summary: Two-cell-like cells (2CLCs), a rare population (~0.5%) in murine embryonic stem cell (mESC) cultures, are in a transient totipotent-like state resembling that of 2C-stage embryos, and their discovery and characterization have greatly facilitated the study of early developmental events, such as zygotic genome activation. However, the molecular determinants governing 2C-like reprogramming remain to be elucidated. Here, we show that ZBTB24, CDCA7 and HELLS, components of a molecular pathway that is involved in the pathogenesis of immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, function as negative regulators of 2C-like reprogramming by maintaining DNA methylation of the Dux cluster, a master inducer of the 2C-like state. Disruption of the ZBTB24-CDCA7-HELLS axis results in Dux hypomethylation and derepression, leading to dramatic upregulation of 2C-specific genes, which can be reversed by site-specific re-methylation in the Dux promoter. We also provide evidence that CDCA7 is enriched at the Dux cluster and recruits the CDCA7-HELLS chromatin remodelling complex to constitutive heterochromatin. Our study uncovers a key role for the ZBTB24-CDCA7-HELLS axis in safeguarding the mESC state by suppressing the 2C-like reprogramming.

overall_design: To decipher whether deficiency in Zbtb24, Cdca7 or Hells promotes 2C-like transcriptome by affecting the chromatin accessibility of 2C-specific genes, we generated Zbtb24-KO, Cdca7-KO and Hells-KO mESC lines by CRISPR/Cas9 technology and performed ATAC-seq on those cell lines, and analyzed their genomic binding/occupancy.

last: Liu


title: Chromatin dynamics at cis-regulatory elements dictate cell fate identities in early embryos [scMultiome]

status: Public on Mar 28 2025

city: Milan

first: Yinxiu

last: Zhan

address: via Adamello, 16

country: Italy

institute: European Institute of Oncology (IEO)

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The establishment of germ layers during early development is crucial for body formation. The Drosophila zygote serves as a model for investigating these transitions in relation to the chromatin landscape. However, the cellular heterogeneity of the blastoderm embryo poses a challenge for gaining mechanistic insights. Using 10× Multiome, we simultaneously analyzed the in vivo epigenomic and transcriptomic states of wild-type, E(z)-, and CBP-depleted embryos during zygotic genome activation at single-cell resolution. We found that pre-zygotic H3K27me3 safeguards tissue-specific gene expression by modulating cis-regulatory elements. Furthermore, we demonstrate that CBP is essential for cell fate specification functioning as a transcriptional activator by stabilizing transcriptional factors binding at key developmental genes. Surprisingly, while CBP depletion leads to transcriptional arrest, chromatin accessibility continues to progress independently through the retention of stalled RNA Polymerase II. Our study reveals fundamental principles of chromatin-mediated gene regulation essential for establishing and maintaining cellular identities during early embryogenesis.

overall_design: Single-cell multiome datasets were generated from 100 embryos of wildtype, CBP-KD and E(z)-KD conditions. Two biological replicates were independently prepared.

first: Francesco

last: Cardamone

first: Annamaria

last: Piva

first: Bastian

last: Eichenberger


title: Chromatin dynamics at cis-regulatory elements dictate cell fate identities in early embryos [RNA-Seq]

overall_design: Three biological replicates were performed for each condition.


title: IL-33 from oligodendrocytes sustains effector differentiation of CD8+ tissue-resident T cells and is a druggable target in CNS autoimmune disease

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: Our study identifies oligodendrocyte-derived IL-33 as a druggable tissue factor regulating the differentiation and survival of self-reactive CD8+ T cell in the inflamed CNS. This finding introduces tissue factors as a novel category of immune targets for treating chronic CNS autoimmune diseases.

overall_design:
Transcriptional activity of FACS-sorted brain CD8 GP33-41+ T cells from WT, MOG-GP, and IL-33 cKO MOG-GP mice at 21 days after rLCMV-GP33 infection.
Transcriptional activity using scRNAseq of FACS-sorted brain CD45+ cells from MOG-GP, and IL-33 cKO MOG-GP mice at 21 days after rLCMV-GP33 infectionfon.

first: Nicolas

last: Fonta

last: Page

first: Doron

last: Merkler


title: SINE-MIR enhancer rewiring by Esrrb architecturally reprogram the pluripotency spectrum [scRNA-Seq]

status: Public on Mar 31 2025

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: scRNA-seq were performed during EPSC differentiation to 3dESC

first: N

middle: O

last: Cipta

first: Y

middle: Y

first: H

last: Li

last: Loh


title: Chromatin dynamics at cis-regulatory elements dictate cell fate identities in early embryos [CUT&Tag]

overall_design: Two biological replicates were performed for each CUT&Tag.


title: Chromatin dynamics at cis-regulatory elements dictate cell fate identities in early embryos [ChIP-Seq]

overall_design: Two biological replicates were performed.

first: Fides

last: Zenk


title: MEG3 Chromatin isolation by RNA purification-DNA sequencing (ChIRP-Seq)  in wild type Mouse emryonic fibroblasts (MEFs) and Beta actin Knock out MEFS

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: In the eukaryotic cell, β-actin plays essential nuclear functions. Actin directly affects genome organization and regulates promoter-enhancer interactions as part of the BAF (SWI/SNF) chromatin remodeling complex. It also binds to the hyperphosphorylated carboxy-terminal domain (CTD) of RNA polymerases II, and depletion of β-actin leads to differential gene expression that impacts key cellular processes such as differentiation. In this study, we investigated whether β-actin controls the level of long non-coding RNAs (lncRNAs). Using a combination of bulk RNA-seq and qPCR analyses on total RNA isolated from WT mouse embryonic fibroblasts (MEFs), β-actin heterozygous (HET) MEFs, and β-actin KO MEFs. Our findings demonstrate that the expression of several lncRNAs is directly affected by β-actin depletion. One of these lncRNAs, Meg3, shows increased expression in a dosage-dependent manner. Using ChIRP-seq, we observed alterations in Meg3 genomic association and Meg3 enrichment at or near enhancer sites following β-actin depletion. These changes were accompanied by increased levels of H3K27 acetylation. At these sites, specific Meg3 enrichment disrupts promoter-enhancer interactions, as revealed by the Activity by Contact (ABC) model, through a sponging effect. Consequently, this leads to the repression of genes involved in metabolic biosynthetic pathways for chondroitin, heparan, dermatan sulfate, and phospholipases, impacting their synthesis. We propose that Meg3 potentially impairs local genome organization (or DNA looping) and negatively affects gene expression through its chromatin sponging effect that interferes with promoter-enhancer interactions.

overall_design: Chromatin isolation by RNA purification of MEG3 in WT MEFs and  KO MEFs, replicates were used using odd and even probes such that WTO1 is replicate one of WT MEFs odd MEG3 probes, WTO2 is replicate two of WT MEFs odd MEG3 probes, WTE1 is replicate one of WT MEFs Even MEG3 probes WTE2 is replicate two of WT MEFs Even MEG3 probes, KOO1 is replicate one of KO MEFs odd MEG3 probes, KOO2 is replicate two of KO MEFs odd MEG3 probes, KOE1 is replicate one of KO MEFs Even MEG3 probes and KOE2 is replicate two of KO MEFs Even MEG3 probes.

first: Nadine

middle: H

last: El Said

first: Syed

middle: R

last: Mahmood


title: Chromatin dynamics at cis-regulatory elements dictate cell fate identities in early embryos [ATAC-Seq]

overall_design: Two biological replicates were performed for each experiment.


title: Single Cell Sequencing Data of Mouse Spinal Cord with Dorsal Column Lesion and Astrocyte-Specific Ryk conditional Knockout

city: San Diego

first: Zhe

last: Shen

state: California

address: 9500 Gilman Dr. MC 0123, La Jolla

country: USA

institute: Devision of Biological Science, UCSD

summary: After the data quality control, a total of 18,203 captured cells were subjected to clustering analysis by leiden and visualized in lower dimension by uniform manifold approximation and projection (UMAP). The results showed that they could be clustered into 17 distinct cell clusters. According to the highest differentially expressed genes (DEGs) and canonical markers used in prior studies, we annotated these 17 clusters as 13 major cell types with distinct expression profiles): Astrocytes (ASC, containing 3 clusters: Astro_2, Astro_5, and Astro_7), microglia (MG, containing 2 clusters: Microglial_6 and Microglial_10), oligodendrocytes (containing 2 clusters: Oligo_4 and Oligo_8), endothelial cells (containing 1 cluster: Endothelial_1), pericytes (Pericytes_9), fibroblasts (Fibroblasts_14), neuronal cells (Neuronal_3), oligodendrocyte progenitor cells (OPC_11), Schwann cells (schwan cells_15), red blood cells (RBC_17), immune cells (Immuno_12), myeloid cells (myeloid Cells_16)

overall_design: We dissociated cells from the spinal cord tissue around the lesion core. Two biological repetitions of single cell suspensions were generated from the mice which uninjured, 1d, 7d, and 14d after SCI with or without Ryk cKO.

first: Bo

last: Feng

first: Timothy

last: Woo

first: Yimin

last: Zou


title: Transcriptomic signatures in peripheral CD4 + T-lymphocytes may reflect melanoma staging and immunotherapy responsiveness prior to ICI initiation

status: Public on Mar 27 2025

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

summary: Background and Purpose: Promoting adaptive immunity with ICIs has drastically improved melanoma prognosis, but not for all patients. Some cases relapse in the first few months, while others keep durable benefit, even after immunotherapy discontinuation. To identify cellular/molecular signatures in peripheral blood that could differentiate advanced from metastatic melanoma and predict dynamics for primary/secondary immune escape, we examined 100 consecutive patients with stage III/IV melanoma scheduled to start ICIs . Materials and Methods: At melanoma diagnosis, a multiparameter flow cytometric analysis and purification scheme using standard conjugated antibodies were performed for all individuals prior to ICI initiation. In each stage (III/IV) according to their RFS/PFS, we retrospectively selected the cases with the clearest clinical outcomes and focused our analysis on the extreme responders (n=7) and non-responders (n=7) to characterize the transcriptomes of circulating CD4+T-cells by bulk RNA-seq, Differential Expression Analysis(DEA)and Gene Ontology (GO) enrichment analysis. Based on our selected patient cohort, we examined for differentially expressed genes (DEGs) and key-pathways that appear preferentially activated in stage III vs. IV melanoma, and in long vs. short immunotherapy responders.Results: Although circulating immune-cells did not numerically differ in both sets of analysis(staging and ICI responsiveness), DEA and GO data showed that patients could be clustered separately, identifying 189vs.92 DEGs in stage IV/III and 101vs.47 DEGs in early progressors/long responders. These DEGs were functionally implicated in distinct pathways. For metastatic cases: inflammatory response (log p-value=-9.2: ADGRE5/2,CYBA,GRN,HMOX1,IRF5,ITGAM), adaptive immunity(log p-value=-7.7: CD1C,CD74,CYBB,NCF2,CTSA,S100A8/9,BCL3,FCER1G), T-cell activation(log p-value=-6.3: BCL3,CD1C,CD74,FCER1G,FGL2)and lipid metabolism/catabolism(log p-value=-2.5/-2.6: ARF3,GPX1,MVD,OCRL,PCCB,CTSA,PNPLA2,NAGLU,GBA2,ABHD4); while in early- progressors to ICIs: immune effector processing(log p-value=-13.7: BCL6,FGR,HLA-DQA1/DQB1,HLA-DRA,HLA- DRB1/DRB5,NKG7,SLC11A1,TYROBP,SPON2,HAVCR2),PD-1(log p-value=-10.2: HLA-DQA1/DQB1,HLA-DRA,HLA-DRB1/DRB5)and IFN signaling(logp-value=-8.5: HLA-DQA1/DQB1,HLA-DRA,HLA-DRB1/DRB5,NCAM1,IFITM3),positive regulation of T-cell activation(log p- value=-7.7: BCL6,HLA-DQA1/DQB1,HLA-DRA,HLA-DRB1/DRB5,SASH3,HAVCR2)and CD28 co-stimulation(log p-value=-10.3: HLA- DQA1/DQB1,HLA-DRA,HLA-DRB1/DRB5), supporting an immune-mediated behavior. Conclusions: Specific pathways and marker genes in the peripheral CD4+T-cells may predetermine melanoma staging and immunotherapy resistance.

overall_design: Analysis of melanoma patients with stage III and stage IV disease (with equal gender distribution) with heterogenous clinical outcomes. RNA-seq on CD4+T-cell subpopulation of PBMCs of  cases that showed most extreme clinical outcomes, including: the 7 best (longest RFS/PFS) and the 7 worst responders to ICIs (shortest RFS/PFS) in each stage (III and IV, total 26 samples) retrospectively. Pairwise comparison (stage IV, S4 vs. stage III, S3) and early progressors (Short RFS/PFS, S) vs. long responders (Long RFS/PFS, L) were performed to identify  DEGs in either group applying the following thresholds |Log2FC| >1 and p-value <0.05, which was considered statistically significant in order to limit the stringency of FDR testing and help us to account for anticipated interpatient variability.

first: Elena

last: Palli

first: Panagiotis

last: Verginis

first: Dimitrios

last: C. Ziogas

first: Helen

last: Gogas


title: The ZBTB24-CDCA7-HELLS axis suppresses the totipotent 2C-like reprogramming by maintaining Dux methylation and repression

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Two-cell-like cells (2CLCs), a rare population (~0.5%) in murine embryonic stem cell (mESC) cultures, are in a transient totipotent-like state resembling that of 2C-stage embryos, and their discovery and characterization have greatly facilitated the study of early developmental events, such as zygotic genome activation. However, the molecular determinants governing 2C-like reprogramming remains to be elucidated. Here, we show that ZBTB24, CDCA7 and HELLS, components of a molecular pathway that is involved in the pathogenesis of immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, function as negative regulators of 2C-like reprogramming by maintaining DNA methylation of the Dux cluster, a master inducer of the 2C-like state. Disruption of the ZBTB24-CDCA7-HELLS axis results in Dux hypomethylation and derepression, leading to dramatic upregulation of 2C-specific genes, which can be reversed by site-specific re-methylation in the Dux promoter. We also provide evidence that CDCA7 is enriched at the Dux cluster and recruits the CDCA7-HELLS chromatin remodeling complex to constitutive heterochromatin, perhaps including the perinucleolar heterochromatin, where the Dux cluster resides. Our study uncovers a key role for the ZBTB24-CDCA7-HELLS axis in safeguarding the mESC state by suppressing the 2C-like reprogramming.

overall_design: HA-CDCA7 was stably expressed in Cdca7-knockout (KO) mouse embryonic stem cells (mESCs), and ChIP-seq was performed with HA antibody. Two stables clones (biological replicates), Cdca7_10 and Cdca7_11, were used.

first: Swanand

last: Hardikar

first: Taiping

last: Chen


title: Circulating miRNAs are associated with successful bone regeneration

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

type: Non-coding RNA profiling by high throughput sequencing

summary: Introduction: Bone healing is a well-orchestrated process involving various bone cells and signaling pathways, where disruptions can result in delayed or incomplete healing. MicroRNAs (miRNAs) are small non-coding RNAs capable of influencing various cellular processes, including bone remodeling. Due to their biological relevance and stable presence in biofluids, miRNAs may serve as candidates for diagnosis and prognosis of delayed bone healing. The aim of this study was to investigate changes in miRNAs circulating in the blood during the healing of rat calvaria defects as biomarkers of successful bone regeneration. Methods: Standardized calvaria defects were created in 36 Wistar rats with a trephine drill and treated with collagen hydroxyapatite (CHA) scaffolds. The treatment groups included CHA scaffolds only, CHA scaffolds containing a plasmid coding for bone morphogenetic protein 2 (BMP2) and miR-590-5p, CHA scaffolds containing mesenchymal stromal cell-derived extracellular vesicles, and empty defects as a control group. After 1, 4 and 8 weeks of healing, the animals were evaluated by microcomputed tomography (microCT), as well as subjected to histological analyses. Blood was sampled from the tail vein prior to surgeries and after 1, 4, and 8 weeks of healing. miRNAs circulating in the plasma were determined using next generation sequencing. Results: Variability of bone regeneration within the four groups was unexpectedly high and did not result in significant differences between the groups, as indicated by the microCT and histological analyses of the newly formed bone tissue. However, irrespective of the treatment group and regenerative activity, we identified miRNAs with distinct expression patterns of up- and downregulation at different time points. Furthermore, rats with high and low regenerative activity were characterized by distinct circulating miRNA profiles. miR-133-3p was identified as the top up-regulated miRNA and miR-375-3p was identified as the top down- regulated miRNA in animals exhibiting good regeneration over all time points evaluated.  Conclusion: Our study indicates that regardless of the treatment group, success or lack of bone regeneration is associated with a distinct expression pattern of circulating microRNAs. While for some of these microRNAs functional association with skeletal regeneration has previously been reported, further research is needed to evaluate whether their levels in the blood can be used as predictive factors of successful bone regeneration.  Keywords: gene-activated scaffold; osteogenesis; bone regeneration, biomarkers, circulating microRNAs

overall_design: Rat calvaria defect regeneration was studied in 3 treatment groups (non-augmented CHA scaffolds, CHA scaffolds with pDNA for BMP2 and miR-590-5p, CHA scaffolds with MSC-EVs) and control untreated defect group. Out of 4 groups, 6 animals exhibiting good and 6 animals exhibiting bad regeneration were selected based on microcomputed tomography scanning (unbalanced between the groups). Analysis of miRNAs circulating in the blood plasma was conduted at timepoints prior to surgery (week 0) and 1, 4, and 8 weeks after surgery.

first: Julia

middle: K

last: Frank

first: Carina

last: Kampleitner

first: Patrck

last: Heimel

first: Gabriele

last: Leinfellner

first: Dominik

last: Hanetseder

first: Simon

last: Sperger

first: Amelie

last: Frischer

first: Barbara

last: Schaedl

first: Stefan

last: Tangl

first: Heinz

last: Redl

first: Matthias

last: Hackl

first: Johannes

last: Grillari

first: Darja

last: Marolt Presen


title: IKAROS modulates CD19 surface expression and CD19-directed CAR-T response [RNA-seq]

city: Palo Alto

first: Pablo

last: Domizi

state: CA

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

summary: To elucidate how IKAROS modulates CD19 surface expression in B cell acute lymphoblastic leukemic cells, we analyzed gene expression profile from isogenic IKAROS wild type (WT) or knock down (KD) B-ALL cell lines.

overall_design: Human B-ALL cell lines (NALM6, REH and SUP-B15) were transduced with IKZF1-specific or scramble shRNA expressing lentivirus. 72 hours post transduction, we compared their gene expression profiles through RNA-seq.

first: Kara

middle: L

last: Davis


title: Sex-specific impact of B cell-derived IL-10 on tuberculosis resistance

status: Public on Mar 26 2025

city: Borstel

first: David

last: Hertz

address: Parkallee 22

country: Germany

institute: Research Center Borstel

summary: Due to the historical dogma, that host defense against intracellular pathogens is mediated by cell-mediated immunity, B cells have been considered unimportant in providing protection against Mycobacterium tuberculosis (Mtb) and remained understudied for decades. However, emerging evidence suggests a more complex and multifaceted role for B cells in tuberculosis (TB) immunity. They accumulate at the side of infection in both animal models and human TB patients, suggesting a potential link to protective immunity. Still, the diverse roles of B cells in TB immunity continue to be unraveled. Apart from antibodies, B cells produce a wide range of cytokines, which can influence the local immune response. Here we addressed the relevance of interleukin 10 (IL-10) secreting B cells in long-term control of the Mtb Beijing strain HN878. Our research highlights the previously unknown role of B cell-derived IL-10 as a negative regulator of protective immunity in TB. For the first time, we demonstrate that mice lacking B cell-derived IL-10 show increased resistance to aerosol Mtb infection, as evidenced by a delayed onset of clinical symptoms and prolonged survival. Notably, this effect was significantly more pronounced in males compared to females, and was accompanied by male-specific immune alterations, indicating a previously unknown sex-specific regulatory role of B cell-derived IL-10 during Mtb infection.

overall_design: We collected the gene expression profile in a Host Response Panel, a custom Code Set which profiled 785 genes in mouse across 55 pathways. Tissue was extracted and analyzed from the lung of B cell IL-10 KO mice (Cd19-cre+/-  IL-10 flox/flox) and their corresponding littermates infected with Mycobacterium tuberculosis HN878 on day 82 post infection.

first: Sebastian

last: Marwitz

first: Rudolf

middle: A

last: Manz

first: Torsten

last: Goldmann

first: Bianca

middle: E

last: Schneider


title: IKAROS modulates CD19 surface expression and CD19-directed CAR-T response [ATAC-seq]

summary: To elucidate how IKAROS modulates CD19 surface expression in B cell acute lymphoblastic leukemic cells, we analyzed chromatin landscape profile from isogenic IKAROS wild type (WT) or knock down (KD) B-ALL cell lines.

overall_design: Human B-ALL cell lines (NALM6, REH and SUP-B15) were transduced with IKZF1-specific or scramble shRNA expressing lentivirus. 72 hours post transduction, we compared their chromatin landscape profiles through ATAC-seq.


title: Treacle’s ability to form liquid-like phase condensates is essential for nucleolar fibrillar center assembly, efficient rRNA transcription and processing, and rRNA gene repair

city: Moscow

first: Artem

last: Luzhin

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: We investigated the role of the nucleolar protein Treacle in organizing and regulating the nucleolus in human cells. Our results support Treacle’s ability to form liquid-like phase condensates through electrostatic interactions among molecules. The formation of these biomolecular condensates is crucial for segregating nucleolar fibrillar centers from the dense fibrillar component and ensuring high levels of rRNA gene transcription and accurate rRNA processing. Both the central and C-terminal domains of Treacle are required to form liquid-like condensates. The initiation of phase separation is attributed to the C-terminal domain. The central domain is characterized by repeated stretches of alternatively charged amino-acid residues and is vital for condensate stability. Overexpression of mutant forms of Treacle that cannot form liquid-like phase condensates compromises the assembly of fibrillar centers, suppressing rRNA gene transcription and disrupting rRNA processing. These mutant forms also fail to recruit DNA topoisomerase II binding protein 1 (TOPBP1), suppressing the DNA damage response in the nucleolus.

overall_design:
ChIP-seq of the full-length Treacle-2S (Treacle-2S full), charge-scrambled Treacle-2S (Treacle-2S CS) or Treacle-2S Δ83-1121 deletion mutant (Treacle-2S Δ83-1121) with Katushka2S antibodies.
Raw data for input samples were previously uploaded (GSM4112817 and GSM4112818) and can be retrieved at SRA under accessions SRR10241419 and SRR10241420.

last: Velichko

middle: V

first: Sergey

last: Razin


title: Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer

city: KALYANI

first: ANIKET

last: KUMAR

state: WEST BENGAL

address: Near Netaji Subhas Sanatorium Post Office

country: India

institute: NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS

summary: Pancreatic ductal adenocarcinoma (PDAC) is the most common and aggressive form of pancreatic cancer with a very low survival rate and limited treatment options. Aberrant expression of MYC oncogene plays a crucial role in the progression of PDAC. Recent reports have established the significance of enhancer RNAs (eRNAs), originated from active enhancer or super-enhancer regions, in controlling gene transcription. Our study has identified how novel MYC eRNAs regulate MYC gene expression during chronic inflammatory condition in pancreatic cells. The higher amount of MYC eRNA has been observed in chronic pancreatitis and in pancreatic cancer patients as well. We have shown that MYC-490 kb eRNA interacts with YEATS2, a histone reader protein of ATAC-HAT complex and augments the association of YEATS2-containing ATAC complex to MYC promoter/enhancer region and thus increases MYC gene expression. A TNF-α induced Tyrosine dephosphorylation cycle regulates the MYC eRNA binding to YEATS2 protein in cancer cell. Thus, our study has added another layer of MYC gene expression regulation by enhancer-driven transcripts which can be used as a potential therapeutic target for treating pancreatic cancer.

overall_design:
Nascent RNA sequencing of untreated and 24 hour TNFα treated cells.
Please note that processed data generated from both replicates are linked to the corresponding rep1 records.

first: Jayita

last: Roy

first: Aniket

last: Kumar

first: Shouvik

last: Chakravarty

first: Nidhan

last: Biswas

first: Srikanta

last: Goswami

first: Anup

last: Mazumder


title: NAT10 and N4-Acetylcytidine restrain R-loop levels and related inflammatory responses

city: Austin

first: Blerta

last: Xhemalce

state: Texas

address: 2500 Speedway

institute: University of Texas at Austin

summary: N4-acetylcytidine (ac4C) is an evolutionarily conserved RNA modification that is deposited on diverse RNAs by N-acetyltransferase 10 (NAT10), a protein with high biological significance for aging and cancer. Here, we performed a comprehensive survey of ac4C using metabolic labeling, sodium cyanoborohydride chemical treatment coupled to next generation sequencing (NGS) and ac4C antibody-based cell and molecular biology techniques. Our NGS analysis confirms robust ac4C modification of rRNA and specific tRNA species in a NAT10-dependent manner, but suggests low or spurious ac4C acetylation in mRNA. Analysis of RNA-seq data also revealed an induction of inflammatory responses as well as mutagenesis at transcriptionally active sites in NAT10-KO cells. This finding led us to further explore the role of NAT10 in R-loops, which have recently been shown to induce APOBEC3B-mediated mutagenesis. Our analysis revealed that R-loops are modified with ac4C in a NAT10-dependent manner. Furthermore, NAT10 restrains the levels of R-loops at a subset of differentially expressed genes in a manner dependent on its catalytic activity. Together with cellular biology data showing ac4C containing RNA in endosomal structures, we propose that increased levels of ac4C-unmodified RNAs, likely derived from R-loops, in endosomal structures induce inflammatory responses.

overall_design: NAT10 knockout and NaCNBH3 treatment were applied individually and jointly to determine their effects on ac4C and gene expression. RNA was profiled from two replicates in each of four total conditions, and either processed for normal RNA-seq or further extracted to retrieve tRNAs. These were also sequenced for a total of 16 samples.

first: Turja

last: Debnath

first: Nathan

last: Abell

first: Yi-Ru

last: Li

first: Sravan

last: Devanathan

first: Enrique

last: Navedo

last: Xhemalçe


title: Single-cell transcriptomic analysis identified resistant MDSCs and a stress-tolerant gene co-expression network as common MDSC features across multiple disease settings

city: Pittsburgh

first: Timothy

last: Billiar

state: PA

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

summary: This experiment validated the inferred SCNV profile derived from scRNA-seq directly from DNA-level evidence using Cyto-SNP array.

overall_design: To provide data at the DNA-level, we cultured and harvested the samples from eight donors under two experimental conditions, control or GM-CSF + IL-6 treated PBMCs. Cytokines were added daily for three days. Then, cells were harvested and flow sorted for CD33+ cells.

first: Tianmeng

last: Chen


title: A type 1 immune-stromal cell network mediates disease tolerance and barrier protection against intestinal infection

status: Public on Mar 25 2025

city: Montreal

first: Irah

last: King

state: QC

address: 1001 Decarie Blvd

country: Canada

institute: McGill University Healthy Centre

summary: Type 1 immunity mediates host defense through pathogen elimination, but whether this pathway also impacts tissue function is unknown. Here we demonstrate that rapid induction of IFNγ signaling coordinates a multi-cellular response that is critical to limit tissue damage and maintain gut motility following infection of mice with a tissue-invasive helminth. IFNγ production is initiated by antigen-independent activation of lamina propria CD8+ T cells following MyD88-dependent recognition of the microbiota during helminth-induced barrier invasion. IFNγ acted directly on intestinal stromal cells to recruit neutrophils that limited parasite-induced tissue injury. IFNγ sensing also limited the expansion of smooth muscle actin-expressing cells to prevent pathological gut dysmotility. Importantly, this tissue-protective response had limited impact on parasite burden, indicating that IFNγ supports a disease tolerance defense strategy. Our results have important implications for managing the pathophysiological sequelae of post-infectious gut dysfunction and chronic inflammatory diseases associated with stromal remodelling.

overall_design: Expression profiling of high throughput sequencing from whole small intestinal tissue infected with Hpb.

first: Maria

last: Gentile

first: Susan

last: Westfall

first: Andrei

last: Bogza


title: Modulation of Gene Expression by Substrate Stiffness via Regulation of Histone H2B Mono-ubiquitination

city: Tianjin

first: Mingwei

last: Feng

state: Tianjin

address: Weijin road No.92

department: SPST

country: China

institute: Tianjin University

summary: Mechanotransduction plays a critical role in regulating cell growth, proliferation, and metabolism. Cells respond to mechanical signals, which ultimately induces gene expression. However, the underlying mechanisms of this gene regulation remain largely unclear. In previous research, we discovered that the ubiquitin-conjugating enzymes UBE2A and UBE2B translocate between the cytoplasm and nucleus in a force-dependent manner. Additionally, we confirmed that UBE2A and UBE2B ubiquitinate histone H2B at lysine 120 (K120) when cells are cultured on a stiff substrate. In this study, we employed Chromatin Immunoprecipitation (ChIP) to investigate the distribution of H2B mono-ubiquitination in human skeletal muscle (hsSKM) cells cultured on substrates of varying stiffness—soft (0.2 kPa) and stiff (64 kPa).

overall_design: chromatin immunoprecipitation for H2BK120ub of hsSKM cell cultured on 64kPa or 0.2kPa hydrogel

first: Fumihiko

last: Nakamura


title: RNA-sequencing demonstrates transcriptional differences between human vocal fold fibroblasts and myofibroblasts

city: Madison

first: Lingxin

last: Cheng

state: WI

address: University of Wisconsin Madison

department: Biomedical Data Science

institute: UW Madison

summary: Background: Differentiation of fibroblasts into myofibroblasts is necessary for wound healing, but excessive myofibroblast presence and persistence can result in scarring. Treatment for scarring is limited largely due to a lack of comprehensive understanding of how fibroblasts and myofibroblasts differ at the transcript level. The purpose of the study was to comprehensively characterize transcriptional profiles of injured fibroblasts relative to normal fibroblasts, utilizing fibroblasts from the vocal fold as a model for other areas of the body. Results: we identified differentially expressed genes between groups of normal fibroblasts, scarred fibroblasts, and fibroblasts treated with transforming growth factor-beta 1 (TGF-β1), which represented an induced-scar phenotype. Principal component analysis revealed clustering of normal fibroblasts separate from the clustering of fibroblasts treated with TGF-β1; scarred fibroblasts were more similar to normal fibroblasts than fibroblasts treated with TGF-β1. Enrichment analyses revealed pathways related to cell signaling, receptor-ligand activity, and regulation of cell functions in scarred fibroblasts, pathways related to cell adhesion in normal fibroblasts, and pathways related to ECM binding in fibroblasts treated with TGF-β1. Although transcriptomic profiles between scarred fibroblasts and fibroblasts treated with TGF-β1 were relatively dissimilar, the most highly co-expressed genes were enriched in pathways related to actin cytoskeleton binding. Conclusions: Transcriptomics of normal fibroblasts differ from myofibroblasts, including from those retrieved from scar and those treated with TGF-β1. Despite large differences in transcriptomics between tVFF and sVFF, tVFF serve as a useful in vitro model of myofibroblasts and highlight key similarities to myofibroblasts extracted from scar pathology, as well as expected differences related to normal fibroblasts from healthy VF.

overall_design:
We collected normal fibroblasts, scarred fibroblasts, and fibroblasts treated with transforming growth factor-beta 1 (TGF-β1), which represented an induced-scar phenotype. We then performed gene expression profiling analysis, and analyzed their differences using gene expression analysis methods.

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first: Michelle

last: Bretl

first: Christina

last: Kendziorski

last: Thibeault


title: IKAROS facilitates antigen escape in the face of CD19- and CD22-targeted therapies for B-cell malignancies

first: Pablo

last: Domizi

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

overall_design: Refer to individual Series


title: Lung-resident memory B cells maintain allergic IgE responses in the respiratory tract.

city: Maywood

first: Yee Ling

last: Wu

state: Illinois

address: 2160 S. First Ave

department: Microbiology and Immunology

institute: Loyola University Chicago

summary: We used single cell RNA sequencing to examine the transcriptome of lung-resident memory B cells early after allergen inhalation (day21) and late (day 77) to explore potential mechanisms that control residency in the lungs.

overall_design: Ragweed pollen and OVA were administered to mice intranasally for 5 days in week 1, followed by OVA alone in weeks 2 and 3. Memory B cells were isolated from the lungs by FACS as B220+CD38+GL7-IgD- excluding dead cells (DAPI+) or circulating cells (intravascular label negative) from two mice per time point (day 21 and day 77). 2,500 cells per sample were partitioned on a 10X Chromium Controller and libraries were prepared using 10X Genomics Next GEM Single Cell 3' Reagents Kits v3 (Dual Index). We compared gene expression and memory B cell subsets present on day 21 and day 77 after allergen exposure to identify potential mechanisms controlling residency in the lungs.

first: Alexander

middle: J

last: Nelson


title: Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma [Hi-C]

city: Boston

first: Matthew

last: Meyerson

state: MA

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Amplification-mediated oncogene overexpression is a critical and widespread driver event in cancer, yet our understanding of how amplification and dosage mediate oncogene regulation is limited. Here, we find that the most significant focal amplification event in lung adenocarcinoma (LUAD) targets a lineage “super-enhancer” near the NKX2-1 lineage transcription factor. The NKX2-1 super-enhancer is targeted by focal and co-amplification with NKX2-1 and controls NKX2-1 expression and regulation. We find that NKX2-1 directly controls enhancer accessibility to drive a lineage-addicted state in LUAD. We precisely map the effects of NKX2-1 dosage modulation upon both overexpression and knockdown and identify both linear and non-linear regulation by NKX2-1 dosage. We find that NKX2-1 is a widespread dependency in LUAD cell lines and that NKX2-1 confers persistence to EGFR inhibitors. Our data suggest a defining role for dosage in the oncogenic regulation of amplified NKX2-1 and that amplified NKX2-1 lineage addiction defines LUAD tumors.

overall_design: Lung adenocarcinoma cancer cell lines (NCI-H2087, NCI-H358, NCI-H441, HCC364) were fixed and prepared for Hi-C genome-wide interaction mapping in duplicate.

first: John

last: Pulice


title: Single-cell transcriptomic analysis of zebrafish fli1b mutants

city: Tampa

first: Saulius

last: Sumanas

state: FL

address: 560 Channelside Dr

department: Department of Pathology and Cell Biology

institute: University of South Florida

summary: To characterize fli1b role in zebrafish hematopoietic development, we obtained samples from zebrafish fli1b mutant and control wild-type embryos at 23-24 hpf stage. Whole embryo single-cell RNA-seq demonstrated reduction in the expression of hematopoietic markers associated with erythroid and myeloid development. A subset of vascular endothelial markers was also reduced in fli1b mutants. These results demonstrate fli1b role in hematopoietic and vascular development.

overall_design: Approximately 40 homozygous fli1b-/- and wild-type zebrafish embryos at 23-24 hpf stage were obtained from incrosses of  fli1b-/- or sibling wild-type parents, respectively. All cells were disaggregated and subjected to single-cell RNA-seq using 10x Genomics Chromium system.

first: Valentina

last: Laverde

first: Luiza

last: Loges


title: Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma [RNA-seq]

overall_design:
Lung adenocarcinoma cancer cell lines (NCI-H441, NCI-H2087, NCI-H1975, PC9, NCI-H1975) were lentivirally infected with indicated constructs, selected, and harvested for ATAC-seq at day 7-10 post infection for constitutive overexpresison and knockdown experiments. NCI-H441 and PC9 cells were prepared in experimental batches, which are distinguished by "Set2".

For TT-seq degron experiments, LUAD cell lines (PC9, NCI-H1975) were lentivirally infected and selected as indicated, then treated for 1 h 45 min with 500nM dTagV-1 or dTagV-1NEG control then for 15min with dTagV-1/dTagV-1NEG as before + 500µM 4-Thiouridine (4sU), then harvested for TT-seq.


title: Deep sequencing of microRNA and total RNA reveals distinct microRNA-mRNA signatures that differentiate pancreatic neuroendocrine neoplasia from non-diseased pancreas tissue

city: Bratislava

first: Natália

last: Matyašovská

address: Ilkovičova 8

country: Slovakia

institute: MultiplexDX

summary: Only a limited number of biomarkers guide personalized management of pancreatic neuroendocrine tumors (PanNETs). Transcriptome profiling of microRNA (miRs) and mRNA has shown value in segregating PanNETs and identifying patients more likely to respond to treatment. Because miRs are key regulators of mRNA expression, we sought to integrate expression data from both RNA species into miR-mRNA interaction networks to advance our understanding of PanNET pathogenesis. We used deep miR/mRNA sequencing on six low-grade/high-risk, well-differentiated PanNETs compared with seven non-diseased tissues to identify differentially expressed miRs/mRNAs. Then we crossed a list of differentially expressed mRNAs with a list of in silico predicted mRNA targets of the top upregulated/downregulated miRs to generate high probability miR-mRNA interaction networks. Gene ontology and pathway analyses revealed several miR-mRNA pairs implicated in cellular processes and pathways suggesting perturbed neuroendocrine function (miR-7 and Reg family genes), cell adhesion (miR-216 family and NLGN1, NCAM1, and CNTN1; miR-670 and the claudins, CLDN1 and CLDN2), and metabolic processes (miR-670 and BCAT1/MPST; miR-129 and CTH). These novel miR-mRNA interaction networks identified dysregulated pathways not observed when assessing mRNA alone and provide a foundation for further investigation of their utility as diagnostic and predictive biomarkers.

overall_design: Non-coding RNA profiling by high throughput sequencing of pancreatic neuroendocrine cancer samples and non-diseased pancreatic tissues delineated from pancreatic adenocarcinoma tissues

first: Natalia

last: Matyasovska

last: Valkova

first: Michal

last: Gala

first: Silvia

last: Bendikova

first: Abdulhameed

last: Abdulhamed

first: Vladimir

last: Palicka

first: Neil

last: Renwick

first: Pavol

last: Cekan

first: Evan

middle: D

last: Paul


title: Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma [ChIP-seq]

overall_design: Lung adenocarcinoma cancer cell lines (NCI-H441, NCI-H2087, NCI-H358, HCC364) were fixed and harvested for ChIP-seq of naïve cell lines.


title: Deep sequencing of microRNA and total RNA reveals distinct microRNA-mRNA signatures that differentiate pancreatic neuroendocrine neoplasia from non-diseased pancreas tissue [RNA-seq]

overall_design: Total RNA profiling by high throughput sequencing of pancreatic neuroendocrine cancer samples and non-diseased pancreatic tissues delineated from pancreatic adenocarcinoma tissues


title: Modulation of Macrophages TLR4-mediated Transcriptional Response by Lacticaseibacillus rhamnosus CRL1505 and Lactiplantibacillus plantarum CRL1506

city: San Miguel de Tucuman

first: Leonardo

last: Albarracin

address: Chacabuco 145

country: Argentina

institute: CERELA

summary: The aim of this work was to gain insight into the mechanisms involved in the immunomodulatory properties of L. rhamnosus CRL1505 and L. plantarum CRL1506 in the context of TLR4-mediated inflammation, particularly focused on macrophages. Therefore, in vitro studies in murine macrophages were conducted to evaluate the ability of the lactobacilli strains to modulate the transcriptomic response after LPS stimulation.

overall_design: Raw 264.7 mouse macrophage cells (5x10^5 cells/well) were inoculated in 12-well plates and incubated overnight. The culture medium was changed, and macrophages were stimulated with lactobacilli strains CRL1505 or CRL1506 (5x10^7 cells/mL) for 24 h. Macrophages were washed to eliminate lactobacilli and stimulated with 50 ng/mL LPS (InvivoGen, San Diego, USA) for 12 h. Total RNA was extracted using the RNeasy Mini kit (Qiagen, Tokyo, Japan). The RNA labelling and hybridization was performed using the SurePrint G3 Mouse GE 8x60K ver2.0 Microarray from Hokkaido System Science Co., Ltd., Sapporo, Japan. Microarray scanning was performed with the Microarray Scanner from Agilent Technologies, while digitalization was done using Agilent Feature Extraction 10.7.3.1.

first: Masahiko

last: Suzuki

first: Haruki

last: Kitazawa

first: Julio

last: Villena


first: Yee Ling

last: Wu

state: IL

address: 2160 S. 1st Ave

summary: We used single cell RNA sequencing to examine the transcriptome and B cell receptor (BCR) sequences of B cells infiltrating mouse lungs 3 weeks after allergen inhalation to investigate the origins of IgE-producing plasma cells.

overall_design: Total non-naïve B cells (CD19+IgD-) were isolated from lungs or lung-draining mediastinal lymph nodes (medLNs) of 3 mice by FACS excluding circulating cells identified by intravascular labeling. Isolated cells from each mouse were hashed with BioLegend TotalSeq-C0301, C0302, and C0303 antibodies prior to pooling. Pooled cells from the lungs or medLNs were partitioned on a 10X Chromium Controller and three libraries were prepared for both samples: gene expression, BCR VDJ, and feature barcode libraries for hashing and demultiplexing biological replicates.

first: Alexander

last: Nelson


title: Mutational signatures define immune and Wnt-associated subtypes of ampullary carcinoma

city: Copenhagen

first: Jesper

middle: Bøje

last: Andersen

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research & Innovation Centre, University of Copenhagen


title: Selict-seq profiles genome-wide off-target effects in adenosine base editing

city: Wuhan

first: qi

last: wei

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

summary: Adenosine base editors (ABEs) facilitate the conversion of A•T base pairs to G•C base pairs, demonstrating significant potential for correcting pathogenic point mutations in humans. However, the off-target editing effects of ABEs remain inadequately characterized. In this study, we present a biochemical method, Selict-seq, designed to evaluate genome-wide off-target editing by ABEs. Selict-seq specifically captures dI-containing single-stranded DNA (ssDNA) and precisely identifies dA-to-dI mutation sites, thereby elucidating the off-target effects induced by ABEs. Through investigations involving three single-guide RNAs (sgRNAs), we identified numerous unexpected off-target edits both within and outside the protospacer regions. Analysis of these off-target sites revealed distinct characteristics of the ABE8e(V106W). These findings significantly advance our understanding of the off-target landscape associated with ABE8e. In summary, our approach enables an unbiased analysis of the ABE editome and provides a widely applicable tool for specificity evaluation of various emerging genome editing technologies.

overall_design:
10 samples are analyzed (6 sgRNA&ABE8e tranfacted sample, 2 ABE_only tranfated sample and 2 background sample)
20 samples are analyzed (8 sgRNA&ABE7.10 tranfacted sample in HEK293T, 4 sgRNA&ABE8e tranfacted sample in HEK293T, 4 sgRNA&ABE8e tranfacted sample in MCF7, 2 ABE8e_only tranfated sample in MCF7 and 2 background sample in MCF7)

first: Kexin

last: Yuan

first: Xin

last: Xi

first: Shaoqing

last: Han

first: Qi

last: Wei

first: Xiang

last: Zhou


title: Mutational signatures define immune and Wnt-associated subtypes of ampullary carcinoma [WES]

summary: Whole exome sequencing in order to characterise genomic alterations from patients with Ampullary carcinoma (AMPAC)

overall_design: The exome sequencing of bulk AMPAC tumors and matched normal

first: Ekaterina

last: Zhuravleva

first: Monika

last: Lewinska

first: Colm

last: O’Rourke

first: Asif

last: Rashid

first: Ann

middle: W

last: Hsing

first: Andrzej

last: Taranta

first: Yu-Tang

last: Gao


title: Progesterone receptor in uterine glands is required for pregnancy establishment in mice

city: Columbia

first: Andrew

last: Kelleher

state: MO

address: 1030 Hitt Street

department: Ob, Gyn Womens Health

institute: University of Missouri

summary: By utilizing Prss29-Cre, Pgr was conditionally deleted to identify the definitive roles of progesterone signaling in the uterine glands during pregnancy. This study provides new insights, demonstrating that PGR-P4 signaling in the glandular epithelium is required for uterine receptivity by regulating LIF on gestation day 4. Furthermore, we have shown that PGR signaling in glands is dispensable post-implantation.

overall_design: The uteri were collected from the wild-type (WT) and Prss29Cre/Cre;Pgrf/f (Pgr gecKO) on GD 4. RNA was extracted and sequenced by Azenta Life Sciences using two replicates for WT and Pgr gecKO. Libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina and sequenced (2 x 150 bp paired end) using Illumina instrument (4000 or equivalent). Raw sequence data (.bcl files) generated from Illumina Hiseq was converted into fastq files and de-multiplexed using Illumina’s bcl2fastq 2.17 software.

first: Greeshma Sai

last: Bayammagari

first: Sai Goutham Reddy

last: Yeddula

first: Sarayut

last: Winuthayanon

first: Francesco

last: Demayo

first: John

middle: P

last: Lydon

first: Thomas

last: Spencer

middle: M


title: Single-cell transcriptomic analysis identified resistant MDSCs and a stress-tolerant gene co-expression network as common MDSC features across multiple disease settings

first: Timothy

last: Billiar

summary:
Background: Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of immunosuppressive myeloid cells. The identification of a molecular signature common to MDSC regardless of tissue source would aid in the classification of cells as MDSCs.
Methods: Single-cell RNA sequencing (scRNA-seq) was performed on GM-CSF+ IL-6 induced human MDSCs to characterize the extent of heterogeneity within monocytic MDSCs (M-MDSCs). Cytokine-treated PBMCs were also cultured in the absence of serum to include an additional element of cell stress. Independent published bulk and single-cell transcriptomic datasets were used for validation.
Findings: A cluster of cells with preserved MDSC features was induced by the combination of inflammatory signals and cell stress in the form of serum starvation (resistant MDSCs, rMDSCs). A gene co-expression module (the yellow module) was identified specific to rMDSCs. The genes upregulated in MDSCs can be further classified into stress-tolerant vs. -sensitive features. This yellow module mostly contained stress-tolerant genes and showed excellant separation for distinguishing M-MDSCs from control cells across a range of in vitro and in vivo conditions (ROC AUC=0.954), a feature not found in the stress-sensitive genes. Importantly, rMDSCs were identified in scRNA-seq datasets of immune cells from multiple human cancer types. Tumor C1Q macrophages, which have been associated with immunosuppression, highly expressed the yellow module gene signature.
Interpretation: These results demonstrate the importance of the combined roles of inflammation and cellular stress in shaping the features of M-MDSCs, and highlights cellular resilience represented by rMDSCs and the role of stress-tolerant features in defining common MDSC features.

overall_design: MDSCs were generated by treating PBMCs with GM-CSF (10ng/mL) + IL-6 (10ng/mL) at 5x10^5 cell/mL in full media at 37C with 5%CO2. Cytokines were added daily for 3 days. PBMCs cultured in full media alone were used as control. Serum starvation was performed using serum-free media.

first: Tianmeng

last: Chen

first: Julia

last: Hughes

last: Conroy


title: Mutational signatures define immune and Wnt-associated subtypes of ampullary carcinoma [methylation]

first: Jesper

last: Andersen

summary: RNA-seq, methylation and Whole exome sequencing in order to characterise genomic alterations from patients with Ampullary carcinoma (AMPAC)

overall_design: Methylation profling of bulk AMPAC tumors and matched normal

first: Ekaterina

last: Zhuravleva

last: Lewinska


title: Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma

first: Matthew

last: Meyerson

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

Amplification-mediated oncogene overexpression is a critical and widespread driver event in cancer, yet our understanding of how amplification and dosage mediate oncogene regulation is limited. Here, we find that the most significant focal amplification event in lung adenocarcinoma (LUAD) targets a lineage “super-enhancer” near the NKX2-1 lineage transcription factor. The NKX2-1 super-enhancer is targeted by focal and co-amplification with NKX2-1 and controls NKX2-1 expression and regulation. We find that NKX2-1 directly controls enhancer accessibility to drive a lineage-addicted state in LUAD. We precisely map the effects of NKX2-1 dosage modulation upon both overexpression and knockdown and identify both linear and non-linear regulation by NKX2-1 dosage. We find that NKX2-1 is a widespread dependency in LUAD cell lines and that NKX2-1 confers persistence to EGFR inhibitors. Our data suggest a defining role for dosage in the oncogenic regulation of amplified NKX2-1 and that amplified NKX2-1 lineage addiction defines LUAD tumors.

last: Pulice


title: Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma [ATAC-seq]

overall_design:
Lung adenocarcinoma cancer cell lines (NCI-H441, NCI-H2087, NCI-H1975, PC9, NCI-H1975) were lentivirally infected with indicated constructs, selected, and harvested for ATAC-seq at day 7-10 post infection for constitutive overexpresison and knockdown experiments. NCI-H441 and PC9 cells were prepared in experimental batches, which are distinguished by "Set2".

For degron experiments, LUAD cell lines (PC9, NCI-H1975) were lentivirally infected and selected as indicated, then treated for 2hr with 500nM dTagV-1 or dTagV-1NEG control then harvested for ATAC-seq.


title: RNA-seq analysis of concentration-response transcriptomic changes induced by cannabinol (CBN) in hepatocytes derived from human induced pluripotent stem cells (iPSCs)

status: Public on Mar 24 2025

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

summary: Currently little is known about the safety of nonintoxicating cannabinoids such as cannabinol (CBN). New approach methodologies (NAMs) based on bioinformatic analysis of high-throughput transcriptomic data are gaining increasing importance in risk assessment and regulatory decision-making of data-poor chemicals. In this study, we conducted a concentration response transcriptomic analysis of CBN in hepatocytes derived from human induced pluripotent stem cells (iPSCs). Biological functions and pathways impacted by CBN exposure were identified, including liver metabolism and cellular oxidative stress. In addition, a transcriptomic point-of-departure (tPoD) value was determined for CBN through benchmark concentration (BMC) analysis of the transcriptomic data. The present study demonstrates the potential utility of transcriptomic BMC analysis as a NAM for hazard assessment of data-poor chemicals, improves our understanding of the possible health effects of CBN, and provides important tPoD data that could contribute to inform human safety assessment of cannabinoid compounds.

overall_design: Cells were exposed to increasing concentrations of CBN (0.1-20 μM) for 24 h. Transcriptomic gene expression was characterizecd using RNA-seq. Three replicates were included for each concentration group including the control (0.0 μM).


title: Glucosidase Alpha Neutral C Promotes Influenza Virus Replication by Inhibiting Proteosome-Dependent Degradation of Hemagglutinin

city: Shenzhen

first: Qian

last: Xie

state: Guangdong

address: School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.

institute: Sun Yat-sen University

summary: The H7N9 influenza virus poses a significant threat to human health, and the mechanism by which it infects humans remains incompletely understood. Our investigation has unveiled significant insights into the role of glucosidase alpha, neutral C (ganc) gene in human H7N9 infections. Through whole genome sequencing (WGS), we identified five low-frequency functional and heterozygous variants of ganc strongly associated with human H7N9 infections compared to healthy controls. Furthermore, we observed a reduction in mRNA and protein expression of GANC following H7N9 virus infection in vitro and in vivo. Subsequent experiments involving GANC demonstrated promotion of H7N9 virus replication in a stable strain with GANC overexpression. Conversely, GANC knockdown exhibited the ability to restrict influenza A virus (IAV) replication, including H7N9, H9N2 and H1N1, both in vitro and in vivo. This inhibition was mediated by GANC's ability to promote the degradation of H7N9 hemagglutinin (HA). Moreover, we discovered that GANC knockdown facilitated the degradation of HA in a proteasome-dependent manner. The inhibition caused by GANC knockdown was mediated by promoting direct binding of HA with the  proteasome 26S subunit, non-ATPase, 1 (PSMD1) and PSMD2. All the five variants in the ganc gene reduced its ability to promote H7N9 virus replication, and also diminished the levels of GANC-induced HA protein expression. Our findings revealed a novel mechanism by which GANC inhibited the proteasome-dependent degradation of HA to promote H7N9 virus replication. These results suggest that GANC may play an important role in IAV replication.

overall_design: A549 cells were transfected with GANC siRNAs, and with or without H7N9 virus infection at a MOI of 0.1, and cells were harvested at 36 h post-infection for RNA-Seq and data analysis.

first: Xinzhong

last: Liao

last: xie

first: Minqi

last: Liang

first: Qijun

first: Bi

last: Huang

first: Shengze

last: Zhang

first: Feng

first: Liangliang

last: Wang

first: Lifang

last: Yuan

first: Xuejie

last: Liu

first: Simin

last: Wen

first: Chuming

last: Luo

first: Dayan

first: Yongkun

first: Huanle

first: Yuelong

last: Shu


title: Mutational signatures define immune and Wnt-associated subtypes of ampullary carcinoma [RNA]

first: Jesper

last: Andersen

summary: Expression profiling by high throughput sequencing in order to analyze the differential profile of RNAs  expression from patients with Ampullary carcinoma (AMPAC)

overall_design: The expression profiles of AMPAC tumors

first: Ekaterina

last: Zhuravleva

first: Monika

first: Colm

last: O’Rourke

first: Asif

last: Rashid

first: Ann

last: Hsing

first: Andrzej

last: Taranta

first: Yu-Tang


title: Identification of potent biparatopic antibodies targeting FGFR2 fusion driven cholangiocarcinoma

city: Cambridge

first: William

last: Sellers

state: Massachusetts

address: 415 Main street

institute: Broad Insititute

summary: Translocations involving FGFR2 gene fusions are common in cholangiocarcinoma and predict response to FGFR kinase inhibitors. However, response rates and durability of are limited due to the emergence of resistance, typically involving FGFR2 kinase domain mutations, and to sub-optimal dosing, relating to drug adverse effects. Here, we develop biparatopic antibodies targeting the FGFR2 extracellular domain (ECD), as candidate therapeutics. Biparatopic antibodies can overcome drawbacks of bivalent monospecific antibodies, which often show poor inhibitory or even agonist activity against oncogenic receptors. We show that oncogenic transformation by FGFR2 fusions requires an intact ECD. Moreover, by systematically generating biparatopic antibodies targeting distinct epitope pairs in FGFR2 ECD, we identified antibodies that effectively block signaling and malignant growth driven by FGFR2-fusions. Importantly, these antibodies demonstrate efficacy in vivo, synergy with FGFR inhibitors, and activity against FGFR2 fusions harboring kinase domain mutations. Thus, biparatopic antibodies may serve as new treatment options for patients with FGFR2-altered cholangiocarcinoma.

overall_design: To investigate the potential role of immune effector functions mediated by biparatopic antibodies in ICC13-7 xenografts, we administered varying concentrations of biparatopic antibodies to mice. At two time points (Day 41 and Day 52), xenografts were surgically removed, flash-frozen in liquid nitrogen, and processed for RNA sequencing.

first: Saireudee

last: Chaturantabut

first: Yao

last: He


title: Transcriptomic analysis of B cells from patients with chronic lymphocytic leukemia

city: Taipei

first: Ho-Yang

last: Tsai

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

department: Genomics research center

country: Taiwan

institute: Academia Sinica

summary: CD22 (also known as Siglec-2) belongs to the Siglec family of glycan-recognition proteins and negatively regulates B-cell receptor-mediated signaling. CD22 is down-regulated in the B cells of patients with chronic lymphocytic leukemia (CLL). However, the mechanism regulating the transcription of CD22 is incompletely understood. In this study, we defined the minimal promoter of the human CD22 gene and identified the transcription factors that bind to the CD22 promoter by proteomic analysis. This transcriptome dataset (by RNAseq of peripheral blood B cells from 6 patients with CLL) was used (1) to validate the positive correlation between the expression levels of CD22 transcript (assessed by RNAseq) and CD22 protein (assessed by flow cytometry), and (2) to test the correlations between the expression levels of CD22 transcript and those of transcription factors that bind to minimal CD22 promoter.

overall_design: B cells were purified from donor blood with CD19 MicroBeads (Miltenyi Biotec). Total RNA was prepared from 5×10^6 cells with RNeasy Mini Kit (Qiagen) and subjected to library preparation with KAPA mRNA HyperPrep Kit (Roche). The next-generation sequencing (20 million paired-end (2 × 150 bp) sequencing per sample) with NovaSeq 6000 (Illumina) was performed. The raw data was mapped and normalized, and transcripts per million (TPM) were calculated for each gene by HISAT2.

first: Shang-Ju

last: Wu

first: Kuo-I

last: Lin


title: CD8+ TEMRA Memory T cells Associate with Asthma Symptom Duration and Escape Proliferation Arrest in Severe but Not Mild Asthma

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

summary: Aberrant immune response is a hallmark of asthma, with 5-10% of patients suffering from severe disease exhibiting poor response to standard treatment. A better understanding of the immune responses contributing to disease heterogeneity is critical for improving asthma management. Here we show a significant association of airway CD8+ effector memory T cells re-expressing CD45RA (TEMRAs), but not CD8+ CD45RO+ or tissue resident memory (TRM) T cells, with asthma duration in patients with severe asthma (SA) but not mild to moderate asthma (MMA). Higher frequencies of IFN-g+ CD8+ TEMRAs compared to IFN-g+ CD45RO+ T cells were detected in SA airways, and the TEMRAs from SA but not MMA patients proliferated ex vivo, although both expressed cellular senescence-associated biomarkers. Prompted by the transcriptomic profile of SA CD8+ TEMRAs and proliferative response to IL-15, airway IL15 expression measured higher in SA compared to MMA patients. Our findings add a new dimension to understanding asthma heterogeneity identifying IL-15 as a potential target for treatment.

overall_design:
Cryopreserved cell suspensions were thawed as above and resuspended in FACS buffer but instead of stimulation were incubated with optimally diluted labeled monoclonal antibodies for 30 min at 0oC. Cells were washed and then sorted on an Aurora CS cell sorter using SpectroFlo software. Up to 100,000 T cells from three populations (CD8+ naïve, CD8+ CD45RO+ memory, and CD8+ TEMRAs) were sorted directly in to 1 mL of RLT buffer (Qiagen).
Libraries were generated with the Takara SMART-Seq Stranded kit using Takara SMARTer RNA Unique Dual Index A and B Kits according to the manufacturer’s instructions. RNA was normalized to 5 ng/uL with water for a total volume of 7 uL of input RNA. RNA fragmentation was carried out for 6 minutes. 10 cycles were used for PCR1, followed by ribosomal RNA depletion using scZapR. No samples were pooled prior to PCR2 where 12 cycles were completed. Library quantification and assessment was done using a Qubit FLEX fluorometer and an Agilent TapeStation 4150/Fragment Analyzer 5300. Libraries were normalized and pooled to 2nM by calculating the concentration based off the fragment size (base pairs) and the concentration (ng/uL) of the libraries. Sequencing was performed on an Illumina NextSeq 2000, using a P3 200 flow cell. The pooled library was loaded at 750 pM. Sequencing was carried out 2x101 bp, with a target of 40 million reads per sample. A custom run chemistry was used to incorporate 3 dark cycles at the start of R2 that mask the 3 bp of the Takara adapter present in the read. Sequencing data was demultiplexed by the on-board Illumina DRAGEN FASTQ Generation software (v3.10.12).

first: Richard

last: Ramonell

first: Anuradha

last: Ray

first: Sally

last: Wenzel

last: MacDonald


title: Immune Evasion Mechanisms in Early Stage-I High-Grade Serous Ovarian Carcinoma: Insights into Regulatory T-Cell Dynamics

city: Rozzano, Milan

first: Paolo

last: Marzano

address: Via Alessandro Manzoni 56

institute: Humanitas Research Hospital

summary: The mechanisms driving immune evasion in early stage-I high-grade serous ovarian carcinoma (HGSOC) remain poorly understood. To investigate this, we performed single-cell RNA-sequencing analysis. Our findings revealed a highly immunosuppressive HGSOC microenvironment, characterized by the infiltration of regulatory T cells (Tregs). Trajectory analysis uncovered differentiation pathways of naïve Tregs, which either underwent activation and proliferation or experienced transcriptional instability. The predicted network of Treg-cell interactions, including those with tumor cells, facilitate Treg mobility, maturation, and reinforced their immunosuppressive function and persistence. Treg-mediated interactions predict the inhibition of CD8+ T cells and antigen-presenting cells, supporting tumor immune escape. Additionally, we observed that more immunogenic tumor conditions, marked by IFNγ production, likely contributed to Treg destabilization. Our findings underscore the pivotal role of Tregs in early immune evasion and provide valuable insights into potential therapeutic strategies targeting Treg cell activity and differentiation fate.

overall_design: scRNA-seq analysis was conducted on tumor lesions and PBMCs from two incidentally diagnosed stage- I HGSOC patients who underwent ovarian resection without prior chemotherapy treatment. scRNA-seq analysis of tumor lesions was conducted on FACS-sorted tumor-associated CD45+ immune cells and their CD45- tumor counterpart.

first: Joanna

last: Mikulak

first: Sara

last: Terzoli

first: Valentina

last: Cazzetta

first: Maurizio

last: D'Incalci

first: Sergio

last: Marchini

first: Domenico

last: Mavilio


title: Transcriptome analysis of Corynebacterium glutamicum ΔtrpP

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: For the establishment of synthetic microbial communities comprising complementary auxotrophic strains, transport processes for common goods are extremely important. Most auxotrophic strains reach wild type level growth with external supplementation of the required metabolite. One exception was the tryptophan auxotrophic strain Corynebacterium glutamicum ΔTRP ΔtrpP, which grew about 35% slower than the wild type in supplemented minimal medium. Corynebacterium glutamicum ΔTRP ΔtrpP lacks the whole tryptophan biosynthesis cluster (TRP) as well as the putative tryptophan transporter TrpP. We wanted to explore the role of TrpP in tryptophan transport or synthesis and to unravel the cause for the growth limitation of the auxotrophic strain.

platform_organism:
Gluconobacter oxydans
Escherichia coli
Bacillus subtilis
Corynebacterium glutamicum
Pseudomonas putida KT2440

overall_design: We performed a transcriptome comparison of WT ΔtrpP and WT in CGXII minimal medium with 2% (w/v) glucose as carbon source. The growth of these two strains was slightly different, thus we might detect altered genes as secondary effects due to the different growth rates. Overall, in WT ΔtrpP, 82 genes had an at least 2-fold reduced transcription and 18 genes had an at least 2-fold increased transcription (3 out of 4 experiments, p<0.05, signal to noise ratio >2). The trpP gene exhibited  the strongest  downregulated apparent gene expression, thereby confirming its deletion.

first: Rico

last: Zuchowski

first: Meike

last: Baumgart


title: An in vivo massively parallel platform for deciphering tissue-specific regulatory function [RNA]

city: Pittsburgh

first: Irene

middle: Miriam

last: Kaplow

address: 5000 Forbes Avenue, Gates-Hillman 7703

department: Computational Biology

institute: Carnegie Mellon University

summary:
Massively parallel reporter assays (MPRAs) have the potential to link differences in genome sequence, including genetic variants, to tissue-specific regulatory function. Whole-animal MPRA (WhAMPRA), where systemic intravenous AAV effectively transduces the plasmid MPRA library to mouse tissues.
This technology simultaneously determines the transcriptional functions of hundreds of enhancers in vivo across multiple tissues

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A plasmid libratry with 642 synthetic enhancers and variants each with 20 DNA barcodes was transduced into C57BL6/J mice or transfected into HMC3 cells.  DNA barcode transcripts from cDNA were then sequenced.

first: Ashley

last: Brown

first: Andreas

last: Pfenning


title: Characterization of the human HSC1L cell line with knockout of NF1

city: Minneapolis

first: David

middle: A.

last: Largaespada

state: MN

address: 2231 6th Street SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

summary: An RNA-seq study of altered gene expression in serum starved human HSC1L cells (an immortalized Schwann cell line) with and without knockout (KO) of NF1.  The analysis of the RNA-seq data led to the identification of a set of genes disregulated in the NF1 KO samples.

overall_design: For the knockouts, CRISPR/Cas9-mediated mutagenesis was used to target exon 10 of NF1 with a single sgRNA to generate indel mutations.  WT controls went through the CRISPR process, but did not result in changes to exon 10 of NF1.

first: S

last: Rathe

first: K

last: Williams

first: D


title: Nuclear AGO2 Supports Influenza A Virus Infectivity By Downregulating Type-I Interferon Response

status: Public on Mar 23 2025

city: Gothenburg

first: Aishe

last: Sarshad

address: Medicinaregatan 9c

country: Sweden

institute: Universiry of Gothenburg

summary: The role of Argonaute (AGO) proteins and the RNA interference (RNAi) machinery in mammalian antiviral response has been debated. Therefore, we set out to investigate how mammalian RNAi impacts influenza A virus (IAV) infection. We demonstrate that IAV infection triggers nuclear accumulation of AGO2, which is directly facilitated by p53 activation. Mechanistically, we show that IAV induces nuclear AGO2 targeting of TRIM71, a proposed AGO2 E3 ligase, and type-I interferon-pathway genes for silencing. Hence, the RNAi machinery is highjacked by the virus to evade the immune system and support viral replication. We demonstrate that the FDA approved drug arsenic trioxide prevents nuclear AGO2:p53 accumulation, thereby increasing interferon response and decreasing viral replication in vitro and in a mouse model in vivo. Our data indicates that targeting the AGO2:p53-mediated silencing of innate immunity may offer a promising strategy to mitigate viral infections.

overall_design: We performed AGO fPAR-CLIP to assess AGO proteins occupancy on RNA in cytoplasmic and nuclear lysates of HEK293 mock infected and PR8 infected cells.

first: Hsiang-Chi

last: Huang

first: Vivian

last: Lobo

first: Karin

last: Schön

first: Iwona

last: Novak

first: Jakub

last: Orzechowski Westholm

first: Carola

last: Fernandez

first: Angana

last: Patel

first: Clotilde

last: Wiel

first: Volkan

middle: I

last: Sayin

first: Dimitrios

middle: G

last: Anastasakis

first: Davide

last: Angeletti


title: Characterization of the human 143B cell line with knockout of SRGAP2

summary: An RNA-seq study of altered gene expression and mutations in human 143B cells (a TK- derivative of the HOS cell line) with and without knockout (KO) of SRGAP2.  The analysis of the RNA-seq data led to the identification of a set of genes downregulated in the SRGAP2 KO samples, as well as a couple of potential off-target CRISPR events.

overall_design: For the knockouts, CRISPR was used to target exon 4 of SRGAP2A, SRGAP2B, and SRGAP2C.  Variations in gene expression as well identification of acquired mutations were studied using various RNA-seq analysis tools.

first: T

last: Marko


title: An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation (CRISPRi screen)

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Microarray analysis of concentration-response transcriptomic changes induced by cannabichromene (CBC) in hepatocytes derived from human induced pluripotent stem cells (iPSCs)

status: Public on Mar 21 2025

first: Xiugong

last: Gao

summary: Transcriptomic changes measured by microarray in iPSC-derived hepatocytes after exposure to varying concentrations of CBC (0.1-40 μM) for 24 h.

overall_design: Cells were exposed to increasing concentrations of CBC (0.1-40 μM) for 24 h. Whole genome gene expression was characterized using Affymetrix GeneChip PrimeView Human Gene Expression Arrays. Three replicates were included for each concentration group including the control (0.0 μM).


title: Epigenetic Alteration of Smooth Muscle Cells Regulates Endothelin-Dependent Blood Pressure and Hypertensive Arterial Remodeling [km_mouse]

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: Long-standing hypertension (HTN) affects multiple organs and leads to pathologic arterial remodeling, which is driven by smooth muscle cell (SMC) plasticity. To identify relevant genes regulating SMC function in HTN, we considered Genome Wide Association Studies (GWAS) of blood pressure, focusing on genes encoding epigenetic enzymes, which control SMC fate in cardiovascular disease. Using statistical fine mapping of the KDM6 (JMJD3) locus, we found that rs62059712 is the most likely casual variant, with each major T allele copy associated with a 0.47 mmHg increase in systolic blood pressure. We show that the T  allele decreased JMJD3 transcription in SMCs via decreased SP1 binding to the JMJD3 promoter.  Using our unique SMC-specific Jmjd3-deficient murine model (Jmjd3flox/floxMyh11CreERT), we show that loss of Jmjd3 in SMCs results in HTN due to decreased EDNRB expression and increased EDNRA expression. Importantly, the Endothelin Receptor A antagonist, BQ-123, reversed HTN after Jmjd3 deletion in vivo. Additionally, single cell RNA-sequencing (scRNA-seq) of human arteries revealed strong correlation between JMJD3 and EDNRB in SMCs. Further, JMJD3 is required for SMC-specific gene expression, and loss of JMJD3 in SMCs increased HTN-induced arterial remodeling. Our findings link a HTN-associated human DNA variant with regulation of SMC plasticity, revealing targets that may be used in personalized management of HTN.

overall_design: mice were treated with saline or angiotensin with 14 days and then aortas were harvested and submitted for scrna-seq

first: Kevin

last: Mangum

first: Johann

last: Gudjonsson

first: Lam

middle: C

last: Tsoi


title: Deciphering shared molecular dysregulation across Parkinson's Disease variants using a multi-modal network-based data integration and analysis

city: Esch sur Alzette

first: Alise

last: Zagare

state: Belval

address: 7 Avenue des Hauts-Fourneaux

country: Luxembourg

institute: University of Luxembourg

summary: Parkinson’s disease (PD) is a progressive neurodegenerative disorder with no effective treatment. Advances in neuroscience and systems biomedicine now enable the use of complex patient-specific in vitro disease models and cutting-edge computational tools for data integration, enhancing our understanding of complex PD mechanisms. To explore common biomedical features across monogenic PD forms, we developed a knowledge graph (KG) by integrating previously published high-content imaging and RNA sequencing data of PD patient-specific midbrain organoids harbouring LRRK2-G2019S, SNCA triplication, GBA-N370S or MIRO1-R272Q mutation with publicly available biological data. Furthermore, we generated a single-cell RNA sequencing dataset of midbrain organoids derived from idiopathic PD patients (IPD) to stratify IPD patients towards genetic forms of PD.

overall_design: Single cell RNA sequencing of midbrain organoids generated from iPSC of idiopathic Parkinson's disease patients and healthy controls.

first: Irina

last: Balaur

first: Claudia

last: Saraiva

first: Adrien

last: Rougny

first: Matthieu

last: Gobin

first: Soumyabrata

last: Ghosh

first: Venkata

last: Satagopam

first: Jens

last: Schwamborn


title: RNA-seq analysis of concentration-response transcriptomic changes induced by cannabichromene (CBC) in hepatocytes derived from human induced pluripotent stem cells (iPSCs)

summary: Currently little is known about the safety of nonintoxicating cannabinoids such as cannabichromene (CBC). New approach methodologies (NAMs) based on bioinformatic analysis of high-throughput transcriptomic data are gaining increasing importance in risk assessment and regulatory decision-making of data-poor chemicals. In this study, we conducted a concentration response transcriptomic analysis of CBC in hepatocytes derived from human induced pluripotent stem cells (iPSCs). Biological functions and pathways impacted by CBC exposure were identified, including liver metabolism and cellular oxidative stress. In addition, a transcriptomic point-of-departure (tPoD) value was determined for CBC through benchmark concentration (BMC) analysis of the transcriptomic data. The present study demonstrates the potential utility of transcriptomic BMC analysis as a NAM for hazard assessment of data-poor chemicals, improves our understanding of the possible health effects of CBC, and provides important tPoD data that could contribute to inform human safety assessment of cannabinoid compounds.

overall_design: Cells were exposed to increasing concentrations of CBC (0.1-40 μM) for 24 h. Transcriptomic gene expression was characterizecd using RNA-seq. Three replicates were included for each concentration group including the control (0.0 μM).


title: An in vivo massively parallel platform for deciphering tissue-specific regulatory function [DNA]

first: Irene

last: Kaplow

state: PA

overall_design: A plasmid libratry with 642 synthetic enhancers and variants each with 20 DNA barcodes was transduced into C57BL6/J mice or transfected into HMC3 cells.  DNA barcodes from viral DNA were then sequenced.

first: Ashley

middle: R

last: Brown

first: Andreas

last: Pfenning


title: Whole genome inducible CRISPR KO screens for HIFa activity

city: Adelaide

first: David

last: Bersten

state: SA

address: Victoria Drive

department: Molecular and Biomedical Sciences

country: Australia

institute: The University of Adelaide

summary: Hypoxic inducible factors control the cellular response low oxygen by transcription regulation of gene programs. In order to understand the genes that control HIFa transcription factor regulated gene expression we generated dual fluorescent dFLASH-HIF reporter cells lines in HEK293T and U2OS cells to monitor HIFa activity. We then generated dox-inducible Cas9-TagBFP expressing reporter lines and performed 3 replicate genome wide KO gain- or loss- of function screens for HIF activity in U2OS  and HEK293T reporter cell lines using the Brunello sgRNA KO library (~79,000 sgRNA, covering ~19,000 genes). High throughput sequencing was used to identify sgRNAs in enriched vs library samples and sgRNA enrichment quantified by either DEseq2 or MAGeck.

overall_design: Library vs Low vs High HIF activity isolated based on DMOG induced Tomato expression in U2OS or HEK293 cell lines


title: Expression profile of mRNA involved in glucocorticoid-induced apoptosis in osteoblasts

city: Guiyang

first: hong

last: luo

address: 9 Beijing Road, Yunyan District

institute: Guizhou medical university

summary: Further study on the mechanism of glucocorticoid (GC) -induced apoptosis of osteoblasts (OB) is of great practical significance for the prevention and treatment of steroid-induced osteoporosis and osteonecrosis. However, the regulatory mechanism of alternative splicing in GC-induced OB apoptosis remains unclear. The aim of this study is to explore the role and mechanism of the splicing regulator serine/arginine-rich splicing factor 1 (SRSF1) in GC-induced OB apoptosis. OBs were treated with 0.4mg/ml hydrocortisone, the active form of GC, for 12 hours, and the mRNA expression profile was obtained by RNA-seq. The key splicing factor SRSF1 mediating GC-induced OB apoptosis was successfully screened, and its role and regulatory mechanism were further determined. Importantly, overexpression of SRSF1 was resistant to GC-induced OB apoptosis.

overall_design: In this study, OBs were treated under normal and GC conditions for 12 hours, with 3 biological replicates per group. The cells are then cleaved to collect total RNA.

first: Hong

last: Luo

first: Tao

last: Wang

first: Wuxun

last: Peng

first: Fei

last: Zhang


title: An in vivo massively parallel platform for deciphering tissue-specific regulatory function


title: A comprehensive analysis of microRNA alteration in ApoE(-/-) mice model of white adipose tissue injury induced by chronic intermittent hypoxia

status: Public on Mar 20 2025

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

summary: In the current study, we first used miRNA-seq technology to identify the miRNA expression profile of CIH-induced WAT dysfunction in a mouse model. Then, Gene Ontology (GO) and KEGG analyses were utilized to analyze the differential expression of mRNA targeting function, followed by RT-qPCR validation. Finally, we constructed a regulatory network for miRNA–mRNA based on the above results. This study contributes to a more detailed description of the WAT dysfunction mechanism associated to OSA.

overall_design: we established an apolipoprotein-deficient(ApoE-/-) CIH mouse model and identifed  differentially expressed miRNAs (DEmiRs) using miRNA_x0002_seq technology. With the help of Gene Ontology (GO) functional enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, we determined the biological functions of these DEmiRs. In addition, RT-qPCR was performed for further evaluation of the sequencing data. Finally, we constructed a conserved negative correlation (CNC) network to expound the relationship between miRNA and target genes.

first: Jinjie

first: Yaopeng

last: GUO

first: Meilin

last: Ji

first: Shu

last: Lin

first: Dexin

last: Liu

first: Qingshi

last: Chen


title: Rictor orchestrates β-catenin/FOXO balance by maintaining redox homeostasis during development of ovarian cancer

city: wuhan

first: xuejiao

last: zhao

state: hubei

address: jiefang avenue 1095#

institute: tongji hospital

summary: Rictor/mTORC2 has been demonstrated to have important roles in cancer development and progression in a number of solid and hematologic malignancies. However, little is known about the role of Rictor/mTORC2 in ovarian cancer pathophysiology. Herein, using conditional Rictor knockout mice, we were able to demonstrate that Rictor deletion disrupted glutathione metabolism through Nrf2-dependent, AKT-independent signaling and induced intracellular oxidative stress during the malignant transformation of Kras/Pten-mutant ovarian surface epithelial cells. Elevated reactive oxygen species and activated FOXO3a in Rictor-deleted cells strikingly shifts the functional interaction of β-catenin from TCF to FOXO3a, which strongly inhibits classical Wnt/β-catenin signaling. Our findings emphasize a pivotal role of Rictor in orchestrating crosstalk between the PI3K/AKT and Wnt/β-catenin signaling in the development of ovarian cancer.

overall_design: We separated OSE cells from ovaries by digestion,then we infected the cultured OSE cells with AdCre-eGFP to activate KrasG12D and delete Pten as well as Rictor.The cultured WT-OSE, KP-OSE and KPR-OSE cells were then used for gene-expression profiling analysis.

first: Xuejiao

last: Zhao


title: Human long noncoding RNA, VILMIR, is induced by major respiratory viral infections and modulates the host interferon response

city: Raleigh

first: Xinxia

address: 1060 William Moore Drive

institute: North Carolina State University

summary: Long noncoding RNAs (lncRNAs) are a newer class of noncoding transcripts identified as key regulators of biological processes. Here we aimed to identify novel lncRNA targets that play critical roles in major human respiratory viral infections by systematically mining large-scale transcriptomic datasets. Using bulk RNA-sequencing (RNA-seq) analysis, we identified a previously uncharacterized lncRNA, named virus inducible lncRNA modulator of interferon response (VILMIR), that was consistently upregulated after in vitro influenza infection across multiple human epithelial cell lines and influenza A virus subtypes. VILMIR was also upregulated after SARS-CoV-2 and RSV infections in vitro. We experimentally confirmed the response of VILMIR to influenza infection and interferon-beta (IFN-β) treatment in the A549 human epithelial cell line and found the expression of VILMIR was robustly induced by IFN-β treatment in a dose and time-specific manner. Single cell RNA-seq analysis of bronchoalveolar lavage fluid (BALF) samples from COVID-19 patients uncovered that VILMIR was upregulated across various cell types including at least five immune cells. The upregulation of VILMIR in immune cells was further confirmed in the human T cell and monocyte cell lines, SUP-T1 and THP-1, after IFN-β treatment. Finally, we found that knockdown of VILMIR expression reduced the magnitude of host transcriptional responses to both IFN-β treatment and influenza A virus infection in A549 cells. Together, our results show that VILMIR is a novel interferon-stimulated gene (ISG) that regulates the host interferon response and may be a potential therapeutic target for human respiratory viral infections upon further mechanistic investigation.

overall_design: To investigate the functional role of VILMIR during the human antiviral response, VILMIR expression was repressed using CRISPR interference. A549 cells expressing dCas9-KRAB and GFP were transduced with two guide RNAs (gRNAs) targeting the 5’ end of VILMIR (VILMIRg1 and VILMIRg2) along with a negative control gRNA targeting GFP expression (Ctrl). In addition, a STAT1 knockdown cell line (STAT1g1) was included for comparison, as STAT1 is well-known to impact the host interferon and antiviral response. All cell lines were treated with or without influenza A virus California/04/2009 (H1N1) for 18 hours in triplicate. RNA-sequencing and differential expression analysis was then performed to identify the impact of VILMIR knockdown on the host transcriptional response to H1N1 infection.

first: Kristen

last: John

first: Ian

last: Huntress

first: Ethan

last: Smith

first: Hsuan

last: Chou

first: Tammy

middle: S

last: Tollison

first: Sergio

last: Covarrubias

first: Elisa

last: Crisci

first: Susan

last: Carpenter


first: Aishe

last: Sarshad

overall_design: We performed gene expression profiling of HEK293 cells with or without PR8 virus infection via RNA sequencing in 3 biological replicates, and carried out differential expression analysis between infected and non-infected cells.

first: Hsiang-Chi

last: Huang

first: Vivian

last: Lobo

first: Karin

last: Schön

first: Iwona

last: Novak

first: Jakub

last: Orzechowski Westholm

first: Carola

last: Fernandez

first: Angana

last: Patel

first: Clotilde

last: Wiel

first: Volkan

last: Sayin

first: Dimitrios

last: Anastasakis

first: Davide

last: Angeletti


title: Injectable ECM-mimetic dynamic hydrogels abolish ferroptosis-induced post-discectomy herniation through in-situ delivery of nucleus pulposus progenitor cell-derived exosomes [miRNA-Seq]

status: Public on Mar 19 2025

city: Chongqing

first: Wenkai

last: Wang

state: Chongqing

address: Gaotanyan main street

institute: Army Medical University

summary: The discectomy-induced ferroptosis stress on nucleus pulposus cells (NPCs) is a major cause for postoperative lumbar disc herniation (LDH) recurrence and intervertebral disc degeneration (IDD). Surprisingly, we discovered that nucleus pulposus progenitor cells (NPPCs) could transmit their ferroptosis-resistant phenotype to recipient NPCs through exosome-dependent cell-cell communication while identifying miR-221-3p as the primary anti-ferroptosis effector molecule therein. Based on these findings, we first developed a synthetically-tailored NPPC-derived exosomes with enhanced miR-221-3p expression and NPC uptake capacity through molecular and cellular engineering, which were then integrated into an injectable hydrogel based on extracellular matrix (ECM) analogues. The ECM-mimetic hydrogel (HACS) serves as a biomimetic filler for the post-operative care of herniated discs, which could be facilely injected into the discectomy-established nucleus pulposus (NP) cavity for localized treatment. HACS-mediated in-situ exosome release in the NP cavity enabled marked ferroptosis inhibition in NPCs that not only prevented LDH recurrence but also reversed the IDD symptoms, leading to robust restoration of NP structure and functions. This study offers a promising approach for the treatment of herniated discs with translational potential.

overall_design: miRNA sequencing analysis performed on nucleus pulposus progenitor cell-derived exosomes and nucleus pulposus cell-derived exosomes.


title: Therapeutic Potential of Emricasan, a Pan-Caspase Inhibitor, in Reducing Cell Death and Extracellular Matrix Accumulation in Fuchs Endothelial Corneal Dystroph

status: Public on Mar 22 2025

city: Kyotanabe

first: Taisuke

last: Numao

state: Kyoto

department: Department of Biomedical Engineering, Faculty of Life and Medical Sciences

country: Japan

institute: Doshisha University

summary: This RNA-Seq dataset captures transcriptomic changes in the corneal endothelium of Col8a2Q455K/Q455K mice, a model of early-onset Fuchs endothelial corneal dystrophy (FECD), following treatment with the pan-caspase inhibitor emricasan. The experiment compared corneal endothelial cells from 28-week-old mice receiving twice-daily 0.1% emricasan eye drops (n=3) versus vehicle control (n=3) from 8 to 28 weeks of age. Differential expression analysis identified 1,345 differentially expressed genes (455 upregulated, 890 downregulated; |Log₂FC| ≥ 1.0, P < 0.05) in emricasan-treated versus control mice. Gene ontology and pathway analyses revealed significant changes in pathways related to ECM production, cell death, and cellular morphology. These transcriptomic changes correlate with the observed improvement in endothelial cell density, hexagonality, and reduction in guttae formation in emricasan-treated mice, providing molecular insights into how caspase inhibition may provide therapeutic benefit in FECD by modulating both apoptotic and ECM production pathways.

overall_design: RNA-seq analysis of corneal endothelium from Col8a2Q455K/Q455K mice treated with 0.1% emricasan eye drops vs vehicle control

first: Sohya

last: Fujimoto

first: Mako

last: Endo

first: Shigehito

last: Tonomura

first: Fuuga

last: Tsuji

first: Hirotaka

last: Haraguchi

first: Kanna

last: Hasegawa

first: Ayaka

last: Izumi

first: Theofilos

last: Tourtas

first: Ursula

last: Schlötzer-Schrehardt

first: Friedrich

last: Kruse

first: Yuki

last: Oyama

first: Masahito

last: Ikawa

first: Albert

last: Jun

first: Noriko

last: Koizumi

first: Naoki

last: Okumura


title: Microarray analysis of concentration-response transcriptomic changes induced by cannabinol (CBN) in hepatocytes derived from human induced pluripotent stem cells (iPSCs)

city: Laurel

first: Xiugong

last: Gao

address: 8301 Muirkirk Rd

institute: US FDA

summary: Transcriptomic changes measured by microarray in iPSC-derived hepatocytes after exposure to varying concentrations of CBN (0.1-20 μM) for 24 h.

overall_design: Cells were exposed to increasing concentrations of CBN (0.1-20 μM) for 24 h. Whole genome gene expression was characterizecd using Affymetrix GeneChip PrimeView Human Gene Expression Arrays. Three replicates were included for each concentration group including the control (0.0 μM).


title: m6A modification regulates cell proliferation via reprogramming the balance between glycolysis and pentose phosphate pathway

city: Guangzhou

first: JianFei

last: Xi

address: 135 Xingang West Road

institute: Sun Yat-sen University

summary: N6-methyladenosine (m6A) stands as the predominant modification in eukaryotic mRNA and is involved in various biological functions. Aberrant m6A has been implicated in abnormal cellular phenotypes, including defects in stem cell renewal and tumorigenesis. However, the precise effects of m6A on cell proliferation and the underlining mechanism of metabolic gene regulation remain incompletely understood. Here, we established a cellular environment with low-m6A levels and observed a severe impairment of cell proliferation. Mechanistic studies revealed that the depletion of m6A on TIGAR mRNA led to increased expression, subsequently inhibiting glycolysis while promoting the pentose phosphate pathway (PPP). A genome-wide CRISPR-Cas9 screen identified extensive genes involved in cell proliferation that are affected by m6A modification, with G6PD emerging as a key regulator. Integration of gene expression and survival data from LIHC patients suggested specific subsets with elevated G6PD expression may exhibit enhanced responsiveness to tumor growth inhibition through m6A suppression. Our findings elucidate the critical role of m6A in cellular metabolic regulation, particularly in the metabolic reprogramming of cell proliferation, offering new insight for cancer therapy.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for HEK293T cells treated by DMSO and 5uM STM2457 for 72h respectively.
To investigate whether m6A inhibitor STM2457 has any preference on specific gene, we utilized MeRIP-seq assay to determine the m6A alteration patterns in HEK293T cells.
We devised a comprehensive CRISPR-centric genetic screen to identify genes that govern cell growth suppression in a low m6A environment. Using lentivirus delivery, we introduced a single guide RNA (sgRNA) library targeting 18,360 protein-encoding genes into HEK293T cells constitutively expressing Cas9. Following a two-week treatment period with either DMSO or STM2457, we employed next-generation sequencing (NGS) to uncover the variation in sgRNA distribution between samples.
To verify the identified genes from our CRISPR screen, we initiated a validation process for a subset. Dual sgRNAs for each gene were transfected into HEK293T cells, and PCR amplification of editing sites followed by NGS sequencing confirmed the editing efficiency.

first: Jianfei

first: Biaodi

last: Liu

first: Guorun

last: Tang

first: Zehui

last: Ren

first: Zhang

last: Zhang

first: Guanzhen

last: Luo


title: Characterization of the Tumor Immune Microenvironment in Gastric Cancer by Single-Cell RNA Sequencing Analysis

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

institute: Kyushu University

summary: Gastric cancer tissues were obtained from patients who underwent gastrectomy at Kyushu University Hospital, and single-cell RNA sequencing was performed on the collected samples.

overall_design:
We performed scRNA-seq analysis from 38 gastric cancers and 16 adjacent normal gastric mucosae. In one case (G77T), no residual cancer cells were observed in the resected specimen.
This study includes samples re-analyzed from GSE201347, GSE231539, and GSE254188. A full list of all re-analyzed samples and their associated SRA, BioSample, and BioProject accession IDs are available at the foot of this record.

first: Kenoki

last: Ohuchida