all major eukaryotic clades, and assigning motifs to the majority of human RBPs. We demonstrate the utility of EuPRI for inferring post-transcriptional function and evolutionary relationships by identifying rapid, recent evolution of post-transcriptional regulatory networks in worms and plants, in contrast to the vertebrate RNA motif set, which has remained relatively stable after a large expansion between metazoan and vertebrate ancestors.

overall_design: Here, we analyze the RNA-binding preferences of 174 diverse eukaryotic RNA-binding proteins using RNAcompete. In the RNAcompete assay, purified GST-tagged RNA-binding protein is incubated with an excess of RNA pool and bound RNA from individual pulldown experiments are directly labeled and hybridized to a custom Agilent 244K microarray.

first: Alexander

last: Sasse

first: Debashish

last: Ray

first: Kaitlin

middle: U

last: Laverty

first: Cyrus

last: Tam

first: Mihai

last: Albu

first: Hong

last: Zheng

first: Yevgen

last: Levdansky

first: Olga

last: Lyudovyk

first: Taykhoom

last: Dalal

first: Kate

last: Nie

first: Cedrik

last: Magis

first: Cedric

last: Notredame

first: Eugene

last: Valkov

first: Matthew

middle: T

last: Weirauch

first: Quaid

last: Morris


title: RNPC3 knockdown in A549 lung adenocarcinoma cells

status: Public on Jun 03 2025

city: Parkville

last: Ritchie

state: Victoria

address: 1G Royal Parade

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Purpose of the study was to investigate the impact of reducing the efficiency of minor (U12-type) splicing on the growth and gene expression of a human cancer cell line. We chose the A549 cell line, derived from a human lung adenocarcinoma, for this study. There are only approximately 700 genes (3.5%) in the human genome that contain a minor intron. Most transcripts (96.5%) require only major (U2-dependent) splicing for correct gene expression. This is carried out by the major spliceosome. A different spliceosome, known as the minor or U11/12-type spliceosome, is required to excise minor introns from pre-RNA transcripts that contain them. One of the unique protein components of the minor spliceosome is a 65kDa protein encoded by the RNPC3 gene. To reduce the efficiency of minor splicing, we used siRNA knockdown methodology to deplete RNPC3 transcripts in A549 cells by approximately 70%. Specifically, A549 cells in growth phase were transfected with siRNA targeted to RNPC3 transcripts for 72h. Control A549 cells were treated in the same experiment with non-targeted (NT) siRNA molecules instead of siRNA targeted to RNPC3.

overall_design: RNA-seq was performed on 8 samples of the A549 human lung adenocarcinoma derived cell line. Of these 8 samples, 4 were treated with non-targeted (NT) siRNA and are the control group, The other 4 were treated with siRNA targeted to RNPC3 and are the test group.

first: Joan

last: Heath

first: Stephen

last: Mieruszynski

first: Alexandra

last: Garnham

first: Xueyi

last: Dong

first: Lucinda

last: Xiao

first: Quentin

last: Gouil

first: Mei

last: Du


title: Tumor cell-intrinsic Decr2 regulates ferroptosis and immunotherapy efficacy

status: Public on Jun 02 2025

city: Chicago

first: Thomas

last: Gajewski

state: IL

address: 929 E 57th St

institute: University of Chicago

summary: We employed a single-cell sequencing approach to analyze CD45+ cells from control and Decr2 knockdown tumors isolated from B6 mice. The aim of this study is to assess the proportion of CD45+ cell populations within the tumor microenvironment and to compare differential gene expression between the two groups across various cell populations.

overall_design: Control or knockdown B16.SIY tumors were subcutaneously injected into B6 mice. Tumor tissues were collected and processed from the mice on day 14 post-injection. Live CD45+ cells were sorted from the tumor tissue and analyzed using scRNA-seq.

first: Shuyin

last: Li

first: Jason

last: W Shapiro

first: Hardik

last: Shah

first: Emily

last: Higgs

first: Lishi

last: Xie

first: Yaopeng

first: Yuanyuan

last: Zha

first: Jonathan

last: Trujillo

last: Cabanov

first: Tyler

middle: A

last: Jones

first: Blake

last: Flood

first: Ken

last: Hatogai

first: Ruxandra

last: Tonea

first: Justin

last: Kline


title: Exploring an essential biomarker in pulmonary fibrosis: an integrated and cross-disease approach with spatial transcriptomics and single-cell RNA sequencing (Spatial Transcriptomics, part 2)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: We cross-sectionally examined various interstitial lung diseases (ILDs) via spatial transcriptomics of human samples. We unveiled crucial gene expression patterns and molecules involving fibrosis, exploring prognostic significance of this molecule in unclassifiable ILDs.

overall_design: We performed spatial transcriptomic analysis on patients with a various ILDs.

first: Kiyoharu

last: Fukushima

first: Takayuki

last: Niitsu

first: Toshiaki

last: Kataoka

first: Koji

last: Okudela


title: A deep learning framework for the reconstruction of gene expression profiles derived from formalin-fixed paraffin-embedded samples

city: Hong Kong

first: Xin

last: Wang

address: 30-32 Ngan Shing Street, Shatin, New Territories

department: Department of Surgery

institute: The Chinese University of Hong Kong

summary: This dataset was utilized to investigate the impact of key preanalytical factors on the preparation of formalin-fixed, paraffin-embedded (FFPE) tissue samples and subsequent library construction for RNA-sequencing analysis. The dataset consists eight RNA-Seq data, derived from two colorectal cancer (CRC) patient samples obtained from Prince of Wales Hospital in Hong Kong.

overall_design: Expression profiling by high throughput sequencing

first: Lingli

last: He

first: Kai

last: Song

first: Ying

last: Li

first: Yujuan

last: Dong

first: Cherry Y N

last: Wong

first: Lin

last: Qi

first: Xianrui

last: Zhang

first: Kristiaan

last: Lenos

first: Tim

last: de Back

first: Clara

last: Elbers

first: Chenchen

last: Xu

first: Yinghan

first: Feng

last: Gao

first: Yufeng

last: Chen

first: Simon Siu-Man

last: Ng

first: Shentao

last: Zhou

first: Louis

last: Vermeulen


title: Transcriptomic signatures associated with regenerative wound  vs. fibrotic repair outcomes to lens post-cataract surgery wounding

city: Philadelphia

first: Janice

middle: Lynn

last: Walker

address: 1020 Locust Street; 571 JAH

department: Pathology and Genomic Medicine

institute: Thomas Jefferson University

summary: RNAseq analysis was used to determine the transcriptomic changes associated with regenerative vs. fibrotic repair to lens injury. Using an ex vivo post-cataract surgery model, we can follow two distinct outcomes to lens injury: 1) A regenerative wound healing response that ensues across the cell-denuded lens capsule basement membrane (BM), culminating in wound closure on Day 3 (D3) post-injury. 2) Induction of fibrosis, which occurs when a wound healing response occurs off the lens capsule, termed the extracapsular zone (ECZ), where transition to a fibrotic phenotype occurs on day 3 post-injury. Here, we report the changes in the transcriptome that occur on D1, D2, and D3 post-injury, a period that covers wound healing across the BM and time points prior to (D1, D2) and after induction of the fibrotic phenotype (D3). Our data provides a molecular map for understanding the gene changes associated with navigating normal and pathological outcomes to lens injury.

overall_design: RNA-seq analysis of regenerative wound vs. fibrotic repair at Day 1, Day 2, and Day 3 post-injury within an ex vivo post-cataract surgery model.

first: J

middle: L

first: M

middle: D

last: Basta


title: Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues [scMAPIT-seq]

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

institute: Peking University

summary: RNA-binding proteins (RBPs) are essential regulators of RNA fate and function. A long-standing challenge in studying RBP regulation has been mapping RNA interactomes within the dynamic transcriptomic landscape, especially in single-cell contexts and primary tissues. Here we introduce MAPIT-seq (modification added to RBP interacting transcript-sequencing), which uses an antibody-directed editing strategy to map genome-wide in situ RBP–RNA interactions and gene expression concurrently. We demonstrate MAPIT-seq’s robustness across multiple RBPs and systematically analyze RNA substrates associated with core polycomb repressive complex 2 (PRC2) components. MAPIT-seq is also applicable to frozen tissue sections, enabling the mapping of RBP roles during brain development. Importantly, we develop high-throughput single-cell MAPIT-seq (scMAPIT-seq) to reveal cell stage-specific RBP regulation. In summary, MAPIT-seq expands multi-omics profiling, providing an effective framework to study post-transcriptional regulation in dynamic biological processes and clinically relevant scenarios.

overall_design: We advanced MAPIT-seq to a high-throughput single-cell format, uncovering cell cycle-specific G3BP1 targets and revealing heterogeneity in RNA-protein interactions at single-cell resolution. High-throughput single-cell MAPIT-seq was performed using DSP fixation in combination with the 10x Genomics platform.

first: Qi-Xuan

last: Cheng

first: Gang

last: Xie


title: Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues

summary:
RNA-binding proteins (RBPs) are essential regulators of RNA fate and function. A long-standing challenge in studying RBP regulation has been mapping RNA interactomes within the dynamic transcriptomic landscape, especially in single-cell contexts and primary tissues. Here we introduce MAPIT-seq (modification added to RBP interacting transcript-sequencing), which uses an antibody-directed editing strategy to map genome-wide in situ RBP–RNA interactions and gene expression concurrently. We demonstrate MAPIT-seq’s robustness across multiple RBPs and systematically analyze RNA substrates associated with core polycomb repressive complex 2 (PRC2) components. MAPIT-seq is also applicable to frozen tissue sections, enabling the mapping of RBP roles during brain development. Importantly, we develop high-throughput single-cell MAPIT-seq (scMAPIT-seq) to reveal cell stage-specific RBP regulation. In summary, MAPIT-seq expands multi-omics profiling, providing an effective framework to study post-transcriptional regulation in dynamic biological processes and clinically relevant scenarios.
This SuperSeries is composed of the SubSeries listed below.


title: Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues [FRISCR_MAPIT-seq]

overall_design: Standard MAPIT-seq of G3BP1 was performed followed by single cell RNA-seq with Fixed and Recovered Intact Single-cell RNA (FRISCR) method, demonstrating that MAPIT-seq could identify RBP targets in individual cells.


title: Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues [long reads]

overall_design: Integrating formaldehyde-fixed and DSP-fixed MAPIT-seq of G3BP1 with long-read sequencing platform Pacbio achieved RBP-RNA interaction detection in isoform-level resolution.


title: NRF2 translation block by inhibition of cap-dependent initiation sensitizes lymphoma cells to ferroptosis and CAR-T immunotherapy

city: miami

first: Jonathan

middle: H

last: Schatz

state: Florida

address: 1580 NW 10th Ave 1st floor

department: Department of Medicine

institute: university of miami

summary: Cancers coopt stress-response pathways to drive oncogenesis, dodge immune surveillance, and resist cytotoxic therapies. Several of these provide protection from ferroptosis, iron-mediated oxidative cell death. Here, we found dramatic sensitization to ferroptosis upon disruption of cap-dependent translation in diffuse large B-cell lymphoma (DLBCL). Specifically, rocaglate inhibitors of the eIF4A1 RNA helicase synergized with pharmacologic ferroptosis inducers, driven by a collapse of glutathione production that protects polyunsaturated fatty acids from ferroptotic oxidation. These effects occur despite initial up-regulation of specific protective factors. We find lost translation of NRF2, oncogenic master regulator of antioxidant gene-expression, is a key consequence of eIF4A1 inhibition. In vivo, combination of the clinical rocaglate zotatifin with a pharmacologically optimized ferroptosis inducer eradicated DLBCL patient derived xenografts. Moreover, we found zotatifin pre-exposure sensitized DLBCL to CD19-directed chimeric antigen receptor (CAR-19) T cells. Translational disruption therefore provides new opportunities to leverage therapeutic impacts of ferroptosis inducers including cytotoxic immunotherapies.

overall_design: This study is done to check the role of Zotatifin in treating DLBCL. We used DHL10 cell lines with control DMSO and Zotatifin. We then performed gene expression analysis using data obtained from RNA-seq of DHL10 cells with Zotatifin and Controal DMSO.

first: Paola

last: Manara

first: Austin

last: Newsam

first: Venu

middle: V

last: Gowda

first: Marco

last: Russ

first: Alicia

middle: B

last: Martinez

first: Nikolai

last: Fattakhov

first: Tyler

last: Cunnigham

first: Abdessamad

middle: Y

last: Alaoui

first: Dhanvantri

last: Chahar

first: Alexandra

last: Carbone

first: Olivia

last: Lightfuss

first: Alexa

last: Barroso

first: Kyle

last: Hoffman

first: Francesco

last: Maura

first: Daniel

last: Bilbao


title: Exploring an essential biomarker in pulmonary fibrosis: an integrated and cross-disease approach with spatial transcriptomics and single-cell RNA sequencing (Spatial Transcriptomics)

first: Daisuke

last: Motooka

summary: We cross-sectionally examined various interstitial lung diseases (ILDs) via spatial transcriptomics and single-cell RNA-Seq (scRNA-seq) analysis of human samples.  We unveiled crucial gene expression patterns and molecules central to fibrosis, establishing prognostic significance of this molecule in unclassifiable ILDs.

overall_design: We performed spatial transcriptomic analysis on 24 cryobiopsy specimens of patients with a variety of ILDs.

first: Kiyoharu

last: Fukushima

first: Takayuki

last: Niitsu

first: Toshiaki

last: Kataoka


title: The transcriptomic data of the Wilms tumor cell line

status: Public on Jun 01 2025

city: Shanghai

first: Cheng

last: Cheng

state: Shanghai

address: NO.1665 Kongjiang Road

institute: Shanghai Jiaotong University School of Medicine affiliated Xinhua Hospital

summary: We conducted RNA sequencing on Wilms tumor cells with or without EHMT2 knockdown to assess the impact of EHMT2 on gene expression in Wilms tumor.

overall_design: RNA sequencing on Wilms tumor cells with or without EHMT2 knockdown was conducted to assess the impact of EHMT2 on gene expression in Wilms tumor.Each group has three replicates.

first: Zhixiang

last: Wu


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) and single-nuclei RNA-seq of flowering plants

city: Berkeley

first: Sharon

last: Greenblum

address: 1 Cyclotron Road

institute: DOE Joint Genome Institute

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

relation:
SuperSeries of: GSE298980
SuperSeries of: GSE298983
SuperSeries of: GSE298988
SuperSeries of: GSE298997
SuperSeries of: GSE299001
SuperSeries of: GSE299004
SuperSeries of: GSE299008
SuperSeries of: GSE299020
SuperSeries of: GSE299024
SuperSeries of: GSE299026
SuperSeries of: GSE297576

sample_organism:
Populus trichocarpa
Arabidopsis thaliana
Brassica oleracea
Solanum lycopersicum
Solanum tuberosum
Oryza sativa
Sorghum bicolor
Thlaspi arvense
Brachypodium distachyon
Fragaria vesca
Arabidopsis lyrata
Capsella rubella
Camelina sativa
Panicum hallii

overall_design:
Refer to individual Series

BioProject ID for single-nuclei RNA-seq of flowering plants: PRJNA1262374


title: Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues [tissue]

first: Yangming

last: Wang

overall_design: To elucidate the developmental dynamics of G3BP1-RNA interactions, we applied MAPIT-seq to OCT-embedded tissue sections from mouse embryos at various stages: whole embryos at E10.5, embryonic brain tissues at E12.5 and E16.5. This approach enabled comprehensive profiling of G3BP1 binding targets throughout critical periods of neurodevelopment.

first: Qi-Xuan

first: Gang

last: Xie


title: Whole blood transcriptomic profiles from older patients

city: London

first: Paula

last: Longhi

address: Charterhouse Square

department: William Harvey Research Institute

institute: Queen Mary, University of London

summary:
The primary objective of this study was to investigate whole blood transcriptomic signatures in older populations and to assess their relationship with peripheral lymphocyte populations.

Whole blood gene expression profiles were evaluated in a cohort of aged individuals undergoing open heart surgery. Transcriptomic signatures were assessed between clinical groupings and proportions of lymphocyte populations from flow cytometry analysis.

overall_design:
Pre-operative whole blood samples were acquired from patients undergoing open heart surgery. Blood samples were collected into PAXgene blood RNA tubes and total RNA extracted according to the manufacturer’s instructions. RNA samples were then hybridized and analyzed using the Clariom S HT microarray.
Gene expression data from human whole blood

first: Balraj

last: Sandhar


title: Starvation activates ECM-remodeling gene transcription and putative enhancers in fibroblasts despite inducing quiescence

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

overall_design: Refer to individual Series


title: Single-cell RNA-seq of mouse androgenetic alopecia models treated with CXCL12-neutralizing antibody

city: Seoul

first: Mi-Ock

last: Lee

address: 1 Gwanak-ro

department: College of Pharmacy

institute: Seoul National University

summary: Androgenetic alopecia (AGA) is a common form of hair loss characterized by follicular miniaturization, dermal fibrosis, and low-grade immune activation, yet the precise mediators linking androgen signaling to these tissue-level changes remain poorly defined. Here, we use single-cell RNA sequencing (scRNA-seq) to map the skin microenvironment in a testosterone-induced mouse model of AGA and assess the therapeutic impact of a CXCL12-neutralizing antibody. We find that androgen receptor-positive dermal fibroblasts are the principal source of CXCL12, which acts in an autocrine manner via ACKR3 to drive TGF-β–mediated extracellular matrix deposition. In parallel, CXCL12 signals through CXCR4 to reprogram a Sox2+ Twist1+ dermal papilla cell population toward a fibrotic, low-inductive state and expand a pro-fibrotic Trem2+ macrophage subset. Blockade of CXCL12 reverses these transcriptional and cellular alterations across stromal, follicular, and immune compartments, restoring a regenerative skin niche and supporting hair regrowth. These findings position CXCL12 as a central mediator of fibroimmune remodeling in AGA and establish its neutralization as a promising therapeutic strategy.

overall_design: Skin samples were collected from three groups of mice: control (Con), androgenetic alopecia (AGA) model induced by testosterone propionate (TP), and TP-induced AGA model treated with a CXCL12-neutralizing antibody (TP+Ab). At the end of the treatment period, dorsal skin tissues were harvested (n = 15 per group) and enzymatically dissociated to generate single-cell suspensions for single-cell RNA sequencing (scRNA-seq).

first: Jong-Hyuk

last: Sung

first: Minsoo

last: Noh

first: Seungchan

last: An

first: Mei

last: Zheng

first: In Guk

last: Park


title: Common AAV gene therapy vectors show nonselective transduction of ex vivo human brain tissue

city: Houston

first: JP

last: McGinnis

state: TX

address: 5306 Creekbend Dr

department: Neurosurgery

institute: Baylor College of Medicine

summary: We have adapted an ex vivo organotypic model to evaluate AAV transduction properties in living slices of human brain tissue. Using single-nucleus RNA sequencing, we found that common AAV vectors show broad transduction of normal cell types, with protein expression most apparent in astrocytes; this work introduces a pipeline for identifying and optimizing AAV gene therapy vectors in human brain samples.

overall_design: Sequencing data includes 10X 3' single-nucleus RNA sequencing of patient samples flash frozen: day 0 control tissue, day 14 cultured tissue without vectors, and day 14 tissue to which vectors were applied. Tissues slices underwent Miltenyi Biotec nuclei isolation followed by nuclei FACS sorting, and were processed with the 3' 10X Genomics single-nucleus RNA isolation protocol.

first: Ben

last: Arenkiel