title: Comparison of phenotypic and transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and PPARα knockout mouse livers

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

institute: ToxStrategies

summary: Recent transcriptomic analyses in vitro comparing the transcriptomic profile of the short-chain per- and polyfluoroalkyl substances (PFAS) HFPO-DA (ammonium, 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate) to that of other chemicals with known MOAs add to the current weight of evidence supporting the peroxisome proliferator-activated receptor alpha (PPARa) activator-induced rodent hepatocarcinogenesis mode of action (MOA) for HFPO-DA-mediated liver effects in rodents. To further inform the MOA of HFPO-DA and evaluate the PPARa-dependence of HFPO-DA-mediated liver effects in vivo, phenotypic and transcriptomic responses in wild-type (WT) and PPARa knockout (KO) mice were investigated following short-term exposure to HFPO-DA or well-established agonists of PPAR (GW7647) and PPARg (rosiglitazone), or cytotoxic agent (acetaminophen [APAP]). Phenotypic and transcriptomic assessment of mouse livers demonstrated a general lack of response to HFPO-DA or GW7647 exposure in PPARa KO but not WT mice, whereas exposure to rosiglitazone or APAP elicited similar, if not greater phenotypic and transcriptomic responses in PPARa KO mice compared to WT mice. Dose-dependent increases in liver weight and increased karyomegaly and mitosis scores via histopathology, as well as increased transcriptomic signaling related to PPARa activation and cell proliferation were observed in HFPO-DA or GW7647-exposed WT mice. The consistent phenotypic and transcriptomic signaling patterns between HFPO-DA and GW7647 in WT mice, and the lack of changes in PPARα KO mice, provide further support that HFPO-DA-mediated liver effects in mice are PPARa-dependent and occur via the PPARa MOA. Thus, these adverse effects in mice are not appropriate for use as the basis of toxicity values for human health risk assessment.

overall_design: Comparative gene expression profiling analysis of TempO-Seq data from FFPE liver tissue of male WT (J:ARC(S) and B6129SF2/J) and PPARa KO mouse strains exposed to various dose levels of HFPO-DA (0, 3, 15, 30 mg/kg-d), or well-established agonists of PPARa (GW7647; 0, 5, 10, 20 mg/kg-d) and PPARg (rosiglitazone; 0, 5, 10, 20 mg/kg-d), or hepatotoxicant (acetaminophen [APAP]; 0, 150, 300, 600 mg/kg) for 5 days via oral gavage or for 6 h via intraperitoneal injection (APAP only).

first: Melissa M

first: Amanda N

last: Buerger

first: Chad M

last: Thompson

first: Laurie C

last: Haws


title: IRX2 and NPTX1 differential regulation of b-catenin underlies MEK-mediated proliferation in human neuroglial cells

status: Public on Apr 21 2025

city: Saint Louis

first: David

middle: H.

last: Gutmann

state: MO

address: 1 Childrens Place Suit 2130

country: USA

institute: Washington University in St. Louis

type: Expression profiling by high throughput sequencing

summary: The two major genomic alterations in pediatric pilocytic astrocytoma (PA) are NF1 loss and KIAA1549: BRAF rearrangement. While these molecular changes result in increased MEK activity and tumor growth, it is not clear exactly how MEK controls human neuroglial cell proliferation. Leveraging human induced pluripotent stem cells harboring these PA-associated alterations, we use a combination of genetic and pharmacological approaches to demonstrate that MEK-regulated cell growth is mediated by b-catenin through independent mechanisms involving IRX2 control of CTNNB transcription and NPTX1 stabilization of b-catenin protein levels. These results provide new mechanistic insights into MEK regulation of human brain cell function

overall_design: Bulk RNA-sequencing of neural cell types (NPCs, GRPs, OPCs, NG2+ progenitor cells, and Astrocytes) comparing control cells to NF1-null cells (homozygous c.2041C > T mutation)

first: Alexander

last: Chen

first: Hannah

last: Wang

first: Xuanwei

last: Li

first: Corina

last: Anastasaki

middle: H


title: The conserved splicing factor PRP21 regulates abscisic acid response and seed germination in Arabidopsis [RNA-Seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

summary: Seed germination is a critical developmental stage in the life cycle of plants, and its regulation is essential for ensuring crop productivity, particularly under adverse environmental conditions. Here, we find that the Arabidopsis thaliana PRE-MRNA-PROCESSING (PRP21) is crucial for the regulation of abscisic acid (ABA) response of seed germination. Our RNA deep sequencing and poly(A) tag sequencing analyses reveal that PRP21 is involved in pre-mRNA splicing, genome-wide gene transcription, and mRNA 3' end processing, highlighting its multifunctional role in gene regulation. Furthermore, we find that PRP21 interacts with various splicing factors and small nuclear ribonucleoproteins, suggesting its involvement in spliceosome assembly. Additionally, we demonstrate that PRP21 negatively regulates the expression of ABA-responsive genes, such as ABSCISIC ACID-INSENSITIVE 3 (ABI3), ABSCISIC ACID-INSENSITIVE 5 (ABI5), EARLY METHIONINE-LABELED 1 (EM1), and EARLY METHIONINE-LABELED 6 (EM6), thereby modulating ABA response and seed germination. Our findings underscore the importance of PRP21 in coordinating transcriptional and post-transcriptional processes, and provide insights into the molecular mechanisms underlying seed germination, potentially guiding crop improvement for stress tolerance.

overall_design: Examination of the mRNA expression of wild type and prp21 mutant in Arabidopsis at  2, 7, and 14 days old.

first: Xinjian


title: SH2D1A Facilitates the Progression of T-Cell Acute Lymphoblastic Leukemia

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: T-cell acute lymphoblastic leukemia (T-ALL) is a highly aggressive hematologic malignancy. The potential of investigating SH2D1A holds promise for more targeted therapies and better outcomes. Knocking down SH2D1A led to decreased T-ALL cell survival and growth both in vitro and in vivo. Cleavage Under Targets and Tagmentation (CUT&Tag) showed the occupancy of ETS1 and RUNX1 at the enhancer loci of SH2D1A in 6T-CEM cells.

overall_design: CUT&Tag using antibody against ETS1 and, RUNX1 in 6T-CEM cells.

first: Juanjuan

last: Yu

first: Wanyan

last: Jiao

first: Jian

last: Pan


title: The conserved splicing factor PRP21 regulates abscisic acid response and seed germination in Arabidopsis [PAT-Seq]

overall_design: Examination of the mRNA expression of wild type and prp21 mutant in Arabidopsis at  14 days old.


title: Pbrm1 loss induces a permissive chromatin state for cholangiocytic differentiation and cholangiocarcinoma formation

city: Taipei City

first: Li-Wen

last: Chiou

address: Chung Shan S. Rd.

department: Pathology

country: Taiwan

institute: National Taiwan University

summary:
Background and Aims:
The SWI/SNF ATP-dependent chromatin remodeling complex regulates transcrip-tional machinery access and is critical in normal physiology and cancer development. Pbrm1, a key subunit of this complex, is frequently mutated in intrahepatic cholan-giocarcinoma (ICC), though how its loss contributes to tumorigenesis remains poor-ly understood. This study aims to explore the role of Pbrm1 in liver physiology and its involvement in ICC development.
Methods:
Liver-specific Pbrm1 knockout (Pbrm1 KO) mice were generated to assess the ef-fects of Pbrm1 loss under various conditions. These mice were exposed to a 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet to induce cholestatic injury and were also subjected to a high-fat diet to evaluate susceptibility to liver steatosis. Chromatin accessibility and gene expression under both normal and injury condi-tions were examined. Additionally, the impact of Pbrm1 loss was analyzed in com-bination with an activating KrasG12D mutation to study cancer development.
Results:
Pbrm1 KO mice exhibited increased susceptibility to cholestatic injury, with an en-hanced ductular reaction. Loss of Pbrm1 reduced chromatin accessibility at hepato-cyte-specific and metabolically important genes, though RNA expression remained unaffected during homeostasis. Following cholestatic injury, hepatocyte-specific gene expression was significantly reduced compared to wild-type controls. Pbrm1 KO mice also showed heightened vulnerability to high-fat diet-induced liver steato-sis. When combined with KrasG12D mutation, Pbrm1 KO/KrasG12D mice had shorter survival and were more likely to develop cholangiocarcinomas, whereas Pbrm1 wild type/KrasG12D mice predominantly developed hepatocellular neoplasms.
Conclusion:
Pbrm1 maintains chromatin accessibility for hepatocyte differentiation-related genes. Its loss promotes differentiation toward cholangiocytes during injury or tu-morigenesis, driving ICC development.

overall_design: To investigate the role of Pbrm1 in liver function and tumorigenesis, we generated Alb-Cre-mediated Pbrm1 knockout mice (referred to as PA in RNA-seq data, whereas wild-type mice referred to as P). Mice were fed a DDC-supplemented diet to initiate liver injury. We then performed RNA-seq in condition with (w/) and without (w/o) DDC to analyze the gene expression differences between Pbrm1 KO and WT mice during liver regeneration.

first: Liwen

first: Yulin

last: Jhuang

first: Chialang

last: Hsu

first: Yungming

last: Jeng


title: SH2D1A Promotes CHI3L2 Expression and Facilitates the Progression of T-Cell Acute Lymphoblastic Leukemia

summary: T-cell acute lymphoblastic leukemia (T-ALL) is a highly aggressive hematologic malignancy. The potential of investigating SH2D1A holds promise for more targeted therapies and better outcomes. Knocking down SH2D1A led to decreased T-ALL cell survival and growth both in vitro and in vivo. RNA-seq analysis was conducted and the differently expressed genes were revealed in the SH2D1A-knockdown Jurkat and 6T-CEM cells in comparison to control group.

overall_design: mRNA profiles of Jurkat and 6T-CEM cells transfected with control shRNA (sh-NC) or sh-SH2D1A were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Yi


title: Gene Expression Profiling and Epigenetic Alterations in RAW 264.7 Cells Following Treatment with Lipopolysaccharide and Methylcobalamin (MCB) [RNA-seq]

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

summary: Methylcobalamin (MCB), an active form of Vitamin B12, demonstrates significant anti-inflammatory and neuroprotective properties by modulating pro-inflammatory cytokines such as TNF-α, IL-1β, and IL-6 (Chopra et al., 2013; Scalabrino et al., 2019). This modulation could potentially ameliorate the hyperinflammatory response known as the "cytokine storm" observed in COVID-19 patients, thereby reducing severity and improving clinical outcomes (Tanaka et al., 2020; Scalabrino, 2005). Beyond its immunomodulatory effects, methylcobalamin supports neuronal health, a critical factor given the neurological complications associated with COVID-19 (Scalabrino et al., 2017; Zhu et al., 2021). Although further clinical trials are necessary to confirm its efficacy, methylcobalamin presents a promising adjunctive therapy for managing the inflammatory and neurological symptoms of COVID-19. However, the precise molecular mechanisms underlying MCB's anti-inflammatory effects remain to be fully elucidated. In this study, we aim to investigate the transcriptional and epigenetic mechanisms through which MCB functions as an anti-inflammatory agent.

overall_design:
To explore the transcriptomic and epigenetic mechanisms through which methylcobalamin (MCB) modulates the inflammatory response induced by lipopolysaccharide (LPS) in macrophages, we conducted RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and Cleavage Under Targets and Tagmentation (CUT & Tag) on the RAW 264.7 cell line.
Initially, we conducted a comprehensive gene expression profiling analysis using RNA-seq data from WT RAW 264.7 cells treated with DMSO, LPS, LPS-MCB, and MCB for 12 hours.
Comparative gene expression profiling analysis of RNA-seq data for DMSO, LPS, LPS-MCB and MCB group.


title: Gene Expression Profiling and Epigenetic Alterations in RAW 264.7 Cells Following Treatment with Lipopolysaccharide and Methylcobalamin (MCB) [ATAC-seq]

overall_design:
To explore the transcriptomic and epigenetic mechanisms through which methylcobalamin (MCB) modulates the inflammatory response induced by lipopolysaccharide (LPS) in macrophages, we conducted RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and Cleavage Under Targets and Tagmentation (CUT & Tag) on the RAW 264.7 cell line.
Initially, we conducted a comprehensive gene expression profiling analysis using ATAC-seq data from WT RAW 264.7 cells treated with DMSO, LPS, LPS-MCB, and MCB for 12 hours.
Comparative ATAC-seq analysis of RNA-seq data for DMSO, LPS, LPS-MCB and MCB group.


title: Human iPS cell-derived respiratory organoids as a model for respiratory syncytial virus infection

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

summary: Respiratory syncytial virus (RSV) is a seasonal respiratory pathogen that primarily affects young children, potentially causing severe lower respiratory tract disease. Despite the high disease burden, understanding of RSV pathophysiology remains limited. To address this, advanced RSV infection models are needed. While HEp-2 cells are widely used due to their high susceptibility to RSV, they do not accurately reflect the host response of the human respiratory tract. In this study, we evaluated human induced pluripotent stem cell-derived respiratory organoids, which contain respiratory epithelial cells, immune cells, fibroblasts, and vascular endothelial cells, for their potential to model RSV infection and support pharmaceutical research. RSV-infected organoids exhibited high viral genome and protein expression, epithelial layer destruction, and increased collagen accumulation. Pro-inflammatory cytokine levels in culture supernatants also increased post-infection. Furthermore, RSV infection was significantly inhibited by monoclonal antibodies (nirsevimab, palivizumab, suptavumab, or clesrovimab), while ribavirin showed limited efficacy. These findings highlight the utility of respiratory organoids for RSV research.

overall_design: The respiratory organoids were mechanically recovered from the culture plates, and then scRNA-seq was performed.


overall_design: The human respiratory organoids were mechanically recovered from the culture plates, and then total RNA was collected and RNA-seq was performed.


title: Effects of fluoro-phenyl-styrene-sulfonamide (FPSS) on transcription factor sigma B regulons in Staphylococcus aureus

city: bangkok

first: Sirirak

last: Supa-amornkul

address: 272 Payatai

department: Microbiology

country: Thailand

institute: Mahidol University

summary: Staphylococcus aureus has been shown to cause various types of tissue and systemic infections in humans and livestock with the mortality rate of 20-30%.  Some isolates can be highly resistant to antibiotics hence the need to identify better drugs and drug targets.  Previous studies have shown that (E)-N-(4-Fluorophenyl)-2-phenylethene sulfonamide (FPSS) could inhibit activities of a bacteria-specific transcription factor sigma B.  Sigma B regulons in Bacillus subtilis and in Listeria monocytogenes, including virulence factor genes in L. monocytogenes, were decreased.  Since sigma B is also presented in S. aureus, we initially postulated the use of FPSS to target S. aureus sigma B activity and to attenuate its virulence gene expression.  Surprisingly, qRT-PCR results revealed that FPSS induced expression of sigma B-dependent gene asp23.  RNAseq results showed 39 S. aureus genes were affected by FPSS (37 genes were downregulated and two genes were upregulated).  FPSS had no effect on expression of sigB operon in S. aureus.

overall_design: To investigate the affect of FPSS  on transcription factor sigma B regulons in Staphylococcus aureus by RNAseq

first: Soraya

last: Chaturongakul


title: Glial differentiation of mouse embryonic-stem-cell-derived neuronal precursors is a sensitive marker for assessing developmental neurotoxicity of insecticides

city: Tsukuba

first: Tomohiro

last: Ito

address: 16-2, Onogawa

institute: National Institute for Environmental Studies

summary: Many epidemiological and animal exposure studies have suggested that exposure to environmental substances is a major risk factor for developmental neurotoxicity (DNT), such as in autism, and is related to the increasing relevance of neurodevelopmental disorders. Recent efforts have led to the development of various in vitro approaches that use cell lines and pluripotent stem cells to assess numerous environmental substances. In this study, we developed a method for assessing DNT using a mouse embryonic stem (mES) cell model that focuses on differentiation into neuronal cells (neural cells and astrocytes). Using this model system, we found that six insecticides inhibited the differentiation of neural precursor cells into astrocytes. Our data indicated that the effects of insecticides on glial differentiation were more sensitive than those of several DNT markers reported in previous studies. This mES cell model can make a quick assessment of DNT potential and may be a useful tool for screening substances with potential to induce DNT.

overall_design: To investigate the mechanisms of developmental neurotoxicity by insecticides, we compared gene expression changes by exposure to each insecticide in neural progenitors.


title: TGFβ determines morphology and key cellular processes of activated CD4+ T cells

city: Rehovot

first: Inbal

last: Eizenberg

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: During an immune response, cells are simultaneously exposed to multiple cytokine signals that collectively determine their phenotype. Transforming growth factor β (TGFβ) is a pleiotropic cytokine acting as a key regulator of T-cell differentiation with activating and suppressive effects on their immune function. Here we identify and analyze the cellular responses of CD4+ T cells to TGFβ across signaling contexts by analyzing the responses of T cells to multiple cytokine mixtures in the presence or absence of TGFβ. We found that TGFβ had a profound dominant effect independent of the presence of other cytokines, modulating the expression of more than 4,000 genes. In the presence of TGFβ, cells exhibit lower expression of translation-related and apoptosis-related genes, accompanied by increased survival of activated T cells. Notably, cells cultured in the presence of TGFβ were smaller in size while preserving their proliferative ability. Accordingly, we identified a dense network of transcription factors that were modulated by TGFβ, suggesting a core gene set connecting TGFβ signaling to the regulation of T-cell size. We found N-Myc to be at the center of this network, and we directly show that TGFβ regulates its gene expression level, protein level, and nuclear localization. Our work provides a system to study cell size control and demonstrate the profound effect of TGFβ in the modulation and regulation of T-cell properties, expanding its role beyond guiding their phenotype.

overall_design:
This work examined the effect of TGFb1 on the cellular state and characteristics of CD4+ T cells. To distinguish the effect of TGFb from that of other cytokines we isolated naïve CD4+ T cells from spleens of mice and cultured the cells under different cytokine mixtures in the presence or absence of TGFb1.
We then examined the gene expression profile of the CD4+ T cells using bulk RNA-sequencing in cells cultured under 10 cytokine conditions. As a control, we added a condition of naïve cells. Each condition had 3 repeats.

last: Eizenberg-Magar

first: Jacob

last: Rimer

first: Stav

last: Miller

first: Yehezqel

last: Elyahu

first: Michal

last: Mark

first: Ziv

last: Porat

first: Shlomit

last: Reich-Zeliger

first: Alon

last: Monsonego

first: Yaron

middle: E

last: Antebi

first: Nir

last: Friedman


title: Gene Expression Profiling and Epigenetic Alterations in RAW 264.7 Cells Following Treatment with Lipopolysaccharide and Methylcobalamin (MCB) [CUT&Tag]

overall_design:
To explore the transcriptomic and epigenetic mechanisms through which methylcobalamin (MCB) modulates the inflammatory response induced by lipopolysaccharide (LPS) in macrophages, we conducted RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and Cleavage Under Targets and Tagmentation (CUT & Tag) on the RAW 264.7 cell line.
Last, we conducted a comprehensive CUT&Tag data from WT RAW 264.7 cells treated with DMSO, LPS, LPS-MCB, and MCB for 12 hours.
Comparative CUT&Tag analysis for DMSO, LPS, LPS-MCB and MCB group.


title: Synovial immune cell dysfunction and pain in late-stage knee osteoarthritis

city: London

first: Holly

last: Philpott

state: Ontario

address: 1151 Richmond St

country: Canada

institute: Western University

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

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: Refer to individual Series


overall_design: The human respiratory organoids were mechanically recovered from the culture plates, and then scRNA-seq was performed.


title: Gene expression profile at single cell level of synovial cells from patients with late-stage knee osteoarthritis

summary: Innate immune cell are increased in the synovium in knee osteoarthritis. We used single cell RNA sequencing to analyze synovial cellular profiles, function, and biological processes.

overall_design: Synovial cells were isolated from 8 patients with late-stage knee osteoarthritis and analyzed in two gorups (more pain vs less pain) by single cell RNA sequencing.

first: Garth

last: Blackler

first: Dan

last: Klapak

first: Alexander

last: Knights

first: Easton

last: Farrell

first: Benoit

last: Fiset

first: Logan

last: Walsh

first: Tristan

last: Maerz

first: Tom

last: Appleton


title: Gene expression analysis after RNAi treatment of different isoforms of vab-3 in C.elegans

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

summary: Progredient accumulation of body fat occurs in diverse species with increasing age, and is linked to reduced longevity in humans. Independently, changes in the relative expression of genetic isoforms have recently been associated with aging, while the functional significance of isoform usage in longevity and healthy aging remains to be elucidated. We here find that modulation of the evolutionarily conserved splicing factor skp-1 improves physical fitness and lifespan in adult C. elegans. By opposing usage of the corresponding promoters, this factor modulates the expression of different isoforms of nematodal vab-3, an orthologue of the endocrine transcription factor Pax6 in mammals. Specifically, preferential usage of the short vab-3c isoform is functionally epistatic to skp-1, and promotes expression of the peroxisomal acox-1.2 gene. Increasing ACOX1 activates AMP-dependent protein kinase (AMPK) to promote healthspan in a redox-dependent manner, but also protects from both lipotoxicity as well as organismal triglyceride accumulation. Accordingly, in human adipose tissue expression of SNW1, the human orthologue of skp-1, is positively correlated with age, and inversely correlated with ACOX1 expression. Moreover, increased ACOX1 expression correlates with decreased adipose tissue mass and improved glucose tolerance in BXD mice. Taken together, these findings indicate that ACOX1 may serve as promising therapeutic targets for ameliorating type 2 diabetes and obesity in an aging population.

overall_design: 8 samples in 3 groups: Control: 2 samples, Vab3 isoform A/N2: 3 samples, RNAi Vab3 isoform C/N2: 3 samples

first: Leonid

last: Rozanov

first: Michael

last: Ristow


title: Spatial profiling of synovial tissue from patients with late-stage knee osteoarthritis.

summary: Marked changes in synovial tissue are seen in knee osteoarthritis and are related to pain; however, the regulation of these processes are not fully understood. Spatial profiling was used to characterize cellular profiles and biological processes within important microenvironments in the synovium (intimal lining, sub-lining, and vessels) between patients that experience more pain compared to those that experience less pain.

overall_design: Synovial tissue from n=32 patients with late-stage knee osteoarthritis were analyzed using spatial profiling and compared between those that experience more pain (n=16) and those that experience less pain (n=16). A tissue microarray was created with all patient samples so they could be analyzed on the same slide. Transcriptomes of intimal lining (CD68+), sub-lining area (CD45+), and vessels (aSMA+) were analyzed separately from each region of interest using GeoMx Digital Spatial Profiler and GeoMx Human Whole Transcriptome Atlas (NanoString).


title: Transcriptomic Profiling of HepG2 Cells under PCCB Depletion Reveals Kpm-Mediated Metabolic Gene Regulation

status: Public on Apr 20 2025

city: Shanghai

first: Liu

last: Fangfang

address: No. 555, Zuchongzhi Road, Pudong New Area, Shanghai, China

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary: Lysine alkylation and acylation serve as crucial links between cellular metabolism and a wide range of biological functions. However, hybrid modifications that combine features of both alkylation and acylation remain largely unexplored. Here, we report the discovery and in-depth characterization of lysine methylpropionylation (Kpm), a hybrid post-translational modification (PTM) defined by the propionylation of monomethyllysine residues. Mechanistically, we show that Kpm is metabolically regulated by propionyl-CoA homeostasis and is markedly upregulated upon depletion of the propionyl-CoA carboxylase beta subunit (PCCB). Genome-wide chromatin immunoprecipitation coupled with transcriptomic profiling revealed that Kpm exhibits distinct genomic distribution compared to canonical Kac and Kpr, with preferential enrichment at promoters of genes involved in metabolic pathways. To investigate the site-specific function of Kpm on non-histone proteins, we developed a genetic code expansion system to incorporate Kpm at defined sites. Using this system, we demonstrate that methylpropionylation of NSMCE3 at lysine 260 disrupts a critical electrostatic interaction with E284, thereby impairing its association with NSMCE4A and compromising DNA damage repair. Together, our findings establish Kpm as a dual-feature PTM that integrates metabolic cues with both chromatin regulation and non-histone protein function, offering a mechanistic framework for understanding metabolism-proteome crosstalk.

overall_design: RNA-seq profiling of the wild-type (WT) and PCCB knockdown HepG2 cells.

first: Fangfang

last: Liu

first: Runhua

last: DU

first: Xinlong

last: Guo

first: Xiaohan

last: Song

first: Xuelian

last: Ren

first: He

last: Huang


title: The effect of PTEN inhibitor on Periodontal ligament cells

city: Bangkok

first: Suphalak

last: Phothichailert

state: --None--

address: 34  Henri-Dunant, Wang Mai, Pathumwan

institute: Chulalongkorn University

summary: Objective: Phosphatase and Tensin Homolog (PTEN) act as a negative regulator of the phosphatidylinositol-3-kinase (PI3k)/Akt pathway, which is involved in cell growth, cell proliferation, differentiation, and survival signaling. This study aimed to investigate the effects of VO-OHpic, a PTEN inhibitor, on periodontal ligament stem cells (PDLSCs).

overall_design: PDLSCs were treated with VO-OHpic at various concentrations (0.625, 1.25, 2.5, and 5 μM). Cell viability was assessed using an MTT assay, and colony forming unit efficiency was determined by Coomassie blue staining. A scratch assay was performed to evaluate cell migration. Multipotent differentiation potential was determined using Alizarin Red S staining or oil red O staining, along with immunofluorescent staining and real-time quantitative PCR for gene expression analysis. High-throughput RNA sequencing techniques were employed to analyze transcriptomic data.

first: Nunthawan

last: Nowwarote

first: Chatvadee

last: Kornsuthisopon

first: Vorapat

last: Trachoo

first: Worachat

last: Namangkalakul

first: Hiroshi

last: Egusa

first: Thanaphum

last: Osathanon


title: Cadherin-11 contributes to the heterogenous and dynamic Wnt-Wnt-β-catenin pathway activation in Ewing sarcoma

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: Ewing sarcoma (ES) is the second most common bone cancer in children, and while patients who present with metastatic disease at the time of diagnosis have a dismal prognosis. ES tumors are driven by the fusion gene EWS/Fli1, and while these tumor are genetically homogenous, the transcriptional heterogeneity can lead to a variety of cellular processes including metastasis. In this study, we demonstrate that in ES cells, the canonical Wnt/-Catenin signaling pathway is heterogeneously activated in vitro and in vivo, correlating with hypoxia and EWS/Fli1 activity.

overall_design: A4573 cells were implanted orthotopically in the pretibial space of mice followed by single cell RNA-seq

first: Masanori

last: Hayashi


title: Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (RNA-seq and RIP-seq)

city: Chicago

first: Boyang

last: Gao

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

summary: 2′-O-methylation (Nm) is an abundant RNA modification exists on different mammalian RNA species. However, potential Nm recognition by proteins has not been extensively explored. Here, we employed RNA affinity purification followed by mass spectrometry to identify Nm-binding proteins. The candidates exhibit enriched binding at known Nm sites. Interestingly, some candidates display nuclear localization and functions. We focused on the splicing factor FUBP1. Electrophoretic mobility shift assay (EMSA) validated preference of FUBP1 to Nm-modified RNA. As FUBP1 predominantly binds intronic regions, we profiled Nm sites in chromatin-associated RNA (caRNA) and found Nm enrichment within introns. Depletion of Nm led to increased exon skipping, suggesting Nm-dependent splicing regulation. The caRNA Nm sites overlap with FUBP1 binding sites, and Nm depletion reduced FUBP1 occupancy on modified regions. Furthermore, FUBP1 depletion induced exon skipping in Nm-modified genes, supporting its role in mediating Nm-dependent splicing regulation. Overall, our findings identify FUBP1 as an Nm-binding protein and uncover previously unrecognized nuclear functions for RNA Nm modification.

overall_design: RNA-seq of HepG2 cells with siFUBP1 controled with siCtrl2, U3KD controled with GFP ASO, and RIP-seq of HepG2 cells with siFBL controled with siCtrl

first: Chuan

last: He


title: Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (CLIP-seq and PAR-CLIP)

overall_design: PAR-CLIP of FUBP1 in HepG2 cells and CLIP-seq of FUBP1 in HepG2 cells with siFBL


title: Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (Nm-mut-seq)

overall_design: Nm-mut-seq of HepG2 chromatin-associated RNA (caRNA)


title: Mycoplasma bovis nucleomodulin MbovP202 modulates gene expression in BoMac cells

city: Wuhan

first: Doukun

last: Lu

address: Huazhong Agricultural University

institute: National Key Laboratory of Agricultural Microbiology

summary: We identified a novel M. bovis nucleomodulin, MbovP202, which functions as a 5-methylcytosine-specific DNA methyltransferase that localizes to the nucleus of the bovine macrophage cell line (BoMac). To investigate its regulatory role, we performed RNA sequencing to compare the mRNA expression profiles between  BoMac and BoMacMbovP202 cells. A total of 2,790 differentially expressed genes (DEGs) were identified between the two groups. Integrated analysis of Whole Genome Bisulfite Sequencing (WGBS) and RNA-Seq data revealed that genes with promoter hypermethylation and concomitant down-regulated expression were predominantly enriched in metabolic and inflammatory pathways.

overall_design: RNA-seq profiling of BoMac  (empty vector control) and BoMacMbovP202 cells (stable monoclonal cell lines expressing MbovP202)

first: Aizhen


title: Single-cell dissection of the genotype-immunophenotype relationship in glioblastoma

city: NEW YORK

first: Alexander

last: Tsankov

state: New York

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: We induced de novo brain tumor in immunocompetent genetically engineered mouse models EGFRvIII, Nf1 and PDGFB KO mice of both genders. We isolated brain tumor cells at the end stage in these mice and performed scRNA seq on these cells to compare their functional differences. scRNA demonstrated the distinct Tumor, Myeloid and Lymphoid cell population. PDGFB sample shows the higher proliferation and Wnt5a ligand expression and Nf1 showed the more mesenchymal type.

overall_design: Using immunocompetent de novo mouse models of GBM , we generated tumors in the right-frontal striatumto represent major subtypes of GBM including (Proneural-PDGFB driven), (mesenchymal-NF1 driven) and (classical-EGFRvIII driven). Each tumor subtype contains the relevant driver mutations found in their human counterparts. Brain tumor cells were isolated at the humane endpoint of these mice, and sc-RNA seq was conducted to compare their functional differences.

middle: M

first: Dolores

last: Hambardzumyan

first: Nishant

middle: K

last: Soni


title: Transcriptomic analysis of lung development in the sheep

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Much of our understanding of human lung development is based on earlier physiological studies in the sheep. Here we investigate lung development in wild-type sheep by transcriptomic analysis of proximal and distal lung tissue from day 65 to term (147 days). We also document the transcriptome of lung development at the same time points in the CF sheep model, enabling comparative studies of the impact of CF on the lung before birth,

overall_design: RNA-seq of sheep (ovis aries) proximal and distal lung epithelial tissue

first: Alekh

last: Paranjapye

first: Shih-Hsing

last: Leir

first: Jenny

last: Kerschner

first: Makayla

last: Schacht


title: Effects of LPS treatment on microglia

city: xi'an

first: Xun

last: Wu

state: Shaanxi

address: No.1 Xinsi Road, Baqiao District

institute: fourth military medical school

summary: Microglia, the most abundant type of brain-resident immune cells, continuously surveil the environment and play a central role in shaping the inflammatory state of the central nerve system (CNS). To explore the mechaniam underlying microglial inflammation， we explored the effects of LPS treatment on microglia using RNA-seq.

overall_design: In order to identify the key regulators involved in mediating microglial activation and inflammation, we conducted RNA-seq analyses in LPS-stimulated BV2 cells

first: Qu

last: yan

first: Ge

last: Shunnan

first: Guo

last: Wei

first: Wu

last: Xun


title: METTL3 regulates microglial inflammation through the m6A modification

summary: Microglia, the most abundant type of brain-resident immune cells, continuously surveil the environment and play a central role in shaping the inflammatory state of the central nerve system (CNS). We discovered that the protein expression of METTL3 (a m6A methyltransferase) were up-regulated in inflammatory microglia. We conducted MeRIP-seq analyses in LPS-stimulated microglial cells with or without METTL3 knockout. In the MeRIP-seq analysis, the m6A modifications are primarily located in a consensus “RRACH” motif, and m6A peaks mainly occur in coding sequences (CDSs), 3′ untranslated regions (3′ UTRs), and near stop codons.Further study identified that METTL3 promoted the expression of Basic Leucine Zipper Transcriptional Factor ATF-Like (BATF), which in turn directly bound to a cohort of characteristic inflammatory cytokines and chemokine genes. Collectively, our findings identified METTL3-m6A-BATF axis as a potential therapeutic target for terminating detrimental microglial inflammation

overall_design: In order to identify the key regulators involved in mediating METTL3-m6A-associated effects on microglial response, we conducted MeRIP-seq and RNA-seq analyses in LPS-stimulated microglial cells with or without METTL3 knockout.  In the MeRIP-seq analysis, the m6A modifications are primarily located in a consensus “RRACH” motif (Figure 4A), and m6A peaks mainly occur in coding sequences (CDSs), 3′ untranslated regions (3′ UTRs), and near stop codons, which were consistent with previous reports. To determine the correlation between m6A modification and gene expression, we plotted the m6A peak data against the RNA-seq data. Given that the knockout of METTL3 leads to the blocking of its methyltransferase activity and the downregulation of global m6A levels, we speculated that mRNA transcripts that carry hypomethylated m6A peaks, including the hypo-up and hypo-down genes, might be the potential targets of METTL3. Setting diffPeak.log2fc to 2 and diffExp.gene.log2fc to 2 resulted in the identification of 15 highly reliable genes with diminished m6A peaks while expression was down- or up-regulated. BATF, the only transcription factor among these genes, was reported to have binding sites in the regulatory regions of numerous inflammatory cytokines and pro-inflammatory genes. Collectively, these results suggest BATF as a vital target of METTL3 in microglia.


title: Expression profiling by high-throughput sequencing to evaluate effects of aroylated phenylenediamine HO53 on transcriptome in human undifferentiated bronchial epithelial cells (BCi-NS1.1 cell line).

city: Reykjavik

first: Iwona

middle: Teresa

last: Myszor

address: Vatnsmyrarvegur 16

country: Iceland

institute: University of Iceland

summary: We used RNA sequencing to exploit molecular mechanisms behind HO53-induced innate immune responses in undifferentiated human bronchial epithelial cells (BCi-NS1.1 cell line). We performed transcriptome analysis of undifferentiated bronchial epithelial cells (BCi-NS1.1 cell line) treated with aroylated phenylenediamine HO53 for different time points 4 h, 8 h and 24 h and compared it to transcriptome of untreated cells. The broad effect of HO53 on the gene expression in undifferentiated human lung epithelial cells (BCi-NS1.1) points towards an epigenetic event. Furthermore, genes involved in metabolic pathways (glycolysis, TCA cycles, pentose phosphate, glycosylation and gluconeogenesis) were particularly affected by HO53 treatement. The expression pattern for few relevant selected genes was reconfirmed by qRT-PCR using SYBR Green reagent.

overall_design: Expression profiling by high-throughput sequencing of HO53-treated vs untreated undifferentiated human bronchial epithelial cells (BCi-NS1.1 cell line).

first: Marjorie

middle: L

last: Barrier

middle: T

first: Snaevar

last: Sigurdsson

first: Gudmundur

last: Gudmundsson


title: Transcriptomic analysis of Arabidopsis thaliana seedlings in response to impaired mitochondrial translation

first: Jiahao

last: Li

address: No. 800 Dongchuan Road, Shanghai

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

summary: The goal of this study is to establish the global gene expression profiles of seedlings under doxycycline (Dox) treatment.

overall_design: RNA-seq was performed using Arabidopsis wild type (Col-0) seedlings exposed to doxycycline (Dox). Three biological replicates were conducted for each condition.

first: Xu

last: Wang


title: HIF1A modulates glycolysis function to governs mouse ovarian microenvironment metabolic plasticity in aging single cell resolution

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

overall_design: Single cell RNA sequencing of aging mouse ovary were generated by deep sequencing using the 10x Genomics Chromium Single Cell Gene Expression Solution

first: Ning

first: Xiaoyu

last: Zhang

first: Gunewardena

last: Sumedha

first: Yan

last: Liu


title: Transcriptomes of Wild Type tomato and slszp1 under +Al treatment

city: Beijing

first: lei

last: zhang

address: Yuanmingyuan West Rd. No.2, Beijing, China

department: College of Horticulture

institute: China Agricultural University

summary:
Purpose: Find SlSZP1 regulated genes
Methods: Total RNA was extracted from 20 days old wild-type tomato and slszp1 mutant plants treated with 60 μM Al solutions (pH 4.7). Three biological replicated samples were collected form each treatment and sequenced.
Results:A total of 40 GB clean data was obtained by transcriptome sequencing. The clean data of each sample was more than 6.11 GB, and the percentage of q30 base was more than 90.98%.
Conclusions: By RNA-seq analysis, we find potential SlSZP1-regulated genes

overall_design: mRNA profiles of 20-day old wild type (WT) and slszp1 mutant.

first: Lei

first: Dan-Hui

last: Dong

first: Yang-Dong

last: Guo


title: Inhibition of METTL3 protect against traumatic brain injury

first: Xun

last: Wu

summary: Researchers recently identified STM2457 as a first-in-class catalytic inhibitor of METTL3 and observed a promising therapeutic effect on acute myeloid leukemia. However, it is crucial to note that the existence of the blood-brain barrier (BBB) limit the efficiency of drugs entering the brain to a large extent. In order to effectively deliver METTL3 inhibitor STM2457 to the brain, we generated RVG29 (a BBB-penetrating peptide)-based modified nanoparticle system loaded with STM2457 (abbreviated as RVG-nSTM system) that targets the brain. Specifically, a mixture of STM2457, PLGA20K-mPEG2K, and PLGA20K-PEG5K-MAL was used to prepare nSTM, which was further modified with RVG29 peptide. We investigated the impact of RVG-nSTM on neuroinflammation post-TBI in mice. We performed a total RNA-seq analysis, and observed distinct gene distributions on the volcano plot. A Venn diagram revealed that 3385 genes were differentially expressed in the TBI group compared to the sham group, and treatment with RVG-nSTM reversed the expression of 1941 of these genes . The subsequent GO and KEGG analyses showed that these 1941 genes were primarily enriched in the context of inflammatory response and inflammation-related pathways. These findings were further corroborated by the observation that RVG-nSTM treatment leads to a substantial reversal of the hyperactive microglial states that are induced by TBI . Above all, RVG-nSTM could be a promising agent for the treatment of neuroinflammation after acute brain injury.

overall_design: In order to investigate whether inhibition of METTL3 protect against traumatic brain injury, we performed RNA-seq on TBI mouse brain with or without the delivery of STM2457 (a first-in-class catalytic inhibitor of METTL3)

first: Qu

last: yan

first: Ge

first: Guo


title: Treatment-associated gene expression in hematopoietic stem/progenitor cells from patients with polycythemia vera (PV)

city: Zurich

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary: The objective of the study was to assess gene expression changes in CD34+ hematopoietic stem/progenitor cells from PV patients upon ex vivo treatment with clusterin (CLU), IKK-16, their combination, with hydroxyurea (HU) or with solvent control.

overall_design: CD34+ hematopoietic stem/progenitor cells from five different PV patients were treated with CLU, IKK-16, their combination, HU or solvent control, resulting in a total of 25 samples.

first: Fabienne

last: Meier-Abt


title: Transcriptional signature for dysplastic epidermal development in human pre-malignant skin

status: Public on Apr 19 2025

city: New York

first: Sida

last: Chen

state: NY

address: 622W 168th Street

institute: Columbia University

summary: Actinic keratosis (AK) is a prolific precancerous skin lesion, which occurs in susceptible individuals due to chronic ultraviolet radiation exposure, with a propensity to develop into malignant squamous cell carcinoma (SCC). The histopathologic features of AKs include a dysplastic epithelium that is frequently, but not always, spatially limited to the interfollicular epithelium. However, the upper follicular epithelium, although equally susceptible to ultraviolet radiation (UVR) exposure, is commonly spared of dysplasia. To address these issues, our approach sought to leverage this phenomenon by profiling UVR-susceptible (interfollicular) versus -refractory (follicular) epithelium using spatial transcriptomic analysis of AK tissue sections. Unsupervised clustering analysis segregated transcriptionally distinct regions of epithelium in AK lesions that spatially overlapped with either normal follicular or dysplastic interfollicular regions and identified a total of 193 dysregulated genes in dysplastic interfollicular epidermal clusters that were conserved across multiple AKs. Next, CellChat analysis identified highly enriched cell-cell communication pathways primarily between dermal and dysplastic epidermal clusters, suggesting that perturbations in dermal-epidermal communication may be early drivers of epidermal dysplasia. Collectively, our findings elaborate a first-of-its-kind transcriptional signature for early dysplastic epidermal development in human pre-malignant skin and provide much needed insight into the longstanding clinical observation of susceptible (interfollicular) versus refractory (follicular) epithelium to ultraviolet radiation-induced dysplasia.

overall_design: Samples are human actinic keratoses specimens. Each sample represents a biological replicate. Variables, dysplastic epidermis and normal epidermis, were contained in each biological replicate.

first: Olga

last: Yarygina

first: Emma

last: Gutierrez

first: David

middle: N

last: Silvers

last: Owens


title: Au18(L-NIBC)14 targets ASC oligomerization for autoimmune disease treatment

city: 武汉WuHan

first: 澄

last: 华

state: 湖北Hubei

institute: Wuhan University of Technology

summary: Gold nanoclusters (AuNCs), unlike conventional nanoparticles, possess molecular characteristics besides ultrasmall nano-features. Recently, we and others showed that AuNCs are promising in treatments of various major diseases. However, the AuNCs used were usually mixtures, and the specific target and their relationship with AuNC structures are unclear, which largely restrict their druggability. Multiple sclerosis (MS) is an autoimmune disease (AID) implicating central nervous system (CNS), in which drug discovery is challenging. Here we used Au18(L-N-isobutyryl-L-cysteine)14 (Au18(L-NIBC)14) and Au25(L-NIBC)18, two AuNCs with the same ligand, to report their much different therapeutic effects in experimental autoimmune encephalomyelitis (EAE). We show that, Au18(L-NIBC)14, but not Au25(L-NIBC)18, specifically targets apoptosis_x0002_associated speck-like protein containing a CARD (ASC) oligomerization, thus inhibit the activation of ASC-dependent inflammasomes, resulting in comprehensive restoration of cytokine homeostasis in the CNS of EAE mice. Au18(L-NIBC)14 significantly prevents axon demyelination, protects blood-brain barrier, blocks immune cell infiltration into CNS, and completely prevents motor deficits and relieve the early-cognitive impairments of EAE mice. Remarkable efficacies were also observed in animal models of inflammatory bowel disease, psoriasis, systemic lupus erythematosus, indicating a broad prospect in AIDs treatments. Especially, definite molecular structure, specific target, clear mechanism, and exact therapeutic effects imply a good druggability of Au18(L-NIBC)14.

overall_design: Cortical tissues were collected, and total RNA was extracted for sequencing. Quality control was performed using FastQC, followed by adapter trimming and low-quality read removal with Fastp. The cleaned reads were aligned to the reference genome using Hisat2, and gene expression levels were quantified with bowtie2. Differentially expressed genes (DEGs) were identified using DESeq2, applying a threshold of |log₂FC| > 1 and false discovery rate (FDR) < 0.05. A Venn diagram was generated to visualize overlapping and unique DEGs between the Naive vs.EAE and EAE vs.Au18(L-NIBC)14 comparisons. KEGG pathway enrichment analysis was performed, with key pathways such as the NOD-like receptor signaling pathway mapped via KEGG Mapper. The expression levels of selected genes were quantified using FPKM normalization, and statistical significance was assessed using student t-tests, with results visualized in a bar plot.


title: Modulation of proteostasis by the ubiquitin-conjugating enzyme UBE2N in immunoproteasome-positive AML

city: Cincinnati

first: Kwangmin

last: Choi

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Altered protein homeostasis through proteasomal degradation of ubiquitinated proteins is a hallmark of many cancers. Ubiquitination, coordinated by E1, E2, and E3 enzymes, involves up to 40 E2-conjugating enzymes in humans to specify substrate and ubiquitin linkages. In a screen for E2 dependencies in AML, UBE2N emerged as the top candidate. To investigate UBE2N's role in AML, we characterized an enzymatically-defective mouse model of UBE2N, revealing UBE2N's requirement in AML without significant impact on normal hematopoiesis. Unlike other E2s, which mediate Lysine-48 (K48) polyubiquitination and degradation of proteins, UBE2N exclusively synthesizes K63-linked chains, stabilizing or altering protein function. Proteomic analyses and a whole genome CRISPR-activation screen in pharmacologically and genetically UBE2N-inhibited AML cells unveiled a network of UBE2N-regulated oncoproteins. UBE2N inhibition reduced their protein levels, leading to increased K48-linked ubiquitination and degradation through the immunoproteasome and revealing UBE2N activity is enriched in immunoproteasome-positive AML. Furthermore, an interactome screen identified TRIM21 as the E3 ligase partnering with activated UBE2N in AML to modulate UBE2N-dependent proteostasis. In conclusion, UBE2N maintains proteostasis in AML by stabilizing oncoproteins through K63-linked ubiquitination and prevention of K48 ubiquitin-mediated degradation through the immunoproteasome. Thus, inhibition of UBE2N catalytic function suppresses leukemic cells through selective degradation of critical oncoproteins in immunoproteasome-positive AML.

overall_design: MLL-AF9 transduced Ube2nWT or Ube2nC87S cells were treated in either 100% ethanol control or 50nM 4OHT for 48 hours in same density in triplicates. The cells were collected, and RNA was extracted using ZYMO RESEARCH Quick-RNA Miniprep kit (#R1055). After the confirmation of the RNA quality using Agilent 2100 Bioanalyzer, the libraries were prepared with polyA selection using the Truseq RNA Library Prep Kit, and the libraries were sequenced at an average depth of 30M paired-end 100bp nucleotide reads. After the quality of reads was examined using FastQC (v0.11.7, https://www.bioinformatics.babraham.ac.uk/projects/fastqc), paired-end reads were aligned against mouse mm10 genome (iGenome,https://support.illumina.com/sequencing/sequencing_software/igenome.html) using HISAT2 (v2.0.5,http://daehwankimlab.github.io/hisat2). The raw gene counts were calculated using featureCounts (v1.5.2, http://subread.sourceforge.net/) and normalized using edgeR (v3.16.5, https://bioconductor.org/packages/release/bioc/html/edgeR.html) in iGEAK (https://pubmed.ncbi.nlm.nih.gov/30841853/). Differentially expressed genes were predicted using limma/voom (v3.30.6, https://bioconductor.org/packages/release/bioc/html/limma.html).

first: Chiharu

last: Ishikawa

first: Laura

last: Barreyro

first: Avery

last: Sampson

first: Kathleen

last: Hueneman

first: Issac

first: Lyndsey

last: Bolanos

first: Mark

last: Wenderlich

first: Andrew

last: Volk

first: Stephanie

last: Watowich

first: Kenneth

last: Greis

first: Daniel

last: Starczynowski


title: Expression data from PrimeView human gene expression array

city: Zhengzhou

first: zhen

address: Dongming Road

institute: Henan Cancer Hospital

summary: Gene expression in MM.1R cells infected with shCtrl or added drug (Epirubicin Hydrochloride) was detected with a PrimeView human gene expression array.

overall_design: Gene expression profiling of shCtrl or added drug MM.1R cells was acquired and analyzed. Differentially expressed genes were identified based on fold change of mean of expression (fold change ≥ 1.3) and FDR (< 0.05) from P value calculated based on linear model of empirical Bayesian distribution. In total, 1055 upregulated genes and 761 downregulated genes were characterized.

first: Zhen

first: Yiran

last: Li


title: Comprehensive Transcriptomic and Translational Profiling of Human Embryonic Stem Cell Differentiation to Definitive Endoderm and Pancreatic Progenitors via RNA-seq and Ribo-seq

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

summary: This study presents a detailed transcriptomic and translational analysis of human embryonic stem cells (hESCs) as they differentiate into definitive endoderm (DE) and pancreatic progenitor stages (PP1 and PP2). We employed RNA sequencing (RNA-seq) to capture the transcriptional landscape and ribosome profiling (Ribo-seq) to assess translational regulation throughout the differentiation process.

overall_design: hESCs were differentiated into definitive endoderm (DE), followed by two stages of pancreatic progenitors (PP1 and PP2). RNA-seq and Ribo-seq were performed at each differentiation stage to assess both transcriptome-wide mRNA expression and ribosome occupancy, respectively.

first: Wei

last: Jiang

first: Chenchao

last: Yan


title: SASP-related signals and SASP gene expression profiles in senescent cells after 18β-GA treatment.

city: Guangzhou

first: 白

last: 可

address: Huangpu Avenue 601

department: College of Life Science and Technology

institute: Jinan University

summary: The accumulation of senescent cells contributes to age-related organ degradation and susceptibility to chronic diseases. These cells exhibit the senescence-associated secretory phenotype (SASP), affecting cellular and overall aging. 18β-GA has anti-inflammatory effects。RNA-seq was used to analyze the changes in SASP genes and signaling pathways in senescent cells after 18β-GA treatment. 18β-GA can effectively inhibit the activation of IL6 downstream signaling pathways and reduce the expression of SASP-related genes in senescent cells.

overall_design: To detect the effect of GA on SASP in senescent cells. Replicatively senescent IMR-90 cells were incubated with or without 18β-GA (50 μM) for 0 h, 2 h, 4 h, 8 h, 12 h, 24 h. Collect cells and analyze using RNA-seq.


title: The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E18.5-cKO_RNAseq]

city: Shenzhen

first: Jian

last: Zhang

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

summary: The reversible epitranscriptomic mark, 5-methylcytosine (m5C) modification, is implicated in numerous cellular processes, but its role in neuronal development remains largely unexplored. In this study, we discovered high expression of the m5C reader Ybx1 in the developing mouse cortex. To elucidate its role in cortical development, Ybx1 was deleted in mouse embryonic cortical neural stem cells (NSCs). Interestingly, the deletion of Ybx1 led to perinatal mortality in mice, along with abnormal cortical development. Cortical progenitor cells lacking Ybx1 exhibited impaired proliferation and differentiation. Multi-omics analysis identified the target mRNAs of Ybx1, which encode the key cell cycle regulatory proteins, such as cyclin D2 (Ccnd2). Ybx1 was found to regulate the stability of its target transcripts. Both knockdown and overexpression of Ybx1 targets via in utero electroporation confirmed that they mediated the Ybx1 regulation of proliferation and differentiation of neural precursor cells. Further mechanistic analysis showed that deletion of Ybx1 resulted in the blocking of G1 to S phase transition in the cortical progenitor cells. This study highlights the crucial function of the m5C reader protein Ybx1 in promoting cell cycle progression of the embryonic cortical progenitors, essential for proper cortical development.

overall_design: We perform high-throughput sequencing of mouse cortex with or without deletion of Ybx1 to profile RNA expression.  For the RNA-seq experiments, we performed 3 batches of sequencing experiments in different biological replicates to account for the technical variation

first: Zhuoxuan

last: Yang

first: Pengfei

last: Che

first: Sheng-Jian

last: Ji


title: The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [RIP-seq]

overall_design: 2 replicates, each containing input and IP samples


title: The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E13.5-cKO_RNAseq]


title: Transcriptome analysis of eutopic endometrial mesenchymal stem cells in patients with adenomyosis by RNA-sequencing

city: Nanjing

first: Tao

last: Gui

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

summary: To identify differentially expressed genes (DEGs) and molecular pathways in endometrial mesenchymal stem cells (eMSCs) from adenomyosis patients and provide a new insight into disease mechanisms at transcriptome level.

overall_design: Gene expression profiling of normal endometrial mesenchymal stem cells (N-eMSCs) and adenomyotic endometrial mesenchymal stem cells(A-eMSCs) were analyzed by using RNA-sequencing.

first: Guiping

last: Wan

first: Meiling

last: Cao


title: The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression.

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

overall_design: Refer to individual Series


title: Incorporating programmable DNA-binding domains enhances the efficiency and flexibility of miniature CRISPR base editors

status: Public on Apr 18 2025

city: Xihu District, Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

summary: The therapeutic application of base editors is currently limited by their large sizes, which are often beyond the packaging capabilities of adeno-associated viral (AAV) vectors. Despite recent progress in mega genome mining that has identified a diverse array of compact CRISPR proteins (e.g. Cas12f, TnpB, and IscB), the resulting miniature base editors are often exhibited reduced activities and a limited targeting scope, leaving a broad spectrum of disease-relevant genetic variants inaccessible. In this study, we have developed a platform, designated as Zinc Finger Proteins (ZFP)-enhanced miniature base editor (zmBE), which integrates programmable DNA-binding domains to enhance the efficiency and expand targeting scope of miniature base editors, including those based on Un1Cas12f1 and OgeuIscB. Utilizing protein language model (PLM) for the design of ZFPs further simplified development and optimization of zmBEs tailored to a specific target. Leveraging these methodologies, we engineered a zmBE that effectively induced the SMN2 exon 7 A6>G conversion and restored SMN2 exon 7 inclusion. Our study thus provides a versatile platform for developing miniature base editors for in vivo therapeutic applications.

overall_design: Using RNA-seq to detect RNA off-target effect induced by dCas12f-ABE and dCas12f-ABE-ZFP, and unedited cells were included as mock.

first: Qianyue

last: Huang

first: Geng


title: TSG-6 activated MSC-derived Extracellular Vesicles present altered micro-RNA contents and ameliorate the inflammatory phenotype of macrophages in vitro

city: Rochester

first: Iker

last: Martinez-Zalbidea

address: 1 Lomb Memorial Dr

department: Department of Biomedical Engineering

institute: Rochester Institute of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Mesenchymal stem cell-derived extracellular vesicles (MSC-EVs) have shown promising immunomodulatory properties; however, strategies to enhance their therapeutic potential remain limited. Here, we employed CRISPR activation of the gene TSG-6 in MSCs to evaluate the impact of elevated TSG-6 on micro-RNA (miRNAs) EV cargo and immunomodulatory function in an in vitro macrophage model. CRISPR-mediated gene activation was confirmed by RT-qPCR, demonstrating more than an 1800-fold increase in TSG-6 mRNA compared to controls. EVs were isolated from TSG-6 overexpressing MSCs and thoroughly characterized by nanoparticle tracking analysis, transmission electron microscopy, and Western blot, confirming their typical size distribution, morphology, and surface markers. Small RNA sequencing of these EVs revealed 15 differentially expressed miRNAs relative to EVs from control MSCs. When THP-1–derived macrophages were stimulated with LPS and treated with TSG-6-overexpressing MSC-EVs, a marked reduction in pro-inflammatory cytokine gene expression (IL-1β, CCL2, CXCL10, and TNF-α) and secreted protein levels (CCL2, TNF-α, CXCL1, and MIP-3α) was observed. Taken together, these findings demonstrate that CRISPR-based TSG-6 activation reprograms MSC-EV miRNA cargo (as well as their protein cargo, as previously shown), which can boost their anti-inflammatory effects. These findings underscore the promise of CRISPR-activation as a novel platform for boosting the bioactive properties of MSC-EVs and enhancing immunotherapeutic efficacy.

overall_design: RNA-seq profiling of Extracellular Vesicles (EVs) obtained from 3 different populations of mesenchymal stem cells. These populations are: Wild-Type, Non-Target controls (a negative control), and TSG-6 activated (CRISPR activation of gene TNFAIP6/TSG-6). Samples are in triplicate, with miR samples labeled as follows: Non-Targets labeled: “NA1_NA2_NA3” “NB1_NB2_NB3” “NTA_EV_RNA_NTB_EV_RNA_NTC”; TSG-6 activated labeled: “TA1_TA2_TA3” “TB1_TB2_TB3” “TSGA_EV_RNA_TSGB_EV_RNA_TSGC_EV_RNA”; Wild type labeled:“WA1_WA2_WA3” “WB1_WB2_WB3” “WTA_EV_RNA_WTB_EV_RNA_WTC_EV_RNA”.

first: Alyssa

last: Rzasa

first: Varun

last: Puvanesarajah

first: Wolfgang

last: Hitzl

first: Karin

last: Wuertz‑Kozak


title: The role of smooth muscle cell-derived IL-18 in uterine immune milieu and fetoplacental growth

city: Tokyo

first: Hajime

last: Ino

address: 1-1-5, Sendagi, Bunkyo-ku

institute: Nippon Medical School

summary: There is a close relationship between pregnancy and immune responses. For example, an anti-inflammatory state is essential for maintaining pregnancy by promoting maternal tolerance toward the semi-allogeneic fetus, whereas pro-inflammatory conditions are crucial for processes such as maternal tissue remodeling during embryo implantation and the induction of labor. Increasing evidence suggests that various cell types within the uteroplacental immune environment contribute to these immune responses, and immunological approaches have been employed to investigate the pathophysiology and potential treatments of pregnancy-related complications. Interleukin-18 (IL-18) is a unique cytokine with both pro-inflammatory and anti-inflammatory properties; however, its roles during pregnancy remain largely unclear. We have found that smooth muscle cells (SMCs) in the uterine myometrium are an important source of IL-18, and that the homeostatic production of IL-18 promotes fetal development by supporting maternal uterine remodeling and placental growth. To further investigate the effects of IL-18 on the uterine immune milieu, we established SMC-specific Il18 conditional knockout (cKO) mice and performed RNA sequencing of uterine immune cells.

overall_design: RNA-sequencing profiles of uterine immune cells collected from Il18-floxed (control) mice and Il18-floxed;Sm22a-cre (SMC-specific Il18 cKO) mice.

first: Yasuyuki

last: Negishi

first: Yumi

last: Horii

first: Eri

last: Koike

first: Richard

middle: A

last: Flavell

first: Shunji

last: Suzuki

first: Rimpei

last: Morita


title: Sex-lethal is recruited to chromatin to promote neuronal tRNA synthesis in males through RNA Polymerase III regulation [RNA-seq]

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

summary: The RNA-binding protein sex-lethal (Sxl) is classically defined as a master regulator of sex determination and RNA splicing in Drosophila melanogaster. However, this role is not conserved in all species and functions beyond this canonical pathway remain largely unexplored. Here, we uncover a splicing-independent function for Sxl at the chromatin level in the Drosophila brain. Using Targeted DamID (TaDa) profiling in larval neurons, we identify widespread recruitment of Sxl to promoter regions, independent of sex and RNA binding activity. Notably, Sxl chromatin occupancy exhibits near-complete overlap with Polr3E (RPC37), an RNA Polymerase III subunit, with Sxl binding abolished upon Polr3E knockdown. Depletion of Sxl in mature male neurons equally induces widespread transcriptional changes, particularly in metabolic genes, and improves negative geotaxis during ageing, phenotypes that closely mirror Polr3E knockdown. Conversely, overexpression of SxlRAC isoform enhances tRNA synthesis and upregulates metabolic gene expression. Together, these findings reveal a previously unrecognised role for Sxl in regulating Pol III activity via Polr3E, promoting tRNA synthesis and supporting neuronal metabolism. Given the emerging tie between Pol III regulation and neuronal ageing, our study highlights Sxl as a novel modulator of neuronal homeostasis.

overall_design: These are RNAseq experiments to examine transcriptional changes when Sxl and Polr3E are knocked down with RNAi, as well as when SxlRAC or SxlRNA (mutated RNA binding sites) are mis/overexpressed. RNAi and mis/overexpression was induced in Drosophila male adult neurons and then whole heads collected for RNAseq.

first: Freya

last: Storer


title: Sex-lethal is recruited to chromatin to promote neuronal tRNA synthesis in males through RNA Polymerase III regulation


title: Temporal Differences in Progenitor Metabolism Shape Regional Brain Growth during Development [scRNA-seq]

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

institute: University of Geneva

summary: Mammalian brain development is characterized by disproportionate forebrain expansion, yet the mechanisms underlying this regional growth specificity remain poorly understood. Here, we provide a single-cell-resolution birthdate atlas of the mouse brain (www.neurobirth.org), which reveals that while hindbrain neurogenesis is transient and restricted to early development, forebrain neurogenesis is temporally sustained through reduced consumptive divisions of ventricular zone progenitors, maintaining its germinal pool. This atlas additionally reveals region-specific patterns of direct and indirect neurogenesis. Using single-cell RNA sequencing, we identify evolutionarily conserved cell-cycle programs and metabolism-related molecular pathways that control regional temporal windows of proliferation. We identify the late forebrain-enriched mitochondrial protein Fam210b as a key regulator using in vivo gain- and loss-of-function experiments. Fam210b elongates mitochondria and increases lactate production, which promotes progenitor self-renewing divisions and, ultimately, larger clonal size of their progeny. Together, these findings indicate spatiotemporal heterogeneity in mitochondrial function regulates progenitor cycling behavior and regional neuronal production during brain development.

overall_design: hPSC differentiated into neocortical and hindbrain neural stem cell were harvested for single cell RNA sequencing at 5, 10, 13,15,17 and 20 days in vitro (DIV)

first: Eleonora

last: Conti

first: Oliver

last: Harshnitz

first: Natalia

last: Baumann


title: Transcriptomic response of apple (Malus x domestica Bork. cv. Húsvéti rozmaring) shoot explants to in vitro cultivation on media containing thidiazuron or 6-benzylaminopurine riboside

city: Nyíregyháza

first: Judit

last: Dobránszki

state: Szabolcs-Szatmár-Bereg

address: Westsik Vilmos út 4-6.

department: Centre for Agricultural Genomics and Biotechnology

country: Hungary

institute: University of Debrecen

summary: The effects of two cytokinins (thidiazuron and 6-benzylaminopurine riboside), each applied at 4.5 μM, were studied on mRNA transcription of in vitro apple shoots. Transcriptomic response was investigated at two time points; at 48 h and 4 weeks (end of the subculture) after the cytokinin application

overall_design: 20-mm-long shoot explants from in vitro maintained shoot cultures of apple (Malus x domestica Borkh. cv. Húsvéti rozmaring) were used as the source for the experiments. In vitro shoots served as explant source were maintained on MS (Murashige and Skoog, 1962) medium supplemented with 2.22 μM 6-benzylaminopurine (BA), 0.49 μM indole butyric acid (IBA), 0.58 μM gibberellic acid (GA3), 3% (w/v) sucrose, and 0.7% (w/v) agar-agar. ). Before autoclaving for 20 min, at 121 °C and 105 Pa, the pH of the medium was adjusted to 5.8. Each culture vessel contained 70 ml of medium and five shoot explants. Shoot cultures were grown at 23±2 °C; under 16/8 photoperiod, at light intensity of 106 µmol s-1 m-2. However, in the last subculture before the experiments, shoots were grown in vitro on cytokinin-free medium to avoid the after-effects of cytokinin in the experiments. 4-week-old in vitro shoots grown on cytokinin-free medium were separated from in vitro mother shoots, cut into 20-mm-long segments and placed on experimental media. Except for the cytokinin content, the experimental media were the same as the medium used for maintenance described above. Three different cytokinin-containing media were used during the experiments; medium without cytokinin (control), media containing 4.5 μM thidiazuron (TDZ) and 4.5 μM 6-benzylaminopurine riboside (BAR), respectively.

first: Dóra

last: Farkas

first: Viktor

last: Ambrus

first: Anita

last: Király

first: Neama

last: Abdalla


title: Long non-coding RNA LOC401312 induces radiosensitivity through upregulation of CPS1 in non-small cell lung cancer

first: Zhengyue

last: Cao

address: No. 27 Taiping Road, Haidian District

institute: State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine

summary: Long noncoding RNAs (lncRNAs), non-protein-coding transcripts exceeding 200 nu-cleotides, are critical regulators of gene expression through chromatin remodeling, transcriptional modulation, and post-transcriptional modifications. While ionizing radiation (IR) induces cellular damage through direct DNA breaks, reactive oxygen species (ROS)-mediated oxidative stress, and bystander effects, the functional in-volvement of lncRNAs in radiation response remains incompletely characterized. Here, through genome-wide CRISPR activation (CRISPRa) screening in non-small cell lung cancer (NSCLC) cells, we identified LOC401312 as a novel radiosensitizing lncRNA, the stable overexpression of which significantly enhanced IR sensitivity. Tran-scriptomic profiling revealed that LOC401312 transcriptionally upregulates car-bamoyl-phosphate synthase 1 (CPS1), a mitochondrial enzyme involved in pyrimidine biosynthesis. Notably, CPS1 overexpression recapitulated the radiosensitization phe-notype observed with LOC401312 activation. Mechanistic investigations revealed that CPS1 suppresses the phosphorylation of ATM kinase (Ser1981) and XRCC1 protein levels, which are key mediators of DNA damage checkpoint activation and base exci-sion repair, respectively. This study establishes the LOC401312-CPS1-ATM/XRCC1 axis as a previously unrecognized regulatory network governing radiation sensitivity, highlighting the potential of lncRNA-directed metabolic rewiring to impair DNA re-pair fidelity. Our findings not only expand the functional landscape of lncRNAs in DNA damage response but also provide a therapeutic rationale for targeting the LOC401312-CPS1 axis to improve radiotherapy efficacy in NSCLC.

overall_design: RNA-seq profiling of A549 cell lines overexpressing LOC401312 using the piggybac system and A549 cell lines transfected with empty vector.

first: Tiantian

last: Wang

first: Fumin

last: Tai

first: Rui

last: Zhai

first: Hujie

last: Li

first: Xiaofei

last: Zheng

first: Changyan


title: Sex-lethal is recruited to chromatin to promote neuronal tRNA synthesis in males through RNA Polymerase III regulation [small RNA-seq]

first: Tony

last: Southall

overall_design: These is a smallRNAseq experiment to examine transcriptional changes of small RNAs when SxlRAC is mis/overexpressed. Mis/overexpression was induced in Drosophila male adult neurons and then whole heads collected for RNA extraction.

first: Freya


title: cGAS Suppresses β-cell Proliferation by a STING-independent but CEBPβ-dependent Mechanism

city: Changsha

first: Zixin

last: Cai

address: Renmin middle road 139

institute: Second xiangya hospital

summary: Aims/hypothesis cGAS (cyclic GMP-AMP synthase) has been implicated in various cellular processes, but its role in β-cell proliferation and diabetes is not fully understood. This study investigates the impact of cGAS on β-cell proliferation, particularly in the context of diabetes. Methods Utilizing mouse models, including cGAS and STING (stimulator of interferon genes) knockout mice, we explored the role of cGAS in β-cell function. This involved β-cell-specific cGAS knockout (cGASβKO) mice, created by breeding cGAS floxed mice with transgenic mice expressing Cre recombinase under the insulin II promoter. We analyzed cGAS expression in diabetic mouse models, evaluated the effects of cGAS deficiency on glucose tolerance, and investigated the molecular mechanisms underlying these effects through RNA sequencing. Results Our study found that cGAS expression is upregulated in the islets of diabetic mice and in response to high glucose conditions in MIN6 cells. Global cGAS deficiency enhanced glucose tolerance, while β-cell-specific cGAS knockout improved glucose intolerance under high-fat diet conditions. Interestingly, STING knockout did not affect pancreatic β-cell mass, suggesting a STING-independent mechanism for cGAS's role in β-cells. Further analyses revealed that cGAS deficiency leads to increased β-cell proliferation and reduced expression of CEBPβ, a known suppressor of β-cell proliferation. This effect appears to be mediated by a STING-independent pathway and is specific to pancreatic tissue. Conclusions/interpretation Our findings indicate that cGAS plays a pivotal role in modulating β-cell proliferation and glucose homeostasis, potentially through regulating CEBPβ expression in a STING-independent manner. This study highlights the importance of cGAS in diabetes pathology and suggests it as a potential therapeutic target for enhancing β-cell proliferation in diabetes treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for islets from WT and cGASβKO mice.

first: Jingjing

last: Zhang


title: Extrachromosomal DNA Couples with ATM-mediated DNA Damage Response for Genome Instability in Tumors

first: haiyun

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology

summary: Extrachromosomal DNA (ecDNA) drives the evolution of cancer cells by conferring survival advantages over normal cells. However, the functional importance of ecDNA replication and maintenance is yet to be evaluated, and the molecular components that contribute to these processes remain largely unknown. Here, using CRISPR-C (circularization of genes and chromosomes by CRISPR) technology and synthetic circular DNA mimicking ecDNA identified in tumors, we generated ecDNA-positive (ecDNA+) cell models. Using these models, we identified the proteins involved in ecDNA replication and maintenance and found that DNA damage response (DDR)-related pathways were significantly enriched. We further demonstrated that ecDNA replication led to increased DDR and genome instability, and DDR was also essential for ecDNA maintenance. This is consistent with observations that ecDNA+ tumors exhibited higher DDR scores than ecDNA-negative (ecDNA–) tumors in patients. ATM, MDC1, and CHK2 were activated in ecDNA+ cells compared to ecDNA– cells. Moreover, ecDNA+ cells were more sensitive to ATM and CHK2 inhibition. We further found that topoisomerases and DNA ligase III (LIG3) are critical regulators for ecDNA replication, maintenance, and related DDR. In summary, our findings of the reciprocal interactions between ecDNA and DDR provide new insights into detection and therapy for ecDNA+ tumors.

overall_design: We performed END-Seq and WGS according to the protocol in our previous studies with some modifications. For WGS, entirely digestion (2 hour) with proteinase K (0.5 mg/ml) and RNase A (0.2 mg/ml) in PBS at 65 ℃, genomic DNA was extracted from cells with phenol:chloroform:isoamyl alcohol (25:24:1, PH 7.8) and precipitated with ethanol. The genomic DNA was resuspended in TE buffer and sonicated (Covaris M220) in AFA milliTUBEs (Covaris. 520045) to obtain 200~500 bp fragments. Sonication parameters: PIP 50, duty factor 10%, cycles 200, processing time 170 s. Then, the DNA was purified using the DNA Clean & Concentrator™-5 (ZYMO, D4004) kit. The WGS libraries were prepared with the fragmented DNA (1 µg) using the VAHTS® Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607). The WGS libraries were sequenced for at least 50 G data with PE150 on NovaSeq 6000. For END-seq, plugs making, DSB end blunting, A-tailing, ligation of END-Seq adapter 1, DNA shearing and extractio and streptavidin capture of labeled DSB ends, blunting, A-Tailing ligation of END-Seq adapter 2, and PCR Library amplification were implemented in sequence.

first: Haiyun

last: Gan

first: Xing

last: Kang

first: Jiaqi

last: Zhou

first: Congcong

last: Tian


title: Sex Lethal is recruited to chromatin  by RNA polymerase III [DamID-seq]

summary: We discovered that the splicing factor Sex lethal (Sxl) also associates strongly with chromatin and that this association is not linked to its RNA-binidng capacity, nor its N- or C-terminal domains. We also found that Sxl is recruited to chromatin by the RNA polymerase III subunt Polr3E.

overall_design: Profiling of Sex lethal (Sxl) and Polr3E DNA binding in larval neurons of the Drosophila brain. Also includes binding of Sxl mutants and Sxl in a Polr3E RNAi background.

middle: D

first: Colin

last: McClure


title: Fatty acid oxidation downregulation in alveolar epithelial 2 cells promotes acute lung injury in obesity

first: Genomics-core-facility

last: WCM

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Obesity is associated with increased risk for acute respiratory distress syndrome (ARDS). High fat diet induced obesity was linked to increased lung injury and bronchoalveolar lavage fluid (BALF) free fatty acids in a hyperoxic model of ARDS. In this study, we show significant transcriptional downregulation of fatty acid oxidation (FAO), the mitochondrial process of breaking down fatty acids, in alveolar epithelial type 2 cells (AEC2) of obese compared to lean mice after hyperoxia. AEC2 from obese mice exhibited increased intracellular lipids, more severe mitochondrial bioenergetic failure and reduced ATP production after hyperoxia compared to lean mice. FAO downregulation in AEC2 through a genetic mouse model targeting carnitine palmitoyltransferase 1A (Cpt1aloxp/loxpSftpcCreERT2+/– mice)  resulted in further increased BALF fatty acids and lung injury in obese mice. High fat diet was associated with markers of impaired alveolar epithelial regeneration after hyperoxia, which include reduced surfactant AEC2 lineage markers, as well as reduced surfactant related phospholipids in hyperoxic AEC2, and increased BALF surface tension. In a reanalysis of a human molecular single-cell lung atlas of COVID19 ARDS, significant downregulation of the FAO signature in AEC2 compared to controls was observed only in ARDS patients with BMI >30, and not those with BMI <30.

overall_design: The aim of this study was to explore the role of FAO in obesity associated acute lung injury. C57BL/6 mice received 60% fat versus ingredient matched 10% fat diet for 12 weeks. Mice were exposed to >95% oxygen to induce lung damage. AEC2 were isolated for RNA sequencing, lipidomics, Seahorse, and Western Blot.

first: E

last: Kallinos

first: Kuei-Pin

last: Chung

first: Lisa

last: Torres

first: Divya

last: Bhatia

first: Baran

last: Ersoy

first: William

middle: Z

first: Heather

last: Stout Delgado

first: Augustine

last: Choi

first: Maria

last: Plataki


title: MeRIP-seq analysis of replicative senescent MEFs and WI-38 cells

first: Zixin

last: Chen

state: 广东

address: Dongchuan Road

institute: Guangdong General Hospital

summary: Cellular senescence is the most intuitive manifestation of individual senescence, and m6A is one of the most common modifications in mRNA, playing an important role in regulating gene expression, splicing, RNA stability, and mRNA degradation. Previous research has suggested that m6A levels play an important role in the occurrence and development of aging and aging-related diseases. However, there are few reports on the role of m6A in cellular senescence. Here, we conducted combined MeRIP-seq and RNA-Seq analyses on non-senescent and senescent MEFs and WI-38 cells. The results revealed substantial disparities in the distribution of m6A sites across the transcriptome between senescent and non-senescent cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We then performed RNA-seq (also as input) and MeRIP-seq analysis using non-senescent and replicative senescence MEFs and WI-38 cells.

first: Liqian

first: Zhongjun

first: Guoxiang

last: Jin


title: Temporal Differences in Progenitor Metabolism Shape Regional Brain Growth during Development [TrackerSeq]

first: Denis

last: Jabaudon

overall_design: CD1 mice embryo were electroporated at E12 with CRIPSRi system with/without Fam210b gRNA and TrackerSeq in the neocortex and collected for 3' single cell transcriptomics at P1

first: Awais

last: Javed

first: Natalia

last: Baumann


title: Temporal Differences in Progenitor Metabolism Shape Regional Brain Growth during Development

overall_design: CD1 mice embryo were electroporated at E14 in the neocortex and collected for 3' single nucleus transcriptomics at E15


title: Design and Biological Activity of a Novel Urea Compound Against Glioblastoma [HK-374]

status: Public on Apr 17 2025

city: Los Angeles

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

institute: UC Los Angeles

summary: Despite advances in surgery and radiotherapy, glioblastoma (GBM) remains the deadliest adult brain cancer with unacceptable low median survival rates. Targeted therapies and biologics have failed to improve outcome and the standard-of-care against GBM has not changed in two decades. GBM, like many solid tumors are thought to be organized hierarchically with a small number of radiation- and chemotherapy-resistant glioma stem cells (GSCs) producing more differentiated progeny and can repopulate tumors after sublethal treatment.In this study we sought to develop novel compounds that cross the blood-brain barrier (BBB), target existing GSCs and interfere with glioma cell plasticity to prevent the induction of GSCs in response to irradiation. We show that novel urea compounds target existing GSCs, prevent the radiation-induced conversion of non-stem glioma cells into GSCs and prolong the median survival in mouse models of GBM with minimal normal tissue toxicity.

overall_design: HK-374 gliomaspheres were plated onto the Poly-D-Lysine/Laminin coated 6-well plate (#354595, Corning) and treated with MXC-017 at a concentration of 10 µM, one hour before receiving a single dose of 4 Gy the next day. Five days post-irradiation, the cells were collected for sequencing.

first: Ling

last: He


title: Neutrophils are immobilized at the ductular reaction and promote biliary epithelium expansion in chronic liver injury

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Neutrophils play a central role in tissue inflammation. However, their dynamic behavior and function in chronic injury is largely unknow. Here, we show that, in chronic liver injury, neutrophils are recruited to the ductular reaction, where they are immobilized for a prolonged period of time, acquiring an aged phenotype and an altered functionality. Moreover, neutrophils depletion or inhibition of their recruitment reduced ductular reaction expansion, which was found to be NETosis and elastase-dependent. Overall, chronic liver injury alters dthe dynamics, phenotype and function of neutrophils, which promote biliary epithelium expansion and maladaptive wound-healing response.

overall_design: Liver and circulating neutrophils from 1 week-treated DDC mice (n=3) were isolated by Ly6G immunomagnetic separation after liver suspension percoll gradient and blood lysis.

first: S

last: Ariño

first: B

last: Aguilar-Bravo

first: M

last: Coll

first: J

middle: J

first: P

last: Sancho-Bru


title: The m5C reader Ybx1 regulates embryonic cortical neurogenesis by promoting the progenitor cell cycle progression [E13.5-KD_RNAseq]

first: Jian

last: Zhang

summary: The reversible epitranscriptomic mark, 5-methylcytosine (m5C) modification, is implicated in numerous cellular processes, but its role in neuronal development remains largely unexplored. In this study, we discovered high expression of the m5C reader Ybx1 in the developing mouse cortex. To elucidate its role in cortical development, Ybx1 was deleted in mouse embryonic cortical neural stem cells (NSCs). Interestingly, the deletion of Ybx1 led to perinatal mortality in mice, along with abnormal cortical development. Cortical progenitor cells lacking Ybx1 exhibited impaired proliferation and differentiation. Multi-omics analysis identified the target mRNAs of Ybx1, which encode the key cell cycle regulatory proteins, such as cyclin D2 (Ccnd2). Ybx1 was found to regulate the stability of its target transcripts. Both knockdown and overexpression of Ybx1 targets via in utero electroporation confirmed that they mediated the Ybx1 regulation of proliferation and differentiation of neural precursor cells. Further mechanistic analysis showed that deletion of Ybx1 resulted in the blocking of G1 to S phase transition in the cortical progenitor cells. This study highlights the crucial function of the m5C reader protein Ybx1 in promoting cell cycle progression of the embryonic cortical progenitors, essential for proper cortical development.

overall_design: We perform high-throughput sequencing of mouse cortex with or without deletion of Ybx1 to profile RNA expression.  For the RNA-seq experiments, we performed 3 batches of sequencing experiments in different biological replicates to account for the technical variation

first: Zhuoxuan

last: Yang

first: Pengfei

last: Che

first: Sheng-Jian

last: Ji


title: Design and Biological Activity of a Novel Urea Compound Against Glioblastoma [HK-244_scRNAseq_MXC-017_in_vitro]

overall_design: HK-244 gliomaspheres were plated onto the Poly-D-Lysine/Laminin coated 6-well plate (#354595, Corning) and treated with MXC-017 at a concentration of 10 µM, one hour before receiving a single dose of 4 Gy the next day. Five days post-irradiation, the cells were collected for sequencing.


title: Identification and characterization analysis of the different  genes in Rag1-/- mouse injected with CD8+TSCM cells induced by CUS using RNA-seq

first: Xiaoyu

last: Yu

state: Jiangsu

address: Dingjiaqiao 87

institute: Southeast univeristy

summary: Whole RNA-sequencing analysis was performed and analyzed by Lc. Biotech Co. Ltd. (Hangzhou, China). hippocampus tissue from the PBS_WT group, PBS_Rag1-/- group, Ctr CD8+TSCM_Rag1-/- group, and  CUS CD8+TSCM_Rag1-/-  group were collected in TRIzol. Total RNAs were extracted from Trizol. UMI technology was used to label each sequence fragment with sequence tags, which minimized the interference of duplication caused by PCR amplification on the quantitative accuracy of the transcriptome. RNA sequencing reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was evaluated by calculating fragments per kilo base of exon per million fragments mapped (FPKM).

overall_design: Examination of different genes by injection of CD8+TSCM cells in Rag1-/- mouse  by RNA-seq.

first: Honghong

last: Yao


title: Modulation of plant immunity and bacterial virulence by phage biocontrol

city: Jülich

first: Sebastian

middle: Hermann

last: Erdrich

state: Nordrhein-Westfalen

address: Wilhelm-Johnen-Straße

department: Institute of Bio- and Geosciences

institute: Forschungszentrum Jülich

summary: Bacteriophages are increasingly recognised as key players in modulating plant-microbe interactions, including their potential in the biocontrol of plant pathogenic bacteria.   In this study, we investigated the tripartite interaction between, Arabidopsis thaliana, the bacterial plant pathogen Xanthomonas campestris pv. campestris (Xcc), and the lytic phage Seregon. Using meta-transcriptomic profiling, we characterized host and pathogen responses during infection and phage treatment. While a single phage treatment did not lead to the eradication of Xcc, treatment with phage Seregon significantly mitigated Xcc-induced disease symptoms, restoring leaf growth to levels comparable to the uninfected control within 14 days post-inoculation. Our data revealed that phage-mediated protection is associated with early bacterial recognition and suppression of jasmonate (JA)-related responses in the host. Analysis of nuclear localized reporter plant cell lines further confirmed a significant reduction in ROS levels in phage-treated plants. Concurrently, Xcc exhibited significant transcriptional downregulation of key virulence factors in the presence of the phage, including the genes encoding the type III secretion system, its associated effectors, and components involved in flagella biosynthesis. Remarkably, phage treatment did not lead to a significant increase in bacterial resistance to phage infection, which is in stark contrast to in vitro conditions. Taken together, this study provides first mechanistic insight into how phages can be harnessed to shape plant-pathogen interactions and highlights their potential role in enhancing plant resilience through targeted modulation of both host immunity and pathogen behaviour.

overall_design: RNA-Seq of a Tripartite interaction consisting of Arabidopsis thaliana Col-0 - Xanthomonas campestris (strain 8004) - Xanthomonas phage Seregon. Day 0, 2 and 7 post inocculation. Samples were double rRNA depleted.

first: Milan

last: Zupunski

first: Ulrich

last: Schurr

first: Guido

last: Grossmann

first: Julia

last: Frunzke

first: Borjana

last: Arsova


title: Extracellular vesicle-derived microRNA crosstalk between equine chondrocytes and synoviocytes – an in vitro approach

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary: We describe a novel technique to analyze the extracellular vesicle (EV)-derived microRNA (miRNA) crosstalk between equine chondrocytes and synoviocytes. Donor cells (chondrocytes, n=8; synoviocytes, n=9) were labelled with 5-ethynyl uridine (5-EU); EVs were isolated from culture media and incubated with recipient cells (chondrocytes [n=5] were incubated with synoviocyte-derived EVs, and synoviocytes [n=4] with chondrocyte-derived EVs). Total RNA was extracted from recipient cells; the 5-EU labelled RNA was recovered and sequenced. Differential expression analysis (using edgeR v3.32), pathway analysis, and miRNA target prediction were performed. Overall, 198 and 213 miRNAs were identified in recipient synoviocytes and chondrocytes, respectively. The top five most abundant miRNAs were similar for synoviocytes and chondrocytes (eca-miR-21, eca-miR-221, eca-miR-222, eca-miR-100, eca-miR-26a), and appear to be linked to joint homeostasis. There were nine differentially expressed (p<0.05) miRNAs (eca miR-27b, eca-miR-23b, eca-miR-31, eca-miR-191a, eca-miR-199a-5p, eca-miR-143, eca-miR-21, eca-miR-181a and eca-miR-181b) between chondrocytes and synoviocytes, which appear to be linked to migration of cells, apoptosis, cell viability of connective tissue cell, and inflammation. In conclusion, the reported technique was effective in recovering and characterizing the EV-derived miRNA crosstalk between equine chondrocytes and synoviocytes and allowed the identification of EV communicated miRNA patterns potentially related to cell viability, inflammation, and joint homeostasis.

overall_design: This study investigated the extracellular vesicle (EV)-derived microRNA crosstalk between equine chondrocytes and synoviocytes. Donor cells (chondrocytes, n=8; synoviocytes, n=9) were labelled with 5-ethynyl uridine (5-EU); EVs were isolated from culture media and incubated with recipient cells (chondrocytes [n=5] were incubated with synoviocyte-derived EVs, and synoviocytes [n=4] with chondrocyte-derived EVs). EV-donor (chondrocytes, n=2; synoviocytes, n=2) and recipient (chondrocytes, n=1; synoviocytes, n=1) control cells were collected from six additional horses and run in parallel. Total RNA was extracted from recipient cells; the 5-EU labelled RNA was recovered and sequenced.

first: Catarina

last: Castanheira

first: James

last: Anderson

first: Emily

last: Clarke

first: Matthias

last: Hackl

first: Victoria

last: James

first: Peter

last: Clegg

first: Mandy

last: Peffers


title: The essential role of connective-tissue cells during axolotl limb regeneration [Agilent]

city: Bar Harbor

first: Prayag

last: Murawala

state: ME

address: 159 Old Bar Harbor Rd, Bar Harbor, ME 04609

institute: MDI Biological Laboratory

summary:
This experiment was performed to obtain an expression profiling of connective-tissue-derived cells at different time points during blastema formation after limb amputation.
RNA extraction was performed  from FACS sorted connective tissue cells from converted Prrx1Cre-ERT;CaggsSTOP/Cherry axolotls. 3 Biological replicates were obtained for each time point analyzed.

overall_design: Sorted-connective-tissue cells were obtain at 1, 3, 5, 7, 10 and 14 days post amputation, and compare their expression levels with connective-tissue cells from the uninjured limb.

first: Damián

last: García-García

first: Dunja

last: Knapp

first: Minjoo

last: Kim

first: Katelyn

last: Jamwal

first: Heath

last: Fuqua

first: Ryan

middle: P

last: Seaman

first: Riley

last: Grindle

first: Sergej

last: Nowoshilow

first: Maria

last: Novatchkova

first: Fred

middle: W

last: Kolling

first: Joel

last: Graber