title: Treatment of mouse breast cancer cell line 4T1 with cepharanthine for RNA-seq

first: Chen

summary: Breast cancer remains a significant global health challenge, with the highly aggressive 4T1 mouse mammary carcinoma cell line serving as a common model for studying triple-negative breast cancer (TNBC) due to its metastatic potential and resistance to therapy. Cepharanthine (CEP), a natural bisbenzylisoquinoline alkaloid, has demonstrated anti-inflammatory, immunomodulatory, and anti-cancer properties in various malignancies. However, its molecular mechanisms in 4T1 cells remain poorly understood. In this study, we treated 4T1 cells with CEP and performed RNA sequencing (RNA-seq) to elucidate transcriptomic alterations induced by this compound.

overall_design: In vitro treatment of the 4T1 cell line with 10 μM CEP or an equal volume of DMSO (as control) for 12 hours, followed by RNA-seq analysis.

first: Bin

last: Chen


title: SUV39H1 regulates KLF4 and chromatin remodeling in smooth muscle cell phenotypic plasticity [ATAC-Seq]

status: Public on May 01 2026

city: New Haven

first: Kathleen

last: Martin

state: CT

address: 300 George Street

country: USA

institute: Yale School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We investigated the role of SUV39H1, a histone methyltransferase that generates H3K9me3, a repressive heterochromatin-associated epigenetic mark, in vascular smooth muscle cell (VSMC) plasticity.

overall_design: We applied ATAC-seq in human coronary artery smooth muscle cells (hCASMCs) with or without SUV39H1 knockdown to assess SUV39H1 functions in VSMC plasticity.

first: Raja

last: Chakraborty

first: Payel

last: Chatterjee

first: Peng

last: Xu


title: SUV39H1 regulates KLF4 and chromatin remodeling in smooth muscle cell phenotypic plasticity [RNA-Seq]

type: Expression profiling by high throughput sequencing

summary: We investigated the role of SUV39H1, KDM4A, and TET2 in vascular smooth muscle cell (VSMC) plasticity.

overall_design: We applied RNA-seq in human coronary artery smooth muscle cells (hCASMCs) with or without SUV39H1, KDM4A, or TET2 knockdown to assess their functions in VSMC plasticity.


title: Differential Gene Expression in Leiomyosarcoma Cell Spheroids in Response to Compressive Force

city: Cincinnati

first: Stacey

middle: C

last: Schutte

state: OH

address: 2901 Woodside Dr.

department: Biomedical Engineering

institute: University of Cincinnati

summary: This purpose of this study was to characterize the cell signaling responses of leiomyosarcoma tumors in response to compressive mechanical force using an embedded spheroid culture model. Spheroids fabricated from a human leiomyosarcoma cell line were embedded in an agarose hydrogel and exposed to compressive force for seven days. RNA sequencing analysis was performed to identify differently expressed genes and signaling pathways altered in leiomyosarcoma cells with compression compared to no compression.

overall_design: Gene expression profiling of RNA-seq data from leiomyosarcoma cell spheroids with and without compression.

first: Rose

last: Dean

first: Carolyn

last: Nietupski


title: ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment.

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

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

overall_design: Refer to individual Series


title: High throughput sequencing study

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute


title: Effect of deletion of UTX expression in NY8.3 progenitor CD8+ T cells [CUT&Tag]

city: Los Angeles

first: Ho Chung

state: CA

address: 609 Charles E Young Dr E

department: MIMG

institute: University of California, Los Angeles

summary: Type 1 diabetes (T1D) is a chronic autoimmune disease resulting from the destruction of insulin-producing beta cells. This persistence is due to the continual replenishment of short-live effector CD8+ T cells (autoimmune mediators, Tmed) in the pancreatic lymph nodes (pLNs) by a long-lived reservoir of stem-like memory CD8+ T cells (autoimmune progenitors, Tprog). We are investigating an epigenetic regulator UTX playing the role in Tprog to Tmed conversion. The NOD mice with T cell-specific UTX deficiency (UTXTCD mice) were protected from T1D. In addition, the deletion of UTX in CD8+ T cells resulted in the accumulation of Tprog and loss of Tmed populations in pLNs. The function of UTX is to demethylate the histone mark, H3K27 tri-methylation, leading to the open chromatin accessibility for gene expression. ATAC-seq and RNA-seq of antigen specific Tprog cells revealed a role of UTX in closing chromatin at progenitor gene loci while enforcing accessibility at effector gene loci. Taken together, these findings point to the potential of targeting UTX-mediated conversion of Tprog into Tmed for interrupting the T1D autoimmune response.

overall_design: To investigate the gene directly bound by UTX, we sorted the Ly108+CXCR6- CD8+ T cells harvested from pancreatic lymph node of NOD.NY8.3 (NY8.3) mice and T cell specific deletion UTX deficient NY8.3 mice (UTXTCD.NY8.3). We then perform UTX CUT&Tag to identify the regions bound by UTX

first: Shirley

last: Zhang

first: Lisa

last: Kohn

first: Hsing Hui

last: Wang

first: David

last: Sailer

first: Ethan

last: McCarthy

first: Maryam

last: Seyedsadr

first: Zikang

last: Zhou

first: Xihui

last: Yin

first: Nicole

last: Wilkinson

first: Melissa

last: Lechner

first: Willy

last: Hugo

first: Maureen

last: Su


title: High throughput sequencing of T cells from donors with Down Syndrome

summary: This is a study designed to probe T-cell activation in the context of Down Syndrome. We obtained blood samples from six donors and stimulated with a mixture of pathogenic peptides designed to elicit and immune response or with DMSO as a control.

overall_design: T-cells from 6 donors with down syndrome were analyzed. From each donor, cells were either stimulated with a CEFX mix of peptides (JPT Peptide Technologies), DMSO as a control and from each donor CEFX activated, DMSO activated and total T cells were sorted and hashtagged.  Sorted cells were processed in three pools. Each pool consisting of cells from the three stimulation conditions from two donors.  Each pool was loaded across one channel of a 10X GEM-X kit for processing with a target capture of 10,000 cells.

first: Cliff

last: Rims

first: Susana

last: Orozco

first: Alice

last: Weideman

first: Peter

last: Linsley

first: Jane

last: Buckner


title: High throughput sequencing of B and T cells in checkpoint inhibitor treated patients

first: Stephanie

last: Osmond

summary: This is a prospective longitudinal study designed to identify biomarkers predictive of the onset of irAEs associated with ICI therapy and determine whether these biomarkers are further related to treatment efficacy. We obtained serial blood samples in patients who will be receiving anti-PD-1/PD-L1 either as a single agent or in combination with other therapy.

overall_design: Samples were collected from a 9 donors before and during checkpoint inhibitor treatment. Three of the donors experienced no immune-related adverse event (irAE), three had thyroid-associated irAEs, and three had skin-associated irAEs. Total B and T cells from each sample were sorted. Sorted cells were processed in three pools with each pool consisting of cells from the two timepoints from three donors (6 hashtagged samples). Each pool was loaded across 3 channels of a 10X GEM-X kit for processing.

first: Ty

last: Botoroff


title: Bcl11b-Cxxc1 axis regulates stage-specific chromatin accessibility during thymocyte development

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

country: Japan

institute: RIKEN Yokohama

summary: A zinc-finger (ZnF) transcription factor Bcl11b plays a pivotal role in T-lymphopoiesis. A mouse strain expressing a truncated form of Bcl11b lacking the C-terminal ZnF exhibited a dusrpted chromatin accessibility in CD4+CD8+ double-positive thymocytes. A comprehensive screen of chromatin modifiers associated with the C-terminal ZnF in Bcl11b identified Cxxc1, a protein known to mediate H3K4me3 as a component of Set1 complex. Cxxc1-deficiency caused a developmental arrest at the transition from CD4-CD8- double-negaitve to CD4+CD8+ double-positive thymocytes, leading to the retention of a double-negative-like chromatin structure in double-positive cells and ectopic expression of double-negative signature genes. Genomic regions bound by Cxxc1 largely overlapped with Bcl11b binding sites, and were altered upon loss of Bcl11b. Consistent with the interaction between Cxxc1 and another Bcl11 family protein, Bcl11a―which is essential for B-lymphopoiesis―Cxxc1-deficiency caused a developmental arrest of B lymphocyte at the transition from BP-1- to BP-1+ stage. These findings reveal that Bcl11 family proteins modulate chhromatin accessibility by recruiting Cxxc1 during lymphocyte development.

overall_design: Chromain accessibility in DN (CD24+TCRb-CD4-CD8a-) and DP (CD24+TCRb-CD4+CD8a+) thymocytes from Cxxc1+/+:Lck-cre and Cxxc1F/F:Lck-cre mice were assessed by ATAC-seq analysis.

first: Ichiro

last: Taniuchi


title: Rifamycin O as a Novel CRBN Ligand for Targeted Degradation of IKZF1/3 Proteins in Hematopoietic Malignancies

city: China

first: Jinlian

last: Wei

state: Shanghai

country: China

institute: ECUST

summary: We found that Rifamycin O could effectively suppressed the hematologic tumors growth in vitro and in vivo. The antitumor effect of Rifamycin O is first identified so far.

overall_design: Examination of Rifamycin O-treated and control group in K562 cells by RNA-seq, in triplicate

first: Liang

last: Liao

first: Qiang

last: Wang

first: Zhengyang

last: Gao

first: Jian

last: Li


title: Neuronal gap junction inhibition induces neuroprotection and partially restores visual function II

city: Changsha

first: Duan

last: peiyun

address: 139 Renmin Zhong Lu,

institute: The second xiangya hospital of central south university

summary: human induced pluripotent stem cell (iPSC)–derived CNS-type neural progenitor cells (NPCs) have the potential to improve understanding of the translational significance of our finding, we also investigated the transcriptional effects of genetic GJs inhibition on iPSC-NPCs. Bulk RNA-seq analysis showed that genetic GJs inhibition induced transcriptional effects on iPSC-NPCs

overall_design: We performed gene expression profiling using bulk RNA-seq on human iPSC-derived NPCs subjected to neuronal gap junction inhibition.

first: Duan Peiyun

last: The Second Xiangya Hospital of Central South University


title: DRG RNA-seq data

city: shanghai

first: GuoFeng

last: Fang

address: No. 1630 Dongfang Road, Pudong New Area

department: Shanghai Institute of Immunotherapy Innovation, Renji Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: RNA-seq analysis of DRG (left T8-T13) at 7 days post-LCMV infection, sequenced via Illumina NovaSeq 6000.

overall_design: RNA samples were isolated  and from freshly-isolated DRG (left T8-T13) tissues (n ≥ 3 biological replicates each group).

first: Guotong

last: Fu

first: Guofeng

first: Tianyu

last: Lei


title: Bcl11b-Cxxc1 axis regulates stage-specific chromatin accessibility during thymocyte development [RNA-seq]

overall_design: Gene expression profiles in DN (CD24+TCRb-CD4-CD8a-) and DP (CD24+TCRb-CD4+CD8a+) thymocytes from Cxxc1+/+:Lck-cre and Cxxc1F/F:Lck-cre mice were assessed by bulk RNA-seq analysis.


title: Neuronal gap junction inhibition induces neuroprotection and partially restores visual function

summary: RGCs were FACS-sorted from mice with genetic GJs inhibition by intraocular AAV2-Cx36. We carried out bulk RNA-seq analysis to study the transcriptional effects of GJs inhibition on RGCs.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of  different mice

first: Peiyun Duan


title: Genome-wide identification of DDM1-regulated small RNA loci in rice

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

institute: Tianjin Normal University

summary: This study conducts small RNA sequencing (sRNA-seq) on panicles from wild-type rice and the ddm1a/1b double mutant to identify DDM1-regulated sRNA loci in genome-wide scale.

overall_design: DECREASE IN DNA METHYLATION 1 (DDM1) is a conserved chromatin remodeler essential for maintaining heterochromatic DNA methylation and transposon silencing. This study generated rice ddm1a/1b double mutant through CRISPR-Cas9 technology, and performed small RNA sequencing of wild-type and ddm1a/1b mutant.

first: Yuanyuan


title: Histone lactylation enhances m6A-mediated PDK4 stabilization to drive osteogenic differentiation in calcific aortic valve disease [RNAseq-PDK4]

city: Nanjing

first: Song

state: Jiangsu province

address: Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Calcific aortic valvular disease (CAVD) is characterized by progressive thickening and calcification of the valvular leaflets. Emerging evidence suggests that glycolysis, particularly regulated by pyruvate dehydrogenase kinase 4 (PDK4), plays a significant role in calcification-related diseases. Nevertheless, the mechanisms by which PDK4 affects glycolysis and influences CAVD remain unexplored. This study investigated the contribution of PDK4 to glycolytic reprogramming and osteogenic differentiation in CAVD. Osteogenic differentiation of human valvular interstitial cells (VICs) and CAVD valves was associated with enhanced glycolysis, leading to increased lactate production that further promoted VICs' calcification. PDK4 expression was significantly upregulated in both osteogenically differentiated VICs and CAVD valves. Silencing PDK4 reduced osteogenic differentiation in VICs, whereas PDK4 overexpression aggravated differentiation and increased glycolytic activity. Mechanistically, PDK4 facilitated nuclear translocation of Yes-associated protein (YAP), a key regulator of the Hippo signaling pathway, thereby enhancing RUNX2 transcription and promoting osteogenic differentiation. Nuclear accumulation of lactate increased H3K18 lactylation, which stabilized PDK4 mRNA through the METTL3-m6A-YTHDF1 pathway, establishing a positive feedback loop. This study identifies mechanisms by which glycolysis drives CAVD progression and highlights PDK4 as a potential molecular target for therapeutic intervention.

overall_design: RNA-seq profiling of human valvular interstitial cells (VICs) transfected with scramble siRNA or PDK4-siRNA.

first: Ying

first: Xiufan

last: Xu

first: Yuqiu

last: He

first: Yefan

last: Jiang

first: Yongfeng

last: Shao


title: mitfa-Independent Melanocyte Progenitors are Highly Susceptible to GNAQ-induced Uveal Melanoma in Adult Zebrafish

city: Iowa City

first: Zhijie

state: IA

address: 285 Newton Road

institute: University of Iowa

summary: Melanocytes reside in diverse microenvironments that influence their susceptibility to oncogenic transformation, however, studying rare melanoma subsets has been hindered by the lack of suitable animal models. We developed a primary, immune-competent zebrafish model to study uveal melanoma (UM), utilizing choroidal-targeted injection and electroporation of plasmids containing human GNAQQ209L and CRISPR/Cas9 cassettes for tumor suppressor gene deletion. Single-cell transcriptional profiling of genetically identical eye- and skin-derived tumors revealed distinct oncogenic pathways, highlighting the importance of studying melanoma subtypes in their correct anatomical context. Additionally, we identified a population of tfec- and pax3a-expressing melanocyte progenitor cells in mitfa-deficient embryos and adult zebrafish eyes, which were highly susceptible to GNAQ-driven transformation. While previous studies have linked mitfa deficiency to accelerated UM onset, our findings suggest that an expanded progenitor population in mitfa-deficient animals drives this susceptibility. Our study establishes a critical role for MITF-independent melanocyte progenitors in UM pathogenesis.

overall_design: Eye and skin tumors were harvested with surrounding tissue from 4-6 month old AB wildtype and casper (mitfa -/-, mpv17 -/-) zebrafish. Uninjected eyes and uninjected regions of skin were also included as controls. Tumors were derived by injecting mitfa:GNAQQ209L-mitfa:GFP, mitfa:Cas9, u6:sgRNA-tp53, u6:sgRNA-ptena, u6:sgRNA-ptenb, PCS2FA Tol2 into either eye or skin of adult zebrafish and electroporated to induce uptake.

first: Julius

last: I. Yevdash

first: Colin

last: Kenny


title: Bcl11b-Cxxc1 axis regulates stage-specific chromatin accessibility during thymocyte development [ChIP-seq]

first: Kazuki

last: Okuyama

overall_design: To explore whether Cxxc1 and Bcl11b occupy genomic regions, ChIP-seq analysis for Cxxc1 in total thymocytes from wild-type and Bcl11b-deficient (Bcl11b-F/F:C4-cre) mice was performed.

first: Ichiro

last: Taniuchi


title: Clonal evolution permits outgrowth of chemoresistant LMPP-like early progenitors in relapsed NPM1c AML [scRNA-Seq]

city: Napels

first: Wout

last: Megchelenbrink

address: Vico de Crecchio 7

department: Precision Medicine

country: Italy

institute: University of Campania "Luigi Vanvitelli”

summary: The most recurrent acute myeloid leukemia (AML) driver in adult patients is a DNA frameshift insertion in the Nucleophosmin 1 (NPM1) gene. This mutation causes a translocation of the coding protein from the nucleus to the cytoplasm (NPM1c).  We have generated paired single-cell multi-omics profiles for ~205,000 bone marrow cells collected from NPM1c AML patients at diagnosis and relapse. Detailed single-cell clonal analysis unveiled the evolution, expansion, and concomitant phenotypic changes of pathogenic AML (sub)clones. Blasts with an internal tandem duplication in the FLT3 gene (FLT3-ITD+ blasts) were often lowly abundant at diagnosis but expanded drastically at relapse at the expense of other blasts. Intriguingly, genetically identical FLT3-ITD+ blasts switched from granulocyte-monocyte progenitor-like at diagnosis toward more immature lympho-myeloid primed progenitor (LMPP)-like blasts at relapse. Our data shows that clonal evolution and the accumulation of a FLT3-ITD, is a key evolutionary event that alters AML blast plasticity with minimal changes in the blast phenotype. Increased plasticity favors the specific selection and expansion of FLT3-ITD+ blasts, which adopt a unique LMPP-like phenotype. The overriding transition between diagnosis and relapse suggests that therapeutic interventions (against proliferating cells) could license or accelerate this shift, highlighting the need for a tailored drug composition to target relapsed NPM1c AML.

overall_design: single cell RNA-Seq profiling of bone marrow mononuclear cells from NPM1c AML patient at Diagnosis and Relapse  using 10x Genomic Chromium platform

first: Yanan

last: Zhai

first: Hendrik

middle: G

last: Stunnenberg


title: Intravitreal delivery of the cationic micelle DMP suppressed the development of choroidal neovascularization

city: Chengdu

first: feipeng

last: jiang

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

institute: west china hospital

summary: Age-related macular degeneration (AMD)-associated choroidal neovascularization (CNV) causes severe vision loss. This study evaluated the therapeutic potential of cationic DMP micelles for CNV. DMP micelles were synthesized by modifying PEG-PCL with DOTAP, to form self-assembled nanoparticles. Cytotoxicity was assessed in 661w and human Müller cells via the MTT assay. BN rats with laser-induced CNV received intravitreal DMP or saline. CNV severity was evaluated via fundus fluorescein angiography (FFA) and IB4-stained neovascular area quantification. Retinal transcriptomes were analyzed by RNA-seq. Cellular uptake mechanisms were studied via the use of endocytosis inhibitors (chlorpromazine, methyl-β-cyclodextrin, filipin III). Endothelial migration was tested via a scratch assay. DMP micelles exhibited favorable properties (86.48 nm, +46.4 mV) and low cytotoxicity (IC50 >300 mg/mL vs PEI25K). DMP significantly reduced the FFA leakage score (1.2±0.4 vs saline 2.5±0.6, p<0.01) and IB4+ area (35,602±5,412 vs 58,341±7,203 μm², p<0.001). RNA-seq revealed upregulated antigen presenting genes (RT1-Da, RT1-Ba, RT1-Db1, RT1-Bb) and the immune modulator Slpi. Cellular uptake involved clathrin- and lipid raft-mediated endocytosis. DMP inhibited endothelial migration in vitro. DMP micelles demonstrate dual antiangiogenic and immune-modulating effects in CNV models with retinal biocompatibility. The ability of DMP to suppress neovascularization and activate antigen presentation pathways highlights their therapeutic potential for wet AMD.

overall_design: Two microliters of DMP (10 mg/mL in H2O) or saline were delivered into the vitreous of the rats, and the retina was isolated for RNA-seq .

first: Yingying

last: Chen

first: Jieping

last: Wu

first: Mohan

last: Liu

first: Jiamei

last: Yang

first: Meixia

last: Zhang

first: Ke

last: Men


title: Clonal evolution permits outgrowth of chemoresistant LMPP-like early progenitors in relapsed NPM1c AML [scTapestri]

overall_design: DNA+protein profiling of bone marrow mononuclear cells from NPM1c AML patient at Diagnosis and Relapse

first: Cristoforo

last: Grasso

first: Brigit

last: te Pas


title: Cell Membrane Maintenance by PhoP is Critical for Methyylglyoxal Resistance in Mycobacterium tuberculosis

city: New York

first: Alejandro

last: Pironti

state: NY

address: 430 E29th Street

department: Microbiology

institute: NYU Grossman School of Medicine

summary: The human pathogen Mycobacterium tuberculosis primarily infects macrophages. Upon activation by IFNγ, infected macrophages produce higher levels of methylglyoxal, a toxic aldehyde. Mycobacterium tuberculosis defense mechanisms against aldehydes have not been elucidated. A transposon mutagenesis screen identified 22 loci required for resistance to methylglyoxal, one of which was phoP. The attenuated phoP mutant was even more attenuated in mice that accumulate MG. Secondary mutations in the fatty acid β-oxidation genes fadE25 or fixB restored methylglyoxal resistance to a phoP mutant by restoring the membrane barrier that is compromised in a phoP mutant. Analysis of transcriptional responses to methylglyoxal suggests that phoP mutants are unable to appropriately respond to methylglyoxal-induced stress. Together, our data suggest that the major virulence factor PhoP is essential for Mycobacterium tuberculosis resistance to methylglyoxal toxicity in vivo.

overall_design: RNA was extracted from quadruplicate biological cultures (OD mathced) of Mycobacterium tuberculosis H37Rv (Wildtype; MHD1) and phoP::Tn (H37Rv with phoP interrupted by Himar transposon; MHD1707) either untreated or treated with 1.6 mM methylglyoxal (MG) for 24 hrs. All cultures were grown in 7H9 (pH 5.5) supplemented with 0.2% glycerol, 0.05% Tween-80, and ADN (0.5% bovine serum albumin, 0.2% dextrose, and 0.085% sodium chloride).

first: Phuong

middle: M

last: Tran

first: Andrea

last: Anaya-Sanchez

first: Daisy

last: Ji

first: Mary

last: Jackson

first: Sarah

middle: A

last: Stanley

first: K

middle: H

last: Darwin


title: Targeting leucyl-tRNA synthetase 1 with leucine restores N-glycosylation and overcomes chemoresistance in ICC

city: Guangzhou

first: Haining

address: Zhongshan road 2

institute: The first affiliated hospital of sun yat-sen university

summary: Chemotherapy shows limited efficacy in intrahepatic cholangiocarcinoma (ICC). Selective mRNA translation enables tumour cells to redistribute resources and withstand chemical stress, but the underlying mechanisms remain poorly understood. Here, we demonstrate that leucyl-tRNA synthetase 1 (LARS1) is significantly decreased in ICC and correlates with poor prognosis. Using overexpression and knockout mouse models, we establish the crucial role of LARS1 in ICC chemoresistance. Mechanistically, LARS1 knockdown selectively suppresses the mRNA translation of N-glycan biosynthesis enzymes in a leucine codon frequency-dependent manner, reducing the N-glycosylation of ABCC1 at the N929 site and promoting ICC chemoresistance. Notably, exogenous leucine supplementation emerges effectively restore LARS1 expression and enhance chemotherapy efficacy in ICC. Our findings provide new insights into the selective mRNA hypotranslation underlying ICC chemoresistance and propose a promising diet-drug combination strategy to improve therapeutic outcomes.

overall_design: RNC-seq was used to study the differential translated genes in the LARS1 knockdown and control cells.

first: Liu

last: Haining

first: Jin

last: Bin


title: Salvianolic acid B upregulates miR-744-5p expression in peripheral blood mononuclear cell–derived extracellular vesicles to alleviate uremic cardiomyopathy

city: Dalian

first: Wang

last: Ziran

state: Liaoning

address: No.9 West Section Lvshun South Road

institute: Dalian Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Uremic cardiomyopathy (UCM) is a severe complication of uremia that lacks effective treatments. The role of immune dysfunction in hemodialysis patients with UCM remains unclear. Peripheral blood mononuclear cells (PBMCs) are major components of the immune system; however, they do not directly contact cardiomyocytes. In general, extracellular vesicles (EVs) function as intercellular communication mediators. Therefore, in this study, we first investigated the role of PBMC-derived EVs (PBMC-EVs) in UCM and identified EV-miR-744-5p as a key molecule involved in PBMC–cardiomyocyte communication. Mechanistically, indoxyl sulfate (IS) downregulated miR-744-5p expression in PBMC-EVs, leading to IGF2R upregulation in cardiomyocytes, thereby exacerbating myocardial injury via induction of hypertrophy, apoptosis, and inflammatory pathway activation in the cardiomyocytes. These files provide sequencing results on altered miRNAs in PBMC-EVs after IS stimulation.

overall_design: Including IS-stimulated PBMC-EVs and untreated (control) PBMC-EVs.

first: Ziran

last: Wang

first: Jiaojiao

last: Hao

first: Yaxi

last: Shang

first: Wenli

last: Ma

first: Weidong

first: Qingzhu

last: Tang

first: Xiangning

last: Du

first: Fan

first: Biaojie

last: Qin

first: Kun

last: Xiao

first: Longkai

last: Li

first: Xianan

last: Guo

first: Shuang

last: Meng

first: Huiyi

last: Song

first: Hongli

last: Lin


title: Prebiotic Intake during Pregnancy Mitigates Long-Term Antibiotic Disturbances in the Gut-Breast Axis and Regulates Mammary Gland Development

city: Ottawa

first: Hamed

last: Yasavoli Sharahi

state: ON

address: 451 Smyth Rd

country: Canada

institute: University of Ottawa

type: Methylation profiling by genome tiling array

summary: The mammary gland undergoes critical remodeling during pregnancy, making it vulnerable to environmental influences such as antibiotics. This study investigates the long-term effects of prenatal and postnatal exposure to low-dose penicillin (LDP) on immune responses and mammary gland development in mice, along with the potential protective role of the prebiotic AHCC. Pregnant dams were treated with LDP and/or AHCC from late gestation to weaning. Immune markers and blood-milk barrier integrity were assessed in dams, while offspring were evaluated for immune profiles, mammary gland morphology, and epigenetic alterations. LDP exposure triggered inflammation and disrupted DNA methylation in key regulatory genes and microRNAs related to mammary development and the ERK/MAPK pathway. AHCC mitigated these effects, supporting its immunomodulatory and protective potential. These findings highlight the impact of early-life antibiotic exposure on breast tissue development and the possible role of prebiotics in preserving long-term mammary gland homeostasis.

overall_design: Sixteen pregnant Balb/c mice were randomly assigned to four groups from gestation day 14 until weaning (postnatal day 21): (1) control (water only), (2) low-dose penicillin V (31mg/kg/day), (3) AHCC® prebiotic (2g/kg/day), or (4) penicillin V plus AHCC, all administered via drinking water. Water intake was monitored daily to ensure consistent dosing. After weaning, treatments ceased and dams were euthanized for collection of blood and mammary tissue. Offspring were separated by sex, re-grouped by treatment, and maintained on standard diet until postnatal day 56, when mammary glands and blood were collected for immune and epigenetic analyses. AHCC® was supplied by Amino Up Co., Ltd. (Japan).

last: Yasavoli-Sharahi

first: Roghayeh

last: Shahbazi

first: Darshan

middle: B

last: Kambli

first: Mary

middle: J

last: Hebbo

first: Maria

middle: F

last: Balcells

first: Nawal

last: Alsadi

first: Benjamin

middle: K

last: Tsang

first: Zdenko

last: Herceg

first: Felicia

last: Lei

first: Chantal

last: Matar


title: ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment [RNA-seq]

first: Fabio

last: Mohn

summary: Short interspersed nuclear elements (SINEs) are abundant non-autonomous transposable elements (TEs) derived from RNA polymerase III (Pol III)-transcribed short non-coding RNAs. SINEs retain sequence features recognized by the Pol III machinery and constitute a substantial portion of vertebrate genomes. Despite their impact on genome stability and evolution, the mechanisms governing SINE transcription remain poorly understood. Although DNA methylation and heterochromatin formation have been implicated in their repression, we find these pathways play only a minor role in mouse embryonic stem cells. Instead, we identify the ChAHP complex as a key repressor of SINE B2 elements. ChAHP directly inhibits Pol III transcription by blocking TFIIIB recruitment without affecting TFIIIC binding. This selective interference prevents transcription initiation and highlights a distinct regulatory mechanism. Our findings establish ChAHP as a non-canonical repressor of Pol III-dependent SINE transcription, offering new insights into the control of this pervasive class of non-coding genomic elements.

overall_design: Total RNA-seq and TT-seq analysis in mESCs after accute ADNP-depletion, GTF3C1-depletion, CTCF-depletion and combined ADNP/CTCF-depletion. RNA-seq and TT-seq experiments were performed in independent triplicates.

first: Jakob

last: Schnabl

first: Michaela

last: Schwaiger

first: Marc

last: Bühler


title: The role of Snail1 in collective migration

first: jing

last: chen

state: shanghai

address: 393 Middle Huaxia Road, Pudong, Shanghai

institute: shanghaitech university

summary: Snail1 is a transcription factor directly associated with epithelial-mesenchymal transition (EMT), but our study reveals its significant role in the collective migration process beyond EMT. Through sequencing, we found that knockdown of Snail1 weakens intercellular connections during migration and diminishes the activity of migration-related pathways. Additionally, the expression of a series of downstream genes related to the cytoskeleton and cell migration is also reduced.

overall_design: To investigate the role of Snail1 in the collective migration process, we conducted in vitro migration experiments with HC11 cells that had been either control-treated or subjected to Snail1 knockdown (KD). Samples were collected for sequencing at 0 hours and 36 hours post-migration.

first: Jing

last: Chen

first: Zhi

middle: x

last: Deng


title: Effect of medium pH on the transcriptomes of Mycobacterium tuberculosis H37Rv parental, Δrv0998 and rv0998 complemented strains

city: London

first: Gerald

last: Larrouy-Maumus

address: South Kensington Campus, Exhibition Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

summary: Mycobacterium tuberculosis (Mtb) survives host defenses by adapting to the environmental conditions during infection. A critical survival strategy involves pH homeostasis, mediated by complex signalling systems that regulate metabolic reprogramming and stress responses. While the lysine acetyltransferase Rv0998 is known to support Mtb hypoxia adaptation and metabolic flexibility, its role in acid stress remains unexplored. Here, we investigate how Rv0998 enables acid tolerance by analysing the transcriptomic profiles of the strains under physiological pH (pH 6.8) and acidic pH that mimics phagosomal environment (pH 5.7).

overall_design: Mtb H37Rv parental, Δrv0998 and rv0998 complemented strains were grown in 7H9 media supplemented with dextrose, NaCl, bovine serum albumin and tyloxapol with pH adjusted to either 6.8 or 5.7. Bacteria wer grown in a static incubator to mid-exponential phase for RNA extraction. Three biological replicates in each group were prepared for RNA extraction.

first: Yi

last: Liu

first: Nadia

last: Fernandez

first: Richard

last: Williams


title: Improved Small Interfering RNA Therapy Targeting the Long, Non-Coding RNA SMILR For Therapeutic Intervention in Coronary Artery Bypass Graft Failure

city: EDINBURGH

first: Andrew

last: Baker

state: Not applicable

address: 47 Little France Crescent

institute: University of Edinburgh

summary: Coronary artery bypass graft (CABG) surgery remains the gold standard of care to prevent myocardial ischaemia in patients with advanced atherosclerosis, however long-term graft patency remains a considerable and long-standing problem. Excessive vascular smooth muscle cell (vSMC) proliferation in the grafted tissue is recognised as central to late CABG failure. We previously showed that siRNA-mediated silencing of SMILR, a human-specific SMC-enriched lncRNA, blocks vSMC proliferation, suggesting that targeting SMILR expression could be a novel way to prevent neointima formation, and thus CABG failure. Here, we describe the design and synthesis of a library of 76 chemically-enhanced SMILR-targeting siRNA. From this library, we identify a lead siRNA, BHF7, which demonstrates potent and reproducible silencing of SMILR expression and which robustly blocks vascular smooth muscle cell proliferation, both in vitro and up to 14 days in the ex vivo human saphenous vein model. We further demonstrate using RNA-sequencing that BHF7 down-regulates the expression of genes associated with proliferation and does not induce the expression of interferon or apoptosis genes, suggesting it has an acceptable safety profile both on and off-target. Finally, we performed TUNEL staining and measured the levels of cleaved caspase-3 after BHF7 treatment which demonstrated that BHF7 does not induce a cytotoxic response either in vitro or ex vivo.  Collectively, this data represents a pre-clinical package into the function and specificity of BHF7 which warrants further investigation into the possibility of utilising BHF7 as a novel, ex vivo RNA therapeutic for the prevention of CABG failure.

overall_design: RNAseq profiling to find the transcriptional effects in saphenous vein smooth muscle cells(SVSMCs) after knockdown of the long non-coding RNA SMILR via an optimised siRNA (BHF7). Transcriptional profiles of quiescent, proliferative and proliferative/transfected SVSMCs were compared.

first: Simon

last: Brown

first: Anna

middle: L

last: Malinowska

first: Matthew

last: Bennett

first: Andrés

last: Correa-Sánchez

first: Laia

last: Valencia

first: Aimee

middle: P

last: Lucignoli

first: Scott

last: Webster

last: Barton

first: Loic

last: Roux

first: Julie

last: Rodor

first: David

middle: E

last: Newby

first: Mark

last: Cunningham


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [RNA-seq]

city: Oxford

first: I-Jun

last: Lau

address: Old Rd

department: Botnar Research Centre

institute: University of Oxford

summary: Transcription factors (TFs) are key effectors of enhancer activity. MYB is a critical hematopoietic TF that is frequently dysregulated in cancer. Despite its well-established role, the exact mechanisms by which MYB influences enhancer function—and the specific stages of enhancer activation at which it operates—remain poorly understood. Using high resolution Micro-Capture-C, we show that upon MYB degradation, highly defined enhancer-promoter interactions at specific MYB binding sites are lost. Loss of these interactions, together with other hallmarks of enhancer activity—reduced H3 lysine-27 acetylation and enhancer RNA transcription—correlates with significant downregulation of target gene expression in leukemia, indicating that MYB mediates transcription activation via maintenance of enhancer function. When anchored to DNA within a gene desert region that is devoid of histone marks and active transcription, the MYB transactivation domain is sufficient and necessary for the nucleation of an enhancer-like region. This results in the activation of transcription from distal cryptic elements and the establishment of long-range chromatin interactions up to 400 kb away from the anchor point. Together, these results indicate that MYB activity alone is sufficient to induce long-range interactions and transcription, achieving this through highly precise enhancer-promoter crosstalk.

overall_design: polyA minus RNA-seq in E14 (TOT2N variant) cell lines containing 1) stable integration of TetR constuct, 2) TetR-MYBTA constuct or 3) wild type.

first: Nicholas

middle: T

last: Crump

first: Thomas

last: Milne


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [ChIP-seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq in the following cell lines: 1. WT SEM cells; 2. SEM cells with MYB endogenously tagged with FKBP12(F36V) ±dTAG13; 3. WT E14 (TOT2N variant) cells; 4. WT E14 (TOT2N variant) cells containing stable integration of TetR constuct ±doxycycline; 5. WT E14 (TOT2N variant) cells containing stable integration of TetR-MybTA constuct  ±doxycycline.


title: Small RNA Seq profiling of tissue specific MSCs derived EVs

city: Delhi

first: Sujata

last: Mohanty

state: Delhi

address: Ansari nagar

department: Stem Cell Facility

country: India

institute: AIIMS, New Delhi

summary: Small extracellular vesicles (sEV) play a pivotal role in intercellular communication and hold immense therapeutic potential. In this study, we aimed to characterize sEV derived from bone marrow mesenchymal stromal cells (BM-MSCs) and Wharton’s jelly mesenchymal stromal cells (WJ-MSCs), cultured under normoxic and hypoxic conditions for elucidating their functional inclinations. Using high-throughput miRNA sequencing, we identified distinct miRNA profiles across cell types and oxygenation states, revealing unique signatures associated with hypoxia-driven cellular adaptations.

overall_design: The small RNA sequencing of sEV derived from respective MSCs was outsourced to Eurofins Genomics India Pvt. Ltd. Briefly, RNA was extracted using the TRIzol reagent (Invitrogen, Shanghai, China) following the protocol provided by the manufacturer, and the samples were shipped in dry ice to the laboratory of Eurofins Genomics India Pvt. Ltd. (a) Illumina NextSeq Small RNA Library Preparation Quality and quantity of the received RNA samples were checked on NanoDrop followed by Agilent Tape station using High Sensitivity RNA ScreenTape. The small RNA sequencing libraries were prepared from the received total RNA samples using Illumina NEBNext® Multiplex Small RNA Library Prep Kit for Illumina (NEB) as per the manufacturer’s instruction. Approximately 1 µg of RNA was processed for 3' adapter ligation followed by 5’ adaptor ligation. The adaptor ligated RNA samples were then converted to cDNA using reverse transcriptase followed by PCR amplification using common primer and indexed primer. The enriched library was then purified using Spin column followed by AMPureXP bead-based size selection. The size selected and purified libraries were analyzed in 4200 Tape Station system (Agilent Technologies) using High sensitivity D1000 Screen tape as per manufacturer instructions. (b) Cluster Generation and Sequencing After obtaining the Qubit concentration for the libraries and the mean peak sizes from Agilent Tape Station profile, the PE Illumina libraries will be loaded onto Illumina NextSeq500 platform for cluster generation and sequencing. Paired-End sequencing allows the template fragments to be sequenced in both the forward and reverse directions on NextSeq500. The kit reagents were used in binding of samples to complementary adapter oligoes on paired-end flow cell. The adapters were designed to allow selective cleavage of the forward strands after re-synthesis of the reverse strand during sequencing. The copied reverse strand will be used to sequence from the opposite end of the fragment. (c) Read Filtering Small RNA sequencing data is known to include reads from other category of small non-coding RNAs such as tRNA, snoRNA, snRNA and piRNA ect. Sample-wise reads were mapped against the customized database of Rfam (Database built after removing miRNA and their precursor sequences from the Rfam) using Bowtie v1.3.1 aligner with default parameters. The unmapped against Rfam database were considered for downstream analysis. Reads having length less than 18 nts and greater than 30 nts were excluded from the analysis. The reads which have length between 18-30 bases were considered for miRNA identification. Reads passed above filtration steps were considered as cleaned putative miRNA population, taken further for known and novel miRNA identification. (d) miRNA Prediction and Analysis Mapper.pl and miRDeep2.pl modules of miRDeep2 tool were used to identify novel miRNAs and precursors in sample(s) using reference genome. The resulting candidate novel precursors were filtered based on: the miRDeep2 score (≥4), significant randfold p-value. Know mature and precursor miRNAs of Homo sapiens were downloaded from miRBase database. Quantifier module of miRDeep2 tool was used to quantify miRNAs in each sample using predicted novel miRNAs, and known miRNAs downloaded from miRBase as reference. The analysis was carried out for miRNAs expressed differentially with p-value < 0.05 reported between control and treated samples respectively. Log2 Fold Change (log2FC) values greater than zero were considered up-regulated whereas less than zero were down-regulated along with p-value threshold of 0.05 for statistically significant results. miRNAs were further shortlisted based on specific criteria, such as differential expression and biological relevance. To identify their functional roles, target genes regulated by the shortlisted miRNAs were predicted using the miRWalk database, and pathway enrichment analysis was performed using the Panther database to uncover key biological pathways influenced by these miRNAs. Subsequently, Venny 2.0 was used to identify common miRNAs across multiple experimental groups by comparing miRNA lists and generating Venn diagrams. The intersection of miRNAs from different groups was analysed to determine shared regulatory roles and conserved pathways. This integrated approach provided valuable insights into miRNAs' biological significance and involvement in key regulatory pathways.

first: Yashvi

last: Sharma


title: Stage-specific degradation of cyclin D3 orchestrates myelopoiesis and restrains MPN development [scRNA-seq]

city: Cleveland

first: Ata

last: Abbas

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

summary: Cyclin D3 is critical for myelopoiesis, with its rapid, stage-specific degradation regulating normal granulocyte-monocyte differentiation. Using a knock-in mouse model with a degradation-resistant cyclin D3 variant (D3T283A), we show that sustained cyclin D3 levels enhance granulocyte-monocyte output, cause microcytic erythrocytes, thrombocytosis, and extramedullary hematopoiesis. Splenic HSPCs from D3T283A mice exhibit increased self-renewal and competitive repopulation advantage. Prolonged D3T283A expression drives a high-penetrance myeloproliferative neoplasm, reducing survival.

overall_design: Single-cell sequencing was performed on spleenocytes from C57BL/6J mice with a CRISPR/Cas9-induced mutation in the CCND3 gene, resulting in a Threonine 283 to Alanine substitution (D3T283A). Mice were bred and maintained as heterozygous knock-in. Specifically, two D3T283A female mice, aged 12 and 16 months, and two age- and sex-matched wild-type (WT) female mice were used. The experiment was conducted on spleenocytes from mice aged 12–16 months, when the D3T283A mouse model exhibits severe symptoms of myeloproliferative neoplasm.

first: Bartosz

last: Mucha

first: Vincenzo

last: Tarallo

first: Shuyuan

last: Zhang

first: Marganit

last: Farago

first: Polly

last: Phillips-Mason

first: Harrison

last: Lindley

last: Cameron

first: Chen

last: Zhao

first: Amar

last: Desai

first: Alan

last: Diehl


title: Molecular markers of response of ENzalutamide in combination with PAClitaxel in a phase II trial for advanced or recurrent endometrioid endometrial adenocarcinoma (ENPAC)

city: HOUSTON

first: anil

middle: k

last: sood

state: TEXAS

address: 7777 knight road, unit 173

department: Gyn Oncology and Rep Medicine

institute: UT MD Anderson Cancer Center

summary: We evaluated the efficacy of paclitaxel, carboplatin, and the androgen receptor (AR) inhibitor, enzalutamide, in a phase II study of advanced or recurrent endometrioid endometrial cancer and identified biomarkers associated with response to therapy. A safety lead-in study (part A) was performed in a small group of patients. The remaining patients (part B) received 160 mg of enzalutamide as a single agent before starting triplet therapy. Biopsies were obtained during the lead-in to evaluate molecular markers. Patients received carboplatin (AUC 5 IV Q3 weeks), paclitaxel (175 mg/m2 IV Q3 weeks), and enzalutamide (160 mg PO daily). Response was assessed every 3 cycles. Fifty-two patients were included (7 in part A and 45 in part B). Paired biopsies were collected for translational studies at two time points: prior to chemotherapy and after the first cycle of treatment, during which patients were receiving chemotherapy in combination with enzalutamide. No dose-limiting toxicities were observed during the safety lead-in. Among 40 evaluable patients, the objective response rate was 67.5% (95% CI, 50.9%–81.4%). The PFS duration was 13.27 months (95% CI, 10.58–25.49); the 6-month PFS probability was 0.79 (95% CI, 0.65-0.88). Mass spectrometry analysis of frozen tissues identified 43 significantly altered proteins (P<0.01) in the pre-treatment samples and 37 in the On-treatment samples between responders and non-responders. Responders had multiple AR-responsive genes enriched in the pre-treatment samples that were downregulated in the On-treatment samples. The combination of enzalutamide, carboplatin, and paclitaxel was tolerable and had promising clinical outcomes in patients with advanced or recurrent endometrioid endometrial cancer. Candidate biomarkers of response were identified and could contribute to further development. Clinical Trial registration number: NCT02684227.

overall_design: Frozen uterine tumor tissues (n =31) from 16 patients collected before (pre) and after (On) enzalutamide therapy

first: Shannon

middle: N

last: Westin

first: Anil

last: Sood


title: Clonal evolution permits outgrowth of chemoresistant LMPP-like early progenitors in relapsed NPM1c AML

first: Wout

last: Megchelenbrink

overall_design: bulk RNA-Seq profiling of bone marrow mononuclear cells from NPM1c AML patient at Diagnosis and Relapse

first: Yanan

last: Zhai

first: Brigit

last: te Pas

first: Elizabeth

last: Schweighart

first: Hendrik

last: Stunnenberg


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [ATAC-seq]

first: I-Jun

last: Lau

overall_design: ATAC-seq in E14 (TOT2N variant) cell lines: 1) wild type, 2) containing stable integration of TetR constuct or 3) containing stable integration of TetR-MYBTA constuct

first: Nicholas

last: Crump

first: Thomas

last: Milne


title: Phenotypic effects of disruption of all four rice HK cytokinin receptors

city: Chapel Hill

first: Joseph

last: Kieber

state: NC

address: 120 South Road

institute: University of North Carolina

summary: The phytohormone cytokinin has diverse functions in plants, most of which have been primarily elucidated in dicots. In order to further characterize the role of cytokinin in a monocot, we used CRISPR-Cas9 to generate rice lines with frameshift alleles in the four putative cytokinin receptors (Histidine Kinases 3,4,5,6) in all single and multiple combinations. The transcriptome of the hk3,4,5,6 mutant is completely insensitive to cytokinin, suggesting that all cytokinin signaling regulating transcription acts through these four HKs, despite the presence of a CHASE-containing Serine-Threonine kinase in rice.

overall_design: RNA-seq profiling of wild-type Kitaake callus and hk3,4,5,6 quadruple mutant callus treated with either 5 μM 6-Benzylaminopurine (BA) or vehicle control for 1 hour.

first: Shouse

last: Eva Mei


title: Investigation of EMT Processes in Migrating Mammary Epithelial Organoids

city: shanghai

first: jing

last: chen

summary: Traditionally, it is believed that epithelial tissue migration must undergo the process of EMT (epithelial-mesenchymal transition). However, our research suggests otherwise. We sequenced samples from different migration stages and found that, during the process of epithelial collective migration, gene expression changes did not exhibit the EMT expression pattern.

overall_design: To investigate at the molecular level whether EMT occurs during the collective migration of mammary epithelium, we conducted in vitro migration experiments by exposing mammary organoids to beads soaked in either BSA or FGF10. Samples were collected at 0, 36, and 72 hours for sequencing analysis.

first: Jing

last: Chen

first: Zhi

last: Deng


title: Projections of BLAFgf2+-VMH and BLANotch2+-DMS distinctly decode visceral pain and itch

city: Suzhou

first: Qiuying

last: Zhao

address: No. 199 Ren'ai Road, Suzhou Industrial Park, Xietang Street

institute: Soochow University

summary: Distinct representation of visceral pain and itch by unique BLA neuronal ensembles and suggested that BLA as a sorting center that distinctly processes visceral pain and itch, providing a new framework for comprehending how the brain processes nociceptive and pruritus information, and identifying potential molecular targets for specific visceral pain and itch processing.

overall_design: Analysis of differential genes in three groups of CRD-labeled, His-labeled and CRD & His labeled cells by RNA-Seq

first: Yongchang

last: Li

first: Jiahe

last: Yao

first: Ruixia

last: Weng

first: Xue

last: Xu

first: Shufen

last: Hu

first: Honghong

last: Zhang


title: Mesenchymal-epithelial transition serves to rapidly, yet transiently, restore the endometrial epithelium during postpartum uterine regeneration

city: Boone County

first: Amanda

last: Patterson

state: MO

address: 1030 Hitt St

institute: university of Missouri

summary: The uterus is a remarkable organ in its ability to undergo extensive tissue damage during menstruation and parturition, yet achieves efficient, scar-free repair. Coordinated regulation of this regenerative process is essential for uterine homeostasis and fertility; however, the underlying mechanisms remain incompletely understood. Here, we demonstrate that mesenchymal-to-epithelial transition (MET) is a critical contributor to postpartum endometrial regeneration using PdgfraCreERT2/+; Rosa26-tdTomatofl/+ lineage tracing mice. Flow cytometry revealed a marked increase in mesenchymal-derived (MD) epithelial cells during active tissue repair. Notably, these cells are transient, undergoing clearance primarily via apoptosis following epithelial restoration. We also identified a migratory population of transitional cells of mesenchymal origin within the mesometrial stroma that incorporate into the luminal epithelium, consistent with an active MET program. Single-nucleus RNA sequencing (snRNA-seq) revealed that MD epithelial cells exhibit gene expression profiles associated with cell adhesion and cytoskeletal remodeling, while transitional cells were enriched for genes involved in junctional assembly and actin dynamics. MET-associated genes were significantly upregulated in both transitional and MD epithelial populations. Cell-cell communication analysis highlighted WNT, BMP, and EPHA signaling as candidate regulators of MET during regeneration. Together, these findings provide confirmation of MET as a physiologic mechanism of postpartum endometrial repair and uncover a coordinated signaling network that drives this process. Disruption of MET may contribute to pathologies such as endometriosis or endometrial cancer, underscoring the importance of understanding mesenchymal-epithelial plasticity in both normal and disease states.

overall_design: scRNA profiling of PdgfraCreERT2-tdTomato mice at E18.5, PPD1, PPD2, PPD3, PPD4 and PPD28 postpartum

first: Zidao

last: Wang


title: TCN2 promotes psoriatic skin inflammation and keratinocyte proliferation via the IL-1β-STAT3 pathway

city: Beijing

first: Jingkai

address: No.2, Cherry Blossom Garden East Street, Chaoyang District

institute: China-Japan Friendship Hospital

summary: Psoriasis, a chronic immune-mediated inflammatory skin disorder, exerts systemic impacts across multiple organs. Although transcobalamin 2 (TCN2) has been reported to be associated with several autoimmune diseases, its role in psoriasis remains elusive. Hence, we investigated the role of TCN2 in psoriasis pathogenesis. Our results indicated that TCN2 was highly expressed in the skin tissues and peripheral blood mononuclear cells (PBMCs) of psoriatic patients, with downregulation following biologic therapy. Moreover, imiquimod (IMQ) - induced psoriasis in mice exhibited heightened TCN2 expression. To further explore the role of TCN2 in psoriasis, we generated Tcn2-deficient (Tcn2-/-) mice and established a psoriasis model using IMQ. IMQ-treated Tcn2-/- mice displayed milder psoriatic lesions and a lower level of inflammation. RNA-seq analysis of lesional skin revealed significant downregulation of inflammatory mediators (S100A7, S100A8, S100A9, IL-1β, IL-6) and suppression of STAT3 signaling in Tcn2-/- mice compared to WT-IMQ mice. Parallel in vitro experiments using TCN2-knockout HaCaT cells demonstrated cell cycle arrest. Collectively, our findings highlight TCN2 as a critical regulator of psoriatic inflammation, proposing it as a novel therapeutic target.

overall_design: TCN2-deficient (Tcn2-/-) mice were generated and a psoriasis model using IMQ was established to investigate the role of TCN2 in psoriasis. RNA-seq analyses were performed on the diseased skin of the mice to compare inflammatory factor and pathway profiles with those of wild-type IMQ mice.


title: Differentially expressed genes by YAP-mediated RPE repair in mouse after sodium iodate injury

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

summary: Damage or degeneration results in RPE atrophy such as in AMD, the leading cause of blindness in the elderly population. In contrast to other epithelial tissues, the mature RPE is postmitotic and does not renew itself. Using sodium iodate (SI) as an injury model in mouse, we have previously shown that genetic overexpression of the Hippo pathway effector Yap (YOE) significantly improves a- and b-wave ERG amplitudes and RPE tissue and cellular integrity 7 days post injury. To elucidate the molecular and cellular mechanisms of RPE repair by YOE, we conducted bulk RNAseq for identifying differentially expressed genes (DEGs).

overall_design: Bulk RNA sequencing for retinal pigment epithelium (RPE) collected from YOE or wildtype mice treated with sodium iodate or saline (4 biological groups), then perform differential expression analysis (DEA), and gene set enrichment analysis (GSEA) to show statistically significant differences between selected biological states.

first: Sabine

last: Fuhrmann

first: Yang

last: Song

first: Angela

last: Jones


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [TOPmentation]

first: I-Jun

last: Lau

overall_design: TOPmentation in SEM cells with MYB endogenously tagged with FKBP12(F36V)

first: Nicholas

last: Crump

first: Thomas

last: Milne


title: Stage-specific degradation of cyclin D3 orchestrates myelopoiesis and restrains MPN development [RNA-seq]

first: Ata

last: Abbas

overall_design: RNA-sequencing was performed on spleenocytes from C57BL/6J mice with a CRISPR/Cas9-induced mutation in the CCND3 gene, resulting in a Threonine 283 to Alanine substitution (D3T283A). Mice were bred and maintained as heterozygous knock-in. Specifically, three D3T283A (12-16 months), and three age-matched wild-type mice were used. The experiment was conducted on spleenocytes from mice aged 12–16 months, when the D3T283A mouse model exhibits severe symptoms of myeloproliferative neoplasm.

first: Bartosz

last: Mucha

first: Vincenzo

last: Tarallo

first: Shuyuan

first: Marganit

last: Farago

first: Polly

last: Phillips-Mason

first: Harrison

last: Lindley

first: Mark

last: Cameron

first: Chen

first: Amar

last: Desai

first: Alan

last: Diehl


title: Inhibition of gill and skin damage by infectious hematopoietic cell necrosis virus in rainbow trout (Oncorhynchus mykiss) by astragalus polysaccharides through promotion of inactivated vaccine efficacy

city: Lanzhou City

first: zhengjie

last: suo

state: Gansu

address: 营门村1号

institute: Gansu Agricultural University

summary: With a growing population and increased awareness of the benefits of consuming fish products, meeting the increasing demand for fish products has become critical to aquaculture activities. However, Infectious Hematopoietic Organ Necrosis Virus (IHNV) causes Infectious Hematopoietic Organ Necrosis (IHN) disease, which in severe cases may lead to 100% mortality in juvenile rainbow trout, and has become a problematic issue in the development of aquaculture.IHNV leads to degenerative necrosis of hematopoietic tissues, and the symptoms, including darkening of the skin color, protrusion of the eyes, pallor of the gills, and distension of the abdomen, pose the greatest threat in the juvenile stage of the fish. Gills and skin are mucosal tissues of fish that are in direct contact with the aquatic environment and are key sites of invasion for a variety of pathogens. Here, we investigated the effect of Astragalus polysaccharide combined with inactivated IHNV vaccine (APS+V) on gill and skin immunity in rainbow trout. Histopathological results showed that APS+V significantly inhibited IHNV-induced skin and gill damage and apoptosis. Astragalus polysaccharide also increased tissue SOD, CAT, and T-AOC activities by enhancing vaccine efficacy. Transcriptome analysis showed that immune-related pathways were significantly enriched in the APS + vaccine group. Key immune genes, including IgM, IgT, IgD, CD4, CD8; APS + vaccine induced the expression of these genes in tissues. Notably, APS + V significantly inhibited IHNV replication in mucosal tissues.

overall_design: There were 150 tails in each of the vaccine group, APS + vaccine group and control group. The vaccine and APS + vaccine groups were injected intraperitoneally with 150 μL of inactivated IHNV and APS vaccine, respectively, and the control group was injected with an equal amount of phosphate buffer solution (PBS). At 14 days postvaccination (D 14), the remaining fish in each group were injected intraperitoneally with 50 μL of IHNV (107 TCID 50 ml-1). For sampling, these fish were anesthetized with 100 mg/L MS-222 (Sigma, USA). Skin and gills were collected at D1, D3, D 7, D 14, D 15, D 21, D 30, and D 60 from six fish from the vaccine group, the APS + vaccine group, and the control group for determination of viral loads, immune-related gene expression, and nonspecific enzyme activities. Notably, at D 7 and D 21, three additional skin and gill samples were removed from each group for transcriptome sequencing. In addition, at D 7, D 14, D 15, D 21, D 30, and D 60, skin and gills were collected from three fish from each group for histopathologic examination.

first: Zhe

last: Liu

first: Zhengjie

last: Suo

first: Jinqiang

last: Quan

first: Yucai

last: Pan

first: Junhao

last: Lu

first: Guiyan

last: Zhao


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [TT-seq]

first: I-Jun

last: Lau

overall_design: TT-seq in SEM cells with MYB endogenously tagged with FKBP12(F36V) ±dTAG13 treatment

first: Nicholas

last: Crump

first: Thomas

last: Milne


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions

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

overall_design: Refer to individual Series


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [Capture-C]

overall_design: Capture-C in E14 (TOT2N variant) cell lines containing stable integration of rTetR-MYBTA or TetR-MYBTA constuct ±doxcycline treatment.


title: A cost-effective method to prepare mesenchymal stem cells (MSCs) from human pluripotent stem cells

city: Guangzhou 510700, China

first: yu

last: liu

address: Guangzhou 510700, China

institute: Guangzhou Future Homo Sapiens Institute of Regenerative Medicine Co., Ltd

summary: Induced mesenchymal stem cells (iMSCs) derived from human pluripotent stem cells (hPSCs) offer several advantages over tissue-derived mesenchymal stem cells (MSCs), including unlimited donor expansion, minimal batch-to-batch variation, a controllable pathogen microbiota, and the potential for large-scale production. However, producing iMSCs has several challenges, such as complex differentiation protocols, high costs, and poor reproducibility. Therefore, more effective differentiation methods are needed. In this study, iMSC differentiation was induced based on the classical method of using TGF-β signaling inhibitors. We discovered that due to the differences in the adhesiveness of gelatin to different cells, target cells can be rapidly selected and further differentiated to obtain high-purity iMSCs. This approach is more straightforward and less cost-effective than previous methods, producing iMSCs with higher purity and greater yield. We revealed that the DGEA active motif in gelatin produced effects similar to those of gelatin, playing an essential role in iMSC differentiation. In summary, our differentiation method addresses many of the issues associated with classical industrialization iMSC differentiation protocols and provides valuable insights into the production of iMSCs for clinical translation.

overall_design: The samples were sequenced using a gene sequencer and an MGISEQ-2000RS high-throughput sequencing reagent kit  to determine the transcriptomic gene expression profiles of H1 cells, H1-iMSCs, and bone marrow-, adipose-, and umbilical cord-derived MSCs.

first: Linli

last: Wang

first: Qiang

last: Li

first: Yuanyuan

first: Jianguo

last: Yang

first: Yu

first: Hong


title: Dlx1&2 Directly Promote Expression of Cxcl14 to Control Synapse Development and Interneuron Survival [ChIP-seq]

city: San Francisco

first: John

last: Rubenstein

address: Box 2611 , Mission Bay 284C

institute: University of California, San Francisco

summary: Dlx genes have fundamental roles in the generation, differentiation and functions of virtually all forebrain GABAergic neurons. Here we focused on defining the key genes that are dysregulated in Dlx1/2 conditional mutants in mouse immature cortical GABAergic interneurons (CINs), and by identifying DLX-bound putative regulatory elements (pREs) of these Dlx-regulated genes. Within the Dlx-expressing lineage, some DLX-bound pREs were specific to CINs, others appeared to be constitutively bound; the latter class having activity in mature CINs. One such pRE and its associated gene, Cxcl14, is strongly activated by Dlx1/2 and is essential for synaptogenesis onto CINs and for CIN survival.

overall_design: This submission includes ChIP-seq data. The dataset is on transcription factor Dlx2 across multiple brain cell types and time points.

first: Yurong

first: Alex

last: Nord

first: Susan

last: Lindtner


title: Transcriptome analysis of PRMT5 in Arabidopsis thaliana group to regulate high temperature stress response

city: Kunming

first: ya

middle: qi

last: xiao

state: Yunnan Province

address: Chenggong Campus of Yunnan University

department: Faculty of Ecology and Environment

institute: Yunnan University

summary: RNA-seq transcriptome analysis was used to detect the differential expression of heat stress-related genes of WT and mutant prmt5 after the end of heat stress

overall_design: RNA-seq transcriptome analysis was used to detect the differential expression of genes related to heat stress in WT and mutant prmt5 at 0 hours and 24 hours after the end of heat stress

first: Yaqi

last: Xiao

first: Zeting

last: Song


title: Dlx1&2 Directly Promote Expression of Cxcl14 to Control Synapse Development and Interneuron Survival [scRNA-seq]

overall_design:
Cortical tissues from wild-type (WT), heterozygous (Het), and conditional knockout (cKO) mice were dissected and analyzed using 10x Chromium scRNA-seq. Two biological replicates were prepared by independent experimenters. The second replicate was sequenced twice, with the second run performed at a higher sequencing depth.

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Submitter states that missing raw files (for 'emilycHet' sample) are due to file corruption.
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first: Jia

last: Hu


title: Seeding-competent early taumultimers are associated with cell type-specific transcriptional signatures

first: Rahel

last: Feleke

address: Ducane Road

institute: Imperial College

summary: The initial molecular alterations of Alzheimer’s disease (AD) are unknown. Established AD is characterized by profound structural and transcriptional alterations in the human brain, with the hallmark neuropathological features being beta-amyloid (Aβ) accumulation in senile plaques and hyperphosphorylated fibrillar tau in neurofibrillary tangles (NFTs). Previous evidence indicates that tau multimerization into small aggregates is one of the earliest molecular alterations, anticipating the accumulation of hyperphosphorylated tau in NFTs. In this study, we investigated the seeding capacity of these early small tau multimers and the transcriptional changes associated with them, aiming to unveil early pathogenic processes in AD-type tau pathology. Early tau multimers visualized with tau proximity ligation assay (tau-PLA) in the post-mortem temporal cortex demonstrated high seeding activity detected by real-time quaking-induced conversion (RT-QuIC) and induction of aggregates in a tau biosensor cell line. Using single-nucleus transcriptomics, we showed that brain tissue harboring seeding-competent early tau multimers, but without significant NFT pathology, is associated with substantial gene expression alterations across diverse cell types when compared to control tissue lacking either multimers or NFTs. Differentially expressed genes, such as APP, MAPT, and PSEN1, exhibited significant enrichment of AD heritability in up-regulated genes within excitatory neurons, astrocytes, and oligodendrocytes. Pseudotime analysis exposed a positive correlation between the progression of tau pathology and the expression of genes marking reactive astrocytes. In summary, our results support the hypothesis that seeding-competent tau multimerization may initiate AD-type tau pathology cascades before the accumulation of tau in NFTs. This research contributes valuable insights into the early molecular events associated with AD, with implications for future diagnostic and therapeutic strategies.

overall_design: SnRNA-seq analysis was performed on the cohort representing 16 subjects with no clinical history of AD.

first: Simona

last: Jogaudaite

first: Elisavet

last: Velentza‑Almpani

first: Jeong Hun

last: Ko

first: Javier

last: Alegre‑Abarrategui


title: Pan-cancer analysis combining RNA-seq reveals that ZNF25 contributes to glioma progression mainly through modulating PI3K-AKT signaling pathway

city: Chengdu

first: Xiaohong

middle: Huang

last: Yi

state: Sichuan

address: 1166 Liutai Avenue, Wenjiang District, Chengdu City

department: School of Basic Medical Science

institute: CDUTCM

summary: Background: ZNF25, a member of zinc finger proteins with KRAB domains family genes, is a transcription factor. Previous reports showed it is a biomarker of ovarian cancer. However, there are rarely reports about ZNF25 in other types of cancer, and its underlying mechanisms are not yet clear. Methods: Based on The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx), cBioPortal, Human Protein Atlas (HPA), IntOGen, TIMER, TIMER2, TISIDB, MethSurv, TISIDB, and Cistrome Data Browser (CDB) databases, we adopted bioinformatics methods to excavate the potential tumor genomic features of ZNF25, including dissecting the correlation with prognosis, gene mutation, immune cell infiltration, and DNA methylation in different tumors, and evaluated the association with tumor heterogeneity and stemness, and co-expression with Tex cells, chemokines chemokine receptors, and immunomodulators in pan-cancer. Additionally, we knocked down ZNF25 in U87-MG cells and performed RNA-seq analysis, then differential expression genes (DEGs) were further analyzed and visualized, like GO, and KEGG to interpret the biological significance. Results: The results show that ZNF25 has early diagnostic potential and was associated with the immune infiltration of different tumors. ZNF25 is associated with most tumor immune-infiltrating cells in pan-cancer, especially in glioma. Additionally, ZNF25 correlates with DNA methylation, tumor heterogeneity, Tex, and stemness in many types of cancers, like glioma. Besides, our findings demonstrate a close relationship between ZNF25 and mutated IDH1 in gliomas. Furthermore, our experiments showed that ZNF25 is involved in cancer pathways, mainly in PI3K-AKT and MAPK pathways.Conclusion: Through pan-cancer analysis combined with RNA-seq data, we discovered that ZNF25 might influence the progression of glioma mainly via the PI3K-AKT signaling pathway, and suggested that ZNF25 could serve as an indicator for tumor diagnosis, treatment, and prognosis across various types of tumors, including glioma.

first: Xianwen

last: Zhang

first: Lijun

last: Huang

first: Yumei


title: Molecular insights into the malignant transformation of endometriosis into clear cell carcinoma

city: Seoul

first: YunSoo

last: Chung

address: Yonseiro 50-1, Yonsei University College of Medicine

department: OBGY

country: South Korea

institute: Severance Hospital

summary: Endometriosis affects approximately 10% of women of reproductive age and increases the risk of ovarian cancer by 50%. It has been hypothesized that endometriosis may transform into ovarian clear-cell carcinoma (OCCC), a hypothesis that has been investigated using molecular analyses. The present study aimed to identify genes with altered expression in OCCC compared to that in endometriosis and to potentially predict the transformation of endometriosis into OCCC.

overall_design: Five patients with endometriosis were included in Group 1, while five patients with OCCC were assigned to Group 4. Additionally, patients with both endometriosis and OCCC were included in the study; among them, five patients with benign ovarian tissue were designated as Group 2, and four patients with malignant tissue were designated as Group 3 ( One omentum tissue and three ovary tissues). RNA levels in ovarian tissue samples were analyzed to identify differentially expressed genes (DEGs) and pathways. To identify genes whose expression changes during the transformation from benign ovarian tissue to malignant OCCC, DEGs were analyzed by comparing Group 1 with Group 3 and Group 1 with Group 4.

first: Yun Soo

first: Jung Eun

last: Sim

first: Jin Kyung

last: Baek

first: Euna

last: Choi

first: Heeyon

last: Kim

first: Bo Hyon

last: Yun

first: Seok Kyo

last: Seo

first: Yong Jae

last: Lee


title: Chemical reversion of mouse post-implantation epiblast directly to totipotent-like cells

city: Guangzhou

first: Man

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

summary: Totipotent cells can give rise to all cell types in an organism. Mouse totipotent-like cells (TLCs) have been generated from undifferentiated pluripotent embryonic stem cells (ESCs). However, it remains unknown whether TLCs can be generated from differentiated cells. Here, we report a novel chemically defined medium which can efficiently induce TLCs from differentiation-committed cells including epiblast-like cells (EpiLCs) and post-implantation epiblast. Comparatively, MERVL-GFP positive cells induced from differentiated cells exhibit closer transcriptome characteristics to 2-cell (2C) embryos in contrast to those induced from pluripotent ESCs. Moreover, differentiated cells exhibit distinct reprogramming kinetics and pathways to TLCs compared to ESCs. They are directly and rapidly reprogrammed into TLCs without passing through a pluripotent intermediate. Notably, TLCs were generated from post-implantation epiblast and demonstrated the capacity to contribute to both embryonic and extra-embryonic lineages in chimeras. Overall, these findings have significant implications for understanding the mechanism of totipotency acquisition and cell plasticity.

overall_design: Mouse ESCs were cultured with 2i/LIF and EpiLCs differentiated from ESCs within the FGF2 plus Activin A medium. EpiLCs were induced with GK15+DNALB in the 3D condition for 2 and 4 days. These cells were enriched by the fluorescence-activated cell sorting and analyzed  using scRNA-seq.

first: Hai

last: Zhou


title: Fibroblastic reticular cells drive sympathetic nerve reinnervation to adapt to lymph node expansion induced by tumor cells

city: Shanghai

first: Hui

last: Li

address: 800 Dongchuan Road

institute: SHSCI

summary: Lymph nodes (LNs) are peripheral immune organs innervated by sympathetic and sensory nerves. Upon diverse stimuli, LNs undergo substantial structural reorganization and volume expansion. However, the adaptation of innervation to these changes remains poorly understood. In this study, whole-mount 3D imaging revealed that sympathetic nerve fibers, rather than sensory nerves, exhibited significant elongation and increased branching over time during tumor-induced lymph node enlargement (TLNE). Single-nucleus RNA Sequencing (snRNA-seq)  analysis demonstrated that throughout TLNE, fibroblastic reticular cells (FRCs) are activatedand engage in neuro-related signaling pathways while secreting substantial amounts of hepatocyte growth factor (HGF). Moreover, the stiffness of the extracellular matrix (ECM) in LNs increased in the context of TLNE, further supporting FRC activation and HGF secretion. The role of HGF in promoting sympathetic nerve fiber outgrowth was confirmed by administering specific HGF inhibitors or using adeno-associated virus (AAV)-mediated HGF silencing. Collectively, HGF secreted by FRCs plays a pivotal role in TLNE, triggering adaptive sympathetic nerve outgrowth and reinnervation within LNs, providing novel insights into neuro-stromal-immune system crosstalk.

overall_design: To investigate the interplay between stromal cells and nerves  during tumor-induced lymph node enlargement (TLNE), we performed single-nucleus RNA sequencing (snRNA-seq) on TLNE from mice.

first: Jun


title: Regulation of the transcription cycle contributes to BET bromodomain inhibitor resistance [RNA-seq]

city: Quebec City

first: Jean-Philippe

last: Lambert

state: QC

address: 2705, boulevard Laurier

department: Molecular Medicine

institute: Université Laval

summary: Bromodomain (BRD)-containing proteins, multi-domain scaffolding molecules implicated in the relay of acetylated lysine (Kac) signals, are tractable targets for cancer therapeutics. However, their functions and the consequences of targeting them have not been systematically characterized. Employing complementary interaction-mapping techniques (affinity purification and proximity-dependent biotinylation), we investigate the interactome of 39 BRD-containing proteins together with 110 additional proteins that physically or functionally associate with them. We uncover 4096 novel interactions, revealing intricate connectivity of the Kac-machinery. We survey interaction landscape rewiring following chemical inhibition for multiple class of BRDs and revealed highly distinctive response following pharmacological intervention between BRD-containing proteins families. Lastly, focusing on the BET protein family, we characterized their interplay with the p38/MAPKAPK2 stress signaling pathway and its contribution to metabolic alterations in the context of metastatic cutaneous melanoma.

overall_design:
To investigate the molecular mechanisms by which the loss of MAPKAPK2 enhance resistance to BET bromodomain inhibitors, we established A375 cells knockout for MAPKAPK2 using CRISPR/Cas9.
Using these cells, we performed RNA-seq analysis following treatment with 500 nM JQ1 or DMSO control over 48 hours

first: Pata-Eting

last: Kougnassoukou Tchara

first: Jérémy

last: Loehr

first: Lucas

last: Germain

first: Zachary

last: Steinhart

first: Beatriz

last: Gonzalez-Badillo

first: Anahita

last: Lashgari

first: François

last: Chartier

first: Pavel

last: Savitsky

first: Monika

last: Tucholska

first: Sarah

last: Picaud

first: James

middle: D

last: Knight

first: Stéphane

last: Angers

first: Nicolas

last: Bisson

first: Colin

last: Goding

first: Étienne

last: Audet-Walsh

first: Panagis

last: Filippakopoulos

first: Anne-Claude

last: Gingras


title: Gene Expression is Co-regulated by Non-nucleolar RNA Polymerase I [Cut & Tag]

city: Evanston

first: vadim

last: backman

state: IL

address: 2170 Campus Drive, Silverman Hall 3627

department: Bioengineering

institute: Northwestern University

summary: Due to its role in mRNA synthesis, many studies of the relationship between transcription and chromatin organization have focused on the regulation of RNA polymerase II (Pol-II) function by supranucleosomal structure and vice-versa. In contrast, there is little work on the function of RNA polymerase I (Pol-I) in non-nucleolar chromatin. Prior work has shown that Pol-I engages with components of Pol-II on rDNA, but it’s role in global transcription and chromatin structure beyond the nucleolus has largely been ignored. By pairing auxin-inducible degron technology with nanoscopic imaging, RNA-Seq, and Hi-C, we found that Pol-I and Pol-II co-regulate conformationally defined chromatin domains and mRNA synthesis. Mechanistically, Pol-I maintains the positioning of intronic and intergenic chromatin within domains for the proper expression of exon elements. Consequently, Pol-I loss disrupts genome connectivity, in situ chromatin domains, and the expression of mRNA, genome-wide.

overall_design: Cut&Tag for histone post translational modifications H3K9me3 and H3K4me3, alonside POLR1A and POLR2A to investigate the spatial relationship between Pol-I and Pol-II and their surrounding chromatin context. Targets were assayed in 3 biological replicates (done seperate days, using a freshly thawed aliquot of HCT116 cells each time).

first: Carter

last: Lucas

first: Backman

last: Vadim

first: Almassalha

last: Luay


title: Oxaliplatin induces cancer-like cachexia through distinct transcriptional pathways in mouse muscle and adipose depots

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

summary: Cancer cachexia is a multifactorial, largely irreversible metabolic disorder characterized by skeletal muscle and adipose tissue depletion that is responsible for 20% of cancer-related deaths. Oxaliplatin, a platinum-based chemotherapeutic, is a common, first-line treatment for metastatic colorectal and other malignancies that result in cancer cachexia. Yet, it is unknown whether oxaliplatin contributes to these effects independently of cancer. To reveal its role in cachexia development, we administered a chronic human-equivalent oxaliplatin dose to non-tumor-bearing C57BL/6 mice. Daily activity, muscle wasting, fat depletion, and metabolic parameters were monitored through metabolic cages and echo-MRI measurements followed by postmortem muscle and fat tissue histology and bulk RNA seq. Our results show that a high accumulative oxaliplatin dose of 80 mg/kg leads to cachexia-like symptoms, characterized by severe loss of body mass, decreased food intake, diminished ambulatory activity accompanied by lowered core body temperature, decreased skeletal muscle mass, and loss of adipose tissue. RNA-seq data from muscle and adipose tissues indicate a complex mechanism that is in part driven by inflammation and adipokine activity. Comparison of oxaliplatin treatment with external human and murine datasets in cancer and fasting settings illustrates that while oxaliplatin shares many differentially expressed genes with these conditions, it also induces unique gene differentiation. These results suggested oxaliplatin alone induces a cachexia phenotype and thus may aggravate cancer-induced cachexia, highlighting the importance of early diagnostic and therapeutic interventions that target cachexia from both cancer and chemotherapy.

overall_design: After 8 weeks of oxaliplatin treatment, mice tibialis anterior muscle, subcutaneous white adipose tissues (WAT) and hypothalamus were collected and total RNA was extracted. There were 23 RNA samples in total: 9 muscle samlpes (4 from control and 5 from oxaliplatin group), 7 fat samples (3 from control and 4 from oxaliplatin group) and 7 hypothalamus samples (3 from control and 4 from oxaliplatin group). All samples that passed the integrity threshold (larger than 8) were used for RNA sequencing. Differentially expressed genes between control and oxaliplatin-treated mice were identified with Partek software to study the effects of oxaliplatin on gene expression profile in mice skeletal muscle, WAT and hypothalamus.

first: Junwei

last: Du

first: Rachel

last: Mintz

first: Leland

middle: C

last: Sudlow

first: John

last: Morley

first: Rachael

last: Field

first: Jonathan

last: Brestoff

first: Gwendalyn

last: Randolph

middle: Y


title: Time-of-day defines the risk of thermally abused frying oil to renal injury by modulating the diurnal dynamics of oxylipins

city: Qingdao

first: Yanjun

last: Liu

state: Shandong

address: Yushan road 5

institute: JIANGNAN

summary: Modulation of circadian rhythms results in impaired homeostasis and susceptibility to disease development. Thus, new perspectives on nutrition emphasize the circadian timing of food intake. Here, we find that fried oil disrupted the conversionof epoxides to diols in kidney, and led to aggravated renal injury. Interestingly, the circadian rhythm of epoxides and its diols in the kidney and plasma showed a significant light-dark manner. We demonstrated that time-imposed feeding of fried oil during the active period showed limited damage to renal function, conversely, renal function was impaired during the inactive period. Remarkably, time-imposed epoxy stearic acid (EpSA) from fried oil during the inactive period disrupted the rhythmicity of epoxide hydrolases and related metabolites, and fueled the progression of renal fibrosis and injury. The effect of EpSA on SMA and E-cadherin, renalfibrosis biomarkers, are lost in knockouts of Ephx1 and Ephx2, which encodes for epoxide hydrolase. Besides, the inhibition of epoxide hydrolases by dietary supplementation of linoleic acid rescues mice from the damages from time-imposed feeding of EpSA. Our findings unveil that the time-of-day dependence of epoxide hydrolases and circadian disruption at the inactive phase by EpSA from fried oil has adverse impacts on kidney function.

overall_design: The cohort of six-week-old mice fed a standard chow diet, a high-fat diet, or a high-fat diet containing 3% EpSA for 14 weeks. Kidney samples were collected at ZT time 1, 5, 9, 13, 17, 21, 25.


title: Programmed DNA double strand breaks fuel chromatin remodeling and potentiate stimulus-dependent gene induction

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd

department: Psychiatry

institute: UT Southwestern Medical Center

summary: Neuronal activity critically depends on rapid transcriptional induction of early response genes (ERGs), yet how ERG promoters achieve fast, robust activation remains unclear. Here, we show that programmed DNA double-strand breaks (DSBs), catalyzed by topoisomerase 2β or introduced via CRISPR/Cas9, serve as a potent and surprisingly resilient mechanism to remodel three-dimensional (3D) genome architecture and drive ERG transcription. Using 4C-seq in both primary neurons and HEK293T cells, we find that a single DSB at an ERG promoter triggers an initial “exploratory” phase in which the promoter broadly expands its cis interactome—encompassing local enhancers as well as other chromatin states—to promote transcriptional activation. Contrary to the classical view of tightly pre-formed enhancer–promoter loops, these breaks enable flexible, compartment-confined sampling of the surrounding regulatory landscape. Strikingly, repeated rounds of DSB formation do not diminish but instead potentiate transcriptional output. Over time, the promoter’s cis interactions become more refined and “pruned,” coinciding with increased trans contacts, and these architectural changes persist long after the breaks have been repaired. Notably, even when DSB repair fidelity is low, ERG induction remains robust, underscoring a remarkable resilience in promoter function. Together, our findings reveal a novel model of transcriptional regulation in which transient DSBs act as powerful catalysts for dynamic and progressively fine-tuned 3D genome reorganization. This work broadens our understanding of how cells leverage controlled DNA breaks to support rapid transcriptional responses, while also facilitating adapted future responses.

overall_design: 4C-seq was conducted using NlaIII and DpnII at Fos and Npas4 promoters following various paradigms of double strand break formation, with three replicates each. In primary cortical mouse neurons 4C-seq was conducted in two experiments with baits at Fos and Npas4 promoters. Exp 1 conditions: Control, ETP, NMDA, ETP rec., ETP NMDA, Exp 2 conditions: Control, ETP x 4 rec., ETP x 5, ETP x 4 NMDA. 4C-seq was also conducted in Hek293T cells in various conditions. Cells were collected 72 hours post transfection with a CRISPR-cas9 construct resulting in Control Gen 1 and CRISPR Gen 1 samples. Hek293T cells were then passaged until cas9 was no longer expressed resulting in Control Gen 5 and CRISPR Gen 5 samples. Control or cas9 recovered Hek293T cells were then starved for 16.5 hours in 0.5% FBS media and then serum stimulated with 18% FBS for 30 min. This resulted in the samples: Control_Starved Control_StarveStim CRISPR_Starved CRISPR_StarveStim. Fos_mm10_primer: GTCTACCCCTGGACCCCTTG Npas4_mm10_primer: CAGGTTTTCCATTACATTCTA Fos_hg38_primer: AGCCTCTCTTACTACCACTC

first: Lance

last: Heady

first: Richard

last: Rueda

first: Amir

last: Segev

first: Krystal

last: Morton


title: Regulation of the transcription cycle contributes to BET bromodomain inhibitor resistance [CUT&RUN]

first: Jean-Philippe

last: Lambert

overall_design:
To investigate the molecular mechanisms by which the loss of MAPKAPK2 enhance resistance to BET bromodomain inhibitors, we established A375 cells knockout for MAPKAPK2 using CRISPR/Cas9.
Using these cells, we performed CUT&RUN analysis following treatment with 500 nM JQ1 or DMSO control over 48 hours with antibodies targeting BRD2, BRD4, H3K27ac and IgG control.

first: Pata-Eting

last: Kougnassoukou Tchara

first: Jérémy

last: Loehr

first: Lucas

last: Germain

first: Zachary

last: Steinhart

first: Beatriz

last: Gonzalez-Badillo

first: Anahita

last: Lashgari

first: François

last: Chartier

first: Pavel

last: Savitsky

first: Monika

last: Tucholska

first: Sarah

last: Picaud

first: James

last: Knight

first: Stéphane

last: Angers

first: Nicolas

last: Bisson

first: Colin

last: Goding

first: Étienne

last: Audet-Walsh

first: Panagis

last: Filippakopoulos

first: Anne-Claude

last: Gingras


title: Single cell transcriptomes of pancreatic pre-invasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity [MERFISH]

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: Hebrew University

summary: In this project, we utilized single-cell RNA sequencing (scRNA-seq) and MERFISH spatial transcriptomics to profile the development of pancreatic cancer in a mouse model, tracing its progression from the pre-invasive stage to full malignancy. By employing a reporter gene, we were able to dissect the heterogeneity of metaplastic acinar cells, identifying and profiling six distinct types and states of these cells. We validated their localization within pre-invasive lesions, assessed the heterogeneity across various lesions, and calculated the colocalization of different acinar metaplastic cells with stromal cells.

overall_design: Tamoxifen was injected into six-eight weeks old Ptf1a-CreER, LSL-Kras-G12D, LSL-tdTomato (PRT) mice, and the pancreas was collected for single cell purification from mice seven months post-tamoxifen injection (PTI)

first: Juan

middle: S

last: Arcila-Barrera


title: Achilles tendon exhibits distinct transcriptomic changes with increased mitochondrial energy production under lunar gravity

city: Tokyo

first: Taro

last: Kasai

address: Bunkyoku Hongo7-3-1

institute: The University of Tokyo

summary: Gravity plays a fundamental role in maintaining the structure and function of biological tissues, particularly within the musculoskeletal system. In space, the absence or reduction of gravitational forces leads to musculoskeletal deterioration, posing significant challenges for astronauts and individuals experiencing prolonged immobilization. Consequently, the effects of microgravity on muscle and bone have been extensively studied. Recent research highlights the crucial role of tendons in force transmission and mechanical stability; however, their transcriptomic response to reduced gravity remains largely unexplored. Here, we examined the adaptations of the Achilles tendons to lunar gravity (1/6 of Earth gravity) using RNA sequencing of tissue samples obtained from mice reared in the International Space Station for 25-26 days. Compared to quadriceps femoris muscles and brown adipose tissue, a greater number of genes were upregulated in the Achilles tendons under reduced gravity. Enrichment analyses revealed a significant upregulation of mitochondrial energy production in the Achilles tendons exposed to reduced gravity. Meanwhile, genes associated with extracellular matrix organization and collagen integrity were downregulated. Although histological examination showed no obvious structural differences between the lunar and Earth gravity groups, the expression of Atp5b, a subunit of ATP synthase, was enhanced in the lunar gravity group. Our findings suggest that mechanical loading regulates tendons by influencing mitochondrial energy production and extracellular matrix composition. These insights may contribute to therapeutic strategies for tendon degeneration associated with aging and disuse-related conditions.

overall_design: RNA-seq profiling of Achilles tendon, muscle, and brown adipose tissue in wild-type mice under Earth and lunar gravity

first: Toshiya

last: Tsubaki

first: Takumi

last: Matsumoto

first: Yasuhide

last: Iwanaga

first: Asuka

last: Terashima

first: Yasunori

last: Omata

first: Sakae

last: Tanaka

first: Taku

last: Saito


title: Identification of the RNA that binds with FAK by high-throughput RIP-seq in MDA-MB-231 cells

first: Man-Li

last: Luo

address: No.107 Yanjiang West Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen Memorial Hospital

summary: FAK is overexpressed and aberrantly activated in various advanced solid tumors and plays a critical role in tumor progression and metastasis. Here, we identified an FAK-interacting lncRNA FAISL, FAISL (FAK Interacting and Stabilizing LncRNA) was frequently overexpressed in TNBC tissues and abundantly enriched in FAK-interacting lncRNAs. FAISL promotes cell adhesion, cytoskeleton spreading, proliferation and anchor-dependent survival of TNBC cells. FAISL doesn’t affect FAK mRNA but positively regulates the FAK protein level by blocking Calpain 2-mediated proteolysis, etc.

overall_design: To identify those lncRNAs that interacts with FAK and functions in TNBC, MDA-MB-231 cells with exogenous Flag-tagged FAK were established and subjected to RNA immunoprecipitation (RIP) using negative control normal mouse IgG and anti-FLAG antibody respectively. RIP-sequencing (RIP-seq) was then performed to identify the lncRNAs that specifically binds to FLAG-tagged FAK but not to normal mouse IgG control.

first: Yunmei

last: Zhang

first: Shiyu

last: Wei

first: Zhengjie

last: Chen


title: Ribosome biogenesis mediates the translational increase of codon non-optimal transcripts during IFN stimulation

city: Abbotsford

first: Brenna

last: Hay

address: 33844 King Rd

institute: University of the Fraser Valley

summary: The interferon response is a signaling pathway unique to vertebrates that links the innate and adaptive immune responses. Interferons signal through a cascade of factors including the JAK-STAT pathway to induce the transcription of hundreds of interferon stimulated genes (ISGs). Although the main interferon signal transduction pathways and ISGs have been elucidated, translational regulation of ISG transcripts has not been fully investigated. Prior work demonstrated that ribosomal protein RPL28 negatively regulates a subset of ISGs; however, we find that this effect may be due to a reduction in overall ribosome availability. Multi-omics analysis of RNA-seq and LC-MS/MS data reveal proteins that are translationally up-regulated during BOP1 knockdown and IFN-β stimulation, including an enrichment of ISGs. Analysis of codon optimality demonstrates a significant reduction in codon optimality for proteins that are translationally up-regulated during BOP1 knockdown and IFN-β stimulation. Extremely codon-optimized and -non-optimized reporter constructs were tested under these conditions and demonstrate that BOP1 knockdown increases translation of the non-optimal reporter during IFN stimulation. We propose that this is a form of translational fine-tuning of the IFN in order to ensure the production of integral proteins during times of cellular stress when translation machinery may be inhibited.

overall_design: A549 cells were transfected with either BOP1 of Firefly luciferase siRNA for 48 hours, then subjected to a mock or  IFN-B stimulation at 1000U/mL for a time course of 8 or 12 hours

first: Rachel

last: Smid

first: Nathan

last: Louie

first: Stephane

last: Flibotte

first: Eric

last: Jan

first: Leonard

last: Foster


title: Functional interaction between the transcription factor Sfp1 and the NuA4 complex in response to nutrient availability[RNA]

city: Quebec city

first: Jacques

last: Cote

address: 9 McMahon Street

department: CHU de Québec-Université Laval Research Center

institute: Laval University

summary: In this study, we investigate gene expression profile upon carbon source shifts in yeast. RNA-sequencing was performed in Sfp1 wild-type strain and K655/657 mutants growing in different carbon sources.

overall_design: RNA-seq of wild-type Sfp1 and K655/657R, K655/657Q mutants growing in 2% glucose, 2% raffinose, and 15min, 30min upon the addition of glucose after raffinose incubation