title: snRNAseq of Cpt1a-conditionally-depleted murine kidneys aged with high fat diet

city: St. Louis

first: Steven

last: Funk

address: 660 S. Euclud Ave

institute: Washington University

summary: To compare the snRNA seq transcriptional profile in renal tubule cells after conditional deletion of Cpt1a to floxed littermate controls, in mice fed a high fat diet for 2 years, and to compare mice aged 2  years with high fat diet to young mice.

overall_design:
Cpt1a-floxed mice and mice conditionally depleted of Cpt1a with Pax8-rTTA;tetO-Cre transgenes aged 2 years with high fat diet or aged 3 months were analyzed and compared by snRNA seq.

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

last: Gewin


title: Single-Cell Sequencing Unveils Distal and Proximal Features of Induced Pluripotent Stem Cell-Derived Intestinal Organoids and cAMP’s role in enhancing multicellularity intestinal lineage specification.

status: Public on Jun 16 2025

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

country: USA

institute: Center for Regenerative Medicine

type: Expression profiling by high throughput sequencing

summary: This study aims to advance intestinal organoid models by characterizing mesenchyme-free regional-specific induced pluripotent stem cell (iPSC)-derived human intestinal organoids (HIOs) at single-cell resolution and investigating the impact of cyclic AMP (cAMP) on intestinal differentiation lineage specification.

overall_design: We evaluated various culture conditions' effects on iPSC-derived HIO differentiation by performing single-cell RNA sequencing (scRNA-seq) on proximal HIOs (n=2), distal HIOs cultured with (n=2), and without cAMP (n=2). Canonical marker analysis and validation against published scRNA-seq datasets were conducted. Immunohistochemistry and immunofluorescence assays supported our findings.

first: Elizabeth

middle: Y

last: Flores

first: Gustavo

last: Mostoslavksy


title: When glucocorticoid receptor meets the mineralocorticoid receptor in human cells

city: Research Triangle Park

first: Tatsuya

last: Sueyoshi

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

summary: Glucocorticoids are widely used to treat a variety of inflammatory diseases.  Mechanistically glucocorticoid ligands induce glucocorticoid receptor (GR) homodimerization and regulation of gene expression. Here we show that GR and mineralocorticoid receptor (MR) form molecular complexes with distinct transcriptional responses that alter the biological roles of GR.  MR inhibited GR interaction with genomic DNA and diminished glucocorticoid-regulated gene expression as well as suppressed cell apoptosis induced by GR signaling.

overall_design: Cell lines expressing GR, MR, or GR + MR were developed using human U-2OS cell line.  These cell lines were treated with dexamethasone (1 nM or 10 nM) or aldosterone (1 nM) and transcriptomes in the cells were compared by RNAseq analyses.  GR and MR functional interaction for the gene regulation was observed.

first: Maria

middle: G

last: Petrillo

first: Xiaojiang

last: Xu

first: Sara

middle: A

last: Grimm

first: John

last: Cidlowski


title: Single-nucleus-RNA-sequencing data from isolated glomeruli from 4-week-old podocyte-specific YAP or TAZ knockout mice

city: Cologen

first: Lioba

last: Ester

address: Joseph Stelzmann Str. 26

country: Germany

institute: University of Cologne

summary: YAP and TAZ are paralougous mechanotranducers and act as co-transcription factors pivotal for podocyte homeostasis. We used single nucleus transcriptomic data from podocyte-specific YAP- or TAZ-deficient mice to investigate their unique and shared roles in podocyte health and disease.

overall_design: Glomeruli from 4-week old podocyte-specific YAP-deficient mice with early - or late-onset of proteinuria (2 mice each), podocyte-specific TAZ-deficient mice (2 mice) and wildtype mice (2 mice) were isolated. Nuclei from the isolated glomeruli were used for single nucleus RNA sequencing.

first: Eva

last: Wiesner

first: He

last: Chen

first: Michel

last: Ventzke

first: Paul

last: Diefenhardt

first: Amrei

middle: M

last: Mandel

first: Helena

last: Petereit

first: Francesca

last: Fabretti

middle: T

last: Brinkkoetter

first: Thomas

last: Benzing

first: Sandra

last: Habbig

first: Martin

last: Kann

first: Inês

last: Cabrita

first: Bernhard

last: Schermer


title: Nucleus-localized S100A9 triggers senescence of human amnion fibroblasts as a heterochromatin buster at parturition

city: Shanghai

first: Wangsheng

last: Wang

state: Please Select

address: 845 Lingshan Rd.

country: China

institute: Shanghai Jiao Tong University

summary: Aging in the amnion is considered to trigger and intensify inflammation for the initiation of labor. However, the inducers of amnion cell senescence await to be identified. Here, we unexpectedly observe that S100A9, a classical cytokines, also localizes in the nucleus of human amnion fibroblasts (hAFs), and reveal that nucleus-localized S100A9 (nS100A9) abundance in hAFs increases at parturition and that nS100A9 triggers hAFs senescence. Mechanistically, nS100A9 interacts with heterochromatin proteins, preventing them from binding and maintaining condensed heterochromatin, resulting in heterochromatin erosion, LINE1 de-repression, and type I interferon response activation via the cGAS-STING pathway. Moreover, we demonstrate that dephosphorylation of S100A9 at Thr 113 is required for its nuclear translocation. Mouse studies show that intra-amniotic injection of nS100A9 induces preterm birth along with LINE1 activation, which is blocked by reverse-transcriptase inhibitor. Together, these findings highlight a novel role for S100A9 as a heterochromatin buster that triggers hAFs aging at parturition.

overall_design: RNA sequencing of  human amnion fibroblasts treated with or without nS100A9 overexpression

first: Wang-sheng

first: Fan

last: Zhang


title: SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT. [CUT&Run]

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Atypical teratoid rhabdoid tumor (ATRT) is a highly aggressive brain tumor of childhood with a poor overall survival. The salient molecular feature of ATRT is the loss of SMARCB1 which results in epigenetic dysregulation of the genome. SMARCB1 loss affects lineage commitment and differentiation by controlling gene expression. We hypothesized that additional epigenetic factors co-operate with SMARCB1 loss to control cell self-renewal and drive ATRT. We identified SIRT2 as a primary dependency in ATRT. Using a combination of RNA-seq, CUT&RUN and single RNA sequencing in model systems ATRT, we observed genome-wide reorganization of active chromatin and significantly changes in genes expression in ATRT cells with genetic (with shRNA) or chemical (with Tenovin or Thiomyristoyl (TM)) SIRT2 deactivation. Single-cell RNA transcriptome analysis of xenograft tumors revealed the elimination of tumor cells expressing stem cell genes and expansion of tumor cells expressing differentiated genes in vivo. Furthermore, SIRT2 inhibition induced apoptosis, decreased tumor growth and prolonged survival in orthotopic xenograft models. In summary we demonstrated that SIRT2 inhibition is a molecular vulnerability in SMARCB1-deleted tumors with therapeutic potential.

overall_design: CUT&RUN data comparing peak height in Atypical teratoid rhabdoid tumor (ATRT) BT16 cells treated with Thiomyristoyl (TM) and DMSO. Thiomyristoyl was bought from MedChem express (HY-101278) and reconstituted in DMSO. BT16 ATRT cells were treated with 20 uM of TM for 24 hours followed by CUT&RUN assay with antibodies for H3K4me (positive control; EpiCypher #13-0041), H3K27ac (Cell signaling #8173), HeK27me3 (Cell signaling#, 9733), IgG (negative control; EpiCypher#13-0042K). For bulk RNA-seq experiment BT16 ATRT cells were treated with DMSO or 30uM TM for 72hrs. RNA-Seq data comparing gene expression in pediatric ATRT treated with TM vs DMSO. Single-cell RNA sequencing on GFP-positive BT16ATRT cells. To study the impact of TM on differentiation in vivo, we performed single-cell RNA sequencing on GFP-positive BT16 ATRT cells. Cell were growing in mice cerebellum and treatment started when tumors were established. Mice were treated with either TM (50 mg/kg IP 3/week for 4 weeks) or Vehichle control.

first: Irina

last: Alimova

first: Dong

first: John

last: Desisto

first: Senthilnath

last: Lakshmanachetty

first: Eric

last: Prince

first: Rajeev

last: Vibhakar


title: SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT. [RNA-Seq]


title: Mineralocorticoid receptor co-expression effect on ligand-induced glucocorticoid receptor interaction with the genome in human cell line

city: Durham

last: Cidlowski

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Our previous results observed glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) physical and functional interactions.  RNAseq study (GSE163506) revealed that MR blunted GR ligand-dependent gene regulation in human cell lines.  In the current study, we developed U-2 OS cell line-derived cells constitutively expressing GR or MR plus GR.  Then, we compared GR – genome interaction before and after dexamethasone treatment.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for glucocorticoid receptor in GR clell and MR/GR cell

first: Maria

last: Petrillo

first: Molly

middle: E

last: Cook

first: Jianying

last: Li

first: Xiaojiang

last: Xu

first: Tatsuya

last: Sueyoshi


title: SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT.

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

overall_design: Refer to individual Series


title: Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [CUTnRUN]

first: Paul

last: Wade

department: Laboratory of Molecular Carcinogenesis

summary: The mechanistic details by which pioneer transcription factors interact with partner transcription factors and chromatin modification/remodeling enzymes to activate enhancers remains an emerging area of study. Here, we utilize inducible expression of the pioneer factor GATA3 and study cofactor association and structural alterations in local chromatin.  ATAC-seq analysis and footprinting revealed co-occurrence of GATA3 with other transcription factors, including AP-1, in newly accessible chromatin. GATA3 and AP-1 co-localize at primed enhancers with p300 and BRG1 where nucleosome positioning is responsive to GATA3 location, not to AP-1. Genetic inhibition of AP-1 binding alters chromatin opening at some, but not most, GATA3-bound loci. Pharmacologic inhibition of SWI/SNF ATPase function results in loss of GATA3-dependent chromatin accessibility, binding, and alterations in local chromatin architecture. We conclude that GATA3-dependent gains in chromatin accessibility require chromatin remodeling and that accessibility at some loci is facilitated by a partner transcription factor, in this case AP-1.

overall_design: Doxycycline (dox) inducible wildtype (wt; 1-444aa) and TA1del (ta1; 126-444aa) GATA3 cell lines were generated in SUM159PT basal breast cancer cell line. CUT&RUN was performed for histone modifications, transcription factor binding and chromatin remodeler binding in +/- DOX conditions and +/- inhibitiors of transcription factor binding  (AFOS) or chromatin remodeling (BRM014).

first: Krystal

last: Orlando


title: Muscle stem cells in Duchenne muscular dystrophy exhibit molecular impairments and altered cell fate trajectories impacting regenerative capacity

city: Montreal

first: Natasha

middle: C

last: Chang

state: Québec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

summary: Satellite cells are muscle-resident stem cells that maintain and repair muscle. Increasing evidence supports the contributing role of satellite cells in Duchenne muscular dystrophy (DMD), a lethal degenerative muscle disease caused by loss of dystrophin protein. We used single cell RNA-sequencing (scRNA-seq) to determine how dystrophin deficiency impacts satellite cell heterogeneity and function. scRNA-seq was performed in satellite cells from mdx and D2-mdx DMD mouse models. DMD satellite cells were enriched in myogenic progenitor clusters and a unique DMD enriched cluster. DMD satellite cells and myogenic progenitors exhibited distinct impairments, including cell death and senescence, respectively. Moreover, dystrophic satellite cells express an impaired myogenic differentiation gene signature and are stalled in their differentiation capacity. We found that inducing autophagy led to enhanced differentiation of dystrophic progenitors. Our findings provide insight into the molecular pathways that are dysregulated in DMD satellite cells and suggest molecular targets to enhance their regenerative capacity.

overall_design: Satellite cells from DMD (mdx and D2-mdx) and their WT counterpart (B10 and DBA) mice were isolated by Fluorescence-activated cell sorting (FACS) (ITGA7+/VCAM+/Lin-) and subjected to single cell transcriptomic sequencing

first: Jules

last: Granet

first: Rebecca

last: Robertson

first: Alessio

last: Cusmano

first: Romina

middle: L

last: Filippelli

first: Tim

middle: O

last: Lorenz

first: Shulei

first: Moein

last: Yaqubi

first: Jo Anne

last: Stratton


title: SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT [bulk RNA-seq]

first: Etienne

last: Danis

summary: Background.  Atypical teratoid rhabdoid tumor (ATRT) is a highly aggressive brain tumor of childhood with a poor overall survival. The salient molecular feature of ATRT is the loss of SMARCB1 which results in epigenetic dysregulation of the genome. SMARCB1 loss affects lineage commitment and differentiation by controlling gene expression. We hypothesized that additional epigenetic factors co-operate with SMARCB1 loss to control cell self-renewal and drive ATRT. We identified SIRT2 as a primary dependency in ATRT. Using a combination of RNA-seq, CUT&RUN and single RNA sequencing in model systems ATRT, we observed genome-wide reorganization of active chromatin and significantly changes in genes expression in ATRT cells with  genetic (with shRNA) or chemical (with Tenovin or Thiomyristoyl (TM) ) SIRT2 deactivation.    Single-cell RNA transcriptome analysis of xenograft tumors revealed the elimination of tumor cells expressing stem cell genes and expansion of tumor cells expressing differentiated genes in vivo. Furthermore, SIRT2 inhibition induced apoptosis, decreased tumor growth and prolonged survival in orthotopic xenograft models. In summary we demonstrated that SIRT2 inhibition is a molecular vulnerability in SMARCB1-deleted tumors with therapeutic potential.

overall_design: Bulk RNA-Seq data comparing gene expression in pediatric Atypical teratoid rhabdoid tumor (ATRT) BT16 cells treated with Tenovin (1um of Tenovin for 72 hours) and DMSO.  Bulk RNA-Seq data comparing gene expression in pediatric ATRT with SIRT2 knockdown(shSIRT) vs. vector control shRNA (shNULL).

first: Irina

last: Alimova

first: Dong

last: Wang

first: John

last: Desisto

first: Danis

last: Etienne

first: Senthilnath

last: Lakshmanachetty

first: Eric

last: Prince

first: Rajeev

last: Vibhakar


title: The oncogenic microRNA miR-222 promotes human LINE-1 retrotransposition

city: Jerusalem

first: Daniel

middle: S

last: Goldenberg

state: Select State

address: Kiryat Hadassah, P.O.B. 12000

department: The Goldyne Savad Institute of Gene and Cell Therapy

country: Israel

institute: Hadassah University Hospital

summary: The Long Interspersed Element-1 (LINE-1) contributes significantly to carcinogenesis and to tumor heterogeneity in many cancer types, including hepatocellular carcinoma (HCC), by its autonomous retrotransposition (RTP) and by its ability to retrotranspose some non-autonomous transposable elements. Previously, multiple proteins and a few microRNAs (miRs) were described as regulators of LINE-1 RTP. Here, we demonstrate that miR-222, which is oncogenic in HCC, promotes LINE-1 RTP in human HCC and some other cell lines in vitro, and that both miR-222-3p and miR-222-5p activate LINE-1 RTP in a cell type-specific manner. We generated miR-222-knockout mutants of the Huh7 and FLC4 HCC cell lines, and performed RNA-seq analysis of Huh7/miR-222-knockout cells and global proteomics analysis of both Huh7 and FLC4 miR-222-knockout mutants. We demonstrate that miR-222 decreases let-7c expression in both Huh7 and FLC4 cells, and that this decrease contributes to promotion of LINE-1 RTP by miR-222 in Huh7 cells.

overall_design: RNA-seq was performed on the stable single clones of Huh7 cellsgenerated using the CRISPR-Cas9 system: Huh7/Cas9/miR-222-KO versus similar control clones expressing a control gRNA that has no targets in the human genome (four clones in each group).

first: Jonathan

last: Monin

first: Tomer

last: Friehmann


title: HDAC1 acts as tumor suppressor in ALK-positive anaplastic large-cell lymphoma: Implications for HDAC inhibitor therapy [RNA-Seq]

city: Vienna

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

country: Austria

institute: Medical University of Vienna

summary: Histone deacetylases (HDACs) are frequently deregulated in cancer, and several HDAC inhibitors (HDACi) have gained approval for treating peripheral T-cell lymphomas. Here, we investigated the effects of genetic or pharmacological HDAC inhibition on NPM-ALK positive anaplastic large cell lymphoma (ALCL) development to elucidate potential contraindications or indications for the use of HDACi for the treatment of this rare T-cell lymphoma. Short-term systemic pharmacological inhibition of HDACs using the class I-specific HDACi Entinostat in a premalignant ALCL mouse model postponed or even abolished lymphoma development, despite high expression of the NPM-ALK fusion oncogene. To further disentangle the effects of systemic HDAC inhibition from thymocyte intrinsic effects, conditional genetic deletions of highly homologous class I HDAC1 and HDAC2 enzymes were employed.  In sharp contrast to the systemic inhibition, T cell-specific deletion of Hdac1 or Hdac2 in the ALCL mouse model significantly accelerated NPM-ALK-driven lymphomagenesis, with Hdac1 loss having a more pronounced effect. Integration of gene expression and chromatin accessibility data revealed that Hdac1 deletion selectively perturbed cell type specific transcriptional programs, crucial for T cell differentiation and signaling. Moreover, multiple oncogenic signaling pathways, including PDGFRB signaling, were highly upregulated. The accelerated lymphomagenesis primarily depended on the enzymatic activity of HDAC1, as the expression of a catalytically inactive HDAC1 protein showed similar effects to the complete knockout. Our findings underscore the tumor-suppressive function of HDAC1 and HDAC2 in T cells during ALCL development, however systemic pharmacological inhibition of HDACs is still a valid treatment strategy, which could potentially improve current therapeutic outcomes.

overall_design: We used transgenic mice in which the human oncoprotein NPM-ALK was expressed under the T cell-specific Cd4 promoter.  NPM-ALK mice were further crossed with Cd4-CRE+ mice with floxed exons 6 of the Hdac1 gene, which produced T cell-specific NPM-ALK transgenic mice with an additional Hdac1  knockout (NPM-ALK Hdac1KO). Differential gene expression was done using RNA-sequencing of tumor tissues from biological replicates (n=4) of NPM-ALK versus NPM-ALK Hdac1KO

first: Masa

last: Zrimsek

first: Anna

last: Malzer

first: Carlos

middle: U

last: Malla

first: Raheleh

last: Sheibani-Tezerji


title: Effect of vitamin D and K on osteoclast differentiation of bone marrow derived macrophages induced by RANKL

city: Guangzhou

first: Yang

last: Zhao

state: Guangdong

address: No. 253 Industrial Avenue

institute: Zhujiang hospital of southern medical university

summary: As essential nutrients for the human body, both vitamins D and K play important roles in bone health. However, little is known about the combined effect of vitamins D and K on osteoarthritis-related subchondral bone osteoclastogenesis. In this study, we aim to elucidate the underlying mechanisms of their synergistic effect in the RANKL-induced osteoclastogensis in vitro model.

overall_design: To investigate the combined effect of vitamin D and K on osteoclast differentiation, we isolated BMDMs from C57BL/6 mice and treated them with RANKL and vitamin D and K. Comparative gene expression profiling analysis was then conducted using data obtained from RNA-sequencing of 3 different groups of cells.


title: HDAC1 acts as tumor suppressor in ALK-positive anaplastic large-cell lymphoma: Implications for HDAC inhibitor therapy [ATAC-Seq]

overall_design: We used transgenic mice in which the human oncoprotein NPM-ALK was expressed under the T cell-specific Cd4 promoter.  NPM-ALK mice were further crossed with Cd4-CRE+ mice with floxed exons 6 of the Hdac1 gene, which produced T cell-specific NPM-ALK transgenic mice with an additional Hdac1  knockout (NPM-ALK Hdac1KO). ATAC-seq was done using nuclei of tumor tissues from biological replicates (n=4) of NPM-ALK versus NPM-ALK Hdac1KO mice


title: Transcriptomes of UFMylation gene knockdown in mouse and human cells treated with hypoxia

city: Dongguan

first: Zhou

last: Junzhi

address: Xincheng Road 1#, Songshan Lake

institute: Guangdong Medicine University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: C1q reprograms innate immune memory [ChIP-seq]

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: Innate immune memory, also called trained immunity, is a metabolic and epigenetically regulated process that enables innate immune cells to recalibrate their inflammatory reactivity in response to pathogenic or endogenous stimuli. In addition to its function in host defense, trained immunity contributes to diverse immune-mediated diseases. We discovered that complement component 1q (C1q) is an effective modulator of innate immune memory, potently suppressing the responsiveness of myeloid cells. We found that C1q leads to profound reprogramming of myeloid cell metabolism, particularly glycolysis, and exerts control over the transcriptional regulation of important metabolic and inflammatory genes. We corroborate our findings by identifying single-nucleotide polymorphisms close to the C1q gene that are linked to induction of trained immunity in healthy volunteers. Our results reveal a novel immunomodulatory role for C1q and provide evidence of a molecular interaction between the complement system and innate immune memory. These findings expand our understanding of innate immune memory and provide a promising new target for therapeutic intervention.

overall_design: Investigate the effects of C1q stimulation on the epigenome of monocytes. Therefore, we stimulated PBMCs with C1q or RPMI medium as control (n=4), and isolated monocytes on day 6 for a comprehensive genome-wide analysis of H3K4me3 through chromatin immunoprecipitation sequencing (ChIP-seq)

first: Inge

last: Jonkman

first: Maaike

last: Jacobs

first: Yutaka

last: Negishi

first: Julia

middle: I

last: van Heck

first: Vasiliki

last: Matzaraki

middle: H

first: Marijke

last: Baltissen

first: Michiel

last: Vermeulen

first: Zahi

last: Fayad

first: Abraham

middle: J

last: Teunissen

first: Willem

last: Mulder

first: Luuk

middle: B

last: Hilbrands

first: Leo

last: Joosten

first: Mihai

last: Netea

first: Musa

last: Mhlanga

first: Nils

last: Rother

first: Raphaël

last: Duivenvoorden


title: C1q reprograms innate immune memory [RNA-seq]

first: Joost

last: Martens

overall_design: Investigate the effects of C1q stimulation on the transcriptome of monocytes. Therefore, we stimulated PBMCs with C1q or RPMI medium as control (n=3), and isolated monocytes on day 1 for RNA-sequencing analysis


title: Cuttag sequencing revealed the regulatory targets of transcription factor c-MYC in human chondrocytes

first: xu

last: wu

address: 83 Fenyang Road

institute: EENT Hospital, Fudan University

summary: The transcription factor MYC can promote chondrocyte differentiation in previous studies, but its target remains unclear. We used cutt sequencing to explore its regulatory targets.

overall_design: Chondrocytes were isolated from human auricular cartilage and cultured in vitro. Then, cuttag-seq was performed on P1  and P3 passage of cells.


title: Impact of nifedipine and tannin acid co-culturing on P3 chondrocytes

summary: Tannic acid(TA) and nifedipine(Nif) may influence genetic changes in chondrocytes cultured in vitro, and here we use RNAseq to explore the effects on the transcriptome

overall_design: Chondrocytes were isolated from human auricular cartilage and cultured in vitro. Then, RNA sequencing was performed on 3rd passage (P3) of cells.


title: Changes in chromatin accessibilityof chondrocytes  identified by ATAC-seq in vitro

summary: Chromatin accessibility change of chondrocytes in vitro remains unclear. We performed ATAC-seq of P1,P3, and P6 cells in vitro to explore chromatin accessibility change.

overall_design: Chondrocytes were isolated from human auricular cartilage and cultured in vitro. Then,ATAC-seq was performed on 1,3, and 6 passage of cells.


title: Regularity of Chondrocyte Phenotypic Changes Identified by Single-cell Sequencing in vitro

summary: The specific mechanism of phenotypic change of chondrocytes in vitro remains unclear. We performed single-cell sequencing of P1,P3, and P6 cells in vitro to explore the mechanisms involved.

overall_design: Chondrocytes were isolated from human auricular cartilage and cultured in vitro. Then, single cell sequencing was performed on 1,3, and 6 passage of cells.


title: Genome assembly of 12 Nigrospora species Assembly

city: hangzhou

first: Chao

last: Liu

state: 浙江

address: 浙江省

institute: 浙江大学

summary: To ascertain which genes were influenced in deletion mutants, we newly generated transcriptome data for deletion mutant vs control for each of three convergent genes (ΔNrURED, ΔNrGMF1, and ΔNrGLA) in N. rubi, respectively. After comparing the differentially expressed genes between all three mutants and controls, we found that 868 genes were identified as co-upregulated and 350 genes as co-downregulated (Figs. S7A and S7B). Gene Ontology (GO) enrichment analysis and KEGG pathway analysis revealed that these differentially expressed genes also are mainly involved in the secretory protein synthesis pathway, such as transmembrane transport, hydrolase activity, and protein processing within the endoplasmic reticulum (Figs. S7C and S7D). These results suggest that deletion of the convergent genes affected secretory protein synthesis, modification, and export.

first: Lei

last: Cai

first: Meiling

last: Guo

first: Chenghui

last: Xu


title: Expression data upon K-Ras elimination in DU, DU RRAS2 G23V and DU PI3KCAAX cells

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

summary:
The expression of an oncogenic version (G23V mutant) of R-Ras2/TC21 can fully compensate for the loss of the three classical Ras proteins in MEFs. This process involves the inhibition of the antiproliferative p53–p21Cip1 retinoblastoma axis known to cause the morphological and proliferative defects found in Ras-deficient MEFs. Unlike the case of normal MEFs, the inhibition of this antiproliferative pathway by R-Ras2G23V in Ras-deficient cells is mediated by PI3Ka–dependent rather than ERK-dependent signaling inputs.
We used microarrays to detail the global programme of gene expression underlying this compensation process.

overall_design: We used triplicates of DU control, RRAS2G23V, and PI3KCAAX cells with and without 4-OHT.

first: Isabel

last: Fernández Pisonero

first: L

middle: F

first: Mattias

last: Drosten

first: Mariano

last: Barbacid

first: Balbino

last: Alarcón

first: Xosé

middle: R

last: Bustelo


title: Yap1 mediates a systemic catabolic resonse during liver growth and repair

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 2730 S Moody Ave

department: CDCB

institute: OHSU

summary: Here, we report the gene expression changes that occur in the mouse liver and quadriceps following the expression of the catalytically active form of Yap1 (Yap1S5A) in the liver. Yap1S5A was delivered to the liver by Adeno-Associated Virus (AAV).

overall_design: Using total RNA-sequencing, we analyzed livers and quadriceps from 4 adult C57BL6/J  male mice, 7 days after YAP1S5A hepatic expression

first: Koniaris

last: Leonidas

first: Yanlin

last: Jiang

first: Tewfik

last: Hamidi


title: ADCY1-mediated cAMP signaling pathway mediates the neuropsychiatric effects of montelukast

city: Hengyang

first: Hongye

last: Yan

state: Hunan

address: 69 Chuanshan Road

institute: The First Affiliated Hospital of University of South China

summary: Human forebrain organoids (day 100) derived from U2F iPS cell line were exposed with or without 20 ng/ml and 400 ng/ml montelukast (MTK) for 7 days. Organoids were then randomly selected for RNA sequencing (RNA-seq). By performing RNA-seq analysis, we showed that MTK exposure in hFOs downregulated expression of genes enriched with multiple neuronal functions including the glutamatergic synapse. These downregulated genes were also significantly overlapped with genes reported to be associated with schizophrenia, bipolar disorder, and autism.

overall_design: We generated human forebrain organoids (hFOs) from U2F iPS cell lines. On day 100 of organoid culture, hFOs derived from U2F were exposed with or without for 20 ng/ml and 400 ng/ml MTK 7 days. Three organoids in each group were randomly pooled together as one mixed sample. Five mixed samples in each group were then used for RNA-seq (BGI DNBseq, paired-end 150 bp) to identify genes affected by MTK exposure. DEGs (adjusted P value < 0.05) that identified in hFOs derived from U2F were used for Gene Ontology and KEGG pathway analysis.

first: Qingtuan

last: Meng

first: Zhenhong


title: Breast cancer cell/adipocyte crosstalk and Tamoxifen Resistance: a potential role for IGF-1/TXNIP axis

city: RENDE

first: INES

last: BARONE

state: Please select an option below

address: VIA P BUCCI

department: Pharmacy and Health and Nutritional Sciences

country: Italy

institute: UNIVERSITY OF CALABRIA

summary: Although endocrine therapy (ET) has improved the outcomes of Estrogen Receptor (ER) α-positive breast cancer (BC) patients, resistance to these treatments remains a major challenge. Evidence proved that a reduced response to ET is tightly dependent on the surrounding microenvironment and on the host characteristics. Indeed, several studies have highlighted that obesity, in addition to promote BC development and progression, represents a heavyweight player driving ET resistance. Here, we evaluated the influence of adipocytes and their secretome on the efficacy of ET. Our findings bring insights on adipocytes and mammary cancer cell crosstalk during endocrine therapy, suggesting the possibility to target IGF-1/TXNIP axis to block this harmful connection, especially in obesity settings.

overall_design: Comparative transcriptomic profile between MCF-7 Tamoxifen-resistant (TR) cells untreated or treated with conditioned medium derived from 3T3L1 mature adipocytes.

first: Ines

last: Barone

first: Stefania

last: Catalano

first: Cinzia

last: Giordano


title: Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes [ChIP-Seq]

city: Helsinki

first: Divyesh

last: Patel

address: University of Helsinki

department: Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine,

country: Finland

institute: University of Helsinki

summary: The combination of epigenetic and immunotherapy is emerging as a promising approach for cancer therapy. Derepression of transposable elements (TE) by epigenetic drugs leads to activation of immune response. However, the molecular mechanism of TE regulation by distinct chromatin modifier enzymes (CME) in context of p53 is still elusive. Here, we used FDA-approved epigenetic drugs to systematically inhibit distinct CMEs in p53 wild-type and p53-mutant colorectal, esophageal, and prostate cancer cells. We show that distinct TE subfamilies are derepressed by inhibition of different CMEs in cell type-specific manner. Co-inhibition of DNMT and HDAC (DNMTi-HDACi) had the most consistent effect across cancer types. Loss of p53 results in stronger TE activation and TE-chimeric transcript expression and this effect is largely mediated by the non-genomic actions of p53. Robust immune response elicited by DNMTi-HDACi is due to induced inverted repeat Alu expression concomitant with reduced ADAR1-mediated Alu RNA editing, whereas SETDB1 inhibition activates ADAR1 expression. Collectively, our systematic analyses provide insights for rational use of epigenetic therapies in distinct cancers.

overall_design: Transcription factor binding  was determined by ChIP-seq in GP5d and OE19 cells. Gene expression profiling for GP5d, OE19, LNCAP-1FP, GP5d p53-KO and LNCAP-1Fo p53-KO cells (DMSO treated, DNMT inhibited, HDAC inhibited, SETDB1 inhibited and DNMT-HDAC co-inhibited, DNMT-SETDB1 co-inhibited, HDAC-SETDB1 co-inhibited) was performed by RNA-seq.

first: Ville

last: Tiusanen

first: Päivi

last: Pihlajamaa

first: Biswajyoti

last: Sahu


title: Investigation of gene expression changes in normal human dermal fibroblasts after exposure to bone marrow mesenchymal stromal cell secretome

city: Oxford

first: Tamiris

last: Borges da Silva

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

summary: Mesenchymal stromal cells (MSCs) are been widely investigated in clinical trials for several clinical conditions. It is known that these cells do not promote their effects by engrafment and differentiation, as they die shortly after intravenous administration.  Extracellular vesicles (EVs) are membrane bound particles that carry bioactive lipids, peptides and nucleic acids and act in cell-cell communication. The aim of this study is to determine the transcriptomic effects of exposure of dermal fibroblasts to fractions of bone marrow MSCs, including conditioned medium (CM), non-small extracellular vesicles (NsEV), small extracellular vesicles (sEVs) and depleted medium (DM). Differential gene expression and gene ontology analysis showed that there enrichment of pathways related to migration and genes within the regulation of cell population proliferation pathway had their expression changed after exposure to MSC-sEVs. This indicates that MSC secretome promotes targeted gene expression change that can be of particular interest in wound healing studies and clinical trials.

overall_design: To study the effects of MSC secretome, we fractioned conditioned medium into non-small extracellular vesicles (nsEV, pellet obtained after centrifuging CM at 10,000 g for 40 minutes), and small extracellular vesicles (sEV, ultracentrifugation at 100,000 g for 90 minutes and washing pellet with PBS on a further ultracentrifugation at 100,000g). We then exposed normal human dermal fibroblasts to the different fractions of secretome for 48 hours; controls were cells exposed only to DMEM 1% Penicillin/Streptomycin. Total RNA was extracted and sent for mRNA sequencing at Novogene Limited (Cambridge, UK).

first: Cathy

last: Ye


title: High-resolution changes in chromatin organization throughout breast cancer progression

city: Bethesda

first: Kathleen

middle: Shaindel Metz

last: Reed

state: MD

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

summary: We used Micro-C to explore conformational changes in the cancer genome, using the MCF10 cell line as a model for breast cancer progression. We have generated 5kb-resolution maps in normal (MCF10A), pre-malignant (MCF10AT1), and metastatic (MCF10CA1a) breast cancer cell lines, and aim to identify differential enhancer-promoter interactions between the different stages of cancer progression that may contribute to oncogenesis.

overall_design: Micro-C in MCF10A, MCF10AT1, and MCF10CA1a cell lines (2 biological replicates per cell line, 4 technical replicates per biological rep). Micro-C was conducted by Cantata Bio.

last: Metz Reed

first: Tom

last: Misteli


title: Histone acetyl transferase HAF2 forms complex with PDC to regulate H3K14ac and H3K23ac in ethylene response

city: Austin

first: Guihua

last: Wang

state: Texas

address: 2506 Speedway

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

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

overall_design: Refer to individual Series


title: Histone acetyl transferase HAF2 forms complex with PDC to regulate H3K14ac and H3K23ac in ethylene response [ChIP-seq]

summary: Next-generation sequencing (NGS) has been used to study the histone acetylation  in Arabidopsis etiolated seedlings under air and ethylene treatment. The goal of this study is to investigate how HAF2 is  involved in histone acetylation changes  in response to ethylene.

overall_design: Three-day-old etiolated Arabidopsis seedling genome histone acetylation profiling by high throughput sequencing of haf2_ko were generated by sequencing, in 2 replications, using Illumina NovaSeq X Plus

first: Chia-Yang

last: Chen

first: Zhengyao

last: Shao

first: Hong

last: Qiao


title: Targeting the Epigenetic Regulator CBX5 Promotes Fibroblast Metabolic Reprogramming and Inhibits Lung Fibrosis

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Idiopathic pulmonary fibrosis (IPF) is characterized by the sustained activation of interstitial fibroblasts leading to excessive collagen deposition and progressive organ failure. Epigenetic and metabolic abnormalities have been shown to contribute to the persistent activated state of scar-forming fibroblasts. However, how epigenetic changes regulate fibroblast metabolic responses to promote fibroblast activation and progressive fibrosis remains largely unknown. Here we show that the epigenetic regulator chromobox protein homolog 5 (CBX5) is critical to the transition of quiescent fibroblasts to activated collagen-producing fibroblasts in response to bleomycin injury. Loss of mesenchymal CBX5 attenuated fibrosis development, and this effect was accompanied by the downregulation of pathogenic fibroblast genes, including Cthrc1, Col1a1, and Spp1, and by the upregulation of metabolic genes with anti-fibrotic activity such as Ppara and Pparg. scRNA-seq and immunohistochemistry analyses revealed that CBX5 expression was enriched in pathogenic fibroblasts and fibroblastic foci of IPF lungs. Bulk RNA-seq analysis combined with metabolic assessments demonstrated that CBX5 silencing in IPF fibroblasts potently inhibited TGF-beta-stimulated glycolysis while enhancing AMPK signaling and mitochondrial metabolism. Finally, we showed that inhibition of the CBX5 pathway in IPF fibroblasts synergistically potentiated metformin-induced AMPK activation and IPF fibroblast quiescence. Collectively, our findings identify CBX5 as an epigenetic regulator linking metabolic maladaptation to the persistent activated state of lung fibroblasts during IPF progression.

overall_design: Analysis of gene expression profiles using RNA-seq data generated from samples treated with scrambled control (Scr), siRNA targeting CBX5 (siCBX5), Scr with TGF-beta, and siCBX5 with TGF-beta.

first: Jeongmin

last: Hong

first: Giovanni

last: Ligresti


title: Single cell analysis reveals immune subtypes associated with CRT treatment

city: Zhengzhou

first: ting

last: sun

address: No. 100 Science Avenue

institute: Zhengzhou University

summary: Cervical cancer (CC) is one of the most prevalent female malignancies globally in low- and middle-income regions, accounting for 7.5% of all female cancer deaths.Despite advancements in medical technology and treatment protocols，the combination of radiation therapy and chemotherapy, known as chemoradiotherapy (CRT), remains the standard of care for locally advanced cervical cancer. However, a substantial proportion of patients do not achieved a complete response to CRT, leading to treatment failure and poor clinical outcomes.Herein, we profiled the transcriptome of 50649 cells derived from six partial responsive(PR) tumor tissues and two complete responsive(CR) tissues of CSCC through scRNA-seq. We displayed a comprehensive cell landscape of the TME and investigated its function and lineage tracking.

overall_design: Advanced CSCC patients(IVA or IVB) received cisplatin(75mg/m2) and paclitaxel(135-175mg/m2) for two cycles. Then, patients received radiotherapy (45Gy for 25 fractions) accompanied by cisplatin treatment(35-40 mg/m2, once a week). At last, patients received four cycles of cisplatin(75mg/m2) and paclitaxel(135-175mg/m2) treatment. The clinical response for each target lesion was evaluated based on RECIST v.1.1 criteria.Eight tumor tissues (two tumor tissues from CR patients and six tumor tissues from non-responsive PR patients) were obtained from post-treatment of CRT in CSCC patients for scRNA-seq.Tumor  tissues were washed three times with PBS and then were sliced into 1-3 mm3 pieces. The tissue pieces were subsequently transferred to a 10-mL digestion medium containing 0.2% collagenase I/II, DNAse I (Sigma), and 25 units dispase in DMEM. The samples were placed on an incubated orbital shaker at 37C and 250 RPM for 15 min. Approximately 20 mL of ice-cold PBS containing 5% fetal bovine serum was added to the samples, and the samples were then filtered through a 40-µm cell strainer. After centrifugation at 1500 RPM for 5 min at 4C, 5 mL of red blood cell lysis buffer was added and mixed for 15 min. The samples were then centrifuged; single cells were resuspended in a sorting buffer, and then counted using an automatic cell counter.

first: Xia

last: Li

first: Yanmei

last: Cheng

first: Juanhua

first: Penghua

last: Zhang


title: Homeostatic Dysregulation of Systemic CD8+ T Cell Compartment in Lung Cancer Patients

city: Hwasun-eup, Hwasun-gun

first: Jae-Ho

last: Cho

state: Jeollanam-do

address: 264, Seoyang-ro

country: South Korea

institute: CHONNAM NATIONAL UNIVERSITY

summary: Cancer adapts to evolve various resistant mechanisms to counteract CD8+ T cell attacks. While this suppression for antigen-specific CD8+ T cells is common within the tumor microenvironment, little is known about how tumors affect overall CD8+ T cell compartment systemically. Here we show a new link in lung cancer patients between tumor-associated homeostatic dysregulation and uncontrolled differentiation of peripheral blood CD8+ T cells. These CD8+ T cells exhibited coordinated alterations indicative of reduced quiescence, increased spontaneous activation, and a progressive transition toward proliferation-incompetent late differentiated effector subsets. This phenomenon was not limited to tumor-reactive cells but was also broadly applicable to tumor non-specific cells, which correlated with poor clinical responses to immune checkpoint inhibitor therapy. Malignant diseases continue to confront newly primed CD8+ T cells, and here we uncover a new mechanism by which cancer impairs potentially tumor-reactive CD8+ T cells via dysregulating homeostasis of systemic CD8+ T cell populations.

overall_design:
CD3+CD8+CD4- cells from peripheral blood mononuclear cells (PBMCs) of 4 healthy individuals and 8 non-small cell lung cancer (NSCLC) patients were isolated using Fluorescence-activated cell sorting (FACS). These cells were stained with CITE-seq antibodies and used for a 12-plexed single cell RNA-sequencing (10X Genomics). Raw data are unavailable due to patient privacy concerns. Data are however available from the authors upon reasonable request and with permission of Chonnam National University Hwasun Hospital.
-------------------------
Authors state "Raw data are unavailable due to patient privacy concerns."

first: Sung-Woo

last: Lee


title: [scRNA-seq]: Inhaled PRR Agonists Reprogram Lung Epithelial Cells to Prevent Type 2 Allergic Inflammation

status: Public on Jun 15 2025

city: Houston

first: Scott

last: Evans

state: TX

address: 6565 MD Anderson Blvd, Unit 1059

department: Pulmonary Medicine

institute: University of Texas MD Anderson Cancer Center

summary: The increasing prevalence of chronic allergic lung diseases demands development of new preventative strategies. We previously demonstrated that therapeutic inhalation of the synergistic agents ODN M362, a TLR9 ligand, and Pam2CSK4, a TLR2/6 ligand (collectively, “Pam2ODN”) protects mice against both infectious challenges and allergic lung disease models, including allergic inflammation caused by mouse house dust mite (HDM) extract. By preventing sensitization, Pam2ODN reduces HDM-induced eosinophilic and lymphocytic inflammation. How Pam2ODN affects the interactions of lung epithelial cells, dendritic cells, and T cells to prevent lung eosinophilic inflammation has not been established. In the present study, we show that a single inhaled dose of Pam2ODN prior to HDM sensitization reduces Th2 polarization of airway CD4+ T cells without affecting the immune responses of Th1 or Treg cells. Furthermore, Pam2ODN pre-treatment inhibits recruitment of lung monocyte-derived dendritic cells (moDCs) and conventional type 2 migratory dendritic cells (DC2s) while preventing HDM-induced decrease of conventional type 1 migratory dendritic cells (DC1s). Bulk RNA-seq of whole lung homogenates reveals that Pam2ODN pretreatment restricts the expression of HDM sensitization-induced proinflammatory transcripts. This tolerogenic effect is also reflected at the single-cell level in lung epithelial cells where many proinflammatory transcripts, pathways and chromatin accessibility are inhibited. These results indicate that Pam2ODN reprograms lung epithelial cells to attenuate allergen-induced lung proallergic DC cytokines while maintaining the population of protective DC1s, which prevents lung injury and Th2 polarization. Collectively, our findings suggest that the development of Th2-induced chronic allergic lung diseases may be mitigated by lung epithelium-targeted immunomodulatory strategies.

overall_design: A single aerosol treatment of PBS or Pam2ODN was administered 7-days before intratracheal sensitization of naïve Balb/c mice with 100 µg HDM. Whole lungs were harvested 12 hours after the HDM administration. Lungs were enzymatically digested, and single cell suspensions prepared for flow cytometry sorting of lung immune cells (CD45+) and epithelial cell populations, followed by subsequent single-cell RNA sequencing analysis.

first: Mbaya

last: Ntita

first: Richa

last: Nayak

first: Celine Shuet Lin

last: Kong


title: Hepatic Yap1 activates systemic catabolism and muscle loss during organ repair: evidence for a common mechanism with cancer cachexia

first: Teresa

last: Zimmers

summary: Here, we report the gene expression changes that occur in the mouse liver and quadricep, 3 days following 70% partial hepatectomy (PHx) in mice.

overall_design: Using total RNA-sequencing, we analyzed livers and quadriceps from 5 adult C57BL6/J  male mice, 3days after 70% partial hepatectomy. Control animals received a sham surgery (laparotomy) with no partial hepatectomy. 3 sham control mice and 5 PHx mice were used for the RNA-Seq analysis.

first: Koniaris

last: Leonidas

first: Yanlin

last: Jiang

first: Tewfik

last: Hamidi


title: [RelA ChIP-seq]: Characterization of transcriptional and chromatin accessibility landscape of human bronchial epithelial cells treated with synergistic immunostimulatory ligands.

summary: Lower respiratory tract infections remain a leading cause of death worldwide. The increasing prevalence of antibiotic-resistant respiratory pathogens has been a key driver of efforts to develop host-directed therapies that protect patients against pneumonia. Our laboratory has previously reported discovery of an immunostimulatory therapeutic comprised of a synthetic diacetylated lipopeptide, Pam2CSK4 (Pam2), and a class C CpG oligodeoxynucleotide, ODN M362 (ODN). When delivered by inhalation, this dyad protects synergistically against pneumonias caused by Gram-positive and -negative bacteria, seasonal and pandemic viruses, and multiple fungi. Protection is achieved by manipulating the immune defense response from lung epithelial cells. Here, we dissect the lung epithelial transcriptional response to explain the observed synergistic signaling, using RNA-seq and dual transcription factor ChIP-seq. We find cooperation of RelA and cJun following Pam2+ODN treatment that synergistically confers broad inducible resistance against respiratory pathogens. Specifically, transcription factor binding site (TFBS) analysis revealed that cJun occupancy at promoter regions of Pam2+ODN-induced genes facilitated increased RelA occupancy during differential expression, demonstrating cJUN-assisted loading of RelA as a key mechanism of the synergistic signaling events. Increased or decreased RelA occupancy at promoter sites dictated gene up- or down-regulation, respectively, while increased or decreased cJun occupancy at promoter sites directed synergistic or antagonistic gene expression patterns. Together, RelA and cJun work at promoter regions to control directionality and magnitude of gene expression after Pam2+ODN stimulation, rapidly reprograming the lung epithelial transcriptome to combat respiratory infections.

overall_design: RelA TFBS changes of HBEC3-KT cells were profiled after 4-hour treatment with PBS (Control), Pam2 (4 uM), ODN (1 uM) or Pam2+ODN (4+1 uM) using ChIP-seq. Input file of the dual TF ChIP-seq is stored under the [RelA ChIP-seq] GEO Series.

first: Jezreel

last: Pantaleón García


title: Bulk RNA sequencing on hepatic tissues from colitis mice treated with a sublethal indirubin dose.

city: Hong Kong

first: Yiqi

last: Xu

address: Room 201-207 of 2/F of Building 15W, Phase Three

country: Hong Kong

institute: Centre for Chinese Herbal Medicine Drug Development Limited

summary: Many plant-derived bioactive molecules with low solubility and permeability can cause hepatocyte injury. However, the mechanism by which they induce hepatic damage without passive diffusion into the hepatic circulatory system remains unclear. In this study, we demonstrate that indirubin, the main component of indigo naturalis with poor aqueous solubility, predisposes mice with chronic colitis to hepatic injury.  This closely mimics the hepatic damage commonly observed in ulcerative colitis patients treated with indigo naturalis. To elucidate the mechanism of indirubin-induced hepatocyte injury in chronic colitis, we performed bulk RNA sequencing on hepatic tissues from DSS-induced colitis mice treated with a sublethal indirubin dose.

overall_design: Chronic colitis was induced in C57BL/6J mice using three cycles of dextran sulfate sodium (DSS) administration. Each cycle comprised 1 week of 1.8% (w/v) DSS in drinking water followed by 1 week of recovery. The mice were randomised into 3 groups: (1) the control group received 200 μL of sterile water orally each day; (2) the DSS group received 200μL of sterile water orally each day; (3) the Indirubin groups were given 1g/kg/day of Indirubin in 200μL sterile water orally each day

last: XU

first: Jingchun

last: SHI

first: Heung-Lam

last: MOK

first: Cheng

last: LYU

first: Junbang

last: CHEN

first: Chunhua

last: HUANG

first: Hongyan

last: QIN

first: Chengyuan

last: LIN

first: Hor-Yue

last: TAN

first: Zhaoxiang

last: BIAN


title: Effects of miR-15a modulation in gene expression in human aortic SMCs

city: Munich

first: Lars

last: Maegdefessel

address: Ismaninger Strasse 22

institute: Technical University of Munich

summary: Among in silico predicted or experimentally confirmed miR-15a targets are many genes of relevance to AAA pathology and known to be down-regulated in AAA conditions. To better understand which of these targets could be linked to the observed detrimental effects of miR-15a on SMC dynamics in vitro, we performed RNA-sequencing of hAoSMCs transfected with miR-15a-modulators (mimic, inhibitor, and scrambled control). Upon transfection with miR-15a-mimic, 1030 genes were significantly down-regulated and 741 were significantly up-regulated, whereas miR-15a-inhibition led to 23 down-regulated and 82 up-regulated genes.

overall_design: Primary human aortic smooth muscle cells (hAoSMCs, lot nr 3003) were purchased from Cell Applications (San Diego, USA) and cultured in complete Human SMC Growth Medium (Cell Applications; 311-500), supplemented with 1% PenStrep. Cells were seeded in 6-well plates at 125.000 cells/well and kept in growth medium overnight. Next morning, cells were starved for 24h in OptiMEM (Gibco, ThermoFisher Scientific) + 2% FBS + 1% PenStrep. Shortly before transfection, medium was changed back to full growth medium as per above. Transfection of miRNA-modulators (miRVana miRNA mimic/inhibitor/scrambled control, ThermoFisher Scientific) was performed using Lipofectamine RNAiMAX (ThermoFisher Scientific) in accordance with manufacturer’s manual and using 7.2 µl RNAiMAX per well and a final modulator concentration of 50nM. Cells were then cultured for 48h. RNA was harvested by pooling two wells of each condition to assure adequate RNA concentration. Extraction was performed using miRNeasy Tissue/Cells Advanced Mini Kit (Qiagen), following the manufacturer’s protocol, including an on-column DNAse digestion step. Extracted RNA from cell lysates stemming from hAoSMCs 48h post-transfection with miR-15a-mimic (n=3), miR-15a-inhibitor (n=3) and scrambled control oligo (n=3) was analysed by a commercial vendor (Novogene UK Company Limited, Cambridge, United Kingdom) using following procedures. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP. The directional library was complete after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and Bioanalyzer for size distribution detection. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq PE150 platform and >40M paired-end reads were generated for each sample. Raw data (raw reads) of fastq format were cleaned by removing reads containing adapter sequence, reads containing poly-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data was calculated. All downstream analyses were based on the clean, high-quality data. Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to quantify reads mapped to each gene. FPKM of each gene was calculated based on the length of the gene and its mapped reads. Differential expression analysis was performed using the DESeq2 R package (1.20.0). The resulting p-values were adjusted for false discovery rate using the Benjamini and Hochberg’s approach. At this point, data was released by the commercial vendor and all subsequent analyses were performed independently by our group. Genes with an adjusted p-value <=0.05 and absolute fold-change >=1.5 were defined as differentially expressed.

first: Greg

last: Winski

first: Ekaterina

last: Chernogubova


title: Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR

city: San Francisco

first: Raunak

last: Shrestha

state: CA

department: Radiation Oncology

institute: University of California, San Francisco


title: Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR [ATAC-seq]

summary: Comprehensively understanding the gene regulatory network that modulates the biology of the Androgen Receptor (AR) oncogene is a central goal of prostate cancer research. To study regulators of AR, we knock-in a split neon green fluorescent protein onto the AR in prostate cancer cells creating an endogenous AR reporter cell line. Using our endogenous AR reporter, we performed a genome-scale fluorescence-activated cell sorting based CRISPRi screen to comprehensively identify genes that modulate AR protein levels. We identify and validate known AR protein regulators including HOXB13, GATA2, GRHL2 as well as unexpected top hits including PTGES3, SAE1 and CSNK2A1. Loss of PTGES3 in multiple models of ARSI-resistant Pca resulted in loss of AR protein and thus AR’s oncogenic activity. Mechanistically, we demonstrate a novel nuclear co-factor function of PTGES3 facilitating AR-mediated transcription aside from its canonical co-chaperone function regulating AR protein levels. Lastly using a disulfide tethering chemical screen, we developed a PTGES3 inhibitor demonstrating PTGES3 is a therapeutically tractable target for the treatment of AR-addicted mCRPC.

overall_design: ATAC-seq was performed in PTGES3 knockdown in LNCaP prostate cancer cells

first: Haolong

last: Li

first: Meng

last: Zhang

first: David

last: Quigley

first: Luke

last: Gilbert

first: Felix

middle: Y

last: Feng


title: Gene expression analysis in human scalp biopsies from lichen planopilaris patients

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a small clinical trial using levia, theradome and plaquenil for the treatment of lichen planopilaris (LPP). Scalp biopsies were obtained at baseline and 6 months, and gene expression was assessed with the NanoString fibrosis panel with additional custom spike-in genes.

overall_design: Gene expression was analyzed using 817 Nanostring probes to analyze 6 patients treated with Levia, 4 with Theradome and 5 with Plaquenil comparing baseline to 6 months (scalp biopsies).

first: Maryanne

last: Senna

first: Ümmügülsüm

last: Yıldız-Altay


title: Endocardial primary cilia and blood flow regulate EndoMT during endocardial cushion development [Single Nuc-RNAseq_IFT]

city: New Haven

first: Kathryn

last: Berg

state: Connecticut

address: 333 Cedar St.

department: Genetics

institute: Yale University

summary: Blood flow is critical for heart valve formation, and cellular mechanosensors are essential to translate flow into transcriptional regulation of development.  Here, we identify a role for primary cilia in vivo in the spatial regulation of cushion formation, the first stage of valve development, by regionally controlling endothelial to mesenchymal transition (EndoMT) via modulation of Kruppel-like Factor 4 (Klf4). We find that high shear stress intracardiac regions decrease endocardial ciliation over cushion development, correlating with KLF4 downregulation and EndoMT progression. Mouse embryos constitutively lacking cilia exhibit a blood-flow dependent accumulation of KLF4 in these regions, independent of upstream left-right abnormalities, resulting in impaired cushion cellularization. snRNA-seq revealed that cilia KO endocardium fails to progress to late-EndoMT, retains endothelial markers and has reduced EndoMT/mesenchymal genes that KLF4 antagonizes. Together, these data identify a mechanosensory role for endocardial primary cilia in cushion development through regional regulation of KLF4.

overall_design: Whole hearts of e9.5 mouse embryos (Ift20+/+ (wildtype), Ift20+/-, Ift20-/-) were microdissected and flashfrozen. Five flashfrozen hearts of each genotype were pooled and prepared for single nuclei RNA-sequencing. Ift20+/+ had 3 replicates of this process; Ift20+/- and Ift20-/- had 2.

first: Faith

last: Lundt

first: Joshua

last: Gorham

first: Jonathan

last: Seidman

first: Martina

last: Brueckner


title: Histone acetyl transferase HAF2 forms complex with PDC to regulate H3K14ac and H3K23ac in ethylene response [RNA-seq]

first: Guihua

last: Wang

summary: Next-generation sequencing (NGS) has been used to study the differential gene expression in Arabidopsis etiolated seedlings under air and ethylene treatment. The goal of this study is to investigate how HAF2 is involved in transcriptional regulation in response to ethylene.

overall_design: Three-day-old etiolated Arabidopsis seedling mRNA profiles of haf2_ko were generated by sequencing, in 2 replications, using Illumina NovaSeq X Plus

first: Chia-Yang

last: Chen

first: Zhengyao

last: Shao

first: Hong

last: Qiao


title: Therapeutic immune cell engineering with an mRNA : AAV-Sleeping Beauty composite system

city: West Haven

first: Kazushi

last: Suzuki

state: CT

address: 850 West Campus Drive

summary: We evaluated the insertion site profile of the MAJESTIC (mRNA : AAV-Sleeping Beauty) CAR generation method.

overall_design: Genomic DNA was extracted from CARs and untreated T cells, and then a two step Splinkerette PCR was performed to generate an insertion site library that was sequenced by a Miseq sequencer.

first: Stanley

last: Lam

first: Sidi


title: Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context [amplicon sequencing]

city: Ithaca

first: Zhou

last: Zhou

state: New York

address: 526 Campus Rd, 417 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

summary: Enhancers are gene-distal cis-regulatory elements that drive cell type-specific gene expression. While significant progress has been made in identifying enhancers and characterizing their epigenomic features, much less effort has been devoted to elucidating mechanistic interactions among clusters of functionally linked regulatory elements within their endogenous chromatin contexts.  Here, we developed a novel recombinase-mediated genome rewriting platform and applied our divergent transcription architectural model to understand how a long-range human enhancer confers a remarkable 10,000-fold activation to its target gene, NMU, at its native locus. Our systematic dissection reveals transcription factor synergy at this enhancer and highlights the interplay between a divergently transcribed core enhancer unit and emerging new types of cis-regulatory elements—notably, intrinsically inactive facilitators that augment and buffer core enhancer activity, and an adjacent retroviral long terminal repeat promoter that represses enhancer activity. We discuss the broader implications of our focused study on enhancer mechanisms and regulation genome-wide.

overall_design: Amplicon-sequencing for genomic DNA extracted from different NMU FlowFISH expression bins and unsorted background samples to count unique element barcodes in each bin; two biological replicates were performed (rep1 = Landing Pad Clone E5; rep2 = Landing Pad Clone D17)

first: Albert

last: Li

first: John

last: Lis


title: Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR [mRNA-seq_181-40]

first: Raunak

last: Shrestha

overall_design: mRNA-seq was performed in LNCaP prostate cancer cells treated with PTGES3 inhibitor 181-40, or DMSO as control.

first: Haolong

first: Meng

last: Zhang

first: David

last: Quigley

first: Luke

middle: A

last: Gilbert

first: Felix

last: Feng


title: Proliferating microglia exhibit unique transcriptional and functional alterations in Alzheimer’s disease

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Proliferation of microglia represents a physiologically process which is accelerated in several neurodegenerative disorders including Alzheimer disease. The effect of such neurodegeneration-associated microglial proliferation on function and disease progression remains unclear. We hypothesized that microglial proliferation into a neurodegenerative environment generates subpopulations displaying transcriptional and functional changes that may contribute to the transition from acute to chronic neuroinflammation. Here, we show that proliferation results in profound alterations of cellular function by providing evidence that newly proliferated microglia show impaired beta-amyloid clearance in vivo. Through sorting of proliferating microglia of APP/PS1 mice and subsequent transcriptome analysis, we define unique proliferation-associated transcriptomic signatures that change with age and beta-amyloid accumulation and are characterized by an enrichment of immune system-related pathways.

overall_design: mRNA sequencing and analysis of proliferating (Ki67+) and non-proliferating (Ki67-) microglia from WT and APP/PS1 mice at 4, 6 and 12 months of age

first: Nàdia

last: Villacampa

first: Kristian

last: Händler

first: Thomas

last: Ulas

first: Marc

last: Beyer

first: Michael

last: Heneka


title: Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR [mRNA-seq]

overall_design: mRNA-seq was performed in PTGES3 knockdown, with GAL4 knockdown as control in LnCaP prostate cancer cells


title: [Bulk RNA-seq]: Characterization of transcriptional and chromatin accessibility landscape of human bronchial epithelial cells treated with synergistic immunostimulatory ligands.

first: Scott

last: Evans

overall_design: Gene expression changes of HBEC3-KT cells were profiled after 4-hour treatment with PBS (Control), Pam2 (4 uM), ODN (1 uM) or Pam2+ODN (4+1 uM) using RNA-seq.

first: Jezreel

last: Pantaleón García


title: Lactylation-driven NSUN2-mediated RNA m5C modification promotes perineural invasion in pancreatic cancer [mRNA-seq]

city: Guangzhou

first: Tianhao

last: Huang

state: Guangdong

address: No.106 Zhong Shan Er Road

institute: Southern Medical University

summary: Lactylation, a metabolic stress-induced modification, plays a pivotal role in regulating diverse biological processes. Its involvement in perineural invasion (PNI) of pancreatic ductal adenocarcinoma (PDAC), however, has not been clearly defined. Our study demonstrates that patients with severe PNI exhibit significantly elevated levels of global lactylation and lactate, correlating with poorer prognosis. We identified NSUN2, a methyltransferase, as a crucial mediator of lactylation-driven PNI. Inhibition of lactylation or NSUN2 markedly reduced the neural infiltration capabilities of tumor cells. Mechanistically, lactate accumulation leads to the lactylation of NSUN2 at lysine 692 (K692), subsequently inhibiting its ubiquitination and degradation. lactylation of NSUN2 mediated m5C modification on CDCP1 and STC11 mRNA, enhanced their mRNA stability. Consistently, analyses using a KPC mouse model demonstrated that the lactylation of NSUN2/CDCP1/STC11 axis enhanced PNI through m5C modification. Our findings reveal that lactylation-driven NSUN2-mediated RNA m5C modification plays a pivotal role in promoting PNI and suggest that targeting NSUN2 could offer a promising therapeutic strategy for PDAC.

overall_design: p1_nc, p1_lac, p1_sinc, p1_si

first: Shangyou

last: Zheng

first: Rufu

last: Chen

first: Xuebiao

last: Wei

first: Chonghui

last: Hu

first: Huimou

first: Honghui

last: Jiang


title: Lactylation-driven NSUN2-mediated RNA m5C modification promotes perineural invasion in pancreatic cancer [RIP-seq]

overall_design: PANC1_lac_IP, PANC1_lac_Input, PANC1_nc_IP, PANC1_nc_Input.


title: [scATAC-seq]: Inhaled PRR Agonists Reprogram Lung Epithelial Cells to Prevent Type 2 Allergic Inflammation

overall_design: A single aerosol treatment of PBS or Pam2ODN was administered 7-days before intratracheal sensitization of naïve Balb/c mice with 100 µg HDM. Whole lungs were harvested 12 hours after the HDM administration. Lungs were enzymatically digested, and single cell suspensions prepared for flow cytometry sorting of lung immune cells (CD45+) and epithelial cell populations, followed by subsequent single-cell ATAC sequencing analysis.

first: Mbaya

last: Ntita

first: Dalia

last: Hassan


title: The Regulatory Logic of Planarian Stem Cell Differentiation [scATAC-Seq]

city: Exeter

first: Jordi

last: Solana

address: Northcote House

department: Health and Life Sciences

institute: University of Exeter

summary: Stem cell differentiation underlies development and regeneration in multicellular organisms. Cell type identity is determined by the expression of specific transcription factors (TFs) regulating target genes (TGs) via binding to open chromatin regions (OCRs). The regulatory logic of differentiation includes factors specific to one or multiple cell types, functioning in a combinatorial fashion. Single cell transcriptomics has emerged as a revolutionary approach to study gene expression with cell type resolution, but integrating it with single cell analysis techniques to study chromatin remains challenging. Planarians, with their pluripotent neoblast stem cells continuously giving rise to all cell types, offer an ideal model to attempt this integration. Despite extensive single cell transcriptomic studies, the transcriptional and chromatin regulation at the cell type level remains unexplored. Here, we investigate the regulatory logic of planarian stem cell differentiation by obtaining an organism-level integration of single cell transcriptomics and single cell ATAC-seq. We identify specific open chromatin profiles for major differentiated cell types and analyse their transcriptomic landscape, revealing distinct gene modules expressed in individual types and combinations of them. Integrated analysis unveils gene networks reflecting known TF interactions in each type and identifies TFs potentially driving differentiation across multiple cell types. To validate our predictions, we combined TF knockdown RNAi experiments with single cell transcriptomics. We focus on hnf4, a TF known to be expressed in gut phagocytes, and confirm its influence on other types, including parenchymal cells. Our results demonstrate high overlap between predicted targets and experimentally-validated differentially-regulated genes. Overall, our study integrates TFs, TGs and OCRs to reveal the regulatory logic of planarian stem cell differentiation, showcasing the potential of single cell methods for characterising differentiation trajectories and their regulation.

overall_design: One 10X scATAC-Seq library of trypsin-dissociated, whole S. mediterranea animals in unperturbed conditions.

first: Alberto

last: Perez-Posada

first: Helen

last: Garcia-Castro

first: Elena

last: Emili

first: Virginia

middle: V

last: Vanni

first: Cirenia

last: Arias-Baldrich

first: Siebren

last: Frolich

first: Simon

last: Van Heeringen

first: Nathan

middle: N

last: Kenny


title: [RNA-seq]: Inhaled PRR Agonists Reprogram Lung Epithelial Cells to Prevent Type 2 Allergic Inflammation

first: Scott

middle: E

last: Evans

summary: The increasing prevalence of chronic allergic lung diseases demands development of new preventative strategies. We previously demonstrated that therapeutic inhalation of the synergistic agents ODN M362, a TLR9 ligand, and Pam2CSK4, a TLR2/6 ligand (collectively, “Pam2ODN”) protects mice against both infectious challenges and allergic lung disease models, including allergic inflammation caused by mouse house dust mite (HDM) extract. By preventing sensitization, Pam2ODN reduces HDM-induced eosinophilic and lymphocytic inflammation. How Pam2ODN affects the interactions of lung epithelial cells, dendritic cells, and T cells to prevent lung eosinophilic inflammation has not been established. In the present study, we show that a single inhaled dose of Pam2ODN prior to HDM sensitization reduces Th2 polarization of airway CD4+ T cells without affecting the immune responses of Th1 or Treg cells. Furthermore, Pam2ODN pre-treatment inhibits recruitment of lung monocyte-derived dendritic cells (moDCs) and conventional type 2 migratory dendritic cells (DC2s) while preventing HDM-induced decrease of conventional type 1 migratory dendritic cells (DC1s). Bulk RNA-seq of whole lung homogenates reveals that Pam2ODN pretreatment restricts the expression of HDM sensitization-induced proinflammatory transcripts. This tolerogenic effect is also reflected at the single-cell level in lung epithelial cells where many proinflammatory transcripts, pathways and chromatin accessibility are inhibited. These results indicate that Pam2ODN reprograms lung epithelial cells to attenuate allergen-induced lung proallergic DC cytokines while maintaining the population of protective cDC1s, which prevents lung injury and Th2 polarization. Collectively, our findings suggest that the development of Th2-induced chronic allergic lung diseases may be mitigated by lung epithelium-targeted immunomodulatory strategies.

overall_design: A single aerosol treatment of PBS or Pam2ODN was administered 7-days before intratracheal sensitization of naïve Balb/c mice with 100 µg HDM. After euthanasia, the thoracic cavity was dissected, lungs were removed and RNA was isolated from whole lungs using Qiagen RNeasy mini kits (Qiagen, CA, USA) according to the manufacturers' instructions, then submitted for RNA sequencing.


title: Cannabinoids shift the basal ganglia microRNA m6A methylation profile towards an anti-inflammatory phenotype in SIV-infected rhesus macaques

city: San Antonio

first: Mahesh

last: Mohan

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: Epitranscriptomic modifications [N6-methyladenosine (m6A)] regulate various diseases, including cancer and inflammation. Despite their functional relevance in neural development and differentiation, the role of m6A modifications in HIV neuropathogenesis is unknown. Using anti-N6-methyladenosine (m6A) antibody-immunoprecipitation and microarray profiling, we identified m6A modifications in miRNAs in basal ganglia (BG) of uninfected (VEH) and SIV-infected Rhesus macaques (RMs) on combination anti-retroviral therapy (cART) and either VEH-treated (VEH/SIV/cART), or THC:CBD-treated (THC:CBD/SIV/cART). HIV/SIV infection promoted an overall hypomethylated miRNA m6A profile. While THC:CBD did not significantly impact the overall hypomethylated m6A profile, specific miRNAs predicted to target proinflammatory genes showed marked m6A hypomethylation compared to VEH-treated RMs. Additionally, specific BG m6A-modified miRNAs were detected in BG-derived extracellular vesicles. Mechanistically, the DRACH motif in the miR-194-5p seed region was significantly m6A hypomethylated in THC:CBD/SIV/cART RMs. Unlike wild-type, in-vitro transfected m6A-modified miR-194-5p mimics failed to downregulate STAT1 protein expression. Further, compared to VEH/SIV/cART RMs, THC:CBD significantly reduced m6A methylation of 44 miRNAs directly involved in regulating CNS network genes. Our findings indicate that m6A epitranscriptomic marks in the seed nucleotides can impair miRNA function and that cannabinoids may preserve it by reducing m6A methylation levels, thus, providing a mechanistic explanation underlying their anti-neuroinflammatory effects in HIV/SIV infection.

overall_design: Differentially m6A methylation on microRNAs was profiled in the basal ganglia of anti-retroviral therapy suppressed  chronically SIV infected RMs administered either THC:CBD (n = 3, duration = 6 months) or VEH (n = 4, duration = 6 months) and uninfected control (n = 4) animals


title: [cJun ChIP-seq]: Characterization of transcriptional and chromatin accessibility landscape of human bronchial epithelial cells treated with synergistic immunostimulatory ligands.

overall_design: cJun TFBS changes of HBEC3-KT cells were profiled after 4-hour treatment with PBS (Control), Pam2 (4 uM), ODN (1 uM) or Pam2+ODN (4+1 uM) using ChIP-seq. Input file of the dual TF ChIP-seq is stored under the [RelA ChIP-seq] GEO Series.

first: Jezreel

last: Pantaleón García


title: Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context [ATAC-Seq]

first: Zhou

last: Zhou

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) profiling of WT K562, CRISPR knockout lines (eNMU/e1/e2 deletion), and recombinant eNMU motif mutants; two biological replicates per genotype

first: John

middle: T

last: Lis


title: Gene expression profile at single cell level from the brain at 3h, 2d, and 7d after hypoxic ischemic encephalopathy

city: Hangzhou

first: Jingyu

last: Wang

state: Zhejiang

address: No.688 Yuhangtang road

institute: Zhejiang University

summary: Hypoxic ischemic encephalopathy (HIE) causes brain paralysis. Here, we used single-cell RNA sequencing (snRNA-seq) to examine brain cell heterogeneity during the hyperacute (3 h), acute (2 d), and subacute (7 d) phases.

overall_design: All cells from the brain of sham mice and HIE mice were isolated and analyzed using scRNA-seq

first: Xianbo

last: Chen


title: Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context [ChIP-Seq]

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) targeting p300 for recombinant eNMU motif mutants; two biological replicates per genotype


title: Unlocking the aggressive potential of ZNF217 Exon-4 Skipping isoform in breast cancer and its contribution to bone metastasis

city: TREVOUX

first: joel

last: lachuer

state: Veuillez sélectionner une région, une état ou une province.

address: 11 allée des acacias

country: France

institute: University Lyon1

summary: Breast cancer remains a major health concern worldwide, with bone metastases presenting a significant threat to patient outcomes. Generation of aberrant splicing variants with oncogenic potential are involved in the development and progression of tumors. this study identifies ZNF217-ΔE4 as a new oncogenic splice variant in breast cancer mediating cell aggressiveness and bone marrow homing, as well as a new indicator of the development of bone metastases. ZNF217-ΔE4 thus represents a novel candidate therapeutic target and a new valuable biomarker in the management of breast cancers, particularly in patients with a higher risk of developing bone metastases

overall_design:
To investigate the role of ZNF217 variant splicing as (ZNF217-deltaE4 variant), HEK293 cells line have been transfected ina  stable manner with vector containing 1) WT ZNF217 gene (called WT group) 2) Vector alone (called CMV group) 3) DeltaE4 ZNF217 variant (called  DE group) 4) G1013 ZNF217 variant (called GLY group)
Transcriptomic analysis by RNA seq  has been realised on 12 samples (3 replicats for each group) (WT1, WT2, WT3); (CMV1,CMV2, CMV3); (DE1, DE2, DE3); (GLY1, GLY2, GLY3)
RNAseq has been performed using DNBseq-G400 from MGI. Libraires have been constructed using the MGIEasy RNA Directional Library Prep Set (MGI). Single read of 100 bases has been realised.
Diffrential expression between groups have been realised using Partek Software with CPM normalisation and DEseq pipeline. Functional analysis was performed with Panther software.

first: Pia

last: Fahmé

first: Lamia

last: Bouazza

first: Martine

last: Croset

first: Farah

last: Ramadan

first: Séverine

last: Croze

first: Mariapia

last: Riso

first: Justin

last: Ferraro

first: Philippe

last: Clézardin

first: Olivier

last: Peyruchaud

first: Joël

last: Lachuer

first: Balázs

last: Győrffy

first: Robert

last: Coleman

first: Pascale

last: Cohen


title: Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context [PRO-Seq]

first: Zhou

last: Zhou

overall_design: Precision nuclear run-on sequencing (PRO-seq) profiling of WT K562, CRISPR knockout lines (eNMU/e1/e2 deletion), landing pad (LP) cell line, and recombinant eNMU motif mutants; two biological replicates per genotype

first: Abdullah

last: Ozer

first: John

last: Lis


title: Actinobacillus pleuropneumoniae enhances the growth and virulence of Pasteurella multocida in co-infection

city: jingzhou

first: Huasong

last: Xiao

address: jingmilu

institute: Yangtze university

summary: In this study, P. multocida (serotype A or D) was co-cultured with A. pleuropneumonia (serotype 1), revealing that the growth rates of P. multocida serotype A and D during their decline phase in the co-culture group were significantly higher than those in the mono-culture group. In addition, when P. multocida (serotype A or D) was co-infected with A. pleuropneumonia (serotype 1) in mice, it was found that the bacterial load in the lung tissues of P. multocida in the co-infection group was significantly higher than that of mono-infection group. Then, we analyzed the differential gene expression profiles of P. multocida between co-culture and mono-culture, and used Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to identify key genes and pathways. The results found that the differentially expressed genes of P. multocida in co-culture were widely involved in key pathways such as metabolism, genetic information processing, and environmental adaptation. Taken together, these data demonstrated that A. pleuropneumonia enhances the growth and virulence of P. multocida by reshaping the transcriptional profile of P. multocida.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for P. multocida between co-culture and mono-culture after 20 h

first: Wendie

last: Zhang

first: Junfeng

last: He

first: Feng

last: Liu


title: Identification of conserved miRNAs in Petunia axillaris and P. inflata young flower buds and their verification in the Petunia genome sequence

city: Davis

first: Blake

last: Meyers

address: 451 Health Sciences Drive

department: Department of Plant Sciences

institute: UC  Davis Genome Center

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are short, endogenous RNAs that play key roles in the regulation of numerous biological processes, including development and metabolic pathways. Here, we present a catalog of conserved miRNAs identified in small RNA data sets from young flower buds of Petunia axillaris (PaxiN) and P. inflata (PinfS6) on the basis of identity to miRNAs known from Arabidopsis and Solanaceae, and confirmed by the presence of (a) corresponding MIR loc(i)(us) in the Petunia genome sequences. We identified 44 miRNAs, belonging to 30 families, and covering 140 MIR loci, representing 120 miRNA*s. An additional 13 miRNAs overlapped at loci, supposedly representing additional family members. Our results are consistent with those in tomato and potato that showed 34 miRNA families, corresponding to 96 and 120 MIR genes, respectively, and other plant species, including monocots. The results are highly comparable between P. axillaris and P. inflata, that showed all but four MIR loci present in both species, and one quarter of the MIRs having identical sequences, whereas the remainder showed minor (< 5 %) sequence variation only. miRNA frequencies were also highly similar between P. axillaris and P. inflata and in good agreement with those reported for tomato and potato buds. miRNA target genes included well-known candidates, such as miRNA156-Squamosa Promoter Binding-like protein (SPL), and hints to flower development and anthocyanin biosynthesis regulatory pathways. The presented MIR sequences allow for functional analysis by using mutants. The high conservation between P. axillaris and P. inflata indicates the usability of our miRNA catalog in the entire genus.

sample_organism:
Petunia axillaris
Petunia integrifolia subsp. inflata

overall_design: We sampled floral buds from two Petunia species at multiple developmental stages. For P. axillaris, we collected young buds at 9 weeks (n = 1), 12 weeks (n = 1), and 18 weeks (n = 3 biological replicates), as well as large buds at 12 weeks (n = 1). For P. inflata, we obtained young buds at 12 weeks (n = 1) and 18 weeks (n = 1), and larger buds at 12 weeks (n = 1) and 18 weeks (n = 2). Total RNA was extracted from each sample, and small RNA libraries were prepared and sequenced.

first: Kitty

last: Vijverberg

first: Nunzio

middle: D

last: Agostino

first: Tom

last: Gerats


title: MVD

first: Fu

last: Gao

address: 55 Prospect Street

summary: We used 10x scRNAseq to explore the MVD mechanism.


title: The Regulatory Logic of Planarian Stem Cell Differentiation [RNA-Seq]

first: Jordi

last: Solana

overall_design: Knockdown treatment consisted in injecting worms with 0.1 μg of either of the following combinations: (i) gfp ; (ii) hnf4 + gfp ;  (iii) hnf4 ; (iv) hnf4+nkx2-2 ; (v) hnf4+foxF-1. dsRNA was injected for 3 consecutive days.

first: Alberto

last: Perez-Posada

first: Helen

last: Garcia-Castro

first: Elena

last: Emili

first: Virginia

last: Vanni

first: Cirenia

middle: C

last: Arias-Baldrich

first: Siebren

last: Frolich

first: Simon

last: Van Heeringen

first: Nathan

last: Kenny


title: Soil metagenome from avocado orchards in Channybearup, Western Australia in 2024

city: Murdoch

first: Viet

last: Dang

address: 90 South Street

country: Australia

institute: Murdoch University

summary: Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.

overall_design: This study aims to capture the diversity, composition, and function of soil organisms at different sites from Avocardo orchards in Channybearup, Western Australia. Soil samples were collected at 0-10cm deep from 2 orchards in 2024 with different designs: grid, longitudinal and zigzag. Total DNA was extracted and sequenced by Amplicon sequencing on Illumina MiSeq 2 × 250-bp PE platform.  Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.

first: Wang

last: Penghao


title: Single cell RNA sequencing of In vivo mouse xenograft tissues from two human TRa1 anaplastic thyroid cancer cell line

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: We used scRNA-seq technology to study mouse xenograft tissues from two human TRa1 anaplastic thyroid cancer (ATC) cell lines. Our analysis demonstrated that TRa1 functions as a transcription factor through multiple signaling pathways to suppress tumor growth. Importantly, scRNA-seq analysis showed that TRa1-induced PAX8, via its transcription program, shifts the cell landscape of ATC toward a differentiated state.

overall_design: ATC cells isolated from human tumors (11T and 16T) were subcutaneously inoculated into mice to grow into xenograft tumors. Single cells were dissociated from the tumors of the 8-week mice and then analyzed by single-cell RNA sequencing (scRNA-seq).

first: Hwang

last: Eunmi

first: Cheng

last: Sheue-yann


title: The effects of YTHDC1 on liver function [YTHDC1 HKO]

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary: The goal of this study is to investigate how YTHDC1 regulates liver function.

overall_design:
mRNA profiles in livers of Ythdc1flox/flox and Ythdc1-HKO mice were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of Ythdc1flox/flox and Ythdc1-HKO mice at 9 weeks old. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38.p6) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.
Our study represents the first detailed analysis of liver transcriptomes from Ythdc1flox/flox and Ythdc1-HKO mice, generated by RNA-seq technology. The RNA-seq analysis showed that 1521 genes were downregulated and 1786 genes were upregulated in the livers of Ythdc1-HKO mice.

first: Xinzhi

last: Li


title: Genome-wide maps of transcription in DEAF1 overexpression(OE) and wildtype(WT) cells in Multiple Myeloma

city: Jiangsu Nanjing

first: Deng

middle: Zhen

last: Dong

address: Xianlin Roud 138

institute: Nanjing University of Chinese Medicine

summary: We found different genes change between WT and OE cells.

overall_design: Examination of 2 different genes changes in 2 cell types.

first: Zhendong

last: Deng


title: Nano-flower-stick S-scheme Au/MoS2/Bi2S3 heterojunction with multiple enzyme-like activity for efficient tumor photothermal and photodynamic combination therapy

status: Public on Jun 14 2025

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

summary: Nano-catalytic therapy mediated by reactive oxygen species (ROS) is a highly promising tumor treatment strategy. However, the unique physiological and biochemical characteristics of tumor microenvironment, such as hypoxia and overexpression of antioxidants and glutathione, limit the production of ROS and their oxidation capacity within the tumor. In this study, an S-scheme heterojunction (Au/MoS2/Bi2S3) with multiple enzyme activities was constructed to achieve significant anti-tumor effects through photothermal/photodynamic combination therapy (PTT/PDT). Under near infra-red irradiation, Au/MoS2/Bi2S3 heterojunction not only provided high fever for PTT but also generated singlet oxygen for PDT. In addition, the Au/MoS2/Bi2S3 heterojunction also could generate H2O2 in-situ (Glucose oxidase-like activity), meanwhile simultaneously complete the decomposition of endogenous H2O2 (Peroxidase-like and Catalase-like activity) and depletion of glutathione (Glutathione-peroxidase-like activity) through the conversion between Mo4+ and Mo6+, further enhancing the generation of ROS. In vitro and in vivo studies demonstrated that the photoactivated Au/MoS2/Bi2S3 heterojunction with multiple enzyme activities could completely eliminate tumors without recurrence, meanwhile this heterojunction also exhibited the high biological safety. This study provided a new perspective for tumor therapy based on nano-catalytic method.

overall_design: 4T1 cells were collected from Au/MoS2/Bi2S3+NIR group and the control group. Total RNA pooled was collected from 4T1 cells of three individuals to construct a cDNA library. 4T1 cells transcriptomics were analyzed by Illumina NovaSeq 6000 for high-throughput deep sequencing.

first: Wei

last: Liu

first: Xinrui

last: Yan

first: Xintong

last: Han


title: Genome-wide maps of chromatin state in DEAF1 overexpression (OE in Multiple Myeloma)

summary: The overexpression of DEAF1, tagged with DYKDDDDK, connnected with the promoter of RAD50.

overall_design: Examination all binding DNA with DYKDDDDK-DEAF1.


title: The effects of FOXA1 and FOXA2 on gene expression in Ythdc1-HKO livers

summary: The goal of this study is to investigate how FOXA1 and FOXA2 regulates gene expression in Ythdc1-HKO livers. Four-week-old male Ythdc1flox/flox mice were injected with AAV8-TBG-βGal via tail vein. Four-week-old male Ythdc1-HKO mice were injected with equal amounts of AAV8-TBG-βGal, AAV8-TBG-FOXA1, or AAV8-TBG-FOXA2 via tail vein. Mice were sacrificed three weeks later.Total RNA was extracted from liver tissues using Tripure Isolation Reagent (Roche, Mannheim, Germany).  RNA-seq was performed using Illumina  novaseq x plus (n=3 for each group).

overall_design: Methods: Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina  novaseq x plus. Paired-end clean reads were aligned to the mouse reference genome(grcm39) with Hisat2 (2.2.1), and the aligned reads were used to quantify mRNA expression by using featureCounts (2.0.6).


title: Identification of mRNAs associated with YTHDC1 in primary hepatocytes

summary: The goal of this study is to identify mRNAs associated with YTHDC1 in primary hepatocytes.

overall_design:
Primary hepatocytes were infected with Ad-FLAG-YTHDC1 adenovirus overnight. RNA immunoprecipitation sequence (RIP-seq) assay was performed to identify mRNAs associated with YTHDC1 in primary hepatocytes.
Then, immunoprecipitated RNA or Input was used for library construction with NEB NextR Ultra™ RNA Library Prep Kit (New England Biolabs). Library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols. Raw data (raw reads) of fastq format were firstly processed using fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low- quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome ( GRCm38/mm10) was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
mRNAs associated with YTHDC1 in primary hepatocytes were characterized.

first: Xueying

first: Chunhong


title: Functional relevance of naturally occurring single nucleotide polymorphisms in bovine leukemia virus-encoded microRNAs.

city: Pulawy

first: Aneta

last: Pluta

state: Lublin

address: Av Partyzantow 57

department: Department of Virology and Viral Animal Diseases

country: Poland

institute: National Veterinary Research Institute

summary:
Background: Bovine leukemia virus (BLV) microRNAs (miRNAs) contribute to viral latency and immune evasion. Naturally occurring single-nucleotide polymorphisms (SNPs) within the BLV miRNA cluster have been associated with persistent lymphocytosis in cattle, yet their functional impact remains unclear.
Aims: This study aims to (1) evaluate how SNPs in BLV miRNAs affect miRNA biogenesis and mature miRNA levels; (2) determine whether specific SNPs alter miRNA–mRNA interactions and identify affected targets; and (3) characterize transcriptomic changes induced by reference versus SNP-bearing miRNAs.
Methods: BLV miRNA loci were PCR-amplified and sequenced from 53 blood samples of infected cattle. Both reference and SNP-containing precursors were cloned into expression vectors and co-transfected with an miRNA-deficient BLV clone into HEK293T cells. Mature miRNA levels were quantified via stem-loop RT-qPCR. Computational target prediction (miRanda) validated changes in mRNA targeting. Gene-expression effects were assessed using Agilent microarrays, with selected findings confirmed by RT-qPCR and subjected to pathway enrichment analysis (IPA).
Significance: This work will elucidate how BLV miRNA polymorphisms modify miRNA maturation and target recognition, reshape host gene networks, and contribute to viral persistence and immune modulation.

overall_design: Fifty‐three blood samples were collected from cattle naturally infected with BLV. BLV miRNA coding regions were PCR‐amplified and sequenced to identify isolates carrying either the reference miRNA sequence or specific SNP variants. Selected miRNA precursors (both reference and SNP‐containing) were cloned into expression vectors and co‐transfected with an miRNA‐deficient BLV clone into HEK293T cells in three independent biological replicates. Mature miRNA levels were quantified by RT‐qPCR. For transcriptomic profiling, total RNA from the three independent transfections for selected miRNA variants (reference, V29, V90) and from two control groups (empty vector ± BLV) were pooled by group and analyzed using Agilent two‐color microarrays in six technical replicates. Differentially expressed genes were validated by RT‐qPCR and then subjected to pathway enrichment analysis (IPA).

first: Kerstin

last: Skovgaard


title: Expression profiling data derived from mouse atrial tissues treated with myocardial infarction (MI) for 0, 1, 3, and 7 days.

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Atrial fibrillation (AF) following myocardial infarction (MI) represents a significant clinical challenge due to the lack of effective therapeutic options. However, the precise mechanisms underlying AF development remain poorly understood. This study systematically characterized the dynamic changes in differentially expressed genes associated with AF post-MI, thereby providing a foundation for a comprehensive molecular understanding of the disease.
We investigated schemia-reperfusion –mediated gene expression alteration associated with the development of cardiac injury by microarray in a mouse model.

overall_design: All mice were euthanized via an overdose of pentobarbital on days 1, 3, and 7 post-myocardial infarction (MI). Total RNA was extracted from atrial tissues (n = 4 per group) at each time point using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. Gene expression profiling was conducted using the Affymetrix GeneChip Mouse Genome 430 2.0 Array following the manufacturer’s protocol (Affymetrix, Inc., Santa Clara, CA). The GeneChip Mouse Genome 430 2.0 Array contains over 45,000 probe sets that analyze the expression levels of more than 39,000 transcripts and variants derived from over 34,000 well-characterized mouse genes.

first: Yun-Long

last: Zhang