title: Nuclear Receptor-SINE B1 Network Modulates Expanded Pluripotency in Blastoids and Blastocysts [RNA-seq 2]

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Embryonic stem cells possess the remarkable ability to self-organize into blastocyst-like structures upon induction. These synthetic embryo models serve as invaluable platforms for studying embryogenesis and therapeutic developments. Nevertheless, the specific intrinsic regulators that govern this potential for blastoid formation remain unknown. Here we demonstrate a novel intrinsic program that plays a crucial role in both blastoids and blastocysts across multiple species. We first establish metrics for grading the resemblance of blastoids to mouse blastocysts, and identify the differential activation of gene regulons involved in lineage specification among various blastoid grades. Notably, abrogation of nuclear receptor subfamily 1, group H, member 2 (Nr1h2) drastically reduces blastoid formation. Nr1h2 activation alone is sufficient to rewire conventional ESC into a distinct pluripotency state, enabling them to form blastoids with enhanced implantation capacity in the uterus and contribute to both embryonic and extraembryonic lineages in vivo. Through integrative multi-omics analyses, we uncover the broad regulatory role of Nr1h2 in the transcriptome, chromatin accessibility and epigenome, targeting genes associated with embryonic lineage and the transposable element SINE-B1. The Nr1h2-centred intrinsic program governs and drives the development of both blastoids and early embryos.

overall_design: Morula embryos injected with siNr1h2 or siNT at 1-cell stage

first: Ka Wai

last: Wong

first: Kiyofumi

last: Hamashima

first: Hu

last: Li

first: Yuin-Han

last: Loh


title: Nuclear Receptor-SINE B1 Network Modulates Expanded Pluripotency in Blastoids and Blastocysts [ChIP-seq 2]

status: Public on Apr 10 2025

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: H3K9me3 and H3K27ac ChIP-seq in ESC with/ without Nr1h2 overexpression and/or T09 treatment


title: Transcription factor reveals interconnected regulation of carbon source utilization and carbon catabolite repression in an oleaginous yeast

city: Ithaca

first: Lori

middle: B

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

country: USA

institute: Cornell University

type: Expression profiling by high throughput sequencing

summary: Cells must sense and respond to available nutrients to utilize available resources and establish fungal colonies. Saprophytic microbes harvest carbon from plant biomass, which contain insoluble, complex carbohydrates that must be degraded extracellularly prior to import into the cell. Filamentous fungi can degrade these complex carbohydrates. However, while many single cellular microbes can utilize the building blocks of these insoluble polysaccharides, they frequently are unable to degrade insoluble carbohydrates. Cellobiose is a disaccharide breakdown product of cellulose, the most abundant component of plant biomass. We investigated the genetic regulation of cellobiose utilization in the oleaginous, basidiomycete yeast Rhodotorula (Rhodosporidium) toruloides using a combination of phylogenetic, genetic, and genomic approaches. We tested the closest R. toruloides homolog of the cellulose degradation regulator CLR-2/ClrB for a role in cellobiose utilization. Deletion of this transcription factor, which we named Cbr1, eliminated the ability of cells to grow on media containing cellobiose as the sole carbon source. Although, the role of CLR-2/ClrB is limited to regulating the expression of genes involved in the utilization of cellulose and hemicellulose, Cbr1 plays a role not only in cellobiose utilization, but also utilization of tricarboxylic acid (TCA) cycle intermediates. Transcriptional profiling revealed that the genes activated by Cbr1 included genes encoding beta-glucosidases and transporters. These beta-glucosidases are secreted and are necessary and sufficient for cellobiose utilization, while one of the transporters is required for utilization of the TCA cycle intermediate, citrate. Additionally, Cbr1 inhibits carbon catabolite repression, specifically during utilization of disaccharides, which may have evolved to limit the repression of genes encoding secreted proteins that cleave disaccharides into glucose extracellularly. The co-regulation of cellobiose and TCA cycle utilization with carbon catabolite repression may shed light on alternative methods of the regulation of carbon catabolite repression in fungi.

overall_design: mRNA-seq profling of Rhodotorula toruloides wild type and cbr1 deletion strains exposed to cellobiose or succinate as the sole carbon source or media lacking a carbon source for 8h. Each experiment was performed in biological triplicate.

first: Brandon

last: Reyes-Chavez

first: Joshua

middle: D

last: Kerkaert


title: Dynamic modelling of EWS::FLI1 fluctuations reveals molecular determinants of phenotypic tumor plasticity and prognosis in Ewing sarcoma [CUT&RUN]

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: The mechanisms underlying tumor cell plasticity driving drug resistance and disease progression remain poorly understood. In Ewing sarcoma (EwS), variations in EWS::FLI1 (EF) activity have been associated with epithelial-mesenchymal plasticity (EMP). Using degron technology, we titrated endogenous EF in an EwS cell line and linked phenotypic states to distinct EF thresholds. Strikingly, modest EF depletion promoted a pro-metastatic phenotype, which was diminished upon near-complete EF loss. Transcriptomic analysis revealed distinct gene clusters with heterogenous response patterns to varying EF dosage. Target genes most sensitive to subtle EF depletion contained GGAA microsatellites in EF-bound enhancers. Furthermore, we identified Krüppel-like zinc-finger transcription factors to be associated with EF-repressed EMP genes. EF rescue after partial depletion for a transient period identified persistently dysregulated genes associated with poor prognosis. This study underscores the therapeutic challenge of insufficient EF inhibition and provides a foundation for exploiting oncoprotein dynamics to uncover therapeutic vulnerabilities in fusion-driven cancers.

overall_design: A673 cells and EF-dTAG clone A2.2 were used for CUT&RUN profiling with various antibodies (FLI1, H3K27ac, H3K27me3, H3K4me3, IgG). In one experiment the EF-dTAG clone was treated with various dTAGV-1 concentrations.

first: Veveeyan

last: Suresh

first: Christoph

last: Hafemeister

first: Andri

last: Konstantinou

first: Sarah

last: Grissenberger

first: Caterina

last: Sturtzel

first: Florencia

last: Cidre-Aranaz

first: Andrea

last: Wenninger-Weinzierl

first: Martha

middle: M

last: Zylka

first: Karla

last: Queiroz

first: Dorota

last: Kurek

first: Ana

last: Sastre

first: Javier

last: Alonso

first: Martin

last: Distel

first: Anna

last: Obenauf

first: Thomas

middle: G

last: Grünewald

first: Heinrich

last: Kovar

first: Valerie

last: Fock


title: Nuclear Receptor-SINE B1 Network Modulates Expanded Pluripotency in Blastoids and Blastocysts [ChIP-seq 1]

first: Yingying

last: Zeng

overall_design: GFP and Nr1h2-FLAG ChIP-seq in ESC with/ without Nr1h2 overexpression and/or T09 treatment, as well as in EPSC with/ without T09 treatment

first: Ka Wai

last: Wong

first: Kiyofumi

last: Hamashima

first: Hu

last: Li

first: Yuin-Han

last: Loh


title: IbinA and IbinB regulate the Toll pathway-mediated immune response in Drosophila melanogaster

city: Tampere

first: Matthew

middle: K

last: Maasdorp

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

summary: To combat infection, an immune system needs to be promptly activated but tightly controlled to avoid destructive effects on host tissues. IbinA and IbinB are related short peptides with robust expression upon microbial challenge in Drosophila melanogaster. Here, we show that Ibin genes are ubiquitously present in flies of the Drosophila subgenus Sophophora, where they replace a different but probably related gene, Mibin, which is found across a much wider range of cyclorrhaphan flies. Using synthetic peptides, we did not observe any direct bactericidal or bacteriostatic activity for either IbinA or IbinB in vitro. Using mutant Drosophila lines lacking the IbinA gene, IbinB gene, or both, we examined their roles in development and during microbial infections. IbinA is expressed in early pupae, and a lack of IbinA and IbinB leads to temperature-dependent formation of melanized tissue during metamorphosis, frequently around the trachea. IbinA and IbinB have distinct effects on susceptibility to microbial infection. For example, IbinB mutant flies, as well as flies lacking both IbinA and IbinB, had improved survival when challenged with Listeria monocytogenes, an intracellular pathogen, whereas a lack of IbinA alone had no effect. RNA sequencing of wildtype and mutant flies infected with L. monocytogenes showed enhanced Toll target gene expression in flies lacking IbinB, suggesting that IbinB acts as a negative regulator of the Toll pathway. In contrast, IbinA mutants had decreased Toll target gene expression in this context. Correspondingly, IbinB mutant flies had improved and IbinA compromised survival in septic fungal infection, where the Toll pathway has a major role. Our study provides insight into the roles of IbinA and IbinB in regulation of the immune response in Drosophila.

overall_design: 2-5 day old males were infected with Listeria monocytogenes by pricking the flies with a tungsten needle dipped in bacterial solution (OD600=0.07). Samples were collected 36 hours post-infection. As controls, uninfected flies of similar age were collected.

first: Susanna

last: Valanne

first: Laura

last: Vesala

first: Petra

last: Vornanen

first: Elina

last: Haukkavaara

first: Tea

last: Tuomela

first: Aino

last: Malin

first: Tiina

middle: S

last: Salminen

first: Dan

last: Hultmark

first: Mika

last: Rämet


title: NAT10 Exacerbates Acute Renal Inflammation by Enhancing N4-Acetylcytidine Modification of the CCL2/CXCL1 Axis

city: hefei

first: jia nan

last: wang

address: 81 Meishan Road

country: China

institute: Anhui medical university

summary: Inflammation plays an essential role in eliminating microbial pathogens and repairing tissues, while sustained inflammation accelerates kidney damage and disease progression. Therefore, understanding the mechanisms of the inflammatory response is vital for developing therapies for inflammatory kidney diseases like acute kidney injury (AKI), which currently lacks effective treatment. Here, we identified N-acetyltransferase 10 (NAT10) as a significant mediator of inflammation. NAT10, the only known ‘writer’ protein for N4-acetylcytidine (ac4C) acetylation, is elevated in renal tubules across various AKI models, human biopsies and cultured tubular epithelial cells (TECs). Conditional knockout (cKO) of NAT10 in mouse kidneys attenuates renal dysfunction, inflammation, and infiltration of macrophages and neutrophils, whereas its conditional knock-in (cKI) exacerbates these effects. Mechanistically, our findings from ac4C-RIP-seq and RNA-seq analyses reveal that NAT10-mediated ac4C acetylation enhances the mRNA stability of a range of key chemokines, including C-C motif chemokine ligand 2 (CCL2) and C-X-C motif chemokine ligand 1(CXCL1), promoting macrophage and neutrophil recruitment and accelerating renal inflammation. Additionally, CCL2 and CXCL1 neutralizing antibodies or their receptor inhibitors, abrogated renal inflammation in NAT10-overexpression TECs or NAT10-cKI mice. Importantly, inhibiting NAT10, either through Adeno-associated virus 9 (AAV9)-mediated silencing or pharmacologically with our newly identified inhibitor Cpd-155, significantly reduces renal inflammation and injury. Thus, targeting the NAT10/CCL2/CXCL1 axis presents a promising therapeutic strategy for treating inflammatory kidney diseases.

overall_design: To investigate the underlying mechanisms of NAT10 in renal inflammation, we performed ac4C-RIP-seq and RNA-seq analyses in H/R-exposed HK2 cells with or without NAT10 silencing

first: Jia nan

last: Wang

first: Xiao ming

last: Meng


title: The glutathione system is essential to maintain the thiol redox balance in the mitochondria, but not in the cytosol, of fission yeast

city: Barcelona

first: Montserrat

last: Vega

state: Barcelona

address: C/ Dr. Aiguader 88, lab 383

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra

summary: Investigate the role of  Pgr1 in the transcriptional response to oxidative stress

overall_design: Gene expression profiling using RNA-seq obtained from a wild-type and Pgr1 deleted strains under untreated conditions and after 30 minutes of 1 mM peroxide treatment

last: de Cubas

last: Boronat

first: Alba

last: Domènech

first: Ferran

last: Gómez-Armengol

first: Alexey

last: Artemov

first: Olga

last: Lyublinskaya

first: Jos

last: Ayté

first: Elena

last: Hidalgo


title: Dynamic modelling of EWS::FLI1 fluctuations reveals molecular determinants of phenotypic tumor plasticity and prognosis in Ewing sarcoma [SLAM-seq]

first: Florian

last: Halbritter

overall_design: A673 cells-derived EF-dTAG clone A2.2 was used for SLAM-seq. Various dTAGV-1 concentrations were used as treatment.

first: Veveeyan

last: Suresh

first: Christoph

last: Hafemeister

first: Andri

last: Konstantinou

first: Sarah

last: Grissenberger

first: Caterina

last: Sturtzel

first: Florencia

last: Cidre-Aranaz

first: Andrea

last: Wenninger-Weinzierl

first: Martha

last: Zylka

first: Karla

last: Queiroz

first: Dorota

last: Kurek

first: Ana

last: Sastre

first: Javier

last: Alonso

first: Martin

last: Distel

first: Anna

last: Obenauf

first: Thomas

last: Grünewald

first: Heinrich

last: Kovar

first: Valerie

last: Fock


title: Oncogene induced senescence and senescence-associated secretory phenotype (SASP) determines the efficacy of palbociclib in PIK3CA mutated colorectal cancer

city: NanJing

first: Pingping

last: Cao

state: Jiangsu

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

department: Department of Cell Biology

institute: Nanjing Medical University

summary: Palbociclib, a classic CDK4/6 inhibitor, has been extensively studied in the context of targeted cancer therapy. We have systematically investigated the applicability of palbociclib in colorectal cancer, utilizing high-throughput sequencing and other methods to explore its resistance mechanisms. Our findings reveal that PIK3CA gene mutations promote a palbociclib-induced senescent phenotype and alter the expression profile of SASP factors. Among these, the SASP factor LCN2 contributes to cellular tolerance to palbociclib by upregulating EGFR protein expression. In summary, our sequencing data provide a molecular framework for the relationship between PIK3CA gene mutations and both palbociclib-induced cellular senescence and resistance.

overall_design: To investigate the role of PIK3CA gene mutations in resistance to palbociclib, we created isogenic cell lines harboring PIK3CA mutations (E545K and H1047R) in the wild-type LOVO cell line using lentiviral vectors. These mutant cell lines were named E545K (2# and 5#) and H1047R (2# and 3#). We then treated both the wild-type and mutant cell lines, E545K (2#) and H1047R (3#), with palbociclib to induce senescence and conducted transcriptome sequencing. Furthermore, we treated cells with conditioned medium containing senescence-associated secretory phenotype (SASP) factors to explore their function through transcriptome sequencing. In-depth, we studied the therapeutic mechanism by treating the PIK3CA mutant cell lines with a combination of palbociclib and erlotinib.

first: Suisui

last: Yang

first: Fan

last: Lin


title: Gut microbiota-mediated hsa_circ_0126925 targets BCAA metabolic key enzyme BCAT2 in exacerbating the progression of colorectal cancer

city: Suzhou

first: Songbing

last: He

address: No 188 Shizi street

institute: Department of General Surgery

summary:
Recent evidence has revealed that a high-fat diet (HFD) can promote the development of tumours, especially colorectal cancer (CRC), by affecting the microbiota. Regulatory circular RNAs (circRNAs) play an important role in modulating host–microbe interactions. However, the specific mechanism by which circRNAs affect cancer progression by regulating these interactions is not yet clear. Here, we report that consumption of a HFD modulates the microbiota by specifically upregulating the expression of the noncoding RNA hsa_circ_0126925 (herein referred to as circ_0126925) in CRC. As a scaffold, circ_0126925 hinders the recruitment of the E3 ubiquitin ligase tripartite motif-containing protein 21 (TRIM21) to branched-chain amino acid transaminase 2 (BCAT2), which leads to reduced degradation of BCAT2. Reducing the targeted degradation of BCAT2 can protect tumours from limited branched-chain amino acids (BCAAs) interference by improving the metabolism of BCAAs in CRC. Taken together, these data demonstrate that circ_0126925 plays a critical role in promoting the progression of CRC by maintaining BCAA metabolism and provide insight into the functions and crosstalk of circ_0126925 in host–microbe interactions in CRC.
Taken together, these data demonstrate that circ_0126925 plays a critical role in promoting the progression of CRC by maintaining BCAA metabolism and provide insight into the functions and crosstalk of circ_0126925 in host–microbe interactions in CRC.

overall_design: The gut microbiota regulated by a high-fat diet can regulate the expression of circ_0126925, thereby promoting the malignant progression of CRC.

first: Huihui

last: Yao


title: Oxidized mitochondrial DNA sensing by plasmacytoid dendritic cells bypasses self-tolerance to trigger Tfh dependent autoantibody production [scRNA-seq]

city: La Jolla

first: Masafumi

last: Ohira

state: California

address: 9500 Gilman Drive

department: Department of Pharmacology

institute: University of California San Diego

summary: Damage associated molecular patterns (DAMP) trigger inflammation and provide co-stimulatory signals to adaptive immune cells, but whether and how recurring innate stimuli circumvent self-tolerance and initiate maladaptive autoimmunity is unknown. We explored if oxidized mitochondrial DNA (Ox-mtDNA), a DAMP released by stressed macrophages, found in higher amounts in diverse metabolic and autoimmune disorders, including systemic lupus erythematosus (SLE), initiates antibody-mediated autoimmunity. Indeed, Ox-mtDNA release induced by repetitive alum challenges elicited germinal center reactions, autoantibody production and nephropathology. These responses were recapitulated by in-vitro generated Ox-mtDNA, while non-oxidized mtDNA was non-pathogenic. Both mtDNA forms, but not nuclear DNA, were internalized by plasmacytoid dendritic cells (pDC), activated NF-kB via TLR9 and induced interferon (IFN)-I. Yet only Ox-mtDNA triggered NLRP3- and gasdermin D-dependent IL-1β secretion, eliciting autocrine production of IL-21 that together with IL-1β, but independently of IFN-I, enabled pDC to convert naïve CD4+ T cells into follicular helper cells. Highlighting Ox-mtDNA as a uniquely immunogenic DAMP that is specifically sensed by pDC and IL-1β as an orchestrator of autoantibody production, these findings explain how chronic inflammation culminates in autoimmunity and unravel new therapeutic targets applicable to SLE, the autoimmune/inflammatory syndrome induced by adjuvants (ASIA) and related diseases.

overall_design: Live freshly peritoneal cells of B6 mice intraperitoneally injected with PBS, Alum, mtDNA, or Ox-mtDNA were analyzed using scRNA-seq.

first: Hongxu

last: Xian

first: Kosuke

last: Watari

first: Jonathan

last: Brito

first: Santino

middle: L

last: Buttice

first: Janset

last: Onyuru

first: Elina

middle: I

last: Zuniga

first: Hal

last: Hoffman

first: Michael

last: Karin


title: Prior Chemotherapy Deteriorates T Cell Quality for CAR T Cell Therapy in B-Cell Non-Hodgkin’s Lymphoma

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

summary: Chimeric antigen receptor (CAR) T cell therapy depends on T cells that are genetically modified to recognize and attack cancer cells. Their effectiveness thus hinges on the functionality of a patient’s own T cells. However, CAR T cell therapy is currently only approved for advanced cancers after at least one line of chemotherapy. To evaluate the potential negative effects of prior exposure to chemotherapy on T cell functionality we studied T cells of two B cell Non-Hodgkin’s lymphoma (B-NHL) patient cohorts, one collected before treatment (pre-therapy) and the other after one or more (median 3) lines of chemotherapy (post-therapy). Leveraging advanced multi-parameter flow cytometry and single-cell RNA sequencing (scRNAseq), we elucidated significant modifications in T cell subsets and their transcriptional profiles post-therapy. Our analysis revealed a discernible shift towards phenotypically more differentiated T cells and an upregulation of markers indicative of T cell exhaustion. Additionally, scRNAseq and DNA methylation analyses revealed gene expression and epigenetic changes associated with diminished functionality in post-therapy T cells. Cytotoxicity assays demonstrated superior killing efficacy of CAR T cells derived from treatment-naïve patients compared to those with chemotherapy history. These findings corroborate that employing T cells collected prior to frontline chemotherapy could enhance the effectiveness of CAR T cell therapy and improve patient outcomes.

overall_design:
We sequenced T cells of a total of 12 B-NHL patients, six of whom did not yet receive any anti-lymphoma treatment (pre-therapy), while the other six received at least one line of therapy (post-therapy). Peripheral blood samples were collected from the above-mentioned patients and T cells were isolated.

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Raw data unavailable due to patient privacy restrictions.
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first: Charlotte

last: Junkuhn

first: Phillip

last: Schiele

first: Anna

last: Walter

first: Frederik

last: Hamm

first: David

last: Busch

first: Olaf

last: Penack

last: Damm

first: Julia

last: Polansky

first: Lars

last: Bullinger

first: Annette

last: Künkele

first: Marco

last: Frentsch

first: Il-Kang


title: Prior chemotherapy deteriorates T-cell quality for CAR T-cell therapy in B-cell non-Hodgkin’s lymphoma

address: Föhrer Str. 15

institute: Charité Universitätsmedizin Berlin

type: Methylation profiling by genome tiling array

summary: Immunotherapies, such as CAR T cell therapy, depend on T cells that are genetically modified to recognize and attack cancer cells. Their effectiveness thus hinges on the quality of a patient’s own T cells. We studied blood samples from B-NHL patients collected both before any treatment (pre-therapy) and following at least two lines of chemotherapy (post-therapy) to evaluate the potential negative effects of prior exposure to chemotherapy on T cell quality. Utilizing advanced multi-parameter flow cytometry and single-cell RNA sequencing (scRNAseq), we discovered notable alterations in T cell composition and gene expression after therapy, such as increasingly differentiated phenotypes and elevated expression of exhaustion markers. Additionally, scRNAseq and DNA methylation analyses revealed gene expression and epigenetic changes associated with diminished T cell function in post-therapy samples. In vitro cytotoxicity studies demonstrated superior killing efficacy of CAR T cells derived from T cells of treatment-naïve patients compared to T cells of patients with treatment history. These findings corroborate that using T cells collected prior to chemotherapy exposure could enhance the effectiveness of CAR T cell therapies  and offer new strategies for improving patient outcomes in B-NHL treatment.

overall_design: The Illumina Methylation EPIC Bead Chip was used to compare DNA methylation patterns of B-NHL patient samples. T cells were isolated before and after patient exposure to chemotherapy and methylation was compared on T cells at time of apheresis (n=22) as well as on the CAR T cell product (n=9).


title: Syndecan-3 positively regulates the pro-inflammatory function of macrophages

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary:
The tumour microenvironment (TME) is a highly structured ecosystem that surrounds a tumour and plays a crucial role
in tumorigenesis. As one of the most abundant cell types in the TME, tumour-associated-macrophages (TAMs) can promote
disease progression and resistance to therapy. Syndecan-3 (SDC3) is a cell-surface heparan sulphate proteoglycan
expressed by TAMs, although its functional relevance in these cells remains unknown. Here, we demonstrated that proinflammatory
cytokines drive the expression of SDC3 on the cell surface of macrophages. Genetic ablation of SDC3
in macrophages led to aberrant proliferation, adhesion and expression of CD40 and CD86 surface markers. Moreover,
SDC3 defective macrophages exhibited distinctive gene expression patterns, leading to impaired tumour cell phagocytosis
and increased tumour cell proliferation. Mechanistically, a decrease in the secretion of pro-inflammatory cytokines
was observed in SDC3 KO macrophages, concomitant with impaired T cell effector functions. Additionally, a higher
angiogenic capacity was observed in endothelial cells when co-cultured with macrophages deficient for SDC3, possibly
mediated through an increased release of VEGFA, PECAM-1 and IL-8 by SDC3 KO cells. Collectively, we have identified
SDC3 as a modulator of macrophage functions aiming at supporting a pro-inflammatory and anti-tumour phenotype
in these cells.

overall_design:
To investigate the effect of Syndecan-3 in the regulation of macrophage pro-inflammatory functions, we established THP-1 cell lines in which Syndecan-3 has been knocked-out by CRISPR/Cas9.
We then performed gene expression profiling analysis using data obtained from RNA-seq of two different cells in response to two different conditions.
Comparative  gene expression profiling analysis of RNA-seq data for IFN-gamma-treated SDC3 KO and WT THP-1 cells.

first: Lorena

last: Pérez-Gutiérrez

first: Lee

middle: Y

last: So

first: Endika

last: Prieto-Fernandez

first: Leire

last: Egia-Mendikute

first: Asier

last: Antoñana-Vildosola

first: Paloma

last: Velasco-Beltrán

first: Alexandre

last: Bosch-Martinez

first: Borja

last: Jimenez-Lasheras

first: Ander

last: de Blas-Martin

first: Jone

last: Etxaniz-Diaz de Durana

first: Eunate

last: Valdaliso-Díez

first: Laura

last: Bozal-Basterra

first: Amaia

last: Ercilla

first: José

middle: E

last: Martin

first: Arkaitz

last: Carracedo

first: Alena

last: Gros

first: Asís

last: Palazón


title: Oxidized mitochondrial DNA sensing by plasmacytoid dendritic cells bypasses self-tolerance to trigger Tfh dependent autoantibody production [RNA-seq]

first: Masafumi

last: Ohira

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS-sorted pDCs treated with vehicle, mtDNA, or Ox-mtDNA.

first: Hongxu

last: Xian

first: Kosuke

last: Watari

first: Jonathan

last: Brito

first: Santino

last: Buttice

first: Janset

last: Onyuru

first: Elina

last: Zuniga

first: Hal

last: Hoffman

first: Michael

last: Karin


title: RNA-seq of Drosophila melanogaster wing imaginal discs during L3 stage

city: Marseille

first: Cédric

last: Maurange

address: Parc Scientifique de Luminy

department: Developmental Biology Institute of Marseille (IBDM)

country: France

institute: CNRS

summary: During the last larval stage (L3) of Drosophila melanosgaster development, wing imaginal discs undergo tremendous growth and initiate differentiation programs. This transcriptomic time course aims at uncovering the the genes that are temporally regulated during the L3 in wing imaginal discs to regulate the dynamics of growth and differentiation.

overall_design: Five time points were analyzed after the L2/L3 molt: 6 hours (hr), 15 hr, 25 hr,  35 hr, and 48 hr (wandering L3) stages

first: Fanny

last: Chazal


title: Nuclear Receptor-SINE B1 Network Modulates Expanded Pluripotency in Blastoids and Blastocysts [RNA-seq 1]

first: Yingying

last: Zeng

overall_design: NrESC at various passages under T09 treatment with ESC as passage-matched control

first: Ka Wai

last: Wong

first: Kiyofumi

last: Hamashima

first: Hu

last: Li

first: Yuin-Han

last: Loh


title: STING aggravates ferroptosis-dependent myocardial ischemia-reperfusion injury by targeting GPX4 for autophagic degradation

city: Jinan

first: Xiaohong

last: Wang

address: Wenhuaxi Road

institute: Qilu Hospital of Shandong University

summary: To investigate the potential signal pathways affected by the deletion of the Sting gene in mice during ischemia-reperfusion (IR), we extracted the myocardial tissues of mice 24 hours after ischemia-reperfusion. Subsequently, we conducted gene expression profiling analysis using the data obtained from RNA-seq of STING-CKO mice and their control counterparts.

overall_design: A comparative gene expression profiling analysis was performed on the RNA-seq data of myocardial tissues from STING-CKO mice and their control counterparts following ischemia-reperfusion (I/R).


title: Highly specific immunoproteasome inhibitor M3258 induces proteotoxic stress and apoptosis in MLL-AF4-driven acute lymphoblastic leukemia.

city: AUBURN

first: Amit

middle: Kumar

last: Mitra

state: AL

address: HARRISON COLLEGE OF PHARMACY

department: DRUG DISCOVERY AND DEVELOPMENT

institute: AUBURN UNIVERSITY

summary: Proteasome inhibitors (PIs) Bortezomib, Carfilzomib and Ixazomib are approved for the treatment of multiple myeloma and mantle cell lymphoma and have clinical activity in acute lymphoblastic leukemia (ALL). The predominant form of proteasome in these hematologic malignancies is the lymphoid tissue specific immunoproteasome. FDA-approved PIs inhibit immunoproteasomes and ubiquitously expressed constitutive proteasomes causing on-target toxicities in non-hematological tissues. Replacing PIs with selective immunoproteasome inhibitors (IPIs) should reduce these toxicities. We have previously shown that IPI ONX-0914 causes apoptosis of ALL cells expressing the MLL-AF4 fusion protein but did not elucidate the mechanism. Here we show that a novel, highly specific IPI M3258 induces rapid apoptosis in ALL cells in vitro and is comparable to bortezomib in its ability to reduce tumor growth and enhance effect of chemotherapy in vivo. Treatment of ALL cells with M3258, ONX-0914 and bortezomib induced proteotoxic stress that was prevented by the protein synthesis inhibitor cycloheximide, which dramatically desensitized cells to PI-induced apoptosis. Thus, like MM, ALL cells are sensitive to PIs and IPIs because they are under proteotoxic stress caused by elevated rates of protein synthesis.

overall_design: RS4;11 cells were treated Bortezomib, M3258, or ONX-0914 and RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s protocol, and total RNA sequencing was performed (150 bp PE, 20 million reads per sample).

first: Mitra

last: Amit Kumar

first: Kisselev

last: Alexei

first: Jenkins

last: Tyler W.


title: Dynamic modelling of EWS::FLI1 fluctuations reveals molecular determinants of phenotypic tumor plasticity and prognosis in Ewing sarcoma [RNA-seq]

first: Florian

last: Halbritter

overall_design: In one part of the experiment, A673 cells in bulk, untagged A673 single cell clones, EF-dTAG clones A2.2 and B3.1 were sequenced without treatment (ssc_experiment). In the other parts, the two EF-dTAG clones were treated with various dTAGV-1 concentrations for various durations with either no ligand washout after treatment, or 7 day washout applied.

first: Veveeyan

last: Suresh

first: Christoph

last: Hafemeister

first: Andri

last: Konstantinou

first: Sarah

last: Grissenberger

first: Caterina

last: Sturtzel

first: Florencia

last: Cidre-Aranaz

first: Andrea

last: Wenninger-Weinzierl

first: Martha

last: Zylka

first: Karla

last: Queiroz

first: Dorota

last: Kurek

first: Ana

last: Sastre

first: Javier

last: Alonso

first: Martin

last: Distel

first: Anna

last: Obenauf

first: Thomas

last: Grünewald

first: Heinrich

last: Kovar

first: Valerie

last: Fock


title: Dynamic modelling of EWS::FLI1 fluctuations reveals molecular determinants of phenotypic tumor plasticity and prognosis in Ewing sarcoma

first: Florian

last: Halbritter

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

overall_design: Refer to individual Series


title: Nuclear receptor-SINE B1 network modulates expanded pluripotency in blastoids and blastocysts.

first: Yingying

last: Zeng

type: Methylation profiling by high throughput sequencing


title: The root-knot nematode effector MiEFF12 targets the host ER quality control system to suppress immune responses and allow parasitism

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

summary: Conclusions: MiEFF12 overexpression modifies the expression of genes important for the ontogenesis of giant cells, notably those involved in microtubule cytoskeleton reorganization and cell cycle regulation, strongly suggesting that MiEFF12-mediated SmD1 inactivation in plants leads to a loss of susceptibility to root-knot nematodes.

overall_design: mRNA profiles of PolyA RNA from WT, MiEFF12 overexpressor and smd1b mutant seedlings PolyA RNA from WT, MiEFF12 overexpressor and smd1b mutant seedlings

first: Bruno

last: Favery

first: Michael

last: Quentin


title: EIF3D Safeguards the Homeostasis of Key Signaling Pathways in Human Primed Pluripotency [Ribo-seq]

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

summary: Pluripotent stem cell identities such as differentiation and infinite proliferation have long been decoded in the frameworks of transcription factor networks, epigenomes, and signal transduction, yet unclear and fragmented. However, directing attention toward translation regulation, the bridge between these events promises to provide new insights into previously unexplained mechanisms. Functional screening led to the discovery that EIF3D maintains primed pluripotency via selective translation regulation. The loss of EIF3D unbalanced the pluripotency-associated signaling pathways, disrupting primed pluripotency. Furthermore, we found that EIF3D safeguards robust proliferation by managing the translation of multiple p53 regulators that maintain low p53 activity in the undifferentiated state. Therefore, this study provides a paradigm for selective translation regulation that defines the primed pluripotent stem cell identity.

overall_design: To investigate the translational effect of EIF3D knockdown, we established cell line for EIF3D knockdown by using CRISPRi system which Cas proteins were induced by with doxycycline (DOX) treatment. iPSCs with non-targeting guide RNAs were used as control. Ribosome Profiling and their accompanying RNA-seq data were obtained 3 days after DOX treatment.

first: Chikako

last: Okubo

first: Michiko

last: Nakamura


title: EIF3D Safeguards the Homeostasis of Key Signaling Pathways in Human Primed Pluripotency [RNA-seq]


title: EIF3D Safeguards the Homeostasis of Key Signaling Pathways in Human Primed Pluripotency

overall_design: We utilized on genome-wide functional screening using the CRISPR interference (CRISPRi) platform with Human Genome-wide CRISPRi-v2 Libraries (https://www.addgene.org/pooled-library/weissman-human-crispri-v2/). Set A were used for d0_1, d0_2, d8_1, d8_2 and d16_1 and Set B were used for d8_3, d16_2, d0_3 and d16_3. We collected samples from day 0 and day 16 after doxycycline (Dox, WAKO) treatment.


title: EIF3D Safeguards the Homeostasis of Key Signaling Pathways in Human Primed Pluripotency [RNA-Seq]

overall_design: To investigate the effect of EIF3D knockdown, we established cell line for EIF3D knockdown by using CRISPRi system which Cas proteins were induced by with doxycycline (DOX) treatment. iPSCs with non-targeting guide RNAs were used as control. RNA-seq data were obtained from 0, 3, 5 days after DOX treatment. To compare with loss of pluripotency states, POU5F1, SOX2 and NANOG knockdown lines were also established and sampled, in addition to endoderm, mesoderm and ectoderm like cells derived from iPSCs. To induce changes observed in EIF3D knockdown PSCs, we employed the chemical compounds and growth factor to including the activation of EGF/MAPK, mTOR, AKT, WNT, and p53, and inhibition of TGFβ.


title: Intratumoral heterogeneity of glioblastoma is attributed to precancerous cells derived from neural stem cells

city: Daejeon

first: Jeong Ho

last: Lee

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary:
Neural stem cells (NSCs) in the subventricular zone (SVZ) have been identified as cells-of-origin carrying driver mutations in glioblastoma (GBM), but there is a lack of understanding how a few NSCs with driver mutations chronologically transform into distant tumor with transcriptional heterogeneity.
We used single cell RNA sequencing (scRNA-seq) to show the precancerous cells arising from mutation-harboring NSCs emerge prior to tumor formation and lead to intratumoral heterogeneity in our spontaneous, somatic mouse model as well as in patients’ tumor-free SVZ tissues.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
In mouse GBM model, the SVZ and corpus callosum (CC) tissues were microdissected for precancerous stage, and tumor tissues were used for the study. Mutation-harboring cells with tdTomato signal were enriched with fluorescent-activated cell sorting (FACS) and analyzed using scRNA-seq.
For human specimens, freshly frozen samples of pathologically normal and tumor-free SVZ tissues, as well as tumors, were obtained from three GBM patients with EGFRvIII, PTEN mutations. Nuclei were isolated by FACS and analyzed using single nucleus RNA-seq.

first: Hyun Jung

last: Kim


title: Targeting glycolysis reduces infection and dampens inflammation in a host-directed therapy for dengue

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

institute: Singapore Immunology Network (SIgN)

summary: To determine transcriptomic difference between uninfected monocytes and infected monocytes

overall_design: RNA sequencing was performed on 10 samples total, 5 donors - uninfected and infected monocytes

last: Loy

first: Amit

last: Singhal


title: DNA methylation markers in peripheral blood as effective diagnostic biomarkers for adult-onset Still’s disease

city: Changsha

first: Shijia

last: Rao

state: Hunan

address: Renmin Road

department: dermatology

institute: Second Xiangya hospital

summary: Genome-wide DNA methylation was analyzed to screen for differentially methylated CpG sites in the discovery phase to explore the role of DNA methylation CpG markers in the diagnosis of adult onset still's disease.

overall_design: DNA methylation array was used to screen for differentially methylated CpG sites in 50 patients with adult onset still's disease, 24 patients with T cell lymphoma, 24 patients with sepsis, 24 patients with drug eruption and 50 healthy controls.

first: Qianjin

last: Lu

first: Ming

last: Zhao

first: Hai

last: Long


title: Expression data from plasma of early-onset acute myocardial infarction patients and health control

city: Beijing

first: ziqian

last: wang

address: No.28 Fu Xing Road, Beijing 100853, China

institute: the PLA general hospital

summary:
CircRNAs are a new class of noncoding RNA and play regulatory roles in a variety of human diseases. However, the clinical significance of circRNAs in early-onset acute myocardial infarction (AMI) remains unknown. Therefore, we sought to explore the expression profile of circRNAs in early-onset AMI.
Microarray was used to screen differentially expressed circRNAs between early-onset AMI patients and matched healthy controls.

overall_design: Five early-onset AMI patients younger than 45 years and 5 sex- and age-matched healthy control subjects were enrolled for for RNA extraction and hybridization on Affymetrix microarrays.

first: Tong

last: Yin

first: Ziqian

last: Wang


title: Ribociclib derivative Rib-CA suppresses breast cancer progression by inducing p53-dependent apoptosis

status: Public on Apr 09 2025

city: Lianyungang

first: Song

middle: meng

last: wei

address: China

institute: Jiangsu Ocean University

summary: RNA sequencing and bioinformatics analysis revealed 2628 differentially expressed genes, with functional enrichment indicating strong associations with the p53 pathway, apoptosis, and G2/M checkpoint regulation

overall_design: In order to investigate the role and mechanism of Rib_CA in Breast Cancer, we treated MDA-MB-231 cells with Rib_CA and without treatment. Then, we performed gene expression profiling analysis using RNA seq data from Rib_CA and DMSO cells.

first: Mengwei

last: Song

first: Jing

last: Ji


title: RNA sequencing - E12 mouse embryonic cortices Emx1-Cre Zbtb7a-flox cKO vs WT

city: Sioux Falls

first: Louis-Jan

last: Pilaz

state: SD

address: 2301 E 60th Street North

department: Pediatrics and Rare Disease

institute: Sanford Research

summary: This is RNA sequencing performed with embryonic day 12 (E12) microdissected mouse cortices with the following genotypes: Emx1 Cre/ +; Zbtb7a +/+ (WT) and Emx1 Cre/+; Zbtb7a fl/fl (cKO). The goal of this study was to understand the impact ot Zbtb7a knockout during cortical development.

overall_design: 3 cortices per condition coming from 2 separate litters

first: Neeraj

last: Tiwari

first: Pratiksha

last: KC


title: Hepatic Mettl14 Knockout Disrupts Bile Acid Homeostasis and Alters Fecal Microbiota Composition

city: Nanjing

first: Xiang

last: Zhong

address: Tongwei Road

institute: Nanjing agricultural university

summary: Bile acids are multifunctional signaling molecules that play significant roles in maintaining microbial homeostasis. N6-methyladenine (m6A), the most abundant epitranscriptomic modification, mediates various biological processes by modulating RNA metabolism. However, the precise regulatory mechanisms of m6A methylation in bile acid metabolism, and its downstream effects on microbiota remain unclear. In this study, liver-specific Mettl14 knockout (Mettl14-LKO) reshaped bile acid profile and expression levels of protein related to bile acid metabolism, namely CYP7A1, FXR, and BSEP. M6A-seq data revealed m6A methylated peaks on CYP7A1. Mettl14-LKO significantly elevated expression of m6A “reader” IGF2BP3. Knockdown of IGF2BP3 inhibited CYP7A1 expression by decreasing mRNA stability. Mechanistically, Mettl14-LKO promoted bile acid synthesis by upregulating CYP7A1 expression in an m6A-IGF2BP3-dependent manner. Interestingly, Mettl14-LKO reduced bile acid content in ileum due to decreased BSEP level in liver. Noteworthy, we discovered for the first time that Mettl14 knockout in the liver altered fecal microbiota composition. Specifically, it changed the abundance of Cyanobacteria and Patescibacteria at phylum level, and Lachnochostridium, Candidatus-Saccharimonas, and Roseburia at genera level. Remarkably, Roseburia was negatively correlated with the bile acid levels and CYP7A1 expression. Our findings provide new insights into the role of METTL14 in regulating bile acid homeostasis and its impact on fecal microbiota. Roseburia emerges as a potential target for addressing metabolic diseases linked to disrupted METTL14 signaling.

overall_design: M6A-seq was used to reveal alterations in m6A methylation patterns in WT and Mettl14-LKO mice.

first: Yaxu

last: Liang

first: Anrui

last: Liu

first: Zhibo

first: Xiaoyun


title: CUT&RUN sequencing - E12 mouse embryonic cortices ZBTB7A - GATAD2B - H3K27ac…

summary: These are CUT&RUN analyses performed with embryonic day 12 (E12) CD1 mouse neocortices. Targets were ZBTB7A, GATAD2B, H3K4Me3, H3K4Me1, H3K27Ac, and IgG control.

first: Jeremiah

last: Tsyporin

first: Bin

last: Chen


title: Single nucleus RNA-seq of subcortical white matter from lysophosphatidylcholine (LPC) and cuprizone toxicity mouse models

city: Notre Dame

first: Katrina

last: Adams

state: Indiana

address: 100 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

summary: We compared the transcriptional changes in the cells of the corpus callosum, focusing on the oligodendrocyte and microglia, between LPC and cuprizone mediate demyelination. We further compared the transcriptional phenotypes to human MS patient samples. We identified distinct disease-associated oligodendrocyte states with shared pathological changes to MS, and observed a common but altered remyelination state between the models. Microglia response to demyelination is highly conserved, but human MS-associated microglia exhibit significantly more heterogeneity than we found in the mouse models. (doi: https://doi.org/10.1101/2025.03.24.645058)

overall_design: LPC: Adult (8-12wk) C57BL6 mice were injected with 1% LPC into the corpus callosum of one brain hemisphere. Saline was injected on the contralateral side. 7 days later, mice were injected with Neutral Red dye by IP 2 hours prior to sacrifice. Mice were anesthetized, perfused with cold PBS for 5mins, and the brain was dissected out into cold PBS. Coronal slices of the brain were made and corpus callosum lesions were identified by the presence of Neutral red stain. The corpus callosum lesion was dissected out and the corresponding region on the contralateral side was also collected. Tissue was placed in Eppendorf tubes, excess liquid was removed as much as possible, and tissue was flash frozen in liquid nitrogen and stored at -80 until single nuclei processing. Cuprizone: Adult (8-12wk) C57BL6 mice were fed 0.2% cuprizone chow for 5 consecutive weeks. Control mice were fed normal chow. Mice were anesthetized, perfused with cold PBS for 5mins, and the brain was dissected out into cold PBS. Coronal slices of the brain were made. The corpus callosum was dissected out for cuprizone-fed mice and normal chow-fed mice. Tissue was frozen as above, and stored at -80 until processing.

first: Erin

last: Aboelnour


title: Global Transcriptomic analysis of PBMC derived from COVID-19 acute-severe patients and convalescents

first: Nicholas

last: Ang

summary: The majority of patients with COVID-19 have a self-limiting upper respiratory tract infection mostly represented by asymptomatic or mild, however a small but relevant proportion of patients develops acute respiratory distress syndrome (ARDS), characterised by an excessive, host immune response with overproduction of proinflammatory cytokines can rapidly lead to multi-organ failure and death. Indeed, immune pathologies are well characterised through deep immune phenotyping, plasma analysis, sc-RNA and chip based methylation analysis, still we lack a molecular understanding of immune pathologies associated with COVID-19 which is urgently needed for new prognostic and therapeutic interventions. In this study, we first time showed a SARS-Cov2 induced severity associated deregulation of immune functions driven through a global reprogramming of immune functions through a epigenetically driven gene regulatory network

overall_design: RNA sequencing was performed on a total of 80 PBMC samples derived from healthy controls (n = 10), acute-Mild (n = 4), Acute-Moderate (n = 6), Acute-Severe (n = 32) and Convalescent = 28

first: Amit

last: Singhal

first: Dilip

last: Kumar


title: Transcriptome profiling of THSG treatment in a dexamethasone-induced muscle atrophy model using C2C12 myotubes

city: Gangneung

first: Hye-Young

last: Youn

address: 679 Saimdang-Ro

institute: KIST

summary: This study investigates the effects of 2,3,5,4′-Tetrahydroxystilbene-2-O-β-D-glucoside (THSG) on gene expression changes in C2C12 myotubes under dexamethasone-induced muscle atrophy conditions. Using RNA-seq, we identified transcriptomic alterations associated with THSG treatment, aiming to elucidate its potential protective role against muscle atrophy.

overall_design: C2C12 myotubes were treated with vehicle (control), dexamethasone (50 µM), or dexamethasone (50 µM) plus THSG (10 µM) for 24 hours.

first: Myungsuk

last: Kim


title: Expression and significance of lncRNAs derived from PBMC in rheumatoid arthritis

city: hefei

first: Xiaoke

last: Yang

address: Sanlian street

department: Department of Rheumatology and Immunology

institute: First Affiliated Hospital of Anhui Medical University

summary: Long non-coding RNAs (lncRNAs) are gaining recognition for their critical Q5 involvement in diverse autoimmune disorders. Here, comprehensive transcriptome sequencing was executed to acquire a lncRNA expression pattern in peripheral blood mononuclear cells (PBMC) of rheumatoid arthritis (RA). Then, we conﬁrmed the sequencing data by real-time quantitative polymerase chain reaction (RT-qPCR). The ﬁndings showed decreased levels of LINC00494, TSP0AP1-AS1, MCM3AP-AS1 and LINC01588, increased levels of OIP5-AS1, in PBMC of RA compared to controls. ROC analysis for the ﬁve dysregulated lncRNAs demonstrated an area under curve (AUC) extending from 0.654 to 0.915, and their combination had high utility for accurate RA diagnosis (AUC = 0.920). There existed a negative relation between RF and LINC00494 expression (P=0.027), positive relation between anti-CCP and MCM3AP-AS1 (P=0.024), and negative relation between CRP and LINC01588 expression (P=0.020). Our study indicated that LINC00494, TSP0AP1-AS1, MCM3AP-AS1, LINC01588 and OIP5-AS1 in PBMC may be the biomarkers for RA.

overall_design: Comprehensive transcriptome sequencing was executed to acquire a lncRNA expression pattern in peripheral blood mononuclear cells (PBMC) of RA. Then, we confirmed the sequencing data by real-time quantitative polymerase chain reaction (RT-qPCR).

first: Zhongling

first: Ziqiang

last: Shuai

first: Mingming

last: Zhang

first: Sheng-qian

last: Xu

first: Zong Wen


title: Non-canonical small noncoding RNAs in the Plasma extracellular vesicles as novel biomarkers in gastric cancer

first: Fangfang

last: Jin

address: 138 Xianlin Avenue, Qixia District

department: Department of Clinical Laboratory, Nanjing Drum Tower Hospital, Drum Tower Hospital Clinical College

institute: Nanjing University of Chinese Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Identifying robust diagnostic biomarkers for gastric cancer (GC) remains a significant challenge. Emerging studies highlight extracellular vesicle (EV)-derived RNAs in cancer biology, but the diagnostic potential of circulating EV-derived small non-coding RNAs (sncRNAs) in GC is poorly understood. Using panoramic RNA display by overcoming RNA modification aborted sequencing (PANDORA-seq), we mapped non-canonical sncRNAs—specifically ribosomal RNA-derived small RNAs (rsRNAs) and transfer RNA-derived small RNAs (tsRNAs)—in plasma EVs. We identified a three-rs/tsRNA signature that discriminates GC patients from healthy individuals with high sensitivity (80.42%) and specificity (87.43%) (143 GC vs 167 controls). For early_x0002_stage GC (stage I), sensitivity and specificity were 81.97% and 81.44%, respectively. Furthermore, the three_x0002_rs/tsRNA signature was evaluated in two independent cohorts, resulting in AUC values of 0.97 and 0.91 for distinguishing GC from healthy controls. Functional analyses revealed that these rs/tsRNAs regulate the ErbB/Hippo pathways, suggesting them in the underlying pathogenesis andtherapeutic potential. This study establishes a novel EV-derived sncRNA signature for early GC detection.

overall_design: This study utilized PANDORA-seq to comprehensively sequence small non-coding RNAs (sncRNAs) in plasma extracellular vesicles (EVs) from gastric cancer (GC) patients and healthy individuals, with a particular focus on ribosomal RNA-derived small RNAs (rsRNAs) and transfer RNA-derived small RNAs (tsRNAs).

first: Ping

first: Zhibo

last: Li

first: Xi

first: Chiyuan

last: Ma

first: Yiyuan

last: Han

first: Xiaoshan

first: Xiaodong

last: Wei

first: Yueyue

last: Lei

first: Tonghui


title: Cyperotundone Promotes Chemosensitivity of Breast Cancer via SRSF1

city: Lexington

first: Xiang

last: Song

state: Kentucky

address: Virginia Ave

institute: University of Kentucky

summary: Breast cancer is among the most common malignancies and the leading cause of cancer-related deaths in women. SRSF1 proteins belong to an important splicing factor (SF) family and bind to different splicing regulatory elements (SREs) to promote or inhibit splicing. Cyperotundone (CYT) is the major bioactive component of sedge and reported to exhibit multiple biological functions. This study aimed to investigate the effects of CYT on breast cancer drug resistance and to explore the molecular mechanisms. CYT significantly suppressed the in vitro and in vivo growth of BC cells without affect the normal cells, induced cell apoptosis, and inhibited the migration and invasion of drug-resistant BC. In comparison with the mono treatment with CYT, combination of CYT and doxrubicin (Dox) enhanced the effects. CYT treatment regulated the RNA and protein levels of epithelial mesenchymal transition (EMT) biomarkers, suppressed the sphere formation ability and expression of cancer stem cell biomarkers in drug resistant BC cells. Results from transcriptome sequencing analysis and experiments identified significantly decreased SRSF1 level in drug resistant cells after CYT treatment. Knockdown of SRSF1 significantly decreased expression of full-length MYO1B protein in drug-resistant BC cells. Overexpression of SRSF1 and MYO1B revered the inhibitory effects of CYT. In conclusion, CYT repressed the growth and metastasis of BC cells and recovered drug sensitivity, via regulating the alternative splicing of RNAs.

overall_design: RNA-seq analysis of gene expression in human breast cancer cell line MDA-MB-231-DR, comparing control group with CYT treated.

first: Chao


title: Quadruple adenine base edited allogeneic CAR T cells outperform CRISPR/Cas9 nuclease engineered T cells [ATAC-seq]

city: Philadelphia

first: Regina

middle: M.

last: Young

state: Pennsylvania

address: 3400 Civic Center BLVD

department: CCI

institute: University of Pennsylvania

summary: Genome editing technologies have enabled the clinical development of allogeneic cellular therapies, yet the optimal gene editing modality for multiplex editing of therapeutic T cell product manufacturing remains elusive. In this study, we conducted a comprehensive comparison of CRISPR/Cas9 nuclease and adenine base editor (ABE) technologies in generating allogeneic chimeric antigen receptor (CAR) T cells, utilizing extensive in vitro and in vivo analyses. Both methods achieved high editing efficiencies across four target genes, critical for mitigating graft-versus-host disease and allograft rejection: TRAC or CD3E, B2M, CIITA, and PVR. Notably, ABE demonstrated higher manufacturing yields and distinct off-target profiles compared to Cas9, with translocations observed exclusively in Cas9-edited products. Functionally, ABE-edited CAR T cells exhibited superior in vitro effector functions under continuous antigen stimulation, including enhanced proliferative capacity and increased surface CAR expression. Transcriptomic analysis revealed that ABE editing resulted in reduced activation of p53 and DNA damage response pathways at baseline, along with sustained activation of metabolic pathways during antigen stress. Consistently, ATAC-seq data indicated that Cas9-edited, but not ABE-edited, CAR T cells showed enrichment of chromatin accessibility peaks associated with double-strand break repair and DNA damage response pathways. In a preclinical leukemia model, ABE-edited CAR T cells demonstrated improved tumor control and extended overall survival compared to their Cas9-edited counterparts. Collectively, these findings position ABE as a superior choice of Cas9 nucleases for multiplex gene editing in therapeutic T cells.

overall_design: ATAC-seq profiling of human CD19 CAR T cells with or without multiplex knockout of 4 genes  (TRAC or CD3E, B2M, CIITA PVR) at the end of primary CAR T expansion (D0) realized by 4 different gene editing strategies (wildtype Cas9 mRNA, SpyFi Cas9 mRNA, SpyFi Cas9 Protein, ABE8e mRNA).

first: Nils

middle: W

last: Engel

first: Kusala

last: Anupindi

first: Samuel

first: Linhui

last: Chen

first: Carl

middle: H

last: June


title: Quadruple adenine base edited allogeneic CAR T cells outperform CRISPR/Cas9 nuclease engineered T cells [RNA-seq]

overall_design: RNA-seq profiling of  human CD19 CAR T cells with or without multiplex knockout of 4 genes (TRAC or CD3E, B2M, CIITA PVR) at two time points (end of primary CAR T expansion, D0; >2 weeks of chronic antigen exposure, end of CAE) realized by 4 different gene editing strategies (wildtype Cas9 mRNA, SpyFi Cas9 mRNA, SpyFi Cas9 Protein, ABE8e mRNA).

last: Kim


title: TLDR (True Length of Diverse capped RNAs)-seq: a method for 5’-to-3’ end sequencing of capped full-length RNAs with or without 3’ polyadenylation [R10]

city: Copengagen

first: Albin

last: Sandelin

address: Ole Maaløes Vej 5

department: Department of Biology, Section for Computational and RNA Biology

country: Denmark

institute: University of Copenhagen

summary: Analysis and understanding of transcript functions is greatly helped by knowing the full-length sequence of individual RNAs. New long-read sequencing devices such as Oxford Nanopore and Pacbio have the potential to sequence full-length transcripts, but standard methods lack the ability to capture true RNA 5’ ends and selects for poly-adenylated (pA+) transcripts. We present a method that, by utilizing cap-trapping and 3’ end adapter ligation, can sequence transcripts from the exact 5’ end to 3’ end regardless of whether they are poly-adenylated, with no need for ribosomal RNA depletion. We show that the method can faithfully detect 5’ ends, splice junctions and 3’ ends, has high reproducibility between runs and gene expression estimates from the method correlate well with short-read sequencing methods. We also demonstrate that the method can detect and sequence full-length pA- RNAs, including lncRNAs, promoter upstream transcripts (PROMPTs) and enhancer RNAs. TLDR-seq is therefore useful for the characterization of diverse capped RNA species.

overall_design: RNA was extracted from WT HeLa S3 cells, WT mouse embryonic stem cells (mES) and knock down mES cells (of either RBM7 or ZCCHC8) and analyzed by TLDR-seq on MinION flow cells

first: Jamie

last: Auxillos

first: Arnaud

last: Stigliani

first: Christian

last: Vaagensø

first: Will

last: Garland

first: Adnan

last: Niazi

first: Eivind

last: Valen

first: Torben

last: Jensen


title: Genome-wide CRISPR Screen Identifies BUB1 Kinase as a Druggable Vulnerability in Malignant Pleural Mesothelioma

city: Izmir

first: Serif

last: Senturk

address: Dokuz Eylul University - iBG

department: Functional Cancer Genomics Lab

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary: Malignant pleural mesothelioma (MPM) is a rare yet highly aggressive malignancy with a severe prognosis. Compounded by the lack of effective treatment modalities, MPM remains a formidable health challenge. Therefore, identification of actionable liabilities is critical for advancing precision medicine to combat this lethal disease. Here, we exploit an unbiased genome-wide CRISPR screen, integrating and cross-comparing three MPM cell lines with nonmalignant mesothelial cells, to selectively map the gene targets whose depletion indicates a common dependency in MPM cells. This systematic approach unveils a cohort of verifiable genes, among which BUB1, a mitotic checkpoint serine/threonine kinase, emerges as a high-confidence hit in cancer cells. Cellular and molecular studies demonstrate that genetic depletion or pharmacological inhibition of BUB1 profoundly impairs MPM cell survival and growth, while inducing G2/M cell cycle arrest, cellular senescence, and apoptosis, and attenuating functional hallmarks of aggressive cancer cells. Transcriptomic profiling of BUB1-depleted cells discloses differential gene expression signatures congruent with cell fate phenotypes, including the reprogramming of mitotic network genes. Mechanistically, BUB1 is indispensable for the proper localization of essential mitotic regulators MAD1, MAD2, and Shugoshin (SGO1), thereby ensuring the functionality of the spindle assembly checkpoint (SAC). Furthermore, BUB1 ablation leads to cytokinesis failure and multinucleation, a phenotype characterized by the downregulation of CDC20, Cyclin A, and Cyclin B, and a reciprocal upregulation of the cyclin-dependent kinase inhibitor p21. Clinically, MPM tumors exhibit elevated levels of BUB1, and high BUB1 expression is associated with shorter patient survival. Our novel findings accentuate comparative CRISPR screens as a powerful platform to explore tumor cell-selective gene essentiality and propose BUB1 kinase as a potential marker and druggable vulnerability with therapeutic implications for MPM.

overall_design: To investigate the role of BUB1 in malignant pleural mesothelioma (MPM), we developed BUB1 knockout H2052, H2452 and H28 cell lines.

first: Senturk

last: Serif

first: Karakülah

last: Gökhan


title: Unravelling the antitumor mechanism of Ocoxin through cancer cell genomics

city: Derio

first: Ana

last: Aransay

address: Parque tecnologico de Bizkaia, Building 801-A

institute: CIC bioGUNE

summary: Cancer is one of the leading causes of death worldwide. Many therapies are being used to treat this disease, however, new treatments are now being implemented, since they are not always effective and their secondary effects represent one of the main reasons for cancer patients’ loss of life quality during the progression of the disease. In this scenario, Ocoxin is a mixture of plant extracts, amino acids, vitamins and minerals, known for its antioxidant, anti-inflammatory and immunoregulatory properties, which has shown to exert antitumor effects in many cancers. The aim of this study is to elucidate the mechanism of action of the compound in colorectal cancer, triple negative breast cancer, pancreatic cancer and prostate cancer. Analyses performed through RNA sequencing revealed that the main effect of Ocoxin appears to be the alteration of cell metabolism, especially inducing the process of ferroptosis. Nevertheless, the modulation of the cell cycle was also remarkable. Ocoxin altered 13 genes in common in all the four cancers that were not only associated to metabolism and cell cycle but were also involved in the integrated stress response and unfolded protein response, suggesting that the compound causes the induction of cell death through several pathways. Although the mechanisms vary according to the type of cancer, this study highlights the potential of Ocoxin as an adjunctive treatment to improve outcomes in cancer therapy.

overall_design: Prostate, Pancreatic and Colorectal adenocarcinoma cultured cells, as well as Triple Negative Breast cultured cells were treated with Ocoxin for 48 hours and their transcriptome was analyzed by RNAseq, to understand the transcriptomic alterations due to the drug.

first: Iera

last: Hernandez-Unzueta

first: Uxue

last: Telleria-Gonzalez

first: Ana M.

first: José E.

last: Martin Rodriguez

first: Eduardo

last: Sanz

first: Joana

last: Márquez


title: Spermidine restricts neonatal inflammation via metabolic shaping of PMN-MDSCs [CUT&Tag]

city: Tianjin

first: Lin

last: Zhu

address: Qixiangtai Road

institute: Tianjin Medical University

summary: Newborns exhibit a heightened vulnerability to inflammatory disorders due to their underdeveloped immune system, yet the underlying mechanisms remain poorly understood. Here we report that plasma spermidine is correlated with the maturity of human newborns and reduced risk of inflammation. Administration of spermidine led to the remission of neonatal inflammation in mice. Mechanistic studies revealed that spermidine enhanced the generation of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) via downstream eIF5A hypusination (eIF5A-Hyp). Genetic deficiency or pharmacological inhibition of deoxyhypusine synthase (DHPS), a key enzyme of eIF5A-Hyp, diminished the immunosuppressive activity of PMN-MDSCs, leading to aggravated neonatal inflammation. The eIF5A-Hyp pathway was found to enhance mitochondrial function via histone acetylation-mediated epigenetic transcription of immunosuppressive signatures in PMN-MDSCs. These findings demonstrated spermidine-eIF5A-Hyp metabolic axis as a master switch to restrict neonatal inflammation.

overall_design: CUT&Tag profiling of PMN-MDSCs after treatment with GC7 and DMSO.

first: Jie

last: Zhou

first: Jiale

last: Chen

first: Zhaohai

last: Cui


title: Spermidine restricts neonatal inflammation via metabolic shaping of PMN-MDSCs [RNA-seq]

overall_design: RNA-seq profiling of PMN-MDSCs from Dhps fl/fl and Dhps fl/fl Lysm cre mice.


title: Modulation of the Pseudomonas aeruginosa quorum sensing cascade by MexT-regulated factors

city: Seattle

first: Andrew

last: Frando

state: WA

address: 1705 NE Pacific Street

department: Pulmonary, Critical Care, and Sleep Medicine

institute: University of Washington

summary: Pseudomonas aeruginosa (Pa) is a ubiquitous bacterium that uses quorum sensing (QS), a cell-cell communication system that enables it to sense cell density and to alter gene expression. Pa has three complete QS circuits controlled by the transcriptional regulators LasR, RhlR, and PqsR (MvfR), that together control hundreds of genes, including virulence factors. In the well-described strain PAO1, QS is organized hierarchically, with PqsR and RhlR activity dependent on LasR. In PAO1, this hierarchy depends on the non-QS transcription factor MexT; by an unknown mechanism, deletion of mexT allows for RhlR activity in the absence of LasR. We aimed to identify how regulators such as MexT modulate the QS architecture in Pa. We compared the transcriptome of PAO1 to that of PAO1ΔmexT and identified 152 differentially expressed genes. MexT does not appear to regulate rhlR or pqsR directly; however, we identified two MexT-regulated operons that may affect the hierarchy in PAO1. These operons encode the drug efflux pump genes mexEF-oprN and the Pseudomonas quinolone signal (PQS) synthesis genes pqsABCDE. We performed genetic experiments to test whether the products of these genes affected the QS hierarchy. As with the mexT knockout mutant, we found that a PAO1 mexEF knockout mutant exhibited RhlR activity earlier, and to a higher magnitude, than wild-type PAO1. MexEF-OprN is known to export the PQS precursor HHQ, and we found that exogenous addition of PQS to PAO1 partially affects RhlR activity, resulting in earlier timing and higher magnitude compared to wild-type PAO1. We further elucidated that this is likely due to positive regulation by PqsE. These data link both the drug efflux pump MexEF-OprN and PQS QS to the regulation of the QS hierarchy in PAO1. We wondered if the same applied to QS architectures in Pa clinical isolates. We discovered that there are alternate QS architectures in clinical isolates, where RhlR activity is not fully dependent on LasR. In these isolates, surprisingly, MexT does not influence the relationship between LasR and RhlR, and this is indicative of a different QS architecture in the clinical isolates. Overall, we further elucidated the regulation of QS architecture in PAO1 and identified unique QS architectures in clinical isolates. Importantly, our work reveals a new suite of factors that regulate QS in Pa, with implications for a variety of Pa behaviors both in the laboratory and clinical settings.

overall_design: Bacteria from wild-type PAO1 and PAO1∆mexT were harvested at mid log and early stationary phase.  RNA was isolated and gene expresion quantified by sequencing.

first: Robert

last: Parsek

first: Jamal

last: Omar

first: Nicole

last: Smalley

first: Ajai

middle: A

last: Dandekar


title: Response to anti-PD-1 + anti-LAG-3 checkpoint blockade is associated with T regulatory cell functional reprogramming and instability

city: Portland

first: venkatesh

last: rajamanickam

state: OR

address: 4805 NE Glisan St, Suite 2N35

institute: Earle A. Chiles Research Institute

summary: We previously identified and validated a pre-treatment peripheral blood biomarker, characterized by a high frequency of LAG-3+ lymphocytes, that predicts resistance in patients receiving anti-PD-1 immune checkpoint blockade. To better understand the mechanism of aPD-1 resistance and select rational therapies to overcome resistance, we identified murine tumor models with a high LAG-3+ lymphocyte frequency (LAG-3hi), which were resistant to aPD-1 therapy, and LAG-3lo murine tumor models that were aPD-1 sensitive, recapitulating the predictive biomarker we previously described in patients. As we hypothesized, LAG-3hi tumor-bearing mice were sensitive to aPD-1+aLAG-3 therapy and the benefit of combination therapy was CD8+ T cell-dependent. Unexpectedly, the benefit of combination therapy was enhanced in LAG-3hi (but not LAG-3lo) mice with depletion of CD4+ T cells. Furthermore, responses to aPD-1+aLAG-3 significantly correlated with T regulatory cell (Treg) phenotypic plasticity in LAG-3hi mice, suggesting a specific role for Tregs in the mechanism of response to this combination. Using Treg fate tracking Foxp3GFP-Cre-ERT2 x ROSAYFP reporter mice we demonstrate that expanded populations of unstable Tregs correlate with response to combination therapy in LAG-3hi mice. Complementing this preclinical data, an increased proportion of unstable Tregs also significantly correlated with higher response rate and improved survival after aPD-1+aLAG-3 therapy in a cohort of patients with metastatic melanoma (n=117). These data indicate that Treg phenotypic plasticity is a key mechanism in aPD-1+aLAG-3 responsiveness, which may represent both a novel biomarker to aid patient selection and a rationale therapeutic target to expand benefit for a subset of PD-1 refractory patients.

overall_design: Subcutaneous implant of CT26 cells, treatment with aPD-1/aLAG-3 (1mg/mL each, IP) on day 7, 10 and 13 post tumor implant. Tumors harvested on day 15 post-tumor implant, prepared for sorting, stained with live/dead, CD45, CD3, CD19, CD11b. Live, CD45+CD3+, CD19-CD11b- cells were sorted and collected for RNA isolation

first: William

last: Redmond


title: Establishing Bovine Embryonic Stem Cells and Analyzing Potential Mechanisms of their Self-Renewal

city: Xianyang

first: Young

last: Tang

state: Shaanxi

address: #22 Xinong Road, Yangling District

department: College of Veterinary Medicine

institute: Northwest A&F University

summary: Bovine pluripotent stem cells (PSCs) hold significant potential for diverse applications in agriculture, reproductive biotechnology, and biomedical research. However, challenges persist in establishing stable bovine PSC lines and understanding the mechanisms un-derlying their pluripotency maintenance. Here, we derived bovine embryonic stem cells (bESCs) from Holstein cattle embryos. These cells exhibited robust differentiation capacity into three germ layers in vitro and in vivo. Transcriptome analysis revealed distinct molecular profiles compared to primed-state bESCs. Notably, bESC proliferation ceased on methanol-treated feeder cells, in contrast to mouse ESCs (mESCs), which proliferated normally. Pathway analysis identified key signaling events critical for bESC survival and proliferation, highlighting species-specific regulatory mechanisms. Furthermore, the derived bESCs demonstrated chimerism capacity in early bovine embryos, underscoring their functional pluripotency. This work provides a foundation for advancing bovine embryology research and stem cell-based biotechnologies in livestock.

sample_organism:
Bos taurus
Mus musculus

platform_organism:
Bos taurus
Mus musculus

overall_design:
RNAseq profiling of our established bESCs and their comparison with the reported RNAseq data from bMSCs (GSM5478616,GSM5478617,GSM5478618), biPSCs(GSM5478624,GSM5478625), primed state bESCs (GSM2976768,GSM2976773), and bovine blastocysts (GSM1265773,GSM1265774,GSM1265775). RNAseq profiling and comparing of bovine ESCs or mouse ESCs cultured on methanol-treated mouse embryonic fibroblasts (MEFs) or regular MEF feeders.

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

last: Li

first: Zhen

last: Yang

first: Yue

last: Su

first: Xiangyan

last: Wang

first: Wenjing

last: Wan

first: Shengcan

last: Xie

first: Anming

last: Lei

first: Jun

last: Liu


title: Rutin ameliorates stress-induced blood‒brain barrier dysfunction and cognitive decline via the endothelial HDAC1‒Claudin-5 axis

first: Zhao-Wei

last: Sun

address: 27# Taiping Road

institute: Beijing Institute of Basic Medical Sciences

summary: Background: Emerging evidence suggests that chronic stress compromises blood‒brain barrier (BBB) integrity by disrupting brain microvascular endothelial cells (BMECs), contributing to the development of cognitive impairments. Thus, targeting the BBB is expected to be a promising treatment strategy. The biological function of rutin has been investigated in neurological disorders; however, its regulatory role in stress-induced BBB damage and cognitive decline and the underlying mechanisms remain elusive. Methods: In a chronic unpredictable mild stress (CUMS) mouse model, a fluorescent dye assay and behavioral tests, including a novel object recognition test and Morris water maze, were performed to evaluate the protective effects of rutin on BBB integrity and cognition. The effects of rutin on BMEC function were also investigated in hCMEC/D3 cells (a human brain microvascular endothelial cell line) in vitro. Furthermore, the molecular mechanisms by which rutin restores BBB endothelium dysfunction were explored via RNA-seq, quantitative real-time PCR, western blotting, immunofluorescence and chromatin immunoprecipitation. Finally, biotinylated tumor necrosis factor-α (TNF-α) was employed to test the influence of rutin on the ability of circulating TNF-α to cross the BBB. Results: We identified that rutin attenuated BBB hyperpermeability and cognitive impairment caused by the 8-week CUMS procedure. Moreover, rutin promoted the proliferation, migration and angiogenesis ability of BMECs through positively regulating the expression of genes involved. Furthermore, rutin impeded histone deacetylase 1 (HDAC1) recruitment and stabilized H3K27ac to increase Claudin-5 protein levels. Ultimately, normalization of the hippocampal HDAC1‒Claudin-5 axis by rutin blocked the infiltration of circulating TNF-α into the brain parenchyma and alleviated neuroinflammation. Conclusions: This work establishes a protective role of rutin in regulating BMEC function and BBB integrity and reveals that rutin is a potential drug candidate for curing chronic stress-induced cognitive deficits.

overall_design: RNA-seq profiling of hCMEC/D3 cells with 0 and 25 μM Rutin treatment for 24 h

first: Zhao-Xin

first: Yun

last: Zhao

first: Ling-Jia

last: Qian


title: Bulk RNA sequencing of skin biopsies from psoriasis patients treated with Dead Sea climatotherapy

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

institute: Aarhus University Hospital

summary: This study investigated the cellular and molecular effects of Dead Sea climatotherapy in psoriasis patients who achieved complete remission.

overall_design: Skin punch biopsies from eight patients, who obtained PASI-100 response with climatotherapy,  were obtained at baseline, end-of-treatment and relapse. Lesional skin (L) were collected at each visit, whereas non-lesional skin (NL) were only collected at the baseline visit. Bulk RNA sequencing was performed on extracted total RNA.


title: PD-1 inhibitor treatment induces gene expression changes at the single-cell level in mouse hearts

city: Rizhao

first: Wei

last: Qin

state: Shandong

address: 669 Xueyuan Road, Donggang District, Rizhao, Shandong, China

institute: Jining Medical University

summary: PD-1 inhibitors, as a type of immune checkpoint inhibitors, have achieved significant success in cancer treatment. However, studies have found the usage of PD-1 inhibitors may cause cardiotoxicity. In this study, single-nucleus transcriptome sequencing (snRNA-seq) was employed to conduct a comprehensive analysis of mouse hearts after treatment with PD-1 inhibitor. Through this method, we aim to reveal the impact of PD-1 inhibitor on the expression network characteristics of heart tissue. SnRNA-seq allows us to obtain the complete transcriptomic information of each cell in the mouse heart , thus enabling the precise identification and quantification of differentially expressed genes in individual cells after PD-1 inhibitor treatment. Through the analysis of snRNA-seq data, we have discovered new mechanisms by which PD-1 inhibitor leads to cardiac dysfunction. These findings provide valuable resources for the research of cardiotoxicity induced by PD-1 inhibitors.

overall_design: The hearts are from mice that received intraperitoneal injections of PD-1 inhibitor (anti-mouse PD-1 antibody ) at a dose of 5 mg/kg on the 1st and 14th days of a 28-day cycle or received intraperitoneal injections of PBS at the same time.

first: Zejin

last: Zhang

first: Zhenzhen

last: Yan


title: Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

institute: Max Planck Institute for Biological Intelligence

summary: Diverse types of GABAergic projection neurons and interneurons of the telencephalon derive from progenitors in a ventral germinal zone, called the ganglionic eminence. Using single-cell transcriptomics, chromatin accessibility profiling, lineage tracing, birthdating, heterochronic transplantation, and perturbation sequencing in mouse embryos, we investigated how progenitor competence influences the maturation and differentiation of these neurons. We found that the progression of neurogenesis over developmental time shapes maturation competence in ganglionic eminence progenitors, influencing how they progress into mature states. In contrast, differentiation competence, which defines the ability to produce diverse transcriptomic identities, remains largely unaffected by the stages of neurogenesis. Chromatin remodeling alongside a NFIB-driven regulatory gene module influences maturation competence in late-born neurons. These findings provide key insights into how transcriptional programs and chromatin accessibility govern neuronal maturation and the diversification of GABAergic neuron subtypes during neurodevelopment.

overall_design: Cut&Run on Nfib and H3K4me3 on mouse ganglionic eminence.

first: Ann Rose

last: Bright

first: Yana

last: Kotlyarenko

first: Florian

last: Neuhaus


title: Rapamycin Enhances CAR-T Control of HIV Replication and Reservoir Elimination in vivo

city: Los Angeles

first: Jeffrey

last: Harding

state: CA

address: 405 Hilgard Avenue

institute: University of California Los Angeles

summary: Chimeric Antigen Receptor (CAR) T cell therapy shows promise for various diseases. Our studies in humanized mice and non-human primates (NHPs) demonstrate that hematopoietic stem cell (HSCs) modified with anti-HIV CAR achieve lifelong engraftment, providing functional anti-viral CAR-T cells that reduce viral rebound after ART withdrawal. However, T cell exhaustion due to chronic immune activation remains a key obstacle for sustained CAR-T efficacy, necessitating additional measures to achieve functional cure. We recently showed that low dose rapamycin treatment reduced inflammation and improved anti-HIV T cell function in HIV-infected humanized mice. Here, we report that rapamycin improved CAR-T cell function both in vitro and in vivo. In vitro treatment with rapamycin enhanced CAR-T cell mitochondria respiration and cytotoxicity. In vivo treatment with low-dose rapamycin in HIV-infected, CAR-HSC mice decreased chronic inflammation, prevented exhaustion of CAR-T cells and improved CAR-T control of viral replication. RNAseq analysis of CAR-T cells from humanized mice showed that rapamycin downregulated multiple checkpoint inhibitors and the upregulated key survival genes. Mice treated with CAR-HSCs and rapamycin had delayed viral rebound post-ART and reduced HIV reservoir compared to CAR-HSCs alone. These findings suggest that HSCs-based anti-HIV CAR-T combined with rapamycin treatment is a promising approach for treating persistent inflammation and improving immune control of HIV replication.

overall_design: RNA-seq profiling of CAR T cells was performed to investigate the transcriptional effects of rapamycin treatment. CAR T cells were treated with rapamycin (0.5 mg/kg, i.p., 3 times/week) and compared to untreated controls. Additionally, the R5-tropic strain HIV-1NFNSXSL9 was generated by transfecting 293T cells with a plasmid containing the full-length HIV-1 genome. Humanized mice were infected with HIV-1NFNSXSL9 (500 ng p24/mouse) via retro-orbital injection and treated with antiretroviral therapy (TDF 80 mg/kg, FTC 120 mg/kg, ELV 160 mg/kg) for 6 weeks. Rapamycin (0.5 mg/kg) was administered i.p. 3 times/week in combination with ART to assess its effects.

first: Wenli

last: Mu

first: Shallu

last: Tomer

first: Nandita

last: Kedia

first: Scott

last: Kitchen

first: Anjie

last: Zhen


title: MicroRNAs Biomarkers and Host Response Pathways in Severe Pulmonary Hemorrhagic Syndrome due to Leptospirosis

city: Bangkok

first: Phu

middle: Nguyen Trong

last: Tran

address: 1873 Rama IV Rd, Pathum Wan

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

summary: Serum microRNA profiling revealed distinct expression patterns between the two phenotypes. From the top 81 significantly expressed microRNAs, seven were selected for validation. Among these, miR-5010-3p and miR-147b-3p had area under the curve (AUC) values of 0.72 (95% CI: 0.62–0.81) and 0.66 (95% CI: 0.55–0.76) for discriminating SPHS. Notably, the two microRNAs could detect SPHS in patients who were yet to manifest chest radiograph shadows at the time of sample collection, with consistent AUC values.

overall_design: Candidate microRNAs were initially discovered through a global profiling of 800 serum microRNAs in five SPHS and seven non-SPHS patients, then validated using real-time polymerase-chain reactions in 28 SPHS and 140 non-SPHS patients.

last: Nguyen

first: Trong

last: Chan

first: Umaporn

last: Limothai

first: Janejira

last: Dinhuzen

first: Sasipha

last: Tachaboon

first: Theerapon

last: Sukmark

first: Chayomon

last: Dokpong

first: Sittiruk

last: Roytrakul

first: David

last: Haake

first: Nattachai

last: Srisawat


title: Human Subcutaneous abdominal adipose tissue RNAseq - NYC sample

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Bulk RNAseq data from abdominal subcutaneous sampling of a racially diverse sample of healthy premenopausal women and men with a range of BMI.

overall_design: We collected preliminary data for further studies of sex differences in human adipose tissues in healthy individuals.

first: Kalyspo

last: Karastergiou

first: Jeanine

last: Albu

first: Susan

last: Fried


title: Spt6-Spn1 interaction is required for RNA Polymerase II association and precise nucleosome positioning along transcribed genes

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Spt6-Spn1 is an essential histone chaperone complex that associates with RNA Polymerase II (RNAPII) and reassembles nucleosomes during gene transcription. While Spt6-Spn1 interaction is important to its histone deposition and transcription functions, a precise understanding of how Spt6-Spn1 association contributes to its functions is still limited. Here, using temperature sensitive alleles of spt6 and spn1 that disrupt their interaction, we show that Spt6-Spn1 association is broadly important for its interaction with the elongating RNAPII complex and nucleosomes. Using micrococcal nuclease (MNase)-based chromatin occupancy profiling, we further find that Spt6-Spn1 interaction is required for maintaining the preferred nucleosome positioning generated from replication-dependent histone deposition at actively transcribed genes. These analyses also reveal an overall shift of nucleosomes towards the 5’ end of genes that correlates with decreased RNAPII levels. While loss of Spt6 and Spn1 function is known to promote cryptic transcription, the nucleosome defects found in spt6 and spn1 mutants that interfere with their interaction were observed broadly across transcribed genes, further highlighting the role of DNA sequence as a mediator of cryptic transcription when nucleosomes positioning is altered. Taken together, these findings reveal Spt6-Spn1 interaction is key to its association with elongating RNAPII and for its ability to precisely organize nucleosomes across transcription units.

overall_design: RNA-seq at 30° and 37° C, MNase-seq at 37° C, and RNA PolII ChIP-seq at 37° C in yeast, across wild-type (S288C), spt6-F249K, spn1-R263D, and spn1-F267E mutant strains.

first: Boning

last: Chen

first: Raghuvar

last: Dronamraju

first: W

middle: R

last: Smith-Kinnaman

first: Sarah

last: Peck Justice

first: Heather

last: MacAlpine

first: Jeremy

last: Simon

first: Amber

last: Mosley

first: Brian

middle: D

last: Strahl


title: Linker histone H1-0 is a specific mediator of the ETV6::RUNX1 transcriptional landscape in preleukemia and B cell acute lymphoblastic leukemia

city: Düsseldorf

first: Vera

middle: Helena

last: Jepsen

address: Moorenstraße 5

institute: University Hospital Düsseldorf

summary: The chimeric hematopoietic transcription factor ETV6::RUNX1 is the most common oncogenic fusion in pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL). It induces a clinically silent preleukemic state that requires secondary mutations for progression to full-blown leukemia. ETV6::RUNX1 functions primarily through repression of RUNX1 binding sites. In order to elucidate the characteristic quiescent state of ETV6::RUNX1 expressing cells, we generated preleukemic human induced pluripotent stem cell (hiPSC) models from two healthy donors using CRISPR/Cas9 gene editing. We identified upregulation of linker histone H1-0 in preleukemic hiPSCs, which was preserved upon hematopoietic differentiation and transformation to overt BCP-ALL. ETV6::RUNX1 induces activity of the H1-0 promoter whereas depletion of H1-0 specifically inhibited ETV6::RUNX1 signature genes, indicating its role as a novel key mediator of the quiescent ETV6::RUNX1 transcriptional profile. Single-cell gene expression analysis revealed that H1-0 levels strongly anti-correlate with cellular transcriptional activity, resulting in particularly high expression in quiescent cells during hematopoietic development. Pharmacologically, H1-0 protein levels correspond to susceptibility of BCP-ALL towards histone deacetylase inhibitor (HDACi) treatment and our data indicate efficacy of combinatorial drug treatment using the potent H1-0-inducing HDACi Quisinostat in BCP-ALL expressing high basal H1-0 levels.

overall_design: To analyze transcriptional changes induced by HDACi treatment, BCP-ALL cell lines were treated with 1 µM Quisinostat or DMSO for 24 hours.

first: Jepsen

last: Vera Helena

first: Fischer

last: Ute


title: Single cell transcriptomics reveals cellular landscape of avian intestinal enteroids

city: Edinburgh

first: Jianxuan

state: Midlothian

address: The University of Edinburgh, Easter Bush Campus

country: United Kingdom

institute: Roslin Institute

summary: Understanding and manipulating the avian gastrointestinal tract, where nutrient absorption and vital host-pathogen interactions occur, is critical for improving poultry health and productivity. To advance research in this area, chicken three-dimensional intestinal enteroid models have been developed and characterised. In this study, we report a comprehensive transcriptome atlas for 43,587 intestinal enteroid cells derived from broiler and layer chickens. Our analyses reveal clusters representing mesenchymal, epithelial, endothelial, immune and neuronal cell lineages. We classified the mesenchymal lineage into nine populations, including fibroblasts, telocytes, myofibroblasts, smooth myocytes, pericytes, and interstitial cells of Cajal, reflecting anatomically distinct intestinal layers. We identified significant heterogeneity within the epithelial lineage, including enterocytes, goblet cells, Paneth cells, tuft cells, and various enteroendocrine cell subtypes. Additionally, we provide evidence for populations of macrophages, monocytes, γδT cell, NK cells, heterophils and dendritic cells. Differential gene expression tests between layer and broiler enteroids revealed extensive cell type-specific variation, pointing at differences in immune function and appetite regulation, with the most pronounced changes in epithelial cell types. Overall, this study offers a cell-resolved perspective of chicken three-dimensional intestinal enteroids, uncovering extensive heterogeneity masked by bulk transcriptomics. Additionally, we provide a catalogue of cell-specific marker genes to explore the function and organization of the chicken gastrointestinal tract.

overall_design: Chicken enteroids were generated from the duodenum, jejunum, and ileum of ED19 embryos, with tissues pooled from four embryos per culture. Dissociated villi (Day 0, n=2 per broiler and layer) and enteroids (Day 3, n=2 per broiler and layer) were collected. Single cell libraries were constructed using the 10x Genomics Chromium platform.

first: Dominika

last: Borowska

first: James

last: Furniss

first: Kate

last: Sutton

first: Daniel

last: Macqueen

first: Lonneke

last: Vervelde


title: Vaccination against oncofetal targets in the tumor vasculature

city: Amsterdam

first: Judy

last: van Beijnum

state: Noord Holland

address: CCA rm 2.52, De Boelelaan 1118

department: Medical Oncology

country: Netherlands

institute: VUMC

summary: Mice were vaccinated with iBoost technology against a tumor vascular target, prior to B16F10 or CT26 tumor inoculation. Tumors from control and target vaccinated mice were excised and subject to RNAseq

overall_design: mRNA profiles of target and control vaccinated mice' B16F10 and CT26 tumor tissue

first: Else

last: Huijbers

first: Arjan

last: Griffioen


title: Generation and characterization of induced pluripotent stem cells of small apes

city: Inuyama

first: Yusuke

last: Hamazaki

state: Aichi

institute: Center for the Evolutionary Origins of Human Behavior, Kyoto University

summary: Small apes (family Hylobatidae), encompassing gibbons and siamangs, occupy a pivotal evolutionary position within the hominoid lineage, bridging the gap between great apes and catarrhine monkeys. Although they possess distinctive genomic and phenotypic features—such as rapid chromosomal rearrangements and adaptations for brachiation—functional genomic studies on small apes have been hindered by the limited availability of biological samples and developmental models. Here, we address this gap by successfully reprogramming primary skin fibroblasts from three small ape species: lar gibbons (Hylobates lar), Abbott’s gray gibbons (Hylobates abbotti), and siamangs (Symphalangus syndactylus). Using Sendai virus-based stealth RNA vectors, we generated 31 reprogrammed cell lines, five of which were developed into transgene-free induced pluripotent stem cells (iPSCs). These iPSCs displayed canonical features of primed pluripotency, both morphologically and molecularly, consistent with other primate iPSCs. Directed differentiation experiments confirmed the capacity of small ape iPSCs to generate cells representing all three germ layers. Particularly, the successful differentiation into limb bud mesoderm cells underscores their utility in investigating the molecular and developmental mechanisms unique to small ape forelimb evolution. Transcriptomic profiling of small ape iPSCs revealed significant upregulation of pluripotency-associated genes, alongside elevated expression of transposable elements. Remarkably, LAVA retrotransposons—a class of elements specific to small apes—exhibited particularly high expression levels in these cells. Comparative transcriptomic analyses with iPSCs from humans, great apes, and macaques identified evolutionary trends and clade-specific gene expression signatures. These signatures highlighted processes linked to genomic stability and cell death, providing insights into small ape-specific adaptations. This study positions small ape iPSCs as a transformative tool for advancing functional genomics and evolutionary developmental biology. By facilitating detailed investigations into hominoid genome evolution and phenotypic diversification, this system bridges critical gaps in comparative research, enabling deeper exploration of the genetic and cellular underpinnings of small ape-specific traits.

sample_organism:
Hylobates lar
Symphalangus syndactylus

platform_organism:
Hylobates lar
Symphalangus syndactylus

overall_design: transcriptome profiles of small ape iPSCs

first: Hiroto

last: Akuta

first: Hikaru

last: Suzuki

first: Kenji

last: Ichiyanagi

first: Takuya

last: Imamura

first: Masanori


title: Characterization and validation of a novel multitarget small-molecule in glioblastoma

city: Donostia

first: Estefania

last: Carrasco-Garcia

state: Guipúzcoa

address: Dr. Begiritsain s/n

department: Oncology

institute: Biodonostia

summary: The development of multitarget small molecules (MSMs) has emerged as a powerful strategy for the treatment of multifactorial diseases such as cancer. Glioblastoma is the most prevalent and malignant primary brain tumor in adults, which is characterized by poor prognosis and a high heterogeneity. Current standards of treatment present limited effectiveness, as patients develop therapy resistance and recur. In this work, we synthesized and characterized a novel multi-target molecule (named DDI199), which is a polyfunctionalized indole derivative developed by juxtaposing selected pharmacophoric moieties of the parent compounds Contilisant and Vorinostat (SAHA) to act as multifunctional ligands that inhibit histone deacetylases (HDACs), monoamine oxidases (MAOs) and cholinesterases (ChEs), and modulate histamine H3 (H3R) and 5-hydroxytryptamine 6 (5-HT6R) receptors. DDI199 exerts high cytotoxic activity in conventional glioblastoma cell lines and patient-derived glioma stem cells in vitro. Importantly, it significantly reduces tumor growth in vivo, both alone and in combination with temozolomide (TMZ). The comparison with SAHA showed higher target specificity and antitumor activity of the new molecule. Transcriptomic and proteomic analyses of patient-derived glioma stem cells revealed a deregulation in cell cycle and neurotransmission activity by the treatment with DDI199. In conclusion, our data reveal the efficacy of a novel MSM in glioblastoma pre-clinical setting.

overall_design: The experiment was performed in patient-derived glioma stem cells (GNS166) treated with DDI199 at 5μM and control for four independent replicates.

first: Matheu

last: Ander