title: The Deubiquitinase USP28 Maintains the Expression of PPARγ and Its Inactivation Protects Mice from Diet-Induced NASH and Hepatocarcinoma

city: hangzhou

first: hangqi

last: luo

state: zhejiang

address: 浙江省杭州市浙江大学华家池校区

institute: zhejiang university

summary: Nonalcoholic steatohepatitis (NASH), a progressive form of nonalcoholic fatty liver disease, is one of the leading causes of liver disease worldwide and may further progress to cirrhosis and cancer. However, the pathogenesis of NASH remains unclear, and there is currently only one FDA-approved drug for its treatment; therefore, new therapeutic approaches are urgently needed. Under high-fat diet or obese conditions, PPARγ is activated in the liver to promote lipid storage as droplets, inducing the progression of NASH. We showed that the expression level of USP28 is elevated in the livers of NAFLD/NASH patients. Through dietary induction, including a methionine-choline deficient (MCD) diet and a Western diet (WD) combined with intraperitoneal injection of carbon tetrachloride (CCl4), we established two severe mouse models of NASH and revealed the role of the deubiquitinase USP28. Mechanistically, the hepatic deubiquitinase USP28 directly binds to PPARγ and prevents its own ubiquitination and degradation, thereby regulating its downstream signaling pathways. In the absence of Usp28 or if the DUB is inhibited, PPARγ is downregulated, and the PPAR signaling pathway is inhibited, allowing the cells to mount a defensive response to excessive fat. Both genetic and pharmacological inactivation of Usp28 significantly attenuated the NASH phenotype induced by the MCD diet or WD-CCl4 regimen, as well as WD-CCl4-induced hepatocellular carcinoma in mice.

overall_design: We generated and utilized USP28 whole-body knockout mice to establish a mouse model of non-alcoholic steatohepatitis (NASH) induced by methionine-choline deficient (MCD) diet. Liver tissues were collected from mice fed with MCD diet for 4 weeks starting at 8 weeks of age, and mRNA was extracted for RNA-seq sequencing to obtain data.


title: microRNAs expression profile in human apheresis platelets during storage

status: Public on Apr 23 2025

city: Beijing

first: Jun

last: Xiao

address: 30 Fucheng Road

country: China

institute: Air Force Medical Center, Air Force Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the microRNAs (miRNAs) expression profiles in human apheresis platelet under platelet storage lesion (PSL), and predict the potential biomarkers in the process of PSL. miRNAs profiles of platelets were tested by illumina HiSeq2500 between PSL and nonPSL. 13 miRNAs were chosen to validate by real-time PCR, the result was consistent with the sequencing results.

overall_design: Platelet samples were collected from 6 male healthy donors with O blood group. Apheresis platelets were stored at 22±2 ℃ in storage tank. The PSL was defined as: samples below the lower limit of the reference range of aggregation ratio (<43.25%), or above one of the upper limit of the reference range of CD62P positive ratio (>43.29%), TNF-α (>252.49pg/mL) or sCD40L (>1575.34pg/mL) according to our previous study. Two groups in these samples were used for sequencing analysis.

first: Huimin

last: Li

first: Cuiying


title: Bulk RNA sequencing for GL261 cells treated with propionate (4h post-treatment)

city: Daejeon

first: Chae Won

last: Kim

address: 291, Daehak-ro, Yuseong-gu  E7 Rm 5101

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

type: Expression profiling by high throughput sequencing

summary: To identify the effect of propionate on GL261 cells, we treated GL261 cells with sodium chloride or propionate and extracted RNA at 4 hours post-treatment

overall_design: Examination of transcriptional changes on GL261 cells post propionate treatment

first: Heung Kyu

last: Lee


title: Mechanisms and consequences of myeloid adhesome dysfunction in atherogenesis II

city: Cleveland

first: Tatiana

middle: V

last: Byzova

state: OH

address: 9500 Euclid Avenue

department: Neurosciences

country: USA

institute: Lerner Research Institute, CCF

summary: Exposure of macrophages to oxLDL in vitro or to oxidized lipids-rich milieu of atherosclerotic lesions induces dysregulation of multiple cellular processes including adhesome-dependent functions. Kindlin3 (K3) is indispensable for integrin activation and is directly involved in all adhesome-dependent cell functions. In the current study, we demonstrated that disturbance of the Kindlin3-integrin axis in myeloid cells leads to proatherogenic phenotype in hyperlipidemic LDLR-/- mice.  We also found that lipid accumulation in macrophages in vivo in atherosclerotic plaque and in vitro after exposure to oxLDL was associated with strongly reduced K3 protein, likely contributing to deficient adhesome function of macrophages in lesions. RNA-seq analysis of BMDM isolated from K3 mutant with disrupted Itgβ binding site revealed multiple dysregulated adhesion-related genes and pathways overlapping with ones dysregulated in WT cells after oxLDL treatment. In addition, many dysregulated genes overlapped with genes involved in atherogenesis. These included dramatically increased expression of OLR1, a gene encoding Lectin-like oxidized LDL receptor-1 (LOX1). Disturbed Kindlin3-integrin axis in macrophages leads to dramatically increased level of LOX1 receptor in macrophages, providing a mechanism for increased uptake of oxLDL and foam cell formation.  A similar proatherogenic phenotype, increased macrophage LOX1 and foam cell formation, was observed in Itgβ1 deficient mice but not Itgβ2 deficient mice, indicating that lack of Kindlin3/Itgβ1 interaction can be, at least partially, responsible for the observed phenotype.

overall_design: To evaluate the transcriptomic changes of macrophages under oxidative stress conditions, we performed bulk RNA-seq analyses of mouse bone marrow-derived macrophages (BMDM) exposed to oxLDL vs non-treated cells.


title: Chemokine Ligand 2 Expressing Fibroblast Recruitment of Macrophages Enhanced in Loeys-Dietz Syndrome Aortic Root Aneurysm Formation [human]

city: Palo Alto

first: Alex

last: Dalal

state: California

address: CT Surgery, 870 Quarry Rd Ext

department: Cardiothoracic Surgery

institute: Stanford University

summary: Loeys-Dietz Syndrome (LDS), caused by a spectrum of mutations in the TGF-β signaling cascade, leads to aggressive thoracic aneurysms. Given the ubiquitous nature of TGF-β signaling machinery, the exact cell type(s) responsible for initiation of LDS pathogenesis is poorly understood.

overall_design: Aortic root and ascending aortic tissue from 5 LDS (Loeys-Dietz Syndrome) and 2 Donor control patients was subjected to tissue digestion and single-cell RNA sequencing. Aortic root and ascending aorta samples were processed as individual libraries from each patient, yielding 12 samples total.

first: A

middle: R

first: M

middle: P

last: Fischbein


title: RNA-seq comparing mesenchymal stem cells co-cultured with megakaryocytes

city: New York

first: Avital

last: Mendelson

state: NY

address: 310 E67 Street

department: LFKRI

institute: NYBC

summary: The role of the bone marrow microenvironment for regulating megakaryocyte and platelet function remains incompletely understood. We examined the mechanism by which MSCs can lower platelet activation through communication with megakaryocytes.

overall_design: Primary murine wild-type bone marrow CD45-Ter119-CD31-CD51+CD140a+ mscs were cultured together with primary murine wild-type megakaryocytes or as a control, primary murine wild-type megakaryocytes were cultured alone. After 18 hours, megakaryocytes were isolated from cultures, separated from platelets, and analyzed by RNA-seq.

first: Chengjie

last: Gao

first: Yitian

last: Dai

first: Paul

last: Spezza

last: Boasiako

first: Alice

last: Tang

first: Giselle

last: Rasquinha

first: Patricia

last: Shi

first: Cheryl

last: Lobo

first: Xiuli

last: An

first: Karina

last: Yazdanbakhsh


title: Mechanisms and consequences of myeloid adhesome dysfunction in atherogenesis I

overall_design: To evaluate the transcriptomic changes of WT macrophages vs K3-mutant under oxidative stress conditions, we performed bulk RNA-seq analyses of mouse bone marrow-derived macrophages (BMDM) isolated from wild-type and Kindlin3-integrin mutant mice exposed to oxLDL vs non-treated cells.


title: Nicotinamide mononucleotide promotes female germline stem cell proliferation by activating the H4K16ac-Hmgb1-Fyn-PLD signaling pathway through epigenetic remodeling

city: Shanghai

first: Ji

last: Wu

state: Shanghai

address: No. 800, Dongchuan Road

institute: Shanghai Jiao Tong University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Nicotinamide Mononucleotide Promotes Female Germline Stem Cell Proliferation by Activating the H4K16ac-Hmgb1-Fyn-PLD Signaling Pathway through Epigenetic Remodeling

summary: Nicotinamide mononucleotide (NMN), an endogenous nucleotide essential for various physiological processes, has an unclear role and regulatory mechanisms in female germline stem cell (FGSC) development. In this study, we demonstrate that NMN significantly enhances FGSC viability and proliferation. Quantitative acetylation proteomics revealed that NMN markedly increases the acetylation of histone H4 at lysine 16 (H4K16ac). Subsequent chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) identified high mobility group box 1 (Hmgb1) as a downstream target of H4K16ac, a finding further validated by ChIP-qPCR. Knockdown of Hmgb1 reduced FGSC proliferation by disrupting cell cycle progression, inducing apoptosis, and decreasing chromatin accessibility. High-throughput chromosome conformation capture (Hi-C) analysis showed that Hmgb1 knockdown induced A/B compartment switching, increased the number of topologically associating domains (TADs), and decreased chromatin loop formation in FGSCs. Notably, the chromatin loop at the promoter region of Fyn proto-oncogene (Fyn) disappeared following Hmgb1 knockdown. ChIP-qPCR and dual-luciferase reporter assays further confirmed the interaction between Hmgb1 and the Fyn promoter. Importantly, Fyn overexpression reversed the inhibitory effects of Hmgb1 knockdown on FGSC proliferation. Proteomic analysis suggested this rescue was mediated through the phospholipase D (PLD) signaling pathway, as Fyn overexpression selectively enhanced the phosphorylation of PLD1 at threonine 147 without affecting serine 561. Furthermore, treatment with 5-fluoro-2-indolyldechlorohaloamide, a PLD inhibitor, nullified the pro-proliferative effects of Fyn overexpression. In summary, our findings reveal that NMN promotes FGSC proliferation by activating the H4K16ac-Hmgb1-Fyn-PLD signaling pathway through epigenetic remodeling. These results deepen our understanding of FGSC proliferation and highlight potential therapeutic avenues for advancing FGSC applications in reproductive medicine.

overall_design: To investigate the effect of Hmgb1-knockdown on the development of female germline stem cells (FGSCs), we treated FGSCs with Hmgb1-knockdown lentivirus in vitro. Subsequently, we utilized RNA-seq data from both the control group and the Hmgb1-knockdown group to conduct differential gene expression analysis.

first: Hong

last: Zhou

first: Yujie

last: Liu

first: Geng

middle: G

last: Tian


title: Argonaute immunoprecipitation reveals mis-annotation of human microRNAs [miRNA-seq]

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

summary: MicroRNAs (miRNAs) form the sequence recognition component of the RNA-induced silencing complex (RISC), bringing Argonaute (AGO) and other RISC-associated proteins to target transcripts where they mediate post-transcriptional gene silencing. High-throughput sequencing has helped to catalogue several thousand human miRNAs, as well as a plethora of other small RNAs derived from larger transcripts. Here, we take a closer inspection of sequencing data derived from cellular fractionation and AGO-RNA immunoprecipitation and find that a subset of small RNAs, despite being denoted as miRNAs, are in fact almost exclusively nuclear and do not associate with AGO. Experimental validation of a select number of these small RNAs also fails to show endogenous miRNA-like activity, suggesting they are degradation products from larger transcripts that have been mis-annotated. Despite this, the presumed miRNA functions of almost 20 of these have collectively been the subject of several hundred publications, emphasising the need to filter unlikely miRNA candidates from sequencing data and large miRNA-sequence repositories.

overall_design: miRNA profiles from sequencing endogenous small RNA libraries prepared from HMLE cells without (control: 'HMLE') or with TGF-β (treatment: 'MesHMLE').

middle: A

first: Klay

last: Saunders

first: Nick

last: Warnock

first: Kate

middle: B

last: Dredge

first: Andrew

last: Bert

first: Greg

last: Goodall

first: Cameron

last: Bracken


title: Argonaute immunoprecipitation reveals mis-annotation of human microRNAs [HITS-CLIP]

overall_design: miRNA profiles from sequencing the small RNA fraction of HITS-CLIP libraries prepared from HMLE cells without (control: 'HMLE') or with TGF-β (treatment: 'MesHMLE').


overall_design: Chromatin immunoprecipitation DNA-sequencing of histone modification H4K16ac (Millipore cat. 07-329, lot/batch 3836421) in FGSCs between the control group and NMN-treated groups.


title: Evolutionary Process Underlying Receptor Gene Expansion and Cellular Divergence of Olfactory Sensory Neurons in Honeybees. [scATAC-Seq]

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

summary: The olfactory system is intricately intertwined with species adaptation in insects. Genomic studies have unveiled significant duplications and expansions of olfactory receptor genes in social behavior insects. However, the precise mechanisms through which these duplicated genes integrate into olfactory neural circuitries to enhance species-specific adaptative functions remain inadequately understood.

overall_design: Honeybee workers were collected from three healthy colonies provided by the Institute of Zoology, Guangdong Academy of Sciences (Guangzhou, Guangdong, China). All colonies were maintained in standard Langstroth hives containing a single hive box with 16,000–20,000 bees and one naturally mated queen. Workers were gathered at there different division of labors (newly emerged worker, nurse and forager), with three biologically replicates per divisor of labors. Newly emerged workers were obtained from capped brood frames when workers emerged from their cells for 1-2 h. To collect age-matched samples of nurse and forager bees, the adult bees that had emerged from their cells were marked on the thorax with paint and returned to the hive. When marked bees were 9 days old, we collected a subset of workers observed performing nursing behaviour (bees with their heads in cells containing larvae). When they were 21 days old, we collected another set of bees observed performing foraging behaviour (returning to the hive carrying pollen loads). For each adult worker, the antennae were separated with surgical scissors and 60 individuals were pooled together.

first: Weixing

last: Zhang

first: Yiheng

last: Li

first: Jin

last: Xu


title: Evolutionary Process Underlying Receptor Gene Expansion and Cellular Divergence of Olfactory Sensory Neurons in Honeybees. [scRNA-Seq]


title: Hippocampus-specific epigenetic profiling of chromatin accessibility after deeper cerebral hypoperfusion in mice

first: Zengyu

address: Dong'an Road

department: Neurology

institute: Fudan University

summary:
Efforts to understand genetic variability involved in hippocampus damage and glial activation support a role for upstream regulation by epigenetic mechanisms.
To investigate hippocampus-specific epigenetic profiling after severe cerebral hypoperfusion in mice

overall_design: Hippocampus-specific epigenetic profiling analysis was performed using data obtained from ATAC-seq of 4 biological replicates in sham and BCAS mice after hypoperfusion

first: Jing

last: Zhao


title: Extracellular ISG15 drives severe respiratory pathology during viral infection

city: San Diego

first: John

last: Teijaro

state: CA

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

summary: Cytokine storm during respiratory viral infection is an indicator of disease severity and poor prognosis. Type 1 interferon (IFN-I) production and signaling have been reported to be causal in cytokine storm associated pathology in several respiratory viral infections, however, the mechanisms by which IFN-I promotes disease pathogenesis remain poorly understood. We report using Usp18-deficient, USP18 enzymatic inactive and Isg15-deficient mouse models that lack of deISGylation during persistent viral infection leads to severe immune pathology characterized by hematological disruptions, cytokine amplification, lung vascular leakage and death. Transcriptional studies of immune cells from mice bearing the enzymatic inactive version of USP18 (Usp18C61A) revealed a neutrophil influx in the lung of these animals during infection, associated with increased immature neutrophil content. These neutrophil differentiation changes were dependent on ISG15 as deletion of Isg15 from C61A animals reversed the accumulation of immature neutrophils. Importantly, neutrophil depletion reversed morbidity and mortality in Usp18C61A mice. In summary, we reveal Usp18 enzymatic function is crucial for regulating extracellular release of ISG15 which are accompanied by altered neutrophil differentiation, cytokine amplification and mortality following persistent viral infection.

overall_design: Cells from individual mice were used as biological replicates; 2 replicates per group were sequenced. A total of 4 biological groups were included, all mice were infected with LCMV Clone 13. The biological groups were wild type mice treated with CD8 T cell depleting antibody (aCD8), wild type mice treated with isotype control antibody (iso), USP18 enzymatic inactive mice treated with CD8 T cell depleting antibody or isotype control antibody (C61A aCD8 and C61A iso, respectively).

first: Jaroslav

last: Zak

first: Namir

last: Shaabani


title: Annonaceous Acetogenins Potentiate FBXW7-Mediated EZH2 and MYC Degradation Triggering Anti-Tumor Activity in Head and Neck Squamous Cell Carcinoma.

city: guangzhong

first: yurui

last: liu

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou City, Guangdong Province

institute: Southern Medical University

summary: To investigate the function of ACGs on head and neck squamous cell carcinoma,we treated SCC15 cells and SCC25 cells with ACGs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cells that before and after ACGs treatment in SCC15 and SCC25 cell.

first: Yin

last: Zhu

first: Yurui

last: Liu

first: Bingxin

last: Hu

first: Tiane

last: Tang


title: Distinct contributions of EMT states to colorectal cancer ferroptosis

city: Nanjing

first: Yutong

last: Ge

state: Jiangsu

address: Changle Road 68

institute: Nanjing Medical University

summary: To investigate how tumor heterogeneity involved in ferroptosis mediated by the physical microenvironment is a breakthrough in solving the therapeutic resistance of colorectal cancer (CRC). Based on the three-dimensional (3D) fibrin gel model, we identified four stages of epithelial-mesenchymal transition (EMT) in vitro that are synergistically regulated by mechanical cues and E-cadherin (ECAD) expression with varying degrees of resistance to ferroptosis. Mechanistically, we elucidated that 3D cells undergoing hybrid EMT fought ferroptosis via WNT/β-catenin-GPXs/ferritin signaling axis, while cells of a late-hybrid EMT state relied on adhesion tension forced mitohormesis to reach super defense against ferroptosis. This work deconstructed the distinct contributions of tumor heterogeneity to ferroptosis from an EMT perspective and uncovered the biomechanical weakness of therapeutic resistance. These findings, in conjunction with tumoroids, were expected to serve for future ferroptosis-based personalized diagnosis and treatment of CRC.

overall_design: 3D, cells cultured in 90-Pa 3D fibrin gels; 2D, cells cultured on rigid plastic dishes.

first: Xiaowei

last: Wei

first: Yaolin

last: Zheng

first: Juan

first: Shijia

last: Huang

first: Nuofan

last: Wang

first: Yuhan

last: Chang

first: Wentao

last: Ha

first: Sunyan

first: Xuanchang

first: Jingwen

last: Chen

first: Xiumei

first: Yawen

first: Yuejin

first: Qiong

last: Jia


title: Effect of Mas KO and a novel MAS agonist on pulmonary gene expression

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary: Although both the Mas knockout and the Mas agonist affect roughly the expected types of genes (cytoskeletal, inflammatory, some metabolic), these data imply that (a) the agonist is under some circumstances an antagonist or partial agonist, and that (b) there is a redundant receptor which regulates nearly the same genes, present even with the Mas knockout.

overall_design: Pulmonary mRNA profiles of 200 day old male wild type (WT) and Mas-/- mice treated for 21 days with a MAS agonist or inactive vehicle control.

middle: D

first: Anandharajan

last: Rathinasabapathy


title: Regulatory T cells enforce self-nonself discrimination by constraining conventional T cells of matched self-specificity during infection

city: Chicago

first: Peter

last: Savage

state: IL

department: Pathology

institute: University of Chicago

summary: During infections, Foxp3+ regulatory T (Treg) cells must control autoreactive conventional T (Tconv) cell responses against self-peptide antigens while permitting those against pathogen-derived “nonself” peptides. We sought to define the basis of this selectivity using mice in which Tregs reactive to a single prostate-specific self-peptide/MHC (self-pMHC) antigen, termed "C4", were selectively depleted ("C4ΔTEC" mice). We demonstrated that Tregs reactive to the C4 peptide were dispensable for the control of Tconv cells of matched antigen specificity at homeostasis but were required to control such Tconv cells and prevent fulminant prostatic autoimmunity following infection with the pathogen L monocytogenes engineered to express the C4 peptide ("Lm[C4]"). We performed the experiment outlined here to understand how the absence of C4-specific Treg cells in C4ΔTEC mice changes the phenotypic state of the C4-specific Tconv cells following Lm[C4] infection to drive autoimmunity. We found that C4-specific Tconv cells adopted preferential and differential cell states in both C4ΔTEC mice and wild-type mice that have C4-specific Treg cells. Specifically, gene expesion data revealed that C4-specific Tconv cells in wild-type mice preferentially adopted a non-proliferating effector state, while C4-specific Tconv in C4ΔTEC mice appeared as proliferating effector cells and proliferating central-memory cells.

overall_design: Wild-type and C4ΔTEC male mice were infected intraveneously with 10^7 CFU of attenuated (ΔActA) Lm[C4]. 4 days post-infection spleens were harvested, CD4+ T cells were enriched using MACS CD4+ negative selection, cells were stained with C4/I-Ab APC- and PE-tetramers, fluorophores were cross-linked with anti-fluor MACS microbeads and tetramer-binding cells were positively selected over an AutoMACS column. Eniched samples from individual mice were stained with surface antibodies and Biolegend hashtag antibodies, then pooled into a sample containing enriched cells from 9 or 10 mice, and FACS purified. This entire process was completed twice, first with 4 wild-type and 5 C4ΔTEC mice, then with 5 wild-type and 5 C4ΔTEC mice, staggering the harvest by ~4 hours. After sorting, there were 2 samples total (Samples A and B), where each sample contained hashtagged C4-tetramer+ cells from 9 or 10 mice, respectively. These samples were loaded into one of two lanes of a sequencing chip and then subjected to Drop-seq (10X Genomics) to coencapsulate individual cells in reverse emulsion droplets in oil together with one uniquely barcoded mRNA-capture bead. Libraries were derived from single cells, then subjected to next-generation sequencing.

first: David

middle: E

last: Klawon

first: Nicole

last: Pagane

first: Christine

middle: H

last: Miller

first: Matthew

middle: T

last: Walker

middle: K

last: Ganci

first: Donald

middle: M

last: Rodriguez

first: Bridgett

last: Ryan-Payseur

first: Ryan

last: Duncombe

first: Erin

middle: J

last: Adams

first: Mark

last: Maienschein-Cline

first: Nancy

last: Freitag

first: Ronald

middle: N

last: Germain

first: Harikesh

middle: S

last: Wong


title: Evolutionary Process Underlying Receptor Gene Expansion and Cellular Divergence of Olfactory Sensory Neurons in Honeybees

first: Yage

last: Nie


title: single cell-RNA sequencing for glioma cells and immune cells from mouse brain tumor following propionate supplementation

first: Chae Won

last: Kim

summary: To identify the effect of propionate on brain tumor microenvironment, we isolated immune cells and brain tumor cells of brain from mice supplemented with sodium chloride as control or sodium propionate in drinking water

overall_design: Examination of transcriptional changes on brain tumor and immune cells post propionate supplementation and GL261 intracranial injection

first: Heung Kyu

last: Lee


title: DIS3L, cytoplasmic exosome catalytic subunit, is essential for development but not cell viability in mice.

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

summary: Among numerous enzymes involved in RNA decay, processive exoribonucleases are the most prominent group responsible for the degradation of the entire RNA molecules. The role of mammalian cytoplasmic 3’-5’ exonuclease DIS3L at the organismal level remained unknown. Herein we established knock-in and knock-out mouse models to study DIS3l functions in mice. DIS3L is indeed a subunit of the cytoplasmic exosome complex, which disruption leads to severe embryo degeneration and death in mice soon after implantation. These changes could not be prevented by supplementing extraembryonic tissue with functional DIS3L through the construction of chimeric embryos. Preimplantation DIS3L KO embryos were unaffected in their morphology and ability to produce functional embryonic stem cells (ES) cells showing that DIS3L is not essential for cell viability. There were also no major changes in the transcriptome level for both ES cells and blastocysts, as revealed by RNA sequencing experiments. Notably, however, DIS3l KO led to inhibition of the global protein synthesis. These results point to the essential role of DIS3l in mRNA quality control pathways crucial for proper protein synthesis during embryo development.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Dis3L WT and KO murine Blastocysts and ES cells.

first: Michał

last: Brouze

first: Anna

last: Hojka-Osińska

first: Andrzej

last: Dziembowski


title: Loss of the 7SK snRNP leads to decreased promoter-proximal pausing

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road, 260 EMRB

department: Biochemistry

institute: University of Iowa

summary: In this study, we assessed the effects of cells without the 7SK RNA or LARP7 on transcription using 14 PRO-Seq datasets and 15 RNA-Seq datasets.

overall_design: The datasets include biological duplicates or triplicates with their accompanying parental cell line.

first: Geoffrey

last: Collins

first: Juan

middle: F

last: Santana


title: Leucegene: AML sequencing (part 7)

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: RNA sequencing of human leukemia

overall_design: The goals of this project are to obtain a comprehensive study of mutations and gene expression in human acute myeloid leukemia (AML). Methods: AML cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an illumina NovaSeq 6000 sequencer.

first: Sébastien

last: Lemieux

first: Josée

last: Hébert


title: bulk RNA sequencing for GL261 cells treated with propionate

summary: To identify the effect of propionate on GL261 cells, we treated GL261 cells with sodium chloride or propionate and extracted RNA at 24 hours post-treatment

overall_design: Examination of transcriptional changes on GL261 cells post propionate treatment


title: Transcriptomics study on AC16 cells treated with 10 nM doxorubicin for 0 min, 10 min, 30 min, 360 min.

first: Yuan

last: Li

address: 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing

department: Post-translational modification

institute: Beijing Proteome Research Center

summary: In this work we studied cellular response to doxorubicin by measuring transcriptomics experiments. The AC16 cells were treated with 10 nM doxorubicin for 10 min, 30 min, 360 min. 1 control group was set (0 min treatment).

first: Ping

last: Xu

first: Tao

last: Zuo


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity [Mouse_CD45_scRNA]

status: Public on Apr 22 2025

city: New York City

first: Andrew

middle: Wayne

last: Daman

address: 1300 York Avenue

institute: Weill Cornell Medical College

summary: Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is the vaccine against tuberculosis and an immunotherapy for bladder cancer. When administered intravenously, BCG reprograms bone marrow hematopoietic stem and progenitor cells (HSPCs), leading to heterologous protection against infections. Whether HSPC reprogramming contributes to the anti-tumor effects of BCG administered into the bladder is unknown. We demonstrate that BCG administered in the bladder colonizes the bone marrow and, in both mice and humans, reprograms HSPCs to alter and amplify myelopoiesis. BCG-reprogrammed HSPCs are sufficient to confer augmented anti-tumor immunity through production of neutrophils, monocytes, and dendritic cells that broadly remodel the tumor microenvironment, drive T cell-dependent anti-tumor responses, and synergize with checkpoint blockade. We conclude that bladder BCG acts systemically through hematopoiesis, highlighting the broad potential of HSPC reprogramming to enhance the innate drivers of T cell-dependent tumor immunity.

overall_design: ATAC-seq on sorted mouse Lin- cKIT+ Sca1+ (LSKs) from either PBS or intra-bladder BCG administered animals after 5 doses of BCG.

middle: W

first: Anthony

middle: C

last: Antonelli

first: Gil

last: Redelman-Sidi

first: Michael

last: Glickman

first: Steven

middle: Z

last: Josefowicz


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity [Human_Multiome_Cohort2

overall_design: Single Cell Multiomics (paired scRNA and scATACseq) on human PBMC enriched for circulating CD34+ cells. Longitudinal human samples, pre or post the 6th consecutive bladder BCG administration as treatment for bladder cancer.


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity [Human_Mulitome_Cohort1]


title: Argonaute immunoprecipitation reveals mis-annotation of human microRNAs

first: Katherine

middle: Anne

last: Pillman

overall_design: Refer to individual Series


title: MUC1-C IS ESSENTIAL FOR INFLAMMATORY MEMORY OF TYROSINE KINASE INHIBITOR RESISTANCE IN NSCLC CELLS

city: Boston

first: Atrayee

last: Bhattacharya

state: Massachusetts

address: 450 Brookline Avenue

department: Medical Oncology

institute: DFCI

summary: This study identifies the oncogenic protein MUC1-C as a key driver of resistance to the EGFR tyrosine kinase inhibitor osimertinib in non-small cell lung cancers (NSCLCs).MUC1-C promotes resistance by activating STAT1 and type I/II interferon pathways, creating an inflammatory memory of the resistant phenotype. This memory is maintained via MUC1-C/STAT1 interaction at one enhancer region (pELS-1) and MUC1-C/JUN/PBAF at another (pELS-2) in the MUC1 gene. MUC1-C also mediates resistance to combination EGFR/MET inhibitors and a fourth-generation EGFR TKI (TQB3804). Importantly, targeting MUC1-C with an antibody-drug conjugate (M1C ADC) is effective both in vitro and in a patient-derived xenograft model, making MUC1-C a promising therapeutic target for TKI-refractory NSCLC.

overall_design: ATAC-seq for WT  H1975 and revertant H1975 (H1975-RT) cells ( cells were treated with Osimertinib for 12 weeks to acquire resistance and then left untreated to make them sensitive to Osi)  and ATAC seq for H1975-RT with Control guide RNA(csgRNA) and MUC1-C guide RNA (MUC1-CsgRNA).

first: Naoki

last: Haratake

first: Shinkichi

last: Takamori


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity [Mouse_LSK_ATAC]


title: Design and Biological Activity of a Novel Urea Compound Against Glioblastoma [HK-217_scRNAseq_MXC-017_in_vitro]

city: Los Angeles

first: Frank

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

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

overall_design: HK-217 gliomaspheres were plated onto the Poly-D-Lysine/Laminin coated 6-well plate (#354595, Corning) and treated with MXC-017 at a concentration of 10 µM, one hour before receiving a single dose of 4 Gy the next day. Five days post-irradiation, the cells were collected for sequencing.

first: Ling

last: He


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity [Mouse_Multiome]

overall_design: Single Cell Multiomics (paired scRNA and scATAC seq) on sorted Lineage negative (Gr1-, CD19-, CD3-, NK1.1-, CD11b-) cells from mouse bone marrow treated with PBS or BCG with 3 weekly doses.


title: Epigenetic library screen reveals novel targets for uveal melanoma

city: Miami

first: Stefan

last: Kurtenbach

state: FL

address: 1501 NW 10th Ave

department: Ophthalmology

institute: University of Miami

summary: Uveal melanoma (UM) is the most common primary ocular cancer in adults, which metastasizes mainly to the liver in around half of the cases. The limited potency of current treatment options for metastatic UM necessitates an urgent exploration of novel therapeutic approaches to improve patient prognosis. We conducted a large epigenetic compound library screen with the currently most well characterized, focused epigenetics library available, which consists of 932 potent, cell permeable, medically active, epigenetic-directed small molecule modulators. Our screening identified two new lead compounds, which so-far have been unappreciated for UM. Romidepsin, an HDAC inhibitor with specificity for class I HDACs, was the most efficient compound in-vitro, as well as the BET inhibitor Mivebresib, which showed minimal toxicity on normal cells. RNA sequencing and pathway analysis revealed an upregulation of PRC-associated gene targets induced by HDAC inhibition, while BET inhibition appears to act through retinoic acid related pathways. Mivebresib treatment in a metastatic uveal melanoma mouse model resulted in longer survival times and reduced metastasis to the spinal cord and brain. The results of our drug screen indicate a vulnerability for HDAC and BET inhibition for UM cells. The BET inhibitor Mivebresib may be a promising candidate for future synergistic and clinical trials.

overall_design: To investigate the effects on transcription of treatment with epigenetic compounds of interest on uveal melanoma cells, we subjected human uveal melanoma cell line MP41 to 24 hours of high dose treatment with each drug. Bulk RNA sequencing followed by analysis through BioJupies was performed to determine differential gene expression in treated cells.

first: Yenisehirli

last: Gulum

first: Kurtenbach

last: Stefan


title: A Novel Combination Therapy with Uridine and Praziquantel effectively Alleviates Schistosomiasis-induced Hepatic Fibrosis through Promoting Adipogenic Differentiation

city: Wuxi

first: Yuzheng

last: Huang

address: 117 Meiyuan Yangxiang

institute: Jiangsu Institute of Parasitic Diseases

summary: Schistosomiasis-induced hepatic fibrosis, a consequence of egg-induced granulomatous lesions, remains untreated by current drugs. Therefore, the development of novel antifibrosis drugs is of paramount importance. Our previous study indicated that aberrant uridine concentrations play a pivotal role in schistosomiasis-induced hepatic fibrosis. This study aimed to explore the inhibitory role of uridine in schistosomiasis-induced liver fibrosis and the regulatory mechanism of uridine on hepatic stellate cell (HSC) activation. The results indicated that uridine could inhibit schistosomiasis-induced liver fibrosis in vivo and TGF-β-induced HSC activation in vitro. Molecular docking revealed a strong interaction between uridine and the adenosine receptor A1 (ADORA1) receptor. Subsequent in vitro investigations demonstrated that uridine modulated the cAMP/PKA/CREB pathway, influencing HSC adipogenic differentiation and exerting an antifibrotic effect. In addition, compared with praziquantel (PZQ) alone, combined uridine and PZQ therapy resulted in a reduced fibrotic area and improved hepatic parameters in vivo. Our study reveals the antifibrosis mechanism of the uridine molecule, which may be a promising drug for the treatment of schistosomiasis-induced liver fibrosis.

overall_design: RNA-Seq profiling of LX-2 cells, TGF-β induced LX-2 cells, and Uridine/TGF-β treated LX-2 cells.

first: Xiangyu

last: Zhou

first: Qingkai

last: Xue

first: Chengwei

last: Wu

first: Xiaojing

last: Li

first: Yuyan

last: Wang

first: Yang

last: Dai

first: Chunrong

last: Xiong

first: Ying

last: Zhang

first: Yongliang

first: Xinjian

last: Liu


title: Microbial cancer immunotherapy reprograms hematopoiesis to enhance myeloid-driven anti-tumor immunity

first: Andrew

last: Daman

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Cell fractionation reveals mis-annotation of human microRNAs

first: Katherine

last: Pillman

institute: Adelaide University

summary: MicroRNAs (miRNAs) form the sequence recognition component of the RNA-induced silencing complex (RISC), bringing Argonaute (AGO) and other RISC-associated proteins to target transcripts where they mediate post-transcriptional gene silencing. High-throughput sequencing has helped to catalogue several thousand human miRNAs, as well as a plethora of other small RNAs derived from larger transcripts. Here, we take a closer inspection of sequencing data derived from cellular fractionation and AGO-RNA immunoprecipitation and find that a subset of small RNAs, despite being denoted as miRNAs, are in fact almost exclusively nuclear and do not associate with AGO. Experimental validation of a select number of these small RNAs also fails to show endogenous miRNA-like activity, suggesting they are degradation products from larger transcripts that have been mis-annotated. Despite this, the presumed miRNA functions of almost 20 of these have collectively been the subject of several hundred publications, emphasising the need to filter unlikely miRNA candidates from sequencing data and large miRNA-sequence repositories.

overall_design: miRNA profiles of nuclear and cytoplasmic fractions of HMLE cells without TGF-β treatment (control) or with TGF-β (treatment) of 2.5 ng/ml for 2 days or 18 days.

middle: A

first: Nick

last: Warnock

first: Ayla

last: Orang

first: Greg

last: Goodall

first: Cameron

middle: P

last: Bracken


title: RNA-seq analysis of subcutaneous white adipose tissue from wild-type mice subjected to six months of calorie restriction reveals altered NCOA2 splicing.

city: Katsushika-ku

first: Yuhei

last: Mizunoe

state: Tokyo

address: 6-3-1 Niijuku

department: Department of Medicinal and Life Sciences

country: Japan

institute: Tokyo University of Science

summary: Caloric restriction (CR) is a well-established intervention that extends lifespan and delays the onset of age-related diseases in various species. While previous studies have demonstrated CR-induced transcriptional changes in white adipose tissue (WAT), the impact of CR on alternative splicing remains underexplored. In this study, we performed RNA sequencing (RNA-seq) to investigate gene expression and alternative splicing in subcutaneous white adipose tissue (sWAT) of wild-type mice subjected to CR for six months, from 3 to 9 months of age. RNA-seq analysis identified 6,058 differentially expressed genes (DEGs) (p < 0.05; absolute log2-fold change >1.0) between ad libitum (AL) and CR conditions, with key upregulated genes related to lipid metabolism, including Elovl6, Fasn, Acc, and Srebp1c. Additionally, we detected 400 significant alternative splicing events (FDR < 0.05), with exon skipping being the most prevalent. Among these, we focused on the metabolism-related transcription factor Ncoa2, which exhibited CR-induced exon 13 inclusion, shifting the balance toward the full-length isoform. Functional analyses suggest that this shift enhances Ncoa2 coactivator activity for nuclear receptors involved in lipid metabolism. This dataset provides raw and processed RNA-seq data, including gene expression and alternative splicing analyses, which can be utilized to further explore the molecular mechanisms underlying CR-induced metabolic adaptations in adipose tissue.

overall_design:
RNA-seq analysis of subcutaneous white adipose tissue (sWAT) from wild-type C57BL/6J mice subjected to calorie restriction (CR) for six months (3 to 9 months of age). This study aims to investigate the effects of CR on gene expression and alternative splicing, with a focus on lipid metabolism and transcriptional regulators such as Ncoa2.
Four biological replicates were analyzed for each condition (ad libitum [AL] and calorie restriction [CR]). Samples were collected at 9 months of age.
PolyA-enriched RNA libraries were prepared and sequenced using paired-end reads on the Illumina NextSeq 500 platform, generating approximately 400 million reads per sample.

first: Mitsuki

last: Kumagai

first: Hiroto

last: Fukai

first: Kazuki

last: Hachiya

first: Yuina

last: Ohtani

first: Yuka

last: Nozaki

first: Kyo

last: Tezuka

first: Masaki

last: Kobayashi

first: Yoshikazu

last: Higami


title: Hypoxia LUAD H1975 cell-derived exosomal miR-671-3p promotes angiogenesis via regulating KLF2-VEGFR2 axis

city: Changchun

first: Kun

address: 1266 Fujin Road, Chaoyang District, Changchun City, Jilin Province, China

institute: Department of Regenerative Medicine, School of Pharmaceutical Sciences, Jilin University

summary: For solid tumors, hypoxia is associated with disease aggressiveness and poor outcomes. In addition to undergoing broad intracellular molecular and metabolic adaptations, hypoxic tumor cells extensively communicate with their microenvironments to facilitate conditions favorable for their survival, growth, and metastasis. This communication is mediated by diverse secretory factors, including exosomes (extracellular vesicles of endosomal origin). Exosomal cargo is altered considerably by hypoxia, with significant impacts on tumor-cell communication with both local and distant microenvironments. Exosomes released by cancer cells influence the tumor environment to accelerate metastasis. While tumor-derived exosomes have been identified as a major driver of premetastatic niche formation at distant sites, this mechanism in lung adenocarcinoma (LUAD) remains unclear. We found that miR-671-3p in exosomes derived from H1975 under hypoxic conditions target Krüppel-like factor 2 (KLF2) to regulate VEGFR2 expression in endothelial cells to promote angiogenesis. In addition, miR-671-3p is expressed at high levels in circulating exosomes isolated from patients with LUAD. Our study suggests that exosome miR-671-3p is involved in the formation of premetastatic niche and may serve as a blood-based biomarker for LUAD metastasis.

overall_design: RNA-seq and miRNA-seq of H1975 cells cultured for 24 hours in a normoxic or hypoxic environment

first: Yi

last: Wang

first: Qisen

last: Li

first: Yujue

first: Jinrui

first: Jintao

last: Zhou

first: Feiyu

last: Song

first: Zhongyi

last: Cong

first: Zhe

first: Ning

last: Kong


title: A whole genomic CRISPR-Cas9 screen identifies the amino acid transporter SLC43A1 (LAT3) as a major determinant of oxaliplatin sensitivity in colorectal cancer cells

city: Bethesda

first: Robert

last: Robey

state: MD

address: 37 Convent Drive Rm 2112

institute: NCI

summary: Colorectal cancer (CRC) is the second leading cause of cancer deaths in the United States, with a five-year survival rate of 65%. Oxaliplatin was the first platinum drug shown to improve CRC patient outcomes and is now a common adjuvant therapy for advanced disease, yet 90% of patients develop resistance. Oxaliplatin was developed as a third-generation derivative of cisplatin, but recent evidence points to divergent modes of action. Here, genome-wide CRISPR activation and knockout screens were conducted to identify genetic changes that confer resistance to oxaliplatin in two CRC cell lines with distinct molecular backgrounds (SW620 and RKO). Guide RNAs corresponding to the neutral amino acid transporter SLC43A1 (LAT3) were the most significantly enriched in knockout screens and depleted in activation screens, suggesting a potential role for LAT3 in modulating oxaliplatin resistance. In vitro CRISPR knockout and overexpression of LAT3 in SW620 and RKO cell lines confirm increased resistance or sensitivity to oxaliplatin, respectively. Further analysis demonstrates that increased LAT3 levels corrrelate with increased intracellular levels of oxaliplatin, increased levels of DNA-platinum adducts and DNA damage, demonstrating that enhanced LAT3-mediated uptake of oxaliplatin can exert its expected mechanism of action and induce cytotoxicity. These findings may lead to a better understanding of oxaliplatin’s mode of action in CRC and can provide new insights into the interplay between essential nutrient uptake and drug transport.

overall_design: Profiling of sgRNA counts in colorectal cancer cells (SW620 and RKO) after 20 days of oxaliplatin treatment or untreated controls in whole-genome CRISPR knockout or activation screens.

first: Nisha

middle: R

last: Pawar

first: Heidi

last: Wade

first: Zoe

last: Jackson

last: Poungpeth

first: Allison

middle: V

last: Mitchell

first: Connor

last: Jewell

first: Dalen

last: Chan

first: Pedro

last: Batista

first: Lisa

last: Jenkins

first: Michael

last: Gottesman


title: The effects of wild-type Usp24 or catalytically inactive USP24 on EgfrL858R-driven lung tumor specimens.

city: Tainan

first: Hung-Chia

last: Hsieh

address: 70101 No.1-3, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

summary: Ubiquitin-specific peptidase 24 (USP24), a cysteine protease, functions as deubiquitinating enzyme that recognizes and removes ubiquitin from the target protein. USP24 is overexpressed in various cancers and regulates the stability of proteins involved in cancer metastasis, cancer stemness, and drug resistance. While the expression profile alteration in tumor microenvironment upon USP24 inhibition is unrevealed. Through RNA-seq, we have characterized that USP24 catalytically inactivation upregulates activation of immune response and lymphocyte activation-related genes in lung tumors from EgfrL858RUsp24C1695A mice

overall_design: Comparative gene expression profiling analysis of RNA-seq for lung tumor specimens from TetO-EgfrL858RUsp24WT or TetO-EgfrL858RUsp24C1695A mice after ten weeks of doxycycline-induction


title: Effect of enhanced early life nutrition on the hypothalamic arcuate nucleus transcriptome of bull calf

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

summary: This study evaluated the effect of enhanced dietary intake during the early life period on hypothalamic arcuate nucleus transcriptome in bull calves. Between 2-12 weeks of age bull calves were offered either a high (HI; n=15) or moderate (MOD; n=15) plane of nutrition, with diets designed to evoke growth rates of 1.0 and 0.5 kg/day, respectively. At 12 wk of age,  arcuate nucleus tissue samples were harvested from all calves and subsequently subjected to mRNAseq.

overall_design: 30 arcuate nucleus RNA samples were analysed for this study, comprising. 15 samples were derived from bull calves fed the High plane of nutrition (HI, n=15) and 15 samples  derived from the calves fed the Moderate plane of nutrition (MOD, n=15). Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates. The MOD plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 0.5 kg of concentrates. All tissue samples were collected at the same time-point (12 weeks of age).

first: Stephen

last: Coen

first: Pat

last: Lonergan

first: Sean

last: Fair

first: David

last: Kenny


title: Essential Roles of Conserved Pseudouridines in Helix 69 for Ribosome Dynamics in Translation

city: Urbana

first: Hong

last: Jin

state: Illinois

address: 600 S Mathews Ave

institute: University of Illinois at Urbana-Champaign

summary: The widespread distribution of pseudouridine (Ψ), an isomer of the canonical uridine base, in RNA indicates its functional importance to the cell. In eukaryotes, it is estimated that around 2% of ribosomal RNA nucleotides are pseudouridines, most of which are located in functional regions of the ribosome. Defects in RNA pseudouridylation induce a range of detrimental effects from compromised cellular protein biosynthesis to disease phenotypes in humans. However, genome-wide changes to mRNA translation profiles by ribosomes lacking specific conserved pseudouridines have not been extensively studied. Here, using a new genomic method called 5PSeq and in vitro biochemistry, we investigated changes in ribosome dynamics and cellular translation profiles upon loss of Ψ2258 and Ψ2260 in helix 69, the two most conserved pseudouridines in the ribosome in yeast cells. We found that inhibiting the formation of these two pseudouridines challenges ribosomes to maintain the correct open reading frame and causes generally faster ribosome dynamics in translation. Furthermore, mutant ribosomes are more prone to pause while translating a subset of GC-rich codons, especially rare codons such as Arg (CGA) and Arg (CGG). These results demonstrate the presence of Ψ2258 and Ψ2260 contributes to the dynamics of the H69 RNA stem-loop, and helps to maintain functional interactions with the tRNAs as they move within the ribosome. The optimality of this ribosome-tRNA interaction is likely to be more critical for those limited tRNAs that decode rare codons. Consistent with the changes in ribosome dynamics, we observe that IRES-mediated translation is compromised in the mutant ribosome. These results explain the importance of Ψ2258 and Ψ2260 in H69 to maintain cellular fitness. The strong conservation of Ψ2258 and Ψ2260 in the ribosomes from bacteria to humans indicates their functional significance in modulating ribosome functions. It's likely that the identified functions of these covalent modifications are conserved across species.

overall_design: 8 samples for 5Pseq experiments using various yeast strains.

first: Xin

last: Chen


title: Effect of enhanced early life nutrition on hypothalamic arcuate nucleus miRNA transcriptome in bull calves.

summary: The aim of this study was to measure the impact of contrasting feeding regimes in the first 12 wk of life, on the molecular control of hypothalamic arcuate nucleus tissue in bull calves. Holstein bull calves  were designated to high (HI; n=15) or moderate (MOD; n=12) dietary groups, with diets designed to provoke growth rates of 1.0 and 0.5 kg/day, respectively. At 12 wk of age, all calves were euthanized, and hypothalamic arcuate nucleus tissue harvested. RNA was extracted from the hypothalamic arcuate nucleus and used for miRNAseq.

overall_design: In total 30 RNA samples were analysed, 15 samples were derived from bull calves fed the High plane of nutrition (HI, n=15) and 15 samples were derived from the calves fed the Moderate plane of nutrition (MOD, n=15). From 2 weeks of age calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates, whilst  te MOD group received 0.5 kg of milk replacer (4 litres) per day and 0.5 kg of concentrates. Tissue samples were collected from all calves at 12 weeks of age.


title: Cloche is a pro-regenerative platelet factor during zebrafish heart regeneration [CUT&Tag]

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

summary: Zebrafish heart regeneration is a complex process consisting of tempo-spatial coordination of cardiomyocyte (CM) and endothelial cell (EC) regeneration, fibrosis and inflammation. While myocardial, endocardial, and epicardial signaling have been reported to modulate this process, little is known about how leukocyte especially platelet signaling is involved in this regenerative process. Here we report that cloche/npas4l (neuronal PAS domain protein 4 like) is a pro-regenerative platelet factor for adult zebrafish heart regeneration. We found that injury triggered npas4l expression as early as 1 h post ventricular amputation, and haploinsufficiency of npas4l disrupted CM and EC proliferation and heart regeneration in clofv087b/+ and clom39/+ mutants after ventricular resection or nitroreductase (NTR)-mediated CM ablation. By constructing a single-cell transcriptomic atlas, we discovered that npas4l was dynamically expressed in platelets in response to heart injury with robust platelet-CM or -EC interactions via ligand-receptor activity analysis. Decreasing platelets in NTR-mediated depletion or mpl mutants impaired CM and EC proliferation, and over-expression of npas4l in platelets sufficiently made uninjured and injured CM reentry into the cell-cycle and rescued CM and EC proliferation in clofv087b/+ mutants. Furthermore, Npas4l positively regulated Bmp6 expression in platelets and either BMP6 inhibitors or siRNAs decreased CM proliferation and heart regeneration. This work demonstrates, for the first time, that injury-induced platelets are essential for zebrafish heart regeneration and Npas4l is a core platelet transcription factor for fine-tuning heart regeneration partially via Bmp6 signaling.

overall_design: The ventricles (30 adult ventricles per sample) were gently chopped, transferred, and digested in digestion buffer for 15 min at 4℃ with constant gentle agitation using a rotator. The digestion was then neutralized with 10% FBS (fetal bovine serum) and the disassociated cells were filtered through a 100 μm-strainer to remove large clumps and pelleted at 500 × g for 10 min at 4℃. The pellet which mainly contained platelets and erythrocytes was re-suspended in Hank’s balance salt solution (HBSS). Then, around 2000,000 cells per sample were fixed in 0.2% formaldehyde for 2 min and neutralized by adding glycine to a final concentration 25 mM. The fixed cells were pelleted at 800 × g for 5 min at 4℃, washed twice with PBS and loaded for CUT&TAG reaction using Hyperactive Universal CUT&TAG Assay Kit for Illumina Pro (Vazyme, TD904) and Mouse anti-HA Tag antibody (Santa Cruz, sc-7392) according to the manufacturer’s instructions. The concentrations of library were measured by a Qubit dsDNA high sensitivity assay. The sequencing was performed on a BGI DNBSEQ-T7 PE150 platform operated by Peking GenePlus Co.

first: Junjie

last: Hou

first: Chenglu

last: Xiao


title: Comparative single-cell transcriptomic profiling of patient-derived renal carcinoma cells in cellular and animal models of kidney cancer

city: Toronto

last: Ohh

state: Ontario

address: 661 University Avenue

department: Department of Laboratory Medicine and Pathobiology

institute: University of Toronto

summary: Clear-cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, which is often resistant to conventional cancer therapies including chemotherapy and radiation therapy.  Targeted treatments including immunotherapies and small molecule inhibitors have been recently developed with positive outcomes.  However, variations in the patient response and resistance to therapies suggest that models that better recapitulate the pathogenesis and metastatic mechanisms of ccRCC are required to improve our understanding and subsequent management of ccRCC.  Here, we examined the transcriptional landscapes of in vitro as well as orthotopic and metastatic NOD/SCID-γ mouse models of ccRCC using the RCC243 cell line established from the primary tumour of a patient that was diagnosed with metastatic ccRCC.  Notably, RCC243 cells developed metastatic tumours using assays in mouse models, and they retained their clear-cell morphology irrespective of model type but exhibited differential gene expression profiles between models of RCC243, highlighting the impact of the cellular environment and the stage of disease progression. Furthermore, we identified prognostic markers that were conserved between RCC243 models and patient ccRCC tumour datasets and showed that genes that were upregulated in the metastatic RCC243 model were associated with worse prognosis in patients. Overall, this study presents a novel metastatic model of ccRCC, highlights the role of the cellular environment on the transcriptome, and demonstrates the importance of the choice of an experimental model.

overall_design: RCC243/RCC243-tdTomato were used to generate cell-line derived xenograft models in both the orthotopic (renal capsule) setting and metastatic (heterotopic) setting. The RCC243 patient-derived xenograft model was also generated in the orthotopic setting. The human tumour cells were isolated after tumour excision using magnetic-activated cell sorting (MACS) and then sent for single-cell RNA-sequencing.

first: Richard

last: Huang

first: Lynn

last: Kee

first: Alexander

last: Gont

first: Jalna

last: Meens

first: Fraser

middle: G

last: Ferens

first: Meredith

last: Irwin

first: Laurie

last: Ailles

first: Scott

last: Yuzwa

first: Claire

last: Robinson


title: SMARCD1 is a dual regulator of PD-L1 expression and cell proliferation facilitating tumor evasion

city: Shanghai

first: Gang

last: Fu

address: 197 Ruijin Rd. II, Shanghai

institute: Shanghai Jiaotong University School of medicine affiliated Ruijin Hospital

summary: Cancer cells often evade immune responses by overexpressing immune checkpoint regulators, such as PD-L1. Here we identify a subunit of mating-type switching /sucrose fermentation (SWI/SNF) complex as a factor that favors tumor evasion by a dual mechanism involving both the induction of PD-L1-mediated immune checkpoint responses and the tumor cell proliferation. SMARCD1 deficient cancer cells exhibit not only reduced PD-L1 expression in vitro but also significantly suppressed tumor growth. Mechanistically, SMARCD1 maintains chromatin accessibility at PD-L1 transcriptional regulatory element thereby promoting PD-L1 expression in cancer cells. Besides, SMARCD1 might promote cancer cell proliferation by effecting several pathways such as AI3K-Akt signaling pathways. Collectively, these studies uncover SMARCD1 as a promising target for colorectal cancer (CRC) treatment.

overall_design: To investigate the function of SMARCD1 in tumor cells, we established MC38 cell lines in which each target gene has been knocked out by sgRNA.


title: Cloche is a pro-regenerative platelet factor during zebrafish heart regeneration [bulk RNA-seq]

overall_design: Tg(CD41.eGFP) and Tg(gata1a:DsRed) zebrafish hearts were dissected and cardiac cells were disassociated at 4℃. Fluorescence-activated cell sorting (FACS) was used to sort for CD41+ cells (clofv087b/+ vs. WT at 3dpa) and gata1a+ cells (Npas4l OE vs. control at 7dpt) according to the presence of eGFP or DsRed. 6000 cells per sample were pooled together to extract RNA, reverse transcribed to cDNA and proceeded to library generation followed by sequencing.


title: CNV data from 133 ccRCC samples

city: Zurich

first: Holger

last: Moch

address: Schmelzbergstrasse 12

department: Institute of Pathology and Molecular Pathology

country: Switzerland

institute: University Hospital Zurich

summary: Approximately 70% of clear cell renal cell carcinoma are characterised by the biallelic inactivation of VHL on chromosome 3p. ELOC-mutated renal cell carcinoma with biallelic ELOC inactivation on chromosome 8q are considered a novel subtype of renal cancer possessing a morphological overlap with ccRCC; however, the frequency and consequences of ELOC alterations in wtVHL and mutVHL is unclear. In this study, we characterise 123 renal tumours with clear cell morphology with known VHL mutation status to assess morphological and molecular consequences of ELOC inactivation. Using Oncoscan and whole exome sequencing we identify 18 ELOC deleted RCC, three of which contain ELOC mutations resulting in the biallelic inactivation of ELOC. Biallelic ELOC and biallelic VHL aberrations were mutually exclusive, although two ELOC-mutated RCC showed monoallelic VHL alterations. Using High Ambiguity Driven Biomolecular Docking we report a novel ELOC variant containing a duplication event disrupting ELOC-pVHL interaction alongside the frequently seen Y79C alteration. Using HRM mass spectrometry we show RCC with biallelic ELOC alterations have significantly reduced ELOC expression but similar CAIX and VEGFA expression when compared to classical ccRCC with VHL inactivation. These data demonstrate that RCC with ELOC and VHL alterations have comparable downstream effects with similar pathways to ccRCC tumourigenesis indicating that both entities are closely related.

overall_design: DNA extracted from FFPE primary ccRCC tumours

first: Aashi

last: Batavia

first: Peter

last: Schraml


title: Whole transcriptome exploration revealed the dysregulated RNAs involved in SARS-CoV-2 spike protein inhibited apoptosis in Calu-3 cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: SARS-CoV-2 induced COVID-19 has been spreading all over the world since 2020. Although the vaccines have been planted and efficiently suppressed the momentum, it is not fully understood how SARS-CoV-2 infects host cells, especially for the functions of its spike (S) glycoprotein. In this study, we investigated the biological and molecular functions of S protein by infecting the commercial pure S protein into human Calu-3 cells and analyzing apoptotic level change and its regulated transcriptome profile using whole transcriptome sequencing method (RNA-seq). Strikingly, we found S protein alone could significantly inhibit apoptotic level with dose dependent manner in Calu-3 cells, with or without ActD treatment. Higher level of S protein has more effective inhibition on cellular apoptosis. ActD-treated RNA-seq data analysis revealed hundreds of mRNAs, lncRNAs, and circRNAs were differentially expressed at post-transcriptional level. Functional enrichment analysis of DE mRNAs and lncRNAs showed they were highly enriched in inflammatory response, cell adhesion, and apoptotic process pathways. Host genes of circRNAs were enriched in metabolic and lysosome pathways. Finally, we constructed an RNA regulatory network involving these three RNA classes that were dysregulated in this study. RT-qPCR experiment was performed to validate the DE RNAs, which showed a high consistency with RNA-seq data. In conclusion, our study demonstrated the novel functions of SARS-CoV-2 S protein in lung Calu-3 cells, which will be helpful to understand the underlying molecular mechanisms during SARS-CoV-2 infection and the development of drugs and vaccines in future.

overall_design: We obtained the purified SARS-CoV-2 S protein and transfected it into human Calu-3 cells, which are frequently used in virus infection experiments. Whole transcriptome sequencing data was utilized to identify its regulated expression pattern of genes, including mRNA, lncRNA, and circRNA genes.

first: Yang

last: Luo

first: Xiaofeng

last: Wei

first: Qiyu

last: Zhang

first: Qiang

last: Li


title: Transcriptomic Responses of Peripheral Blood Leukocytes to Cardiac Surgery after Acute Inflammation, and Three Months Recovery

city: Hampton

first: Eric

last: Lewallen

state: Virginia

address: 130 William R. Harvey Way

department: Biological Sciences

institute: Hampton University

summary: Traumatic perioperative conditions may trigger early systemic responses, activate leukocytes and reprogram the immune system. We hypothesize that leukocyte activation may not revert to pre-surgical states, and that protracted activation may emerge with increased risks of comorbidities. We tested this concept by examining the transcriptomes of monocytes and T cells in a representative observational cohort of patients (n=13) admitted for elective cardiac surgery. Transcriptomes in T cells and monocytes were compared from before surgery (t0), and monocytes were analyzed longitudinally after acute (t24hr), and convalescent (t3m) time points. Monocytes and T cells expressed distinct transcriptomes, reflected by statistically significant differential expression of 558 T cell related genes. Monocytes expressed genes related to protein degradation and presented atypical activation of surface markers and cytoplasmic functions over time. Additionally, monocytes exhibited limited transcriptomic heterogeneity prior to surgery, and long-term patterns of gene expression associated with atherosclerosis showed three temporally distinct signatures. These data establish that post-cardiac surgery transcriptomes of monocytes differ even at three months compared to baselines, which may reflect latent (‘smoldering’) inflammation and persistent progression of tissue degenerative processes that should inform clinical care.

overall_design: Whole blood was collected before the onset of surgery (t0), at 24 hours (t24hr), and during a final follow-up occurring at three months (t3m). Monocytes were separated from other peripheral blood cell types using a Ficoll-Hypaque density gradient. Monocytes were further purified by removal of B cells, NK cells and T cells using the negative separation technique. RNA was isolated from MO samples using commercial kits and protocols (Qiagen, Germantown, MD). The integrity of each RNA sample was validated using the Agilent 2100 Bioanalyser System (Agilent Technologies, Santa Clara, CA). The Next-Generation Sequencing Core at the University of Pennsylvania assisted with generating barcoded libraries. They also provided RNA-seq data using an Illumina NovaSeq 6000. Data outputs were stored as raw FASTQ files and returned to the investigative team for downstream analysis.

first: Da

last: Liu

first: Jake

last: Karwoski

first: Wilson

last: Szeto

first: Andre

last: van Wijnen

first: Krzysztof

last: Laudanski


title: Copy number variants in autism spectrum disorders

city: Cairo

first: Amal

last: Mohamed

address: El-Bohooth

department: Human Cytogenetics

country: Egypt

institute: National Research Centre

type:
Genome variation profiling by SNP array
Genome variation profiling by array

summary: Our cohort comprised 40 non-syndromic ASD children.We conducted genome wide analysis using Affymetrix Cytoscan-HD microchips. We identified pathogenic CNVs in 7 patients (17.5%), other variant classified as variants of uncertain significance (VUS) or benign.

overall_design: Our design of the project aimed to identify and assess CNVs and their associated gene impacts in Egyptian ASD patients. Correlate the pathological CNVs to the ASD diagnostic parameters. Also we aimed to identify if ASD with pathological CNVs has certain clinical manifestations in comparison to other ASD patients.

first: Ola

last: Eid

first: Nagwa

last: Meguid


title: ATF4:p52 Complex Activates Oncogenic Enhancers in Multiple Myeloma via p300/CBP Recruitment to Regulate BACH1

status: Public on Apr 21 2025

city: Singapore

first: Yinghui

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Multiple myeloma (MM) is a B-cell malignancy accounting for 20% of all blood-associated cancers. MM patients with a poorer prognosis and high-risk stratification were previously observed to be causally linked to the constitutive activation of non-canonical NF-kB (ncNF-kB) pathway. Consistent with this, the ncNF-kB p52 transcription factor was earlier found to regulate the enhancer landscape of MM to potentiate oncogenic transcription. However, the mechanism by which aberrant p52 expression is involved in coordinating enhancer activity has not been well explored. In this study, we analysed H3K27ac ChIP-seq and ATAC-seq data from MM cell lines and patient samples to screen for putative transcription factors that cooperate with p52 to regulate enhancers activated in MM. We report that ATF4 interacts with p52 and together, this complex mediates the activity of a subset of MM-associated enhancers through the recruitment of histone acetyltransferases (HATs), p300 and CBP (CREB-binding protein). We also identified a novel ATF4:p52 regulated target gene BACH1 under the regulation of a proximal super-enhancer, which was found to drive oncogenesis in MM by promoting cell cycle progression and proliferation. Together, our findings provide further mechanistic insights into how aberrant enhancer activation observed in MM tumours could lead to disease progression.

overall_design: Assay for transposase-accessible chromatin with DNA-sequencing (ATAC-seq) in KMS-11 subjected to ATF4 knock down.

first: Daniel

last: Ang

first: Nathan

last: Harmston


title: Single-Cell Transcriptomic Atlas of Ovine Placenta Reveals Dynamic Cell Fate Transitions and Regulatory Networks Across Gestation

city: Nanjing

first: Zhibo

last: Wang

state: --- Select One ---

address: Tongwei Road, Nanjing City, Jiangsu Province, China

institute: Nanjing agricuture University

summary: This study employed single-cell RNA sequencing (scRNA-seq) to systematically map the cellular landscape of Hu sheep placental tissues across three gestational stages (50, 80, and 120 days), uncovering dynamic cell fate transitions and regulatory mechanisms. Analysis of 51,808 high-quality single-cell transcriptomes identified 14 cellular clusters, including uninucleate trophoblasts (UNCs, 58.83%), binucleate trophoblasts (BNCs, 21.82%), endothelial cells, fibroblasts, and immune cells. UNCs were subdivided into five subtypes expressing PAG2 and GATA3, while BNCs formed four subtypes marked by CSH2, PAG4, and PRP2. Functional enrichment revealed stage-specific activation of hypoxia-inducible factor 1 (HIF-1), vascular endothelial growth factor (VEGF), and MAPK signaling pathways, alongside shifts in proliferation, adhesion, and autophagy. Pseudotemporal trajectory analysis delineated a developmental continuum from UNCs to BNCs, highlighting dynamically expressed genes linked to MAPK signaling and HIF-1 responses. Immunofluorescence validated the spatial expression of key regulators, such as GCM1 and GATA3, in trophoblasts. This comprehensive atlas provides novel insights into molecular programs driving ovine placental maturation, offering potential targets to enhance reproductive efficiency and fetal development.


title: Feeding-Induced Discordance: Protein-mRNA Correlation Varies by Zone, Sex, and Fasting in Mouse Hepatocytes

city: Bronx

first: Jeffrey

middle: E

last: Pessin

state: NY

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: The mammalian liver plays an essential role in maintaining metabolic homeostasis in response to fasting and feeding. Additionally, the liver exhibits sex dimorphism and zonation. To investigate how these factors interact, we performed RNA-seq and proteomics on periportal and pericentral hepatocytes isolated from male and female mice under fed and starved conditions. We developed a classification system to assess protein-mRNA relationship and found that most zonation genes showed strong concordance between mRNA and protein. Classical growth hormone regulated sex-biased genes also exhibited concordance, while a significant subset of sex genes showed protein-level bias without corresponding mRNA differences. Transition between feeding and starvation triggered widespread changes in mRNA expression alongside rapid modulation of functional de novo lipogenesis. However, key lipogenic enzymes—such as ACC, ACLY, and FAS —showed little to no corresponding change at the protein level. To facilitate further exploration of these findings, we developed Discorda, a web-based database for interactive data analysis. Our findings reinforce the principle that mRNA changes do not reliably predict corresponding protein levels (and vice versa), particularly in the context of sex and acute metabolic regulation.

overall_design: Mice were trained for 3 days by removing food at 5PM and feeding at 9:00 the next day (16h fasting overnight and 8h feeding daytime). On the day of experiment, mice were provided food with drinking water that contained 20% of sucrose. The fed (0h) mice were sacrificed at 13:00 equal to 4h of feeding (0h). For fasted mice, the food and sucrose water were taken out at 13:00, then sacrificed at 13:00 the next day for fast 24h (24h).

first: Austin

last: Landgraf

first: Li

first: Kosaku

last: Shinoda


title: Genome wide transcriptional change by oligomycin or manipulation of mitochondrial membrane potential

city: Dallas

first: Mangyu

last: Choe

state: Texas

address: 6000 Harry Hines Blvd

department: Pediatrics

institute: University of Texas Southwestern

summary: Oligomycin, an inhibitor of ATP synthase (Complex V), increases mitochondrial membrane potential (ΔΨm) and induces ISR. Since direct manipulation of mitochondrial membrane potential using the genetic reagent that we developed (UCP1) rescued the effect of oligomycin on ISR, we performed RNAseq to investigate the effect of direct manipulation of ΔΨm by UCP1 on transcription. RNAseq analysis showed that direct manipulation of ΔΨm does not induce a major transcriptional program. However, oligomycin treatment caused a significant change in the expression of many genes, and the activation of UCP1 under oligomycin treatment rescued most of the transcriptional changes.

overall_design: C2C12 cells were infected with lentivirus carrying doxycycline-inducible UCP1. After 24 hr of seeding, Dox or water was added to induce protein expression. After 24 hr, various treatments (51 uM BSA, 300 uM oleic acid, 1 uM oligomycin + 300 uM oleic acid)were started in the presence of Dox or same volume of water. RNA was extracted 16 hr after the treatment and analyzed by RNA-sequencing.

first: Denis

last: Titov


last: Li

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the transcription factor ATF4 and BACH1, co-factors P300 and CBP, and the histone modification H3K27ac in multiple myeloma cell lines (MMCL). ATF4 ChIP-seq in KMS-11 and MM1.144. BACH1, CBP and P300 ChIP-seq in KMS-11. H3K27ac ChIP-seq for ATF4 knockdown in KMS-11 and MM1.144. H3K27ac ChIP-seq for BACH1 knockdown in KMS-11.


title: Expression data from macrophages sorted from Human Aortic Smooth Muscle Cells treated by PM2.5

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Transcriptomic analysis implicated that PM2.5 could influence genes involved in the IRE1α-mediated unfolded protein responses and reduce the expression of DNAJB9, a co-chaperone formed a complex with BiP/IRE1α to inhibit the activation of endoplasmic reticulum (ER) stress.
We investigate the mRNA expression of Human Aortic Smooth Muscle Cells induced by PM2.5 exposure by microarray.

overall_design: Human Aortic Smooth Muscle Cells were treated with PM2.5 (50 μg/mL) containing medium for 24 h. Total RNA was harvested using TRIzol reagent (Thermo, USA).

first: Linyuan

last: Huang

first: Ruiyang

last: Ding

first: Kanglin

last: Yan

first: Junchao

last: Duan

first: Zhiwei

last: Sun


title: Pbrm1 loss induces a permissive chromatin state for cholangiocytic differentiation and cholangiocarcinoma formation [ATAC-seq]

city: Taipei City

first: Li-Wen

last: Chiou

address: Chung Shan S. Rd.

institute: National Taiwan University

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

overall_design: To investigate the role of Pbrm1 in liver function and tumorigenesis, we generated Alb-Cre-mediated Pbrm1 knockout mice. We performed ATAC-seq to examined chromatin accessibility changes between Pbrm1 KO and WT liver.

first: Liwen

first: Yulin

last: Jhuang

first: Chialang

last: Hsu

first: Yungming

last: Jeng


title: Single-cell gene expression of control mandibular bone marrow cells and mandibular bone marrow cells under bisphosphonate-related osteonecrosis of the jaw (BRONJ)

city: Chengdu

first: Yixin

last: Shi

state: Sichuan

address: No.14, Section 3, Renmin South Road, Wuhou District, Chengdu, Sichuan, China

institute: Sichuan University

summary: Single-cell gene expression of mandibular bone marrow cells and mandibular bone marrow cells under the stimulation of BRONJ were determined by scRNAseq.

overall_design: Nine C57/B6 female mice with BRONJ or control mice were used to acquire single-cell suspensions. Mandibles were dissected with soft tissues were removed. Then, mandible tissue was digested to acquire single cell suspension, which enriched with CD45- cells using Meiteni Mouse CD45 MicroBeads. Cellular suspensions were loaded into Chromium microfluidic chips and barcoded with a 10x Chromium Controller (10x Genomics).

first: Junyu

last: Chen


title: Whole proteome and transcriptome analysis of cancer-derived EVs overlap in specific pathways and distinct EV population

city: Phoenix

first: Kendall

last: Van Keuren-Jensen

state: AZ

address: 445 N. 5th Street

institute: Translational Genomics Research Institute

summary: Extracellular Vesicles (EVs) are particles of different sizes, covered by a lipid bilayer membrane and containing highly heterogeneous cargo. Cancer cell-derived EVs have been the main object of an extensive investigation in the field because they carry cancer-specific molecular cargo and can promote cancer progression. Cancer-derived EVs include populations of atypically large EVs (L-EVs), which have been referred to as tumor microvesicles, large oncosomes, or simply L-EVs. While small EVs (S-EVs), which include exosomes, have been investigated by a plethora of reports, little is known about L-EVs. The paucity of studies comparing protein cargo of L- and S-EVs and studies focusing on protein-coding RNA, and the absence of integrative analyses to compare the protein and gene expression in different EV fractions, prompted us to perform mass spectrometry to profile three different, size-based EV fractions generated by three cancer cell models (glioma, prostate and breast cancer). We identified protein signatures for L- and S-EVs either common to all cell types or specific to each of them individually. The proteins enriched in prostate cancer cell-derived L-EVs were also identified in L-EVs from patients with metastatic prostate cancer by a SWATH proteomic assay. We also performed RNA-Seq on the prostate cancer model and integrated proteomic and transcriptomic datasets. GSEA revealed that mitochondrial function was enriched in L-EVs versus S-EVs at both the RNA and protein level. The mitochondrial signature at the transcriptome level was confirmed by single cell RNA-Seq of L- EVs in vitro. The integrated L-EV proteomic and transcriptomic signature enabled distinction between benign and localized prostate cancer, as well as between localized cancer and metastatic castration-resistant cancer.

overall_design: Extracellular vesicle (EV) isolation was performed using a PC3 cell line at three different centrifugations

first: T

last: Vagner

first: E

last: Hutchins

first: W

last: Zhao

first: Y

last: Ciani

first: J

last: Mariscal

first: A

last: Chin

first: M

last: De Simone

last: Ko

last: Kittel

first: S

last: Parker

last: Van Evk

last: Yang

last: Posadas

last: Buzas

last: Guarnerio

last: Zihlstra

last: Nolan

first: C

last: Thery

first: F

last: Demichelis

first: P

last: Boutros

first: K

first: D

last: Di Vizio


title: Increased HSD11β1 Expression in Human Leiomyomatous Uteri: Implication for Enhanced Glucocorticoid Signaling

city: Tampa

first: Umit

middle: Ali

last: Kayisli

state: Florida

address: 560 Channelside Dr,

department: Ob/Gyn

institute: USF Morsani College of Medicine

summary: Abstract: FK506-binding-protein-51 (FKBP51) is a glucocorticoid-induced co-chaperone protein previously shown to bind glucocorticoid receptor (GR), inhibiting its transcriptional activity. We previously found increased FKBP51 levels in uterine leiomyoma versus paired myometrium. To test the hypothesis that elevated FKBP51 levels contribute to leiomyoma pathogenesis by altering GR signaling. Material Method: RNA-sequencing was performed in leiomyoma cell cultures transfected with scrambled or FKBP5-siRNA for 48-h, then treated with vehicle or dexamethasone (DEX) for 24-h. Differentially expressed genes, including HSD11B1, CNN1, and LAMA2 were analyzed by qPCR. Hydroxysteroid 11-beta dehydrogenase 1 (HSD11β1) expression was analyzed in leiomyoma, leiomyoma-adjacent paired myometrium, myometrium from patients without leiomyoma, and human endometrial stromal cells (HESC) by qPCR and immunohistochemistry in women with or without uterine leiomyoma. HSD11B1 mRNA and protein levels in leiomyoma, paired and normal myometrium, and HESC cells and tissue. Results: HSD11β1 expression was higher in paired myometrial and leiomyoma tissues versus normal myometrium (P<0.02). DEX treatment increased HSD11B1 transcription in normal myometrial and HESC cultures, but to a significantly greater extent in leiomyoma. However, FKBP5-silencing blunted DEX-induced HSD11B1 transcription. DEX-treatment reduced LAMA2 and increased CNN1 levels (coding for extracellular matrix and smooth muscle proteins, respectively) in FKBP5-silenced versus scrambled-siRNA leiomyoma cultures. Conclusions: FKBP51 not only inhibits but can augment GR-mediated transcription. Importantly, FKBP51-GR interactions increase HSD11B1 levels in leiomyoma cells, generating a pathological FKBP51-GR-HSD11β1 circle, altering transcription of downstream extracellular matrix and smooth muscle genes to induce a myofibroblast phenotype, thereby possibly contributing to leiomyoma pathogenesis.

overall_design: RNA-sequencing was performed in pooled samples from leiomyoma cell cultures transfected with scrambled or FKBP5-siRNA for 48-h, then treated with vehicle or dexamethasone (DEX) for 24-h (n=4/group).

first: Carrie

last: Malcom

first: Ozlem

last: Guzeloglu‑Kayisli

first: Erika

last: New

first: Xiaofang

last: Guo

first: Charles

last: J. Lockwood


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

first: xinjian

last: He

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

institute: National Institute of Biological Sciences

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

overall_design: Examination of Pol II level in wild type, prp21 mutant.

first: XinJian


title: Cloche is a pro-regenerative platelet factor during zebrafish heart regeneration [10x scRNA-seq]

first: Yabing

last: Song

address: Chaoyang District

institute: Chinese Academy of Sciences

summary: Zebrafish heart regeneration is a complex process consisting of tempo-spatial coordination of cardiomyocyte (CM) and endothelial cell (EC) regeneration, fibrosis and inflammation. While myocardial, endocardial, and epicardial signaling have been reported to modulate this process, little is known about how leukocyte especially platelet signaling is involved in this regenerative process. Here we report that cloche/npas4l (neuronal PAS domain protein 4 like) is a pro-regenerative platelet factor for adult zebrafish heart regeneration. We found that injury triggered npas4l expression as early as 1 h post ventricular amputation, and haploinsufficiency of npas4l disrupted CM and EC proliferation and heart regeneration in clofv087b/+ and clom39/+ mutants after ventricular resection or nitroreductase (NTR)-mediated CM ablation. By constructing a single-cell transcriptomic atlas, we discovered that npas4l was dynamically expressed in platelets in response to heart injury with robust platelet-CM or -EC interactions via ligand-receptor activity analysis. Decreasing platelets in NTR-mediated depletion or mpl mutants impaired CM and EC proliferation, and over-expression of npas4l in platelets sufficiently made uninjured and injured CM reentry into the cell-cycle and rescued CM and EC proliferation in clofv087b/+ mutants. Furthermore, Npas4l positively regulated Bmp6 expression in platelets and either BMP6 inhibitors or siRNAs decreased CM proliferation and heart regeneration. This work demonstrates, for the first time, that injury-induced platelets are essential for zebrafish heart regeneration and Npas4l is a core platelet transcription factor for fine-tuning heart regeneration partially via Bmp6 signaling.

overall_design: Wild type and clofv087b/+ adult zebrafish hearts (injured or uninjured) were dissected and cardiac cells were disassociation at 4℃. Fluorescence-activated cell sorting (FACS) was used to remove cell debris and sort for single cell according to hochest signal intensity. Sorted cell concentration and vaibility were determined on a Countstar Rigel system. 12,000 cells with more than 85% cell vaibility were loaded into 10x Genomics Chromium chip and proceeded to single-cell RNA library construction and sequencing.

first: Junjie

last: Hou

first: Chenglu

last: Xiao


title: Single Cell RNA Sequencing after Moderate Traumatic Brain Injury: Effects of Therapeutic Hypothermia

city: Miami

first: Nadine

last: Kerr

address: 1095 NW 14th Terrace

department: The Miami Project to Cure Paralysis

institute: University of Miami

summary: Traumatic brain injury (TBI) initiates a cascade of cellular and molecular events that promote acute and long-term patterns of neuronal, glial, vascular, and synaptic vulnerability leading to lasting neurological deficits.  These complex responses lead to patterns of programmed cell death, diffuse axonal injury, increased blood-brain barrier disruption, neuroinflammation, and reactive gliosis, each a potential target for therapeutic interventions. Posttraumatic therapeutic hypothermia (TH) has been reported to be highly protective after brain and spinal cord injury and studies have investigated molecular mechanisms underlying mild hypothermic protection while commonly assessing heterogenous cell populations. In this study we conducted single-cell RNA sequencing (scRNAseq) on cerebral cortical tissues after experimental TBI followed by a period of normothermia or hypothermia to clarify multiple cell type-specific transcriptional responses. C57BL/6 mice underwent moderate controlled cortical impact (CCI) injury or sham surgery and then placed under sustained normothermia (37⁰C) or hypothermia (33⁰C) for 2 hrs. After 24 hours, cortical tissues including peri-contused regions were processed for scRNAseq. Unbiased clustering and differential expression tests revealed cellular heterogeneity, reactive astrocytes, microglia, and leukocyte infiltration at this subacute posttraumatic time point. The analysis also revealed vascular and immune subtypes associated with neovascularization and debris clearance, respectively. Compared to normothermic conditions, TH treatment altered the abundance of specific cell subtypes and induced reactive astrocyte-specific modulation of neurotropic factor gene expression. In addition, an increase in the proportion of endothelial tip cells in the hypothermic TBI group was documented compared to normothermia. These data emphasize the importance of early temperature-sensitive glial and vascular cell processes in producing potentially neuroprotective downstream signaling cascades in a cell-type-dependent manner. The use of single cell sequencing to address cell-specific mechanisms underlying therapeutic treatments provides a valuable resource for identifying targetable biological pathways for the development of neuroprotective and reparative interventions.

overall_design: Twelve male C57BL/6 mice (2–3 months old) were randomly assigned to four groups (n=3 per group): 1. TBI–Normothermia 2. Sham–Normothermia 3. TBI–Hypothermia  4. Sham–Hypothermia A moderate controlled cortical impact (CCI) traumatic brain injury (TBI) was administered, followed by a 2-hour selective brain hypothermia (33°C) or normothermia (37°C) protocol starting 30 minutes post-injury. Mice were sacrificed at 24 hours post-injury or sham surgery, and the ipsilateral cortex was dissected for single-cell RNA-sequencing. One sample corresponds to one individual animal, for a total of 12 samples.

first: James

last: Choi

first: Simone

middle: Y

last: Mohite

first: Praveen

middle: K

last: Singh

first: Helen

middle: M

last: Bramlett

first: Jae

last: Lee

first: W

middle: D

last: Dietrich


title: A Novel Squaramide Derivative, HR-19011, Induces the Integrated Stress Response via the HRI-eIF2α-ATF4 Pathway, Effectively Inhibiting Hematologic Malignancies

city: Busan

first: Min Jung

last: Kim

address: 262, Gamcheon-ro, Seo-gu

department: Biochemistry

institute: Kosin university college of medicine

summary: We investigated the therapeutic potential and mechanisms of HR-19011, a novel eIF2α phosphorylation inducer, with a focus on its effects on the integrated stress response (ISR) pathway and cell cycle regulation in K562 cells. Our findings revealed that HR-19011 exerts its anticancer effects primarily through the activation of heme-regulated inhibitor (HRI), leading to the phosphorylation of eukaryotic translation initiation factor 2 (eIF2)α, the induction of ISR signaling, and subsequent G1/S cell cycle arrest. RNA sequencing analysis further highlighted significant changes in gene expression associated with the ISR pathway, particularly those involving the key components, activating transcription factor 4 (ATF4) and CHOP, underscoring the specific targeting of HRI by HR-19011. Additionally, HR-19011 suppressed the mTORC1 pathway, a critical regulator of cell growth and metabolism, through the downregulation of components such as phosphorylated (p)-S6K and p-4EBP1, mediated by ATF4 and CHOP. In vivo studies demonstrated that HR-19011 effectively inhibited tumor growth in a K562 xenograft model, without significant toxicity, and its broad efficacy across various hematologic malignancies further suggests its potential as a versatile anticancer agent. Our findings position HR-19011 as a promising candidate for targeting the HRI-eIF2α axis in cancer treatment, warranting further investigation and optimization for clinical application.

overall_design: RNA-seq profiling of K562 cells treated with 0.1% DMSO (vehicle) or 10 µM HR-19011 for 24 hours

first: Min-Jung

first: Hyung Seok

first: Jee-Yeong

last: Jeong


title: Fungal susceptibility and early flowering in pennycress (Thlaspi arvense) are conferred by naturally occurring mutations in histone demethylase Jumonji 14

city: Saint Louis

first: Jennette

last: Codjoe

state: Missouri

address: 1005 N Warson Rd, Suite 305

institute: CoverCress Inc.

summary: Pennycress (Thlaspi arvense) is a winter oilseed domesticated recently to be incorporated as an intermediate crop between the existing cropping systems of the US Midwest. We show that a natural accession of pennycress, 2032, is more susceptible to the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Alternaria japonica than the reference pennycress accession MN106. A previously identified marker associated with earliness in pennycress was found to be present in in a gene homologous to Arabidopsis Jumonji 14 (JMJ14). It has been reported that AtJMJ14 promotes disease resistance and represses flowering, and greenhouse studies of breeding populations confirmed this phenomenon in pennycress. Plants with the 2032 TaJMJ14 allele were more susceptible to fungi and flowered early. CRISPR-Cas9 editing was used to generate additional TaJMJ14 alleles. A 9 bp deletion in TaJMJ14 showed trends of early flowering and S. sclerotiorum susceptibility, whereas a complete loss-of-function allele led to infertility. We further investigated the transcriptomes of MN106 and 2032 plants in the early stages of S. sclerotiorum and A. japonica infection to identify potential resistance and susceptibility genes. Differences in the expression of pathogen-associated molecular pattern-triggered immunity (PTI)-associated genes led us to discover that 2032 plants have defects in elicitor-triggered oxidative bursts. The transcriptional responses unique to each accession lay a foundation for future gene-editing and breeding approaches to keep the beneficial early flowering phenotype conferred by 2032 but uncouple it from disease susceptibility.

overall_design: RNAseq of pennycress leaves infected with Sclerotinia sclerotiorum (for 3 and 6 hours) or Alternaria japonica (6 and 12 hours) with mock-infected, control samples for each time point.

first: Alice

last: Kujur

first: Jammi

last: Prasanthi Sirasani

first: Anastasia

last: Shamin

first: Thomas

last: Sauer

first: Krishan

last: Rai

first: Tim

last: Ulmasov

first: Ratan

last: Chopra

first: Dilip

last: Shah