title: Type IV pili and TLR2 dependent endocytosis of episymbiotic Saccharibacteria attenuates immunoactivation

city: Seattle

first: Jeffrey

middle: S

last: McLean

state: WA

address: 1959 NE Pacific St, Box 357444

department: Periodontics

institute: University of Washington

summary: Saccharibacteria are episymbionts that require host-bacteria to grow. They are positively associated with inflammatory diseases within the human microbiome, yet their mechanisms for interacting with the human host and contributing to inflammatory diseases remain unknown. This study investigated interactions between a Saccharibacterium (Nanosynbacter lyticus), its host-bacteria (Schaalia odontolytica), and oral epithelial cells. The host-bacteria induced proinflammatory cytokines (IL8, GROα, and MCP-1) in epithelial cells, while Saccharibacteria were immune silent. Remarkably, Saccharibacteria dampened cytokine responses to host-bacteria during coinfection. This effect resulted from Saccharibacteria directly interacting with TLR2 receptors via T4P, becoming endocytosed by epithelial cells, and subsequently inhibiting TLR2 activation by the host-bacteria. Super-resolution imaging showed that intracellular Saccharibacteria colocalized with endosome markers, eventually trafficking to lysosomes. Moreover, a subset survives endocytosis, escapes epithelial cells, and reinfects host-bacteria, highlighting a mechanism for persistence in the oral microbiome and a vital role in mammalian immune system modulation.

overall_design: RNA seq profilling of human oral keratinocyte cell- wildtype TIGK cells and TIGK cells infected with S. odontolyticus strian XH001, N. lyticud strain TM7x and their coculture.

first: Deepak

last: Chouhan

first: Batbileg

last: Bor

first: McLean

last: Jeffrey

first: Kerns

last: Kristopher


title: miRNA signatures in Burkitt leukemia and lymphoma in children and young adults

status: Public on Feb 09 2026

city: Rostock

first: Teresa M.

last: Cardesa-Salzmann

address: Ernst-Heydemann Strasse, 8

country: Germany

institute: Universitätsmedizin Rostock. Klinik für Kinder- und Jugendmedizin

summary: miRNA expression analysis in Burkitt leukemia and lymphoma in children and young adults. Comparison of clinicopathological subgroups. Evaluation of differential expression.

overall_design: Evaluation of the expression profiles of 800 miRNAs in 33 Burkitt leukemia (B-AL) and Burkitt lymphoma (B-Ly) samples taking advantage of the NanoString nCounter System. Comparison of groups based on tumor and normal control lymphoid tissue (NCLT) (n=4) as well as comparisons based on clinical characteristics was performed to evaluate miRNAs deregulated in B-AL and B-Ly.

first: Björn

last: Schneider

first: Teresa

middle: M


title: Respiratory syncytial virus infection induces heterologous protection against SARS-CoV-2 via induction of trained immunity and SARS-CoV-2 reactive mucosal T cells

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

country: USA

institute: UTMB NGS Core

type: Expression profiling by high throughput sequencing

summary: The respiratory viruses can concurrently or sequentially infect a host and influence the trajectory of each other. The underlying immune mechanisms are not well understood. Here, we investigated whether respiratory syncytial virus (RSV) infection affects host vulnerability to subsequent SARS-CoV-2 infection in both BALB/c and the K18 hACE-2 transgenic mouse models. We found that RSV infection- induced heterologous protection against subsequent SARS-CoV-2 infection was dose and time dependent. RNA-seq and immunological analyses revealed that RSV infection triggered antigen presenting cell (APC)s and SARS-CoV-2 reactive mucosal T cell activation in the lung at day 9, which declined at 1 month. RSV infection induced the expansion and the upregulation of cellular metabolic pathways of gd T cells. Furthermore, RSV infection in TCRd-/- mice, which are deficient of gd T cells triggered a lower SARS-CoV-2 reactive mucosal T cell response. Following SARS-CoV-2 infection, TCRd-/- mice with prior RSV infection had increased viral loads and higher levels of virus-induced inflammatory responses in the lung compared to the WT group. In summary, our results suggest that RSV infection provides heterologous protection against subsequent SARS-CoV-2 infection via induction gd T cell- mediated trained immunity in the lung and SARS-CoV-2 reactive mucosal T cell responses.

overall_design: 7- to 8-week-old  C57BL/(B)6 mice were infected intranasally (i.n) with 5 × 106  of RSV. At day 9 post RSV infection, mice were challenged with 1 × 104 PFU of the SARS-CoV-2 CMA4 strain. infected mice were euthanized at day 2 for tissue collection.

first: Awadalkareem

last: Adam

first: Tian

last: Wang


title: Transcriptomes of capsule swapped-strains in Klebsiella

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

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

overall_design: Refer to individual Series


title: Minor spliceosome inhibition via ablation of its U11 snRNA gene results in multiple defects in murine spermatogenesis

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

summary: Minor intron-containing genes (MIGs), which require the minor spliceosome (MiS) for their splicing, are highly represented among genes involved in mouse spermatogenesis. Leveraging gene- and intron-level ortholog data, we show that conservation of these genes as MIGs is particularly strong in chordates but not in other species groups, suggesting lineage-specific changes to their splicing regulation. A role for the MiS in splicing during spermatogenesis was reinforced by the cell-type specific expression patterns of MiS snRNAs and directly tested using Stra8-Cre mediated ablation of Rnu11, which encodes for the MiS U11 snRNA. Rnu11 mutant testes were smaller, and presented with multiple mitotic and meiotic defects, increased cell death, and a reduction in mature sperm at matched timepoints. RNA sequencing of P14 whole testes revealed minor intron retention and alternative splicing events in MIGs that are key regulators of genomic stability, cell cycle progression, and gene expression regulation, contributing to the variable cellular defects. RT-PCR of fractionated cell types of the testes confirmed splicing defects of key MIGs in cell-type enriched samples. The multifaceted molecular disruption resulted in defective meiotic recombination, telomere morphology, chromosome synapsis and XY-chromosome association. Overall, we highlight the molecular and cellular processes that are regulated by the MiS.

overall_design: RNA-seq profiling of postnatal day 14 whole-testes dissected from control and mutant (Rnu11-cKO) animals (n=3). Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Sample Prep Kit with ribosomal RNA depletion by RiboZero, and sequenced on the Illumina NovaSeq 6000 platform.

first: Kazumasa

last: Takemoto

first: Kaitlin

last: Girardini

first: Abigail

last: Boria

first: Jade

last: Rosado

first: Taveena

last: Konakanchi

first: Shreyesh

last: Vachhani

first: Saren

last: Springer


title: Extensive enhancer crosstalk governs the induction of PPARG2 expression during adipogenic lineage commitment [Capture-C]

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Transcriptional master regulators drive cell fate transitions. Peroxisome proliferator- activated receptor γ (PPARγ) is the master regulator of adipogenesis, and its expression must therefore be tightly regulated and efficiently induced in response to adipogenic cues. Here we show that the PPARG locus is primed for activation in the mesenchymal stem cell state by a highly connected enhancer (HICE) community. By systematically deleting 9 individual enhancers, spanning upstream, promoter-proximal, and downstream super-enhancer constituents, we demonstrate elaborate enhancer crosstalk in cis involving stabilization of C/EBPβ recruitment prior to chromatin remodeling. We show that the super-enhancer constituent E+102 plays a dual role in cis crosstalk and feedback activation and is obligate for activation of PPARG expresison. Non-coding genetic variants associated with cardiometabolic traits and predicted to regulate PPARG expression map E+102 and other essential enhancers in the community, thereby supporting the importance of these enhancers in human physiology and disease.

overall_design: Chromatin interactions using Capture-C for PPARG2 TSS and selected enhancer in the PPARG locus during adipocyte differentiation of control and enhancer deletion human mesenchymal stem cells with iducible expression of Cas9 (hMSC-TERT4-iCas9-4).

first: Anna

last: Cetnarowska

first: Mette

last: Hyldahl

first: Marcus

last: Nygård

first: Bo

last: Vagner Hansen

first: Laura

middle: K

last: Holm

first: Kaja

last: Madsen

first: Maria

last: Stahl Madsen

first: Vallari

last: Shukla

first: Esra

last: Durmaz Mitchell

first: Alexander

last: Rauch

first: Jesper

last: Grud Skat Madsen

first: Melina

last: Claussnitzer


title: Profiling Immune-Independent Response to Immune Checkpoint Inhibitors on Stem Cell-derived Cardiac Organoids [scRNAseq_Mouse]

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: The use of antibody based immune-checkpoint inhibitors (ICIs) have been highly successful in clinical treatment of several cancers. Despite the compelling efficacy of these drugs with their high binding affinity, there is incomplete understanding of non-target interactions in vivo. In this regard, ICIs are also known to cause immune-related adverse events (iRAEs) arising from infiltration of immune cells in tissues such as the heart. Due to the frequency of ICI treatments, extended half-life and the late onset of cardiac events, concerns have been raised regarding potential direct interactions of ICIs with major cellular cell types of the heart. The direct effects of these drugs in patients are limited due to rare incidence, and difficulty in obtaining patient heart biopsies in the pre- or post-symptomatic phase. Therefore, in order to study both functional and molecular changes in vitro and in vivo,  we utilized a human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), cardiac organoids (COs), and immunocompromised NOD/SCID mouse models.

overall_design: In this experiment, NOD/SCID mice were injected with immune chekpoint inhibitors (ICIs), pembrolizumab (PEM), atezolizumab (ATZ), or isotype control at day 0 and day 7. On day 14, the animals were sacrificed and hearts were harvested (Pooled, n=3/group) for single cell sequencing (10X Genomics).

first: Dilip

last: Thomas


title: Ontogeny-independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis [scRNA-seq]

city: York

first: Paul

last: Kaye

state: North Yorkshire

address: University of York, Heslington

country: United Kingdom

institute: Hull York Medical School, University of York

summary: Granulomas are organized inflammatory lesions that form in response to persistent stimuli such as infections. Murine infection with Leishmania donovani results in the formation of granulomas around infected Kupffer cells in the liver and serves as a well-defined model of immune granuloma formation. The formation and resolution of granulomatous inflammation requires dynamic shifts in immune cell activation states, imposing significant metabolic demands. As mediators of energy homeostasis and cell signaling, lipids and lipid metabolism play a key role in regulating immune cell function during inflammation and the response to infection. However, the extent to which alterations in lipids are spatially linked to altered immune cell transcription has yet to be resolved. In this study, we performed a multimodal imaging analysis combining MALDI mass spectrometry, spatial and single cell transcriptomics, proteomics of flow-sorted macrophages and histopathology of L. donovani induced hepatic granulomas. Using this spatially-integrated approach, we identified LPCAT2-mediated membrane re-modelling of myeloid cells as a novel feature of these granulomas. Our study provides new insights into local immunometabolic changes associated with granuloma formation and macrophage activation.

overall_design: Adult female C57BL/6J mice were maintained and bred at the University of York, UK. The mice were housed in ventilated cages under specified pathogen-free conditions with access to food and water ad libitum. Identification of the mouse colony was confirmed through genetic profiling of microsatellite markers, verifying C57BL/6J genetic background with minor variations at 3 markers. Healthy (6-8 week old females) were infected intravenously with 3x107 amastigotes of the Ethiopian LV9 strain of Leishmania donovani to establish visceral infection. At 28 days post-infection, mice were euthanized by CO2 inhalation followed by cervical dislocation according to Home Office regulations. Livers were harvested after euthanization and the major lobe cut and snap-frozen in liquid nitrogen while bathed in isopenane and then kept in -80 degrees until used. The remaining liver was harvested in 2% fetal calf serum (FCS) in 1x PBS and immediately processed into a single cell-suspension. Age-matched uninfected female mice from the same colony were used as baseline controls for liver tissue. For single-cell RNA seq 6 infected mice were run as individual samples selected from 2 independent experiments and the 2 naive samples were each pooled from 3x uninfected mice.

first: Shoumit

last: Dey

first: Jian-Hua

last: Cao

first: Benjamin

last: Balluff

first: Nidhi

first: Lesley

last: Gilbert

first: Sally

last: James

first: Adam

middle: A

last: Dowle

first: Grant

last: Calder

first: Peter

last: O'Toole

first: Ron

last: Heeren


title: Comprehensive profiling of N6-methyladnosine (m6A) readouts reveals novel m6A readers that regulate human embryonic stem cell differentiation [GLORI-seq]

city: Beijing

first: Yuan

last: Zhou

address: 38 college road

country: China

institute: Peking University

summary: GLORI-Seq is an antibody-independent sequencing, which can detect m6A sites at single-base. The core of GLORI-Seq is to find a catalytic system of glyoxal and nitrite through chemical reaction combination screening, which efficiently deaminate unmethylated adenosine A to form inosine (A-to-I, > 98%). Inosine is read to guanosine (G) in the sequencing process, forming A-to-G conversion. GLORI-Seq enables single base detection of single base m6A by detecting the proportion of “A” in the sequenced read sequence.

overall_design:
A549, hESCs and JURKAT cells were analyzed with 2 duplications for GLORI-Seq.
METTL3-knockdown A549, hESCs and JURKAT cells were analyzed with 2 duplications for GLORI-Seq.

first: Zhou

last: Huang

first: Rucong

first: Zibaguli

last: Wubulikasimu

first: Wanqing

last: Zhao

first: Jiaqi

first: Jiaxuan

last: Wang

first: Rui

last: Fan

first: Wei

last: Kong

first: Qinghua

last: Cui

first: Yang

last: Li


title: PHIP suppresses NuRD to enable the growth of SWI/SNF-mutant cancers [ChIP-seq]

city: Memphis

first: John

last: Navarro

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SWI/SNF chromatin remodeling complexes are perturbed in 20% of all cancers and several developmental disorders, yet the mechanisms by which these mutations dysregulate transcription and drive disease are poorly understood. To both elucidate these mechanisms and identify vulnerabilities caused by these mutations, we leveraged genome-wide CRISPR-Cas9 screening in hundreds of cancer cell lines and identified the chromatin reader protein PHIP as a specific dependency in cancers with broadly disrupted SWI/SNF function. Mechanistically, we reveal that PHIP cooperates with SWI/SNF to facilitate transcriptional activation by ubiquitinating and suppressing subunits of the repressive Nucleosome Remodeling and Deacetylase (NuRD) complex. We demonstrate that loss of SWI/SNF results in NuRD complexes accumulating at promoters where they would otherwise cause widespread transcriptional silencing if not antagonized by PHIP. Collectively, we identify PHIP as a regulator of the interplay between distinct chromatin regulators that function in development and disease and as a targetable vulnerability in cancers with broad SWI/SNF inactivation.

overall_design: ChIP-seq of G401 in siCtrl, siPHIP, PHIP OE, and PHIP-rescue conditions

first: Hayden

last: Malone

first: Jacquelyn

last: Myers

first: Charles

last: Roberts


title: SETD2 methyltransferase activity aids gene definition by promoting correct transcription initiation and efficient pre-mRNA 3’ cleavage [RCC_POINTseq]

city: Fukuoka

first: Takayuki

last: Nojima

state: Japan

address: Maidashi

department: Medical Sciences

country: Japan

institute: Kyushu University

summary: SETD2 is a key histone methyltransferase responsible for depositing histone H3 lysine 36 trimethylation (H3K36me3). Loss of its enzymatic activity has been implicated in various cancers, including renal cell carcinoma (RCC). In RCC, SETD2 mutations have been linked to defects in transcription termination, though the underlying mechanism remains unclear. Here, using nascent transcriptomics in SETD2 knockouts and RCC patient-derived cells, we show that SETD2 loss leads to delayed transcription termination, but only in a subset of genes. POINT-seq analysis reveals widespread transcriptional readthrough beyond canonical termination sites upon SETD2 loss/mutation, affecting 15–24% of genes. We demonstrate that defective termination following SETD2 loss/mutation is driven by a combination of increased cryptic transcription initiation and impaired 3′ pre-mRNA cleavage. In contrast, genes that maintain proper termination show significant downregulation. Additionally, we find that SETD2 ensures proper termination independently of alternative polyadenylation, underscoring the distinction between transcription termination and 3′ end processing. Our findings highlight that methyltransferase activity of SETD2 is a crucial regulator of transcriptional integrity, preventing cryptic initiation and promoting efficient 3′ end processing

overall_design: POINTseq performed for ACHN and A498 cells. 2 biologicl replication.

first: Magda

last: Kopczyńska

first: Chihiro

last: Nakayama

first: Agata

last: Stępień

first: Shoko

last: Ito

first: Koshi

last: Imami

first: Michal

middle: R

last: Gdula

first: Kinga

last: Kamieniarz-Gdula


title: Ontogeny-independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis [Spatial Transcriptomics]

first: Paul

last: Kaye

overall_design: Adult female C57BL/6J mice were maintained and bred at the University of York, UK. The mice were housed in ventilated cages under specified pathogen-free conditions with access to food and water ad libitum. Identification of the mouse colony was confirmed through genetic profiling of microsatellite markers, verifying C57BL/6J genetic background with minor variations at 3 markers. Healthy (6-8 week old females) were infected intravenously with 3x107 amastigotes of the Ethiopian LV9 strain of Leishmania donovani to establish visceral infection. At 28 days post-infection, mice were euthanized by CO2 inhalation followed by cervical dislocation according to Home Office regulations. Livers were harvested after euthanization and the major lobe cut and snap-frozen in liquid nitrogen while bathed in isopenane and then kept in -80 degrees until used. For spatial gene expression, 4 infected and 4 uninfected liver sections from individual mice were processed using 10x Visium.

first: Shoumit

last: Dey

first: Jian-Hua

last: Cao

first: Benjamin

last: Balluff

first: Gaia

last: Mazza

first: Helen

last: Ashwin

first: Lesley

last: Gilbert

first: Sally

last: James

first: Adam

last: Dowle

first: Grant

last: Calder

first: Nidhi

first: Peter

last: O'Toole

first: Ron

last: Heeren


title: The Notch ligand Jagged1 regulates extracellular matrix production and organization in triple-negative breast cancer

city: Turku

first: Marjaana

last: Parikainen

address: Tykistökatu 6

country: Finland

institute: Åbo Akademi University

summary: The extracellular matrix (ECM) in the tumor microenvironment plays an essential role in the progression of cancer. Here, we show that expression of the Notch ligand Jagged1 correlates with poor patient survival in aggressive breast cancer and that Jagged1 promotes in vivo tumor growth and invasion of triple-negative breast cancer cells. Using transcriptomics, proteomics, and imaging approaches of cancer cell/fibroblast co-cultures, both in vitro and in vivo, we demonstrate that Jagged1 drives fibroblast activation, increased collagen deposition, and aligned organization of ECM fibers. Jagged1 increases transforming growth factor beta (TGFβ) related signaling in fibroblast co-cultures and the Jagged1-induced ECM alignment can be prevented by a TGFβ inhibitor. Thus, Jagged1 regulates ECM remodeling upstream of TGFβ. With the emergence of safe therapeutics targeting specific Notch ligands and receptors, Jagged1 modulation may offer a path to therapeutically target invasive breast cancer.

overall_design: RNA-seq profiling of wildtype MDA-MB-231 breast cancer cells and their derivative cell lines (Jag1KO, Jag1KO+rescue, Jag1KO+ctrl, siCtrl, and siJag1) with altered expression of JAG1, grown for 7 days as 3D Matrigel cultures. 3 biological replicates of each sample.

first: Ujjwal

last: Suwal

first: Pekka

last: Rappu

first: Jyrki

last: Heino

first: Cecilia

last: Sahlgren


title: Role of visfatin (Nampt) on early embryogenesis in normal weight and obese mice. Studies on siRNA induced knockdown model.

city: Kyoto

first: Shinnosuke

last: Honda

address: Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto-shi

institute: Kyoto University

summary: We obtained transcriptomic profiles in HFD or ND mouse blastocysts (96 h post-insemination (hpi)) which had been electroporated with non-targeting or Nampt-targeting siRNA at the one-cell stage (3–6 hpi).

overall_design: In vitro produced mouse blastocysts were processed to RNA-Seq. The experiments were duplicated using ten embryos per group.

first: Patrycja

last: Kurowska

first: Genta

last: Tanaka

first: Gao

last: Yuwei

first: Naojiro

last: Minami

first: Agnieszka

last: Rak

first: Shuntaro

last: Ikeda


title: Deciphering the impact of RAC1-SPTAN1 in ARPKD cystogenesis using multifaceted models

city: Charlestown

first: Ryuji

last: Morizane

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

summary: RNAseq of kidney organoids derived from stem cells with SPTAN1 mutation and cultured under flow conditions.

overall_design: Total RNA was isolated from flow-cultured kidney organoids using TRIzol from two biological replicates per condition (SPTAN1+/+ clone 1, SPTAN1+/+ clone 2, SPTAN1+/- clone 1, SPTAN1+/- clone 2). RNA-Seq data was generated using the NovaSeq X Plus (Novogene).

first: Shohei

last: Kuraoka


title: Early versus late hidradenitis suppurativa: Type 17 T-cell and B-cell inflammation precedes dermal tunnel and tertiary lymphoid structure formation

city: Sacramento

first: JAEHWAN

last: KIM

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

summary: Hidradenitis suppurativa (HS) is a debilitating inflammatory skin disease that progresses from superficial nodules in early stages to deep dermal tunnels, tertiary lymphoid structures (TLSs), and fibrosis in later stages. Interplays between dermal tunnel keratinocytes, TLSs, and fibroblasts promote pathogenic T-cell and B-cell inflammation in late-stage disease. However, whether T-cell and B-cell inflammation sequentially precedes or follows the late-stage structure formation is unclear. The study aims to elucidate the sequence of inflammation from early- to late-stage HS by comparing their single-cell transcriptomes with those of psoriasis. We analyzed gene expression differences between early-stage HS and late-stage HS using single-cell RNA sequencing. The result showed plasma cell expansion, multifunctional B-cells expressing pro-inflammatory cytokines, major histocompatibility complex molecules, and immunoglobulins in HS. Unlike in late-stage HS, T-cells were the primary producers of the B-cell chemoattractant CXCL13 in early-stage HS.

overall_design: Early-stage hidradenitis suppurativa (HS), late-stage HS, psoriasis lesional skin, and psoriasis non-lesional skin specimens were collected by skin biopsy procedures. All the human tissue specimens were collected with informed consent in accordance with the Declaration of Helsinki, and local ethics review boards approved the study. Collected skin tissues were incubated in culture medium for 48 hours. Emigrating cells from the skin tissues after 48-hour incubation were harvested and studied by droplet-based single-cell RNA sequencing.

first: Jaehwan

last: Kim

first: James

middle: G

last: Krueger

first: Jongeun

last: Lee


title: U2AF1 Mutant Myeloid Neoplasms are Preferentially Sensitive to In Vivo Inhibition of Nonsense-Mediated RNA Decay

city: St Louis

first: Sridhar

last: Nonavinkere Srivatsan

address: 660 S Eucild Ave

institute: WashU School Of Medicine

summary: Expression of mutant spliceosome proteins (e.g., U2AF1S34F, SF3B1K700E, or SRSF2P95H) alters RNA splicing in myeloid neoplasms, leading to increased production of nonsense transcripts. We have previously shown that inhibiting the nonsense–mediated RNA decay (NMD) pathway, which is responsible for degradation of nonsense transcripts, preferentially kills cells expressing mutant spliceosome proteins. In this study, we used a novel inhibitor (SMG1i-63) of the kinase SMG1, a key regulator of NMD, to provide in vivo evidence that NMD is also a therapeutic vulnerability for splicing factor mutant myeloid neoplasms. We show that primary mouse acute myeloid leukemia cells and human K562 leukemia cell lines expressing splicing factor mutants were more sensitive than wild-type cells to in vivo inhibition of SMG1 (SMG1i). Disruption of NMD activity by SMG1i led to increased R-loops levels in spliceosome wild-type cells, which are further increased in U2AF1S34F treated cells. This R-loop accumulation was accompanied by an increase in DNA damage. Degradation of R-loops with RNase H1 rescued spliceosome mutant cells from NMD inhibition-induced cell death, indicating that R-loop formation is a primary mechanism of drug sensitivity. In U2AF1S34F cells, SMG1i led to increased detection of NMD transcript isoforms (with reduced but detectable protein levels) for DNA repair genes, including ATR and RAD51. Consequently, SMG1i-induced cell death in splicing factor mutant leukemias could be further enhanced by inhibition of the DNA damage response proteins ATR or RAD51. This study shows that in vivo targeting of NMD is a therapeutic strategy to treat myeloid neoplasms with aberrant splicing.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA was isolated from sorted GFP+ mouse MLL::AF9 BM cells after SMG1i-63 or vehicle treatment using the Quick-RNA MicroPrep Kit (Fisher-Zymo, No. R1050). Quality of isolated RNA was determined using Agilent RNA 6000 Nano chip using the Agilent 4200 TapeStation platform. Quantification was performed using Qubit Fluorometer (Thermo-Fisher Scientific). Total RNA samples with RNA integrity number (RIN) >9 were selected for Illumina sequencing library preparation. The RNA-Seq libraries were prepared using the KAPA RNA Hyper Prep Kit with RiboErase (Roche). After amplification, approximately 300 bp fragments were sequenced on Illumina NovaSeq 6000. The reads were then mapped using STAR (v2.7.0) against the GRCm38.95 version of the mouse genome from the Ensembl consortium. In parallel, gene level counts for mutant and control samples were processed using kallisto (v0.43.1). Differentially expressed genes were identified using DESeq2 (version 1.26.0). Additional filtering was applied to require genes to have 5 reads in at least half the samples, and an FDR < 0.1. TPM values were calculated using StringTie (version 1.3.3). Splicing event classification was per- formed using rMATS-turbo (version 4.1.0). Gene enrichment analysis was performed using clusterProfiler (version 3.10.1). Pathway enrichment analysis was performed using fgsea (version 1.17.0) against GO, Reactome, and MSIGDB gene sets (FDR < 0.1). For K562 same protocol was used for library preparation. The reads were then mapped using STAR (v2.7.0) against the GRCh38.95 version of the human genome from the Ensembl consortium. Pathway enrichment analysis for NMD predicted transcritps was performed using Enrichr.

first: Claudia

last: Cabrera Pastrana

last: Srivatsan

first: Matthew

middle: J

last: Walter


title: Transketolase regulates endoplasmic reticulum stress independent of its enzymatic activity in the retina

city: Chengdu

first: feipeng

last: jiang

address: #37 Guoxue Alley, Wuhou District, Chengdu, Sichuan Province, P.R.China

institute: west china hospital

summary: Transketolase is an enzyme in the pentose phosphate pathway, with nuclear localization and non-metabolic functions reported in various cancer and other cell types. This study explores the role of transketolase in the retina, with a focus on its involvement in endoplasmic reticulum (ER) stress. Using a VEGF-overexpressing mouse model of age-related macular degeneration (AMD), we examined transketolase expression and enzymatic activity. Our results show that while transketolase expression remains stable, its enzymatic activity is significantly reduced in the AMD retina. Chromatin immunoprecipitation sequencing revealed that transketolase regulates genes involved in cellular metabolism and ER protein processing, with pathways linked to neurodegenerative diseases. We also demonstrated that transketolase directly downregulates Ern1 expression. In human Müller cells, knockdown of transketolase resulted in increased ERN1 levels and aggravated ER stress. Interestingly, inhibiting transketolase’s enzymatic activity did not affect the ER stress response, while knockdown of transketolase did not affect the cellular metabolism. These findings suggest that knockdown of transketolase regulates Ern1 translation and ER stress in the retina, independent of its enzymatic function.

overall_design: ChIP-seq of Transketolase in VEGF-overexpressing Mouse Model of AMD. Two retinas from induced Tet-opsin-VEGFA mice and two retinas from noninduced Tet-opsin-VEGFA mice were collected separately.

first: Yingying

last: Chen

first: Feipeng

last: Jiang

first: Ni

last: Han

first: Xinran

last: Wu

first: Tengxiao

last: Mao

first: Meixia

last: Zhang


title: PHIP suppresses NuRD to enable the growth of SWI/SNF-mutant cancers [RNA-seq]

first: John

last: Navarro

overall_design: RNA-sequencing of A204, G401, BIN67 and CHLA266 cells in siCtrl and siPHIP samples

first: Hayden

last: Malone

first: Jacquelyn

last: Myers

first: Charles

last: Roberts


title: Epi-transcriptome analysis reveals the absence of m6A modifications in two watermelon-infected RNA viruses [GLORI-Seq]

first: Jia-xian

last: Jing

address: Beijing Academy of Agriculture and Forestry Science

summary: We carried  GLORI-seq with ribo-minus RNAs extracted from virus-infected watermelon leaves and the corresponding IVT RNAs to evaluate m6A enrichment on viral RNAs.

overall_design: GLORI-seq of virus-infected watermelon leaves and the corresponding IVT RNAs

first: Fuan

last: Pan

first: Jiaxian

first: Xueping

last: Zhou

first: Shaofang

last: Li


title: Single-cell RNA sequencing analysis of lung tissue from Tubb3-/- mice in a bleomycin-induced pulmonary fibrosis model

city: Bethesda

first: Ryo

last: Sato

state: MD

address: 10 Center Dr

department: NHLBI

institute: National Institutes of Health

summary: Whole lung cells and mural cell-enriched mesenchymal cells were isolated by cell sorting from Tubb3-/- mice and their wild-type (WT) littermates 14 days after bleomycin administration, followed by single-cell RNA sequencing analysis.

overall_design:
Tubb3-/- mice and their wild-type (WT) littermates were treated with bleomycin, and lung tissues were harvested 14 days post-treatment. Two biological replicates were prepared for each genotype. The isolated lungs were dissociated and processed to obtain both whole cell samples and mural cell-enriched mesenchymal cell samples. For whole cell samples, erythrocytes were removed by magnetic negative selection using rat anti-mouse TER-119 antibody followed by sheep anti-rat Dynabeads. For mesenchymal cell samples, cells were enriched by magnetic negative selection using rat anti-mouse antibodies against CD31, CD45, EpCAM, and TER-19, followed by sheep anti-rat Dynabeads. Following negative selection, both cell samples were counted and labeled with oligonucleotide tags for multiplexing using the 10x Genomics 3′ CellPlex Kit Set A (1000261). The labeled samples from all four mice were pooled according to sample type (whole cell or mesenchymal cell) and stained with DAPI (0.1 μg/mL) prior to cell sorting. For the pooled whole cell sample, live cells were sorted. For the pooled mesenchymal cell sample, MCAM+ PDGFRα- (mural cells) and MCAM- (non-mural cells) populations were sorted and mixed at a 1:1 ratio to achieve mural cell enrichment. Single-cell isolation, RNA capture, cDNA preparation, and library preparation were performed according to the manufacturer's protocol (Chromium Next GEM Single Cell 3' Reagent Kit, v3.1 chemistry, 10x Genomics). Libraries were sequenced on an Illumina NovaSeq 6000 S4 flow cell.
Please note that processed data files were generated from both GEX and CMO raw data, and are linked to the corresponding GEX sample records.

first: Sato

last: Ryo

first: Yoshida

last: Teruhiko

first: Mukouyama

last: Yoh-suke


title: The alterations of gene expression profiling induced by ORM1 knockdown in HCT116 cells.

city: weifang

first: Jiaqiu

address: Baotong west street No.7166

institute: shandong second medical university

summary: Recently, ORM1 was found to play an oncogenic role in in several cancers. Here we report gene expression profiles of HCT116 cells treated with ORM1 siRNA. This study reveals a novel role of ORM1 in downstream gene regulation and provides a new explanation of ORM1’ s function in colorectal cancer.

overall_design: RNA-seq after knockdown of ORM1 by siRNA in HCT116 cells.


title: Binding of MYC to nascent RNA suppresses innate immune signaling by R-loop-derived RNA-DNA hybrids [DRIPc]

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: In response to perturbed transcription elongation, the MYC oncoprotein multimerizes and undergoes a phase transition; the underlying mechanisms and their function are unknown. Here, we show that MYC relocalizes from its canonical location on DNA to RNA in response to the accumulation of intronic RNA. MYC directly binds RNA, which promotes its multimerization. MYC multimers concentrate the nuclear exosome, a 3'-5' RNA exonuclease, and its targeting complexes around double-stranded RNA and R-loops. RNA binding of MYC suppresses activation of the innate immune kinase TBK1. Upon MYC depletion, intron-derived dsRNAs, including RNA derived from small nucleolar RNAs, and RNA-DNA hybrids accumulate on TLR3, a pattern recognition receptor that activates TBK1. RNA binding of MYC is required to suppress the accumulation of R-loop-derived RNA-DNA hybrids on TLR3. Our data show that the phase transition of MYC is an RNA-driven stress response that suppresses the accumulation of immunogenic RNAs.

overall_design: The first aim was to investigate how the treatment with CBL0137 affects R-loop levels in cells expressing oncogenic MYC levels. To investigate this, DRIPc-sequencing was performed in U2OSMYC-Tet-On cells treated with doxycycline to induce oncogenic MYC levels and CBL0137 (5 µM, 2 h) or DMSO as control. To further evaluate how MYC RNA binding affects R-loop levels and distribution, DRIPc-sequencing was performed in KPC cells depleted of endogenous MYC and exogenously expressing WT MYC or RBRIII MUT MYC. Additionally, we determined the effect of Exosc10 depletion on R-loops in KPC cells in the presence of either WTMYC or RBRIIIMUTMYC.

first: Sinah

last: Löbbert

first: Francisco

last: Montesinos


title: Effect of depletion of MALAT1 on gene expression during LPS stimulation on THP-1 derived differentiated macrophages

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

summary: Long non-coding RNAs (lncRNAs) are known for their diverse roles in regulating gene expression, cellular functions, and metabolic pathways. Among them, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been extensively studied in cancer and inflammation. Here, we report a newly discovered interaction between MALAT1 and HADHB—a key enzyme in mitochondrial fatty acid oxidation (FAO)—which reveals additional regulatory roles for MALAT1 in human macrophages. Our findings show that MALAT1 binds to hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit beta (HADHB), significantly enhancing its thiolase activity and its expression during the inflammation.By targeting HADHB, MALAT1 influences both inflammatory and metabolic pathways, providing insights into its potential as a therapeutic target for modulating macrophage activity and metabolic balance in chronic inflammatory diseases. This study not only identifies HADHB as a new target of MALAT1 but also underscores the conserved functional roles of lncRNAs across species, particularly in immune and metabolic regulation.

overall_design: To explore the function of MALAT1 in the different time points stimulated by LPS, we performed human THP-1 derived macrophages in which the MALAT1 is been knocked down by siRNA. We then performed gene expression profiling analysis using  data obtained from RNA-seq of two different cells at four time points. Comparative gene expression profiling analysis of RNA-seq data for THP-1 derived macrophages transfected by negative control (siControl)  and its KD derivatives (siMALAT1). Each sample has three replicates.

first: Yuxiang

last: Liu

first: Katsuhito

last: Fujiu


title: Binding of MYC to nascent RNA suppresses innate immune signaling by R-loop-derived RNA-DNA hybrids [ChIP_Rx]

summary: In response to perturbed transcription elongation, the MYC oncoprotein multimerizes and undergoes a phase transition. The underlying mechanisms and their function are unknown. Here, we demonstrate that MYC globally relocalizes from its canonical positions on DNA to nascent RNA in response to the accumulation of intronic RNA. Binding of MYC to RNA induces MYC to form multimers that concentrate the nuclear exosome - a 3'-5' RNA exonuclease - and its targeting complexes around double-stranded RNA and R-loops. MYC harbors four RNA-binding regions (RBRI–IV), which overlap with evolutionarily conserved regions. Of these, RBRIII promotes MYC multimerization and is necessary for recruiting the exosome to R-loops. While RBRIII is dispensable for MYC-dependent transcriptional activation and pancreatic tumor cell proliferation in culture, it is indispensable for sustaining tumor growth in vivo. Via RBRIII, MYC suppresses the accumulation of R-loop-derived RNA-DNA hybrids and prevents them from binding to the pattern recognition receptor TLR3 and activating the innate immune kinase TBK1. Our data demonstrate that MYC has mechanistically distinct functions in transcription and RNA metabolism, and that its phase transition is an RNA-driven stress response that suppresses the accumulation of immunogenic RNA-DNA hybrids.

overall_design: One aim of the study was to investigate how treatment with CBL0137 and PlaB affects the DNA binding of MYC. To investigate this, ChIP-Rx using MYC Y69 antibody was performed in U2OSMYC-Tet-On cells treated with doxycycline to induce oncogenic MYC levels and CBL0137 (5 µM, 2 h), PlaB (1 µM, 4 h) or DMSO as control. To further evaluate the behavior of RNAPII and RNAPIIpS2 under these treatment conditions, RNAPII and RNAPIIpS2 ChIP-Rx experiments were additionally performed. 10% murine NIH 3T3 cells were added to each sample as a spike-in. Additionally, a comparison was made of the DNA binding of WTMYC and RBRIIImutMYC in U2OS-AID and KPC cells. For the U2OS-AID experiments, cells were treated with auxin (500 µM, 24 hours) and doxycycline to deplete the endogenous MYC and express either WT or RBRIIImutMYC. The binding behavior was examined in the absence or presence of CBL0137 (5 µM, 2 h). For KPC cells, samples were treated for 48 h with doxycycline to simultaneously deplete endogenous, murine MYC and express WT or RBRIIImut MYC. For U2OS-AID cells, HA-antibody was used for ChIP-Rx. 10% murine NIH 3T3 cells were added to each sample as a spike-in, but not used for further analysis. For murine KPC cells, ChIP-Rx was performed with MYC antibody (Y69), and samples contain 10% of human spike-in. EtOH condition or IgG served as pulldown controls.

first: Theresa

last: Endres

first: Leonie

last: Uhl

first: Peter

last: Gallant

first: Amel

last: Aziba


title: IRF7 Modulates Inflammatory Pain through upregulating IFNβ in mice

city: GuangZhou

first: Jia

last: Shilin

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Institute of Stomatological Research, Sun Yat-sen University

summary: Interferon regulatory factors (IRFs) are a family of transcription factors and function primarily in the immune system, which also play critical roles in other biological processes, such as pain. To date little is known about the functions of the interferon regulatory factor 7 (IRF7) involving in pain. Here we investigate the role of IRF7 signaling in nociceptive processing, using RNA interference strategies or pharmacological approaches. We show that the expression level of IRF7 and interferon (IFN) β is upregulated in primary sensory neurons in a mouse model of inflammatory pain.IRF7-IFNβ signal is involved in regulating neuronal hypersensitivity and pro-inflammatory cytokines production. The results identify IRF7-IFNβ signaling as a critical mediator of neuroinflammation that involve in pain development at the level of the primary sensory ganglion. This pathway may be suggested as a potential target for pain management, particularly in orofacial inflammatory pain.

overall_design: High-throughput sequencing was performed on TG tissues from mice injected with either CFA or saline (n = 3) at 3 dpi. Tissue collection followed the protocol described above, and samples were immediately processed for sequencing. Library preparation for Illumina sequencing was conducted using KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Stranded-mRNA was performed sequenced on Illumina Platform NovaSeq 6000.

first: Shilin

last: Jia

first: Lijia

last: Mai

first: Fang

last: Huang

first: Wenguo

last: Fan


title: EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Mammalian genomes are pervasively transcribed into long noncoding RNAs (lncRNAs), whose functions and modes of action remain poorly understood. EPB41L4A-AS1 is an evolutionary conserved and broadly and highly expressed lncRNA that produces the H/ACA snoRNA SNORA13 from one of its introns. We studied the consequences of EPB41L4A-AS1 perturbation in breast cancer cells and found that it acts both in cis to enhance expression of the proximal EPB41L4A gene, and in trans by broadly regulating gene expression, including expression of snoRNAs, transcription of genes involved in nucleolar biology and the distribution of nucleolar proteins. These effects are phenocopied by loss of SUB1, an interactor of EPB41L4A-AS1 and are observed following transient perturbations of EPB41L4A-AS1 that do not affect steady-state SNORA13 levels. Exogenous expression of the full-length EPB41L4A-AS1 locus but not SNORA13 expression can rescue the trans-acting transcriptional effects of its perturbation. The EPB41L4A-AS1 gene is thus a versatile locus producing RNA molecules acting on multiple levels and important for key cellular functions.

overall_design: RNA-seq, CUT&RUN and SLAM-seq from MCF-7 breast cancer cells after perturbing the expression of EPB41L4A-AS1, SUB1 or GAS5.

first: Alan

last: Monziani


title: RNA-mediated MYC multimerization suppresses innate immune signaling [mRNA]

first: Martin

last: Eilers

summary: In response to perturbed transcription elongation or splicing, MYC proteins multimerize and undergo a phase transition; the underlying mechanisms and the biological function of this transition are poorly understood. Here, we show that MYC proteins globally bind to nascent RNA in tumor cells and relocalize from their canonical location on DNA to RNA in response to the accumulation of intronic RNA. Blocking nascent RNA degradation induces MYC multimerization and MYC multimers are hubs that concentrate the nuclear exosome, a 3'-5' RNA exonuclease, and its targeting complexes around double-stranded (ds)RNA and R-loops. MYC binds RNA directly, and RNA binding promotes MYC multimerization and the recruitment of the exosome to R-loops. RNA binding of MYC has no role in transcriptional regulation but suppresses activation of the innate immune kinase TBK1 by the TLR3 pattern recognition receptor. Upon MYC depletion, intron-derived dsRNAs, including RNA derived from several classes of repetitive elements and small nucleolar RNAs (snoRNAs), accumulate on TLR3. TLR3-bound snoRNAs recovered from MYC-depleted cells carry aberrant 3’-ends, indicating defective exosomal processing. Our data show that the phase transition of MYC is a stress response driven by its binding to RNA that suppresses the accumulation of aberrant RNAs, which would otherwise activate innate immune signaling.

overall_design: To characterize the phenotypes of the MYC RBRIIIMUT, we performed mRNA-seq to compare the gene expression profile between MYC WT and the MYC RBRIIIMUT; shMYC was used as control. For this experiment, KPC cells expressing both, two doxycycline-inducible shRNAs targeting MYC as well as exogeneous, doxycycline-inducbible MYC WT or MYC RBRIIIMUT constructs or no additional exogenous construct for the shMYC condition. All cell lines were treated with doxycycline (1 µg/ml) for 48 h. For each of the conditions, 3 biological replicates have been produced.

first: Toshitha

last: Kannan


title: The XPO7-NPAT axis represents key vulnerabilities in TP53-mutated acute myeloid leukemia (scRNA-Seq)

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

summary: Mutation of TP53, a tumor suppressor in cancer, is common and leads to extremely poor prognosis. To identify vulnerabilities in TP53-mutated tumors, we performed genome-wide CRISPR/Cas9 screens using isogenic Trp53 wild-type and knockout mouse acute myeloid leukemia (AML) lines. Here, we show that histone gene regulation governed by the XPO7-NPAT pathway is essential for survival of TP53-mutated AML cells. In TP53 wild-type cells, XPO7 enhances p53 nuclear localization and functions as a tumor suppressor, but in TP53-mutated cells, XPO7 promotes cell proliferation by retaining NPAT, a histone gene activator, in the nucleus. NPAT depletion led to genome-wide histone loss, enhancing vulnerability to genotoxic stress. Human AML cases show predominant expression of XPO7 and NPAT when TP53 is mutated, suggesting a potential therapeutic vulnerability.

overall_design: To assess intra-patient profiles of NPAT/XPO7 mRNA expression and their correlation with TP53 mutational status at single-cell levels, we performed single-cell RNA-seq (scRNA-seq) using BM cells from two TP53-mutated AML cases.


title: Epi-transcriptome analysis reveals the absence of m6A modifications in two watermelon-infected RNA viruses [m6ARIPseq]

first: Jia-xian

last: Jing

institute: Beijing Academy of Agriculture and Forestry Science

summary: We carried m6ARIP-seq with ribo-minus RNAs extracted from virus-infected watermelon leaves and the corresponding IVT RNAs to evaluate m6A enrichment on viral RNAs.

overall_design: m6ARIP-seq of virus-infected watermelon leaves and the corresponding IVT RNAs

first: Fuan

last: Pan

first: Jiaxian

first: Xueping

last: Zhou

first: Shaofang

last: Li


title: Epi-transcriptome analysis reveals the absence of m6A modifications in two watermelon-infected RNA viruses [DRS]

summary: We carried  DRS with ribo-minus RNAs extracted from virus-infected watermelon leaves and the corresponding IVT RNAs to evaluate m6A enrichment on viral RNAs.

overall_design: DRS of virus-infected watermelon leaves and the corresponding IVT RNAs


title: HyperTRIBE analysis of the m6A reader YTHDF1 in HEK293T cells

first: Yuan

address: 38 college road

summary:
TRIBE/HyperTRIBE has been developed as an alternative method for transcriptome-wide mapping of the RNA targets of RBPs. This method involves fusing an RBP to the catalytic domain of the Drosophila RNA editing enzyme ADAR. When these fusion proteins are expressed in target cells, they direct A-to-I editing at residues in proximity to RNA binding sites.
To demonstrate the utility of HyperTRIBE approach, we applied HyperTRIBE to the m6A reader YTHDF1 in HEK293T cells.

overall_design: Both mCherry-ADAR control and YTHDF1-ADAR cells were analyzed with 3 duplications for HyperTRIBE.

first: Zhou

first: Rucong

last: Liu

first: Zibaguli

last: Wubulikasimu

first: Wanqing

last: Zhao

first: Jiaxuan

last: Wang

first: Qinghua

last: Cui

first: Yang


title: Decoding the total RNAs bound to human HADHB in the THP-1 derived macrophages

first: Ichiro

last: Manabe

overall_design: To explore the RNAs bound to human HADHB, RNA immunoprecipitation sequencing (RIP-seq) for human HADHB was performed in THP-1 derived macrophages stimulated by LPS for 24H.

first: Yuxiang

first: Katsuhito

last: Fujiu

first: Yukiteru

last: Nakayama


title: Cellular function of the GndA small open reading frame-encoded polypeptide during heat shock

city: West Haven

first: Sarah

last: Slavoff

address: 600 West Campus Dr

department: Chemistry

institute: Yale University

summary: Over the past 15 years, hundreds of previously undiscovered bacterial small open reading frame (sORF)-encoded polypeptides (SEPs) of fewer than fifty amino acids have been identified, and biological functions have been ascribed to an increasing number of SEPs from intergenic regions and small RNAs. However, despite numbering in the dozens in Escherichia coli, and hundreds to thousands in humans, same-strand nested sORFs that overlap protein coding genes in alternative reading frames remain understudied. In order to provide insight into this enigmatic class of unannotated genes, we characterized GndA, a 36-amino acid, heat shock-regulated SEP encoded within the +2 reading frame of the gnd gene in E. coli K-12 MG1655. We show that GndA pulls down components of respiratory complex I (RCI) and is required for proper localization of a RCI subunit during heat shock. At high temperature GndA deletion (ΔGndA) cells exhibit perturbations in cell growth, NADH+/NAD ratio, and expression of a number of genes including several associated with oxidative stress. These findings suggest that GndA may function in maintenance of homeostasis during heat shock. Characterization of GndA therefore supports the nascent but growing consensus that functional, overlapping genes occur in genomes from viruses to humans.

overall_design: Several strains of E. coli were created that contain mutations to the gnd locus to assess the transcriptome effects of the small open reading frame encoded peptide GndA that is nested within it. The resulting cells were exposed to increased temperature (45 °C) to induce a heat shock response, after which cellular RNA was extracted and sequenced.

first: Jessica

last: Mohsen


title: Binding of MYC to nascent RNA suppresses innate immune signaling by R-loop-derived RNA-DNA hybrids [seCLIP]

first: Martin

last: Eilers

overall_design: A primary objective of the study was to determine whether MYC binds to RNA in cells. To this end, seCLIP experiments were performed in K562 cells (with endogenous MYC) and in U2OSMYC-Tet-On cells that were treated with doxycycline to induce oncogenic MYC levels or with ethanol (EtOH) as a control to represent endogenous MYC levels. To evaluate whether MYC binds to nascent RNA, MYC eCLIPs were performed after CDK9 inhibition and subcellular fractionation into nucleoplasmic and chromatin-associated fractions. Additionally, we sought to determine the effect of chemical treatment with CBL0137, PlaB, or siRNA-mediated EXOSC5 knockout on MYC RNA binding. Furthermore, seCLIP experiments were performed for TLR3 to compare TLR3 RNA binding in KPC cells with and without MYC (shMYC). To demonstrate that RBRIIImut affects MYC RNA binding in cells, we performed MYC eCLIPs in KPC cells that were depleted of endogenous MYC (shMYC) and that had exogenously inducible WTMYC and RBRIIIMUTMYC alleles. A complementary eCLIP aimed to investigate whether MYC RNA binding changes in stressed (CBL0137-treated) U2OS cells. Thus, MYC-AID cells that express doxycycline-inducible, HA-tagged WTMYC and RBRIIIMUTMYC alleles were treated with auxin and doxycycline.

first: Leonie

last: Uhl

first: Tim

last: de Martines

first: Francisco

last: Montesinos

first: Dimitrios

last: Papadopoulos


title: HyperTRIBE analysis of the m6A readers in hESCs

first: Yuan

last: Zhou

institute: Peking University

summary: TRIBE/HyperTRIBE has been developed as an alternative method for transcriptome-wide mapping of the RNA targets of RBPs. This method involves fusing an RBP to the catalytic domain of the Drosophila RNA editing enzyme ADAR. When these fusion proteins are expressed in target cells, they direct A-to-I editing at residues in proximity to RNA binding sites. The control plasmid, mammalian expression plasmid, containing mCherry ADAR control and p2A GFP reporter can be obtained from Addgene (Plasmid #154786). As for RBP-TRIBE plasmid, using standard restriction enzyme-based cloning to clone RBP (DDX6, FUBP3, FXR2 or L1TD1) into TRIBE plasmid in hESCs.

overall_design: All RBP-ADAR cells were analyzed with 3 duplications for HyperTRIBE.

first: Zhou

last: Huang

first: Rucong

first: Jiaqi

first: Rui

last: Fan

first: Wei

last: Kong


title: Non-mitogenic FGF19 mRNA-based therapy for the treatment of experimental metabolic dysfunction-associated steatotic liver disease (MASLD)

city: Pamplona

first: David

last: Ruiz Guillamón

state: Navarra

address: Av. de Pío XII, 55

department: Programa de Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación de Medicina Aplicada (CIMA) - Clínica Universidad de Navarra

summary: Metabolic dysfunction-associated steatohepatitis (MASH), represents a threat to global health. MASH pathophysiology involves hepatic lipid accumulation and progression to severe conditions like cirrhosis and, eventually, hepatocellular carcinoma. Fibroblast growth factor (FGF)-19 has emerged as a key regulator of metabolism, offering potential therapeutic avenues for MASH and associated disorders. We evaluated the therapeutic potential of a non-mitogenic (NM)-FGF19 mRNA-formulated in liver-targeted lipid nanoparticles (NM-FGF19-mRNAs-LNPs) in C57BL/6NTac male mice with diet-induced obesity and MASH (DIO-MASH).  NM-FGF19-mRNAs-LNPs or control (C-mRNA-LNPs) were administered (0.5 mg/kg, i.v.) weekly for six weeks. NM-FGF19-mRNAs-LNPs treatment in DIO-MASH mice resulted in reduced body weight, adipose tissue depots, and serum transaminases, along with improved insulin sensitivity. Histological analyses confirmed the reversal of MASH features, including steatosis reduction without worsening fibrosis. NM-FGF19-mRNAs-LNPs reduced total hepatic bile acids (BA) levels and changed liver BA composition, markedly influencing cholesterol homeostasis and metabolic pathways as observed in transcriptomic analyses. Extrahepatic effects included the downregulation of metabolic dysfunction-associated genes in adipose tissue. This study highlights the potential of NM-FGF19-mRNA-LNPs therapy for MASH, addressing both hepatic and systemic metabolic dysregulation. NM-FGF19 demonstrates efficacy in reducing liver steatosis, improving metabolic parameters, and modulating BA levels and composition. Given the central role played by BA in dietary fat absorption, this effect of NM-FGF19 may be mechanistically relevant. Overall, our study underscores the high translational potential of mRNA-based therapies in addressing the multifaceted landscape of MASH and associated metabolic perturbations.

overall_design: 24-week-old C57BL/6NTac male mice were feeded with normal chow diet or high-fat diet (HFD) in parallel for 21 weeks. HFD mice where separated into baseline, control and NM-FGF19 groups. Baseline mice were sacrificed the week before treatment to verify that HFD mice had reached the MASH stage. All mice were then treated weekly for six weeks with mRNAs-LNPs while mantaining diet. In lean mice (normal chow) and control HFD mice a Control-mRNA was used, while NM-FGF19 group was treated with NM-FGF19 containing mRNA-LNPs. 24 hours after last mRNA-LNPs administration mice were sacrificed and liver tissues prepared for RNA extraction and sequencing.

first: Amaya

last: Lopez-Pascual

first: Matias

last: Avila

first: Pedro

last: Berraondo

last: Ruiz-Guillamon


title: Neuronal TDP-43 regulates myelin formation via neurexin 1 mRNA stabilization

city: Nagoya

first: Jiayi

last: Li

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Neurology

institute: Nagoya University Graduate School of Medicine

summary: TAR DNA-binding protein 43 (TDP-43) is a major pathological protein inextricably linked to Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Hypomyelination was detected in neuronal- specific TDP-43 knockout (TDP-43cKO) mice, and this impairment was recovered by the supplementation of cytoplasmic TDP-43 in neurons. We herein investigated the mechanisms that neuronal TDP-43 regulating neuron-oligodendrocyte interactions using the TDP-43cKO mice.

overall_design:
AAV-FLEX-GFP or AAV-FLEX-TDP-43mNLS-GFP was injected into the hippocampus of TDP-43cKO or control (CamKIIcre/-) mice. GFP-positive cells were sorted from brain suspensions pooled from 3-4 animals in each group by FACS. RNAs were extracted from the isolated cells and applied for RNA-seq.
We then performed gene profiling analysis using data obtained from RNA-seq  of AAV-FLEX-GFP injected control moue (NC-GFP), AAV-FLEX-GFP injected TDP-43cKO mouse (TDP-43cKO-GFP) and AAV-FLEX-TDP-43mNLS-GFP injected TDP-43cKO mouse (TDP-43cKO-TDP-43mNLS).

first: Yohei

last: Iguchi

first: Masahisa

last: Katsuno


title: Dual-Targeted Microspheres Reshape the Metabolic-immune Microenvironment and Reverse Multiple Dilemmas Post-embolization in Hepatocellular Carcinoma_GM VS GZM

status: Public on Feb 08 2026

city: Suzhou

last: Jiang

address: No. 899, Pinghai Road, Gusu District

department: Department of Interventional Radiology

institute: The First Affiliated Hospital of Soochow University

summary: Transarterial embolization (TAE) efficacy in hepatocellular carcinoma (HCC) is limited by post-embolization hypoxia-driven angiogenesis and metabolic reprogramming. To address these challenges, pH-responsive gelatin microspheres encapsulating zinc sulfide (ZnS) nanoparticles (ZnS@GMs) were developed for the dual delivery of hydrogen sulfide (H2S) gas and Zn2+ ions.

overall_design: ZnS@GMs significantly suppressed tumor growth through suppression of the HIF-1α/VEGF axis and glycolytic metabolism, alongside promoting vascular normalization and immune activation. Mechanistically, H2S disrupted mitochondrial respiration, increasing oxygen levels and destabilizing HIF-1α, whereas Zn2+ inhibited hexokinase and lactate dehydrogenase, depleting ATP and biosynthetic intermediates. Furthermore, ZnS@GMs induced immunogenic cell death, which triggered dendritic cell maturation, cytotoxic T-cell infiltration, and macrophage repolarization, thereby enhancing the efficacy of anti-PD-1 therapy. In a rabbit orthotopic liver tumor model, intra-arterial infusion of ZnS@GMs confirmed potent antitumor effects and excellent embolic performance. This work establishes ZnS@GMs as a multifunctional platform to overcome TAE resistance in HCC.


title: Pre-Clinical Assessment of Composition of Chronic Venous Occlusion Formed in a Pig

city: Chicago

first: Kenneth

last: Bader

address: 5835 S Cottage Grove Ave

institute: University of Chicago

summary: Venous thrombosis that transition to chronic occlusions that are difficult to address with current interventions. Histotripsy is a focused ultrasound therapy that ablates tissue through bubble cloud activity. Pre-clinical studies indicate acute thrombosis is sensitive to histotripsy, but outcomes for chronic disease require further investigation. This study developed a porcine model to test the hypothesis that histotripsy will disrupt disorganized extracellular matrix within chronic venous occlusions. Thrombi were formed in the femoral vein of female mixed breed pigs via selective catheterization. The occlusion was monitored for 30 days with ultrasound imaging, after which the femoral bundle was resected for analysis with bulk RNA-seq (N = 3). Changes to the occlusion appearance were noted throughout aging. At 30 days, obstructed venous tissue was composed primarily of collagen (mean: 39.7% by area) with activated macrophages (mean: 22.2% of cells) and fibroblasts (mean: 21.6% of cells).

overall_design: Thrombi were formed in the femoral vein of female mixed breed pigs via selective catheterization. After 30 days, the vascular bundle was resected and embedded in parafin. Histological regions of interest on control chronic occlusions were identified and annotated on H&E-stained images. The corresponding tissue areas were dissected and processed for RNA isolation using the RNeasy FFPE kit (QIAGEN Cat#73504) according to the manufacturer instructions. Selected regions were deparaffinized, digested with Proteinase K and crosslinks were reversed before RNA purification. The resulting purified product was subsequently used for RNA sequencing. Strand-specific RNA-seq libraries were prepared using an TruSEQ total RNA-SEQ library protocol (Illumina provided). Library quality and quantity was assessed using an Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ-X2. The data were processed to count tables using the nf-core/rnaseq pipeline. Reads were trimmed using Trim Galore and then mapped to the Sscrofa11.1 genome assembly using STAR. Quantification of gene counts was done using Salmon. FastQC and MultiQC were used for data quality checking. The online version of CYBERSORTx was used for deconvolution. The safeTME matrix was exported from the spatialDecon R package and used as the signature matrix in CYBERSORTx. The raw count table was normalized by library size, scaled by gene length, and log2 transformed to be used as the mixture file in CYBERSORTx. The "Impute Cell Fractions" analysis module was run with the following parameters: Batch correction - disabled, Disable quantile normalization - true, Run mode (relative or absolute) - relative, Permutations - 1. The top 200 highly expressed genes in the RNAseq sample were overlapped with the safeTME signature genes to verify the deconvoluted major cell types.   Two sections were processed for each control chronic occlusion with residual thrombus (N = 6 sections total from 3 venous occlusions).

first: Bader

last: Kenneth


title: The RNA 5-methylcytosine writer NSUN5 promotes hepatocellular carcinoma cell proliferation via a ZBED3-dependent mechanism

city: Zhengzhou

first: xue

last: chen

address: NO.101 Kexue Road High-Tech Development Zone Of States Zhengzhou

institute: Zhengzhou University

type: Methylation profiling by high throughput sequencing

summary: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide. Nop2/Sun domain family member 5 (NSUN5), a conserved RNA 5-methylcytosine methyltransferase, is generally considered oncogenic, but its role in the development of HCC remains unknown. In this study, we discovered that NSUN5 expression was remarkably elevated in both tumor tissues of patients as well as HCC cell lines, and was also correlated with poor clinical outcomes. NSUN5 knockdown and overexpression significantly inhibited and promoted HCC cell proliferation, respectively. Additionally, combining methylated RNA immunoprecipitation sequencing (MeRIP-seq) with RIP-seq, we identified zinc finger BED domain-containing protein 3 (ZBED3) as a novel downstream target of NSUN5. We further discovered that overexpression of ZBED3 rescued the tumor-suppressing effect of NSUN5 knockdown, and simultaneously revered the inhibition of Wnt/β-catenin signaling pathway. In conclusion, we discovered the oncogenic role of NSUN5 in the development of HCC and identified ZBED3/Wnt/β-catenin signaling pathway as its downstream target. This study provides a new therapeutic target that can be further developed for HCC treatment.

overall_design: We integrated methylated RNA immunoprecipitation sequencing (MeRIP-seq) data with transcriptomics data to reveal the m5C profiles in NSUN5-knockdown cells. Zinc finger BED domain-containing protein 3 (ZBED3) was identified as a novel target of NSUN5.

first: Xinyu

last: Gu

first: Penghui

first: Xiaohui

last: Gao

first: Yi

last: Ru

first: Chen

last: Xue

first: Shujun

last: Zhang

first: Yafeng

last: Liu

first: Xinjun

last: Hu


title: Landscape of m6A readouts across multiple cell types

city: Beijing

first: Yuan

last: Zhou

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

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

overall_design: Refer to individual Series


title: Dual-Targeted Microspheres Reshape the Metabolic-immune Microenvironment and Reverse Multiple Dilemmas Post-embolization in Hepatocellular Carcinoma_HCC VS TAE


title: Landscape of m6A readouts across multiple cell types [RNA-seq]

summary: RNA modification-driven epitranscriptome regulations play important roles on gene expression at the post-transcriptional level. N6-methyladenosine (m6A) modification is one of the most prevalent RNA modification types. As one of the core component of human epitranscriptome, the functional consequences of m6A modification, also known as m6A readouts, have been suggested to cover various aspects including but not limited to the alterations of the stability, alternative splicing or translation efficiency of the modified RNA transcripts. Of note, previous studies have shown the m6A readouts could be diverged between different transcripts and depend on the binding of various RNA-binding protein (RBP) regulators. Our analysis of the public data further suggested the readouts are also cell type-dependent, with the contribution of RBP regulators also varied between different cell type. Therefore, for a comprehensive understanding of the regulatory mechanism of m6A readouts, a multiple cell type profiling of m6A readouts have been performed here. More specifically, the three major aspects of m6A readouts, i.e. alterations of the stability, alterations of alternative splicing and alterations of translation efficiency, were evaluated by the time-series RNA-Seq, ultra-deep RNA-Seq and Ribo-Seq comparing m6A modification enzyme METTL3 knockdown (siMETTL3) with the siControl group, respectively. With those high-throughput sequencing data, the cell type-dependent responses to m6A perturbation were described. Further integrative analysis with the public transcriptome-wide m6A modification site profiles and RBP binding site profiles revealed the potentially important RBP regulators in different context. In all, our analysis provide an informative resource to decipher the landscape of m6A readouts and the underlying complicated post-transcriptional regulatory network.

overall_design: 80 samples were used for time-series and ultra-deep RNA sequencing, containing two contrasting group (siControl and siMETTL3), five cell lines (A549, H9, HEK293T, HUVEC and JURKAT) and four sampling time points (0h, 1h, 3h and 6h) in two biological replications. All time point data were used for transcript half-life estimation, while the 0 time-point (ultra-deep RNA sequencing) data were used for alternative splicing event analysis.

first: Zhou

last: Huang

first: Wubulikasimu

last: Zibaguli

first: Rucong

first: Wannqing

last: Zhao

first: Jiaqi

first: Wei

last: Kong

first: Qinghua

last: Cui

first: Yang


title: Profiling Immune-Independent Response to Immune Checkpoint Inhibitors on Stem Cell-derived Cardiac Organoids [scRNA-seq]

city: Palo Alto

first: Yu

address: 1215 Welch Road

institute: Stanford University

summary: The use of antibody based immune-checkpoint inhibitors (ICIs) have been highly successful in clinical treatment of several cancers. Despite the compelling efficacy of these drugs with their high binding affinity, there is incomplete understanding of non-target interactions in vivo. In this regard, ICIs are also known to cause immune-related adverse events (iRAEs) arising from infiltration of immune cells in tissues such as the heart. Due to the frequency of ICI treatments, extended half-life and the late onset of cardiac events, concerns have been raised regarding potential direct interactions of ICIs with major cellular cell types of the heart. The direct effects of these drugs in patients are limited due to rare incidence, and difficulty in obtaining patient heart biopsies in the pre- or post-symptomatic phase. Therefore, in order to study both functional and molecular changes in vitro, here we utilized a human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) and multicellular cardiac organoids (COs).

overall_design: In this study, COs were generated from three healthy iPSC lines (#1, #2, and #3) using an established protocol, comprising of cardiomyocytes (CMs), endothelial cells (ECs) and cardiac fibroblasts (CFs) in 7:2:1 ratio, respectively. After 1 week in culture, spontaneously beating COs  were exposed to ICIs, pembrolizumab (PEM), atezolizumab (ATZ), or isotype control at day 1 and day 3 . On day 5, COs were digested into a single cell suspension, labeled with sample-specific “hashtags" and processed for single-cell sequencing (10X Genomics).

first: Dilip

last: Thomas


title: Profiling Immune-Independent Response to Immune Checkpoint Inhibitors on Stem Cell-derived Cardiac Organoids

overall_design: In this study, iPSC-CMs were generated from three healthy iPSC lines (#1, #2, and #3) using an established protocol. Day 23-25 iPSC CMs were exposed to ICIs, pembrolizumab (PEM), atezolizumab (ATZ), or isotype control at day 1 and day 3. On day 5, cells were collected for bulk RNA sequencing.


title: Taldo1 Knockdown impaired NADPH production in CD8+ T cells

city: Wuhan

first: Huafeng

address: Hangkong Road #13

institute: Huazhong University of Science and Technology

summary: Transaldolase (TALDO1), is a key enzyme in the non-oxidative pentose phosphate pathway. However, the impact of Taldo1 disruption on CD8+ T cell differentiation and function remains undefined. Here, we found that knockdown of Taldo1 in CD8+ T cells impairs NADPH production, causes ribose-5-phosphate accumulation, elevates oxidative stress, reduces lipid synthesis, induces mitochondrial dysfunction, and compromises effector cell proliferation, cytokine production, and antitumor efficacy, whereas enhancing Taldo1 promotes memory T cell differentiation, persistence, and recall responses during immune challenges.

overall_design: RNA-seq profiling of samples collected from biological replicates of three shNC and three shTaldo1 CD8+ P14 T cells were isolated 7 dpi with LCMV-Arm.

first: Jingyu

last: Feng

first: Qian


title: Single-nucleus RNA-seq results of AR-97Q and AR-24Q mice at 8 weeks of age.

first: Tomoki

last: Hirunagi

department: Neurology

institute: Nagoya University GraduateSchool of Medicine

summary: To understand the early pathogenesis of motor neuron degeneration in spinal and bulbar muscular atrophy (SBMA), we conducted single-nucleus RNA-seq (snRNA-seq) on the spinal cords of AR-97Q and AR-24Q mice at 8 weeks of age. REST target genes were up-regulated in motor neurons of AR-97Q mice.

overall_design: snRNA-seq was conducted on spinal cord samples from AR-97Q and AR-24Q mice at an early stage (8 weeks of age). Spinal cords from three mice were pooled per sample for homogenization and nuclear isolation.

first: Kentaro

last: Sahashi

first: Madoka

last: Iida

first: Masahisa

last: Katsuno


title: A disease-causing Isoleucyl-tRNA synthetase variant leads to altered protein complex formation and cellular stress response

city: Toronto

first: Haissi

address: 80 St George St

country: Canada

institute: University of Toronto

summary: Aminoacyl-tRNA synthetases are key enzymes in protein synthesis, as they catalyze the attachment of amino acids to their designated, cognate tRNAs. As such, mutations in aminoacyl-tRNA synthetases are associated with severe diseases, such as neurodevelopmental disorders. Many of these mutations occur in the catalytically active site or tRNA binding domains, however, others can affect domains associated with multisynthetase complex formation. Here, we investigate a disease-causing mutation in the UNE-I domain of Isoleucyl-tRNA synthetase (IARS1, IleRS), which mediates IleRS interactions within the multisynthetase complex. Interestingly, levels of the resulting protein were severely reduced in comparison to wildtype IleRS. While bulk protein synthesis and cell proliferation were not affected, the integrated stress response signaling pathway was altered. This change was exacerbated in low glucose medium, suggesting that mutant cells could respond differently to cellular stress. Our study hints at a possible underlying disease mechanism, where catalytic activity might not be affected but instead complex formation and protein stability.

overall_design: IARS I1174N mutant HEK293T, wt HEK 293T, tRNA sequencing

first: Rasangi

last: Tennakoon

first: Han

last: Gao


title: Landscape of m6A readouts across multiple cell types [Ribo-seq]

first: Yuan

overall_design: 20 samples were used for ribosome sequencing (Ribo-Seq), convering two contrasting group (siControl and siMETTL3) and five cell lines (A549, H9, HEK293T, HUVEC and JURKAT) in two biological replications.

first: Zhou

first: Wubulikasimu

first: Rucong

first: Wannqing

last: Li


title: Mechanism of Action of Self-Assembled Nanoparticles from Cornus officinalis in Alleviating Chemotherapy-Induced Myelosuppression.

city: Nanjing

first: po

last: hu

state: jiangsu

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

institute: 南京中医药大学

summary: Myelosuppression is a major side effect of chemotherapy, with a lack of ideal therapeutic approaches. In this study, self-assembled nanoparticles (PCFNPs) were prepared from Cornus officinalis. It was found that in myelosuppression models induced by cyclophosphamide, 5-fluorouracil, and cisplatin, PCFNPs effectively improved blood parameters, reduced atrophy of immune organs, and decreased DNA damage and apoptosis. Mechanistic studies revealed that PCFNPs activate the YAP1-TWIST1 signaling axis, regulating the expression of key genes in the ECM-receptor interaction pathway (Col1a1, Col1a2, Ibsp, Tnc), thereby repairing the bone marrow microenvironment. Safety evaluation showed no significant toxicity at high doses of PCFNPs. This study is the first to reveal that Cornus officinalis nanoparticles alleviate myelosuppression via the YAP/TWIST-ECM axis, providing a new mechanism and strategy for nanomedicine-based treatment in traditional Chinese medicine.

overall_design: The submitted materials contain bone marrow cell samples from mice assigned to different experimental groups. The experimental conditions include a blank control group, a CTX-induced myelosuppression model group, and a treatment group receiving self-assembled nanoparticles from Cornus officinalis. All groups include biological replicate samples.

first: Yan

last: Wang


title: CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination [VDJ-Seq]

city: Shenzhen

first: Wanyu

last: Bai

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital of Sun Yat-Sen University

summary: Histone H3K4me3 broad domain (BD) is a unique epigenetic feature to mark cell identity-associated genes, but its physiological role in lineage differentiation remains unclear. Here we show that CFP1, an integral component of the Setd1A/B methyltransferase complex, is critically required for functional H3K4me3-BD installation and B cell fate determination. Cfp1 deletion impairs H3K4me3-BDs on a subset of B-lineage genes and redistributes H3K4me3 from active genes to bivalent promoters. Transcription of subsets of H3K4me3-BD-bound gene is diminished in part due to reduced RNA Pol II at the promoter and gene body. Specifically, CFP1 ablation abolishes H3K4me3-BD at the recombination center and distal PAIR elements in the immunoglobulin heavy chain (IgH) gene, severely compromises its locus contraction for efficient V-to-DJ recombination and consequently arrests cells at the pro-B stage. Moreover, Cfp1-deficient pro-B cells upregulate a panel of progenitor and myeloid-specific genes with elevated H3K4me3 marks and can trans-differentiate into various myeloid cell types. Therefore, our study reveals pivotal roles for CFP1-mediated H3K4me3-BDs in the transcriptional regulation of cell lineage fate specification and commitment.

overall_design: We performed CUT&Tag, ChIP-seq, RNA-seq, V(D)J-HTGTS and 4C-HTGTS in murine pro-B cells to study roles of CFP1-regulated epigenetic program in early B cell development.

first: Yalin

last: Yang

first: Yanan

first: Shuoxu

last: Gong

first: Yimiao

last: Lu

first: Zhonghui

last: Xue

first: Lie

first: Fei-Long

last: Meng

first: Chun

last: Chen

first: Junchao

last: Dong


title: TTNPB Promotes Pluripotent-to-Neural Stem Cell Transition through Modulating Chromatin Accessibility and Choline Metabolism [ATAC-seq]

city: Hohhot

first: Chen

last: Yanglin

address: Xilin road

institute: Inner Mongolia University

summary: Efficient derivation of neural stem cells (NSCs) from human pluripotent stem cells (PSCs) is crucial for developmental biology and regenerative medicine. Here, we established a chemically defined system using CHIR99021 and TTNPB to generate advanced NSCs (ANSCs). Integrated chromatin accessibility, transcriptomic, and metabolomic analyses revealed molecular mechanisms underlying neural fate commitment. TTNPB synergistically enhanced CHIR99021-mediated neural induction by globally increasing chromatin accessibility and activating neural-specific transcription factors. Compared to NSCs and PSCs, ANSCs exhibited robust upregulation of neural markers and enhanced chromatin remodeling. Metabolomic profiling identified significant metabolic reprogramming during the PSC-to-ANSC transition, with specific enrichment of S-adenosylhomocysteine (SAH), ADP, and glutathione in ANSCs correlating with elevated neural gene expression. Functionally, choline supplementation—regulated via the PEMT pathway—enhanced NESTIN expression and promoted neuroectodermal fate commitment. Our findings establish CHIR99021/TTNPB as a potent synergistic pair for efficient NSC induction and identify choline metabolism as a critical axis governing neuroectodermal lineage specification.

overall_design: ATAC-seq of human pluripotent stem cells (W24 and H9) and their derivatives NSC and ANSC. The pluripotent stem cells were collected from passage 30. The NSC and ANSC both were collected from passage 20.

first: Yanglin


title: CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination [RNA-Seq]

last: Zhao


title: Remodelling of the bone marrow vasculature induced by venetoclax and azacitidine damage

city: LONDON

first: Giuseppe

middle: Alessandro

last: D'Agostino

state: ENGLAND

address: 1 Midland Road

institute: The Francis Crick Institute

summary: The Bcl2 inhibitor venetoclax in combination with the hypomethylating agents azacitidine (ven/aza) has become increasingly utilised clinically for the treatment of haematological malignancies. Whilst its impact on the malignant cells have been extensively studied, its impact to the surrounding bone marrow microenvironment (BME) remains unexplored.  In this study, we report that ven/aza therapy causes significant damage to the BME of immunodeficient mice. Comparatively, high Bcl2 expression in the sinusoidal endothelial cell compartment (SEC) results in high sensitivity to ven/aza treatment, causing a loss of SECs and breakdown in cell-cell communication pathways in the endothelial cell (EC) network. Furthermore, our detailed transcriptomic and imaging studies reveal significant downregulation of essential adhesion molecules in residual SECs, leading to significant defects in human hematopoietic stem/progenitor cell (HSPC) homing and engraftment of hematopoietic stem cells (HSCs). Interestingly, although the vascular niche undergoes partial restoration from therapy induced damage, short-term exposure to ven/aza was sufficient to cause longer-term transcriptional changes to the EC compartment, negatively impacting HSC engraftment in mice receiving HSPC transplantation following endothelial cell recovery.  To conclude, our study showcases that maintaining SEC integrity in response to ven/aza therapy may play a key factor in achieving effective engraftment of donor derived HSCs.

overall_design: Single cell RNA sequencing of murine bone marrow stroma from 3 conditions (Vehicle, Ven/aza, Recovery) hashed using Cell Multiplexing Oligos

first: Steven

last: Ngo

first: Dominique

last: Bonnet


title: A lung specific escape of intravascular metastatic breast cancer cells from cytotoxic T cell killing

first: Marina

last: Kizner

address: 234 Herzel st.

institute: Weizmann Institute of Science

summary: The lungs are a major organ of cancer metastasis. Despite advances in the usage of tumor-specific cytotoxic T cells (CTLs) with potent killing activity (i.e., tumor infiltrating T cells, TILs) for killing of primary tumors, how these T cells encounter and kill metastatic lesions at remote organs is still poorly understood. In the present study we compared the ability of potent neoantigen specific CTLs to kill two types of cancer cells that share the same neoantigen and generate distinct metastatic lesions in the lungs of immunocompetent recipient mice. We have used ovalbumin (OVA) as a neoantigen model and found that the OVA-specific OT-I transgenic CD8 CTLs, when intravenously introduced, readily eliminated primary tumors of OVA-expressing breast cancer E0771 cells. Nevertheless, similar OT-I CTLs failed to clear OVA-expressing breast cancer E0771 cells that colonized the lungs. In contrast, similar intravenously introduced OT-I CTLs efficiently eliminated lung metastatic OVA-expressing B16 melanoma cells, ruling out that the intravenous CTLs were exhausted upon entering the lungs. Three-dimensional (3D) imaging of whole lungs revealed that in both experimental and spontaneous metastasis models, the OVA E0771 cells survived inside lung blood vessels but did not recruit circulating OT-I CTLs to their vicinity. Furthermore, canonical vascular adhesion molecules recognized by the CTLs like ICAM-1 and VCAM-1 were not upregulated nearby the lung-residing intravascular E0771 cells as a potential means to recruit lung circulating CTLs to the vicinity of the intravascular tumor cells. Strikingly, the lung residing OVA-expressing E0771 cells lost expression of their OT-I specific OVA-derived SIINFEKL-H-2Kb pMHC complexes while retaining MHC-I expression. This loss was accompanied by a lung-specific transcriptional reduction of key regulators of MHC-I presentation. A temporal loading of OVA-derived SIINFEKL-H-2Kb pMHC complexes on E0771 cells did not result, however, in cancer cell killing inside the lungs. Nevertheless, direct and stable SIINFEKL peptide presentation on these cells overcame their lung specific escape from OT-I mediated killing. Our study is a first indication that subsets of cancer cells that reside in the lungs rapidly downregulate the expression of neoantigen derived peptide MHC-I complexes and thereby evade killing by intravenously introduced tumor antigen-specific CTLs.

overall_design: 106 OVA-RFP E0771 cells were introduced i.v., and 3 days later fluorescent cells were sorted from whole lungs using FACS Aria III Cell Sorter. Cells were collected in the presence of Actinomycin D (Sigma-Aldrich, cat. A1410) in order to minimize ex vivo RNA transcription. RNA was purified from the sorted cells using the QIAGEN Rneasy kit. A second experimental group consisted of 103 OVA- RFP E0771 cells implanted in mammary fat pads to generate primary tumors. Cells from primary tumors were similarly isolated and sorted on day 14 post implantation.

first: Nehora

last: Levi

first: Carmel

last: Sochen

first: Julia

last: Ryvkin

first: Ofer

last: Regev

first: Alexander

last: Zarbock

first: Lea

last: Eisenbach

first: Moshe

last: Biton

first: Ronen

last: Alon


title: TTNPB Promotes Pluripotent-to-Neural Stem Cell Transition through Modulating Chromatin Accessibility and Choline Metabolism [RNA-seq]

sample_organism:
Homo sapiens
Rattus

platform_organism:
Homo sapiens
Rattus

overall_design: To investigate the role of TTNPB in the differentiation of pluripotent stem cells (PSCs) into neural stem cells (NSCs), we induced the differentiation of human PSCs into NSCs and advanced neural stem cells (ANSCs). RNA sequencing was performed on ANSCs.  Moreover, ANSC , NSC and normal saline (Sham group) were stereotactically injected into the hippocampal region of depressed rats, respectively. Seven days post-injection, the hippocampal tissues of these rats were harvested. Meanwhile, hippocampal tissues from depressed rats without any injection (Depressed group) and normal rats receiving no treatment (Control group,) were collected for transcriptome sequencing.


title: CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination

first: Wanyu

last: Bai


title: The alterations of gene expression profiling induced by EXOSC10-AS1 knockdown in HCT116 cells.

city: weifang

first: Jiaqiu

last: Li

address: Baotong west street No.7166

institute: shandong second medical university

summary: Long noncoding RNAs (lncRNAs) have been identified to play increasingly important roles in tumorigenesis, and they may serve as novel biomarkers for cancer therapy. Here we report gene expression profiles of HCT116 cells treated with EXOSC10-AS1 siRNA. This study reveals a novel role of EXOSC10-AS1 in downstream gene regulation and provides a new explanation of EXOSC10-AS1’ s function in colorectal cancer.

overall_design: RNA-seq after knockdown of EXOSC10-AS1 by siRNA in HCT116 cells.


title: FANCD2 restrains fork progression and prevents fragility at early origins upon re-replication

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

summary: DNA replication is tightly regulated to ensure a single round of chromosome duplication per cell division. DNA licensing restricts origin firing to once-per-cell-cycle while aberrant licensing promotes re-replication and genome instability. Here, we investigate the mechanisms that protect genome integrity following re-replication induced by depletion of the licensing inhibitor Geminin. We find that re-replicating cells require FANCD2 to prevent genome instability. FANCD2 is rapidly recruited to chromatin upon Geminin loss, where it limits unrestrained fork progression and prevents single strand DNA gap accumulation and fork breakage. Genome-wide analyses reveal that upon re-replication, FANCD2 localizes to early origins within highly transcribed regions prone to accumulate R-loops and enriched in early replicating fragile sites. Importantly, reducing transcription and R-loops alleviates re-replication-induced genome fragility, whereas PARP inhibition exacerbates it. Our study uncovers a role for FANCD2 in safeguarding genome integrity during re-replication, offering avenues for selective targeting of cancer cells.

overall_design: ChIP-seq of FANCD2 in K562 cells (lymphobalst; myelogenous leukemia) with siRNA-induced silencing of Geminin (siGMNN) and control cells (non targeting siRNAs; siC).

first: Badra-Fajardo

last: Nibal

first: Karydi

last: Elena

first: Bayona-Feliu

last: Aleix

first: Gómez-González

last: Belén

first: Preza

last: Ourania

first: Arbi

last: Marina

first: Kalogeropoulou

last: Argyro

first: Rantala

last: Juha K.

first: Taraviras

last: Stavros

first: Aguilera

last: Andrés

first: Lygerou

last: Zoi


title: RNA-seq of sipinal cord of WT, AR-24Q, AR-97Q, testosterone-treated AR-97Q mice, Scramble-ASO-treated AR-97Q mice, and Rest4-ASO #3-treated AR-97Q mice at P7

first: Tomoki

last: Hirunagi

summary: Testosterone (20 mg) was subcutaneously adminstered to AR-97Q mice at postnatal day 1 (P1). Scramble-ASO and Rest4-ASO #3 were intracerebroventriculary administred to AR-97Q mice at P1.Gene expression profiles were analysed in the spinal cord of WT, AR-24Q, AR-97Q, testosterone-treated AR-97Q mice, Scramble-ASO-treated AR-97Q mice, and Rest4-ASO #3-treated AR-97Q mice at P7.

overall_design: RNA-seq analysis was performed in the mouse spinal cord at P7 (WT, AR-24Q, AR-97Q, testosterone-treated AR-97Q mice , Scramble-ASO-treated AR-97Q mice, and Rest4-ASO #3-treated AR-97Q mice).

first: Kentaro

last: Sahashi

first: Masahisa

last: Katsuno


title: Tkt knockdown impaired NADPH production in CD8+ T cells

first: Huafeng

last: Zhang

summary: Transketolase (TKT) is a key enzyme in the non-oxidative pentose phosphate pathway. However, the impact of Taldo1 disruption on CD8+ T cell differentiation and function remains undefined. Here, we found that knockdown of Taldo1 in CD8+ T cells impairs NADPH production, causes ribose-5-phosphate accumulation, elevates oxidative stress, reduces lipid synthesis, induces mitochondrial dysfunction, and compromises effector cell proliferation, cytokine production, and antitumor efficacy, whereas enhancing Taldo1 promotes memory T cell differentiation, persistence, and recall responses during immune challenges.

overall_design: RNA-seq profiling of samples collected from biological replicates of three shNC and three shTkt CD8+ P14 T cells were isolated 7 dpi with LCMV-Arm.

first: Jingyu

last: Feng

first: Qian


title: Global Characterization of Functional Microglia Heterogeneity in Relation to Neovascularization and Regression Phases of Oxygen-Induced Retinopathy in Mice

city: Guangzhou

first: Yuan

last: Ma

address: No.7 Jinsui road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: Retinal neovascularization (RNV) is manifested in various retinal pathological conditions, often leading to irreversible blindness. Oxygen-induced Retinopathy (OIR) mouse model proves to be useful for understanding RNV. The OIR vasculatures exhibited two distinct phases: neovascularization and regression, with microglia playing a pivotal role. Most studies concern microglia functions in promoting RNV; however, global retinal microglia dynamics and functional molecular features during RNV formation and regression have yet to be illustrated. Here, we enriched retinal microglia from normoxia (NOX) and OIR mice retinas at different timepoints of RNV progression and regression and performed single-cell RNA sequencing (scRNA-seq).This approach enabled a detailed analysis of microglia dynamics and functional heterogeneity during retinal neovascularization and regression in OIR mice, providing novel mechanistic insights with potential therapeutic implications for retinal diseases involving pathological neovascularization.

overall_design: Microglia from NOX and OIR mice retinas at P17 and P21 were isolated and enriched by CD11b magnetic-activated cell sorting (MACS) and analyzed using scRNA-seq.


title: RNA-seq of sipinal cord of AR-97Q and WT mice at P7 and 13 weeks of age

summary: Antisense oligonuleotides targeting human AR (AR-ASO) or Rest4 (Rest4-ASO) are intracerebroventriculary injected to AR-97Q mice at postnatal day 1 (P1). Gene expression profiles were analysed in the spinal cord of WT and AR-97Q mice at P7 and 13 weeks of age.

overall_design: RNA-seq analysis was performed in the mouse spinal cord at P7 (WT vs. AR-97Q vs. AR-ASO treated AR-97Q, Scramble-ASO vs. Rest4-ASO treated AR-97Q) and 13 weeks of age (WT vs. AR-97Q).


title: CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination [Cut&Tag]

first: Wanyu

last: Bai

first: Yalin

last: Yang

first: Yanan

last: Zhao

first: Shuoxu

last: Gong

first: Yimiao

last: Lu

first: Zhonghui

last: Xue

first: Lie

last: Wang

first: Fei-Long

last: Meng

first: Chun

last: Chen

first: Junchao

last: Dong


title: CRISPR screening using Human PSC-derived cardiomyocytes reveals TAOK1 as a potential therapeutic target for doxorubicin-induced cardiomyopathy I

city: Kyoto

first: Tomoya

last: Kitani

address: 465 Kajii-cho Kawaramachi-Hirokoji Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary: Doxorubicin (DOX) is one of the most effective chemotherapeutic agents for various types of cancers. However, DOX often causes cardiotoxicity referred to as DOX-induced cardiomyopathy (DIC). Despite extensive research aimed at identifying therapeutic targets for DIC, only a limited number of effective treatments are available. In this study, we identified a member of the STE20 kinase family, thousand and one amino acid protein kinase 1 (TAOK1) as a potential regulator for DOX-induced cardiomyocyte death using a kinome-wide CRISPR gene knockout screen in human cardiomyocytes derived from pluripotent stem cells (hPSC-CMs). TAOK1 suppression improved DOX-induced cardiomyocyte dysfunction in hPSC-CMs and rescued cardiac function in a DIC mouse model. Mechanistically, we found that TAOK1 regulated p38 MAPK-mediated cardiomyocyte apoptosis induced by DOX. Our results indicate TAOK1 as a promising therapeutic strategy for treating DIC in cancer patients, and highlight the advantage of hPSC-CMs as a platform to study drug-induced cardiotoxicity.

overall_design: To gain insight into the mechanism underlying the protective effect of the TAOK1 knockout on DOX-induced cardiomyocyte death and dysfunction, we performed global gene expression analysis using RNA-seq in TAOK1- and Ctrl-KO hPSC-CMs treated with DOX.


title: CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination [ChIP-Seq]


title: Isoliensinine promotes the clearance of senescent vascular smooth muscle cells by natural killer cells [MOVAS]

status: Public on Feb 07 2026

first: po

last: hu

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

summary: Atherosclerosis (AS) is an age-related disease whose incidence increases with advancing age. During disease pathogenesis, vascular smooth muscle cells (VSMCs) undergo senescence within the plaques and secrete senescence-associated secretory phenotype (SASP) factors, which contributes to the development and destabilization of atherosclerotic plaques. As key effector cells of the innate immune system, natural killer (NK) cells can specifically recognize and eliminate senescent cells; however, their role in inhibiting AS progression and the underlying mechanisms remain unclear. Isoliensinine (IsoL) is a bisbenzylisoquinoline alkaloid extracted from lotus plumule, which exerts anti-inflammatory and immunomodulatory effects. Studies have shown that IsoL can effectively enhance the immune clearance of tumor cells by NK cells, suggesting that this compound may also have the potential to inhibit AS progression by regulating the recognition and elimination of abnormal target cells by immune cells.

overall_design: This submitted sample set includes mouse aortic vascular smooth muscle cell samples from different experimental groups. The experimental groups consist of the control group, Doxorubicin or hydrogen peroxide-induced cellular senescence group and the isoliensinine treatment group, with biological replicates set up for all groups.

first: XiaoNi


title: CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination [4C-Seq]