title: Streptococcus suis Stk1 Sensitizes Epithelial Cells to Ferroptosis and Exacerbates Disruption of the Respiratory Epithelial Barrier

city: wuhan

first: lang

last: tian

state: hubei

address: 1 Shizishan Street, Hongshan District

institute: huazhong agricultural university

summary: Streptococcus suis serotype 2 (SS2), a significant zoonotic pathogen, initiates systemic infection by breaching the respiratory epithelial barrier. Ferroptosis, an iron-dependent form of regulated cell death driven by lipid peroxidation, is increasingly implicated in the pathogenesis of various infectious diseases, yet its role in SS2-induced epithelial barrier dysfunction remains unknown. Here, we demonstrate SS2 infection sensitizes airway epithelial cells to ferroptosis, leading to the accumulation of lipid peroxides, upregulation of the transcriptional repressor Snail1, and subsequent downregulation of intercellular junction proteins. This cascade compromises epithelial integrity and promotes bacterial translocation. Mechanistically, we found SS2 overwhelms the cellular redox defense system and identified bacterial eukaryotic-like serine/threonine kinase 1 (Stk1) as the key mediator of this process. Stk1 directly interacts with host protein Keap1, which stabilizes the Keap1-Nrf2 complex. This stabilization enhances the ubiquitination and subsequent proteasomal degradation of Nrf2, the master regulator of antioxidant response, thereby crippling cell’s ability to neutralize lipid peroxides. In summary, this study unveils a novel virulence mechanism wherein SS2 effector Stk1 promotes Nrf2 degradation to trigger ferroptosis, ultimately leading to the disruption of respiratory epithelial barrier. These findings suggest that inhibiting ferroptosis could represent a promising therapeutic strategy for clinical prevention and treatment of SS2 infections.

overall_design: To elucidate the molecular mechanism by which SS2 induces ferroptosis, we performed RNA sequencing (RNA-seq) on SS2-infected NPTr cells. The comparison of FPKM density distributions for genes and transcripts and the principal component analysis (PCA) of high-throughput transcriptome sequencing samples collectively satisfied the quality control criteria for RNA-seq data. Clustering analysis and differential gene expression volcano plots identified 196 significantly differentially expressed genes , with KEGG pathway analysis showing strong enrichment for pathways related to adherens junctions, tight junctions, and ferroptosis.

first: Lang

last: Tian

first: Ruicheng

last: Yang

first: Xiangru


title: ATAC-seq and RNA-seq analysis of Eriocheir sinensis muscle in molt stage

status: Public on Mar 04 2026

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

country: China

institute: College of Life Sciences, Tianjin Normal University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: The chromatin accessibility and gene expression of muscle in E. sinensis in molt (E) stage were sequenced by Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) and RNA-seq, respectively. The data was used to analysis the differentially expressed genes (DEGs) in muscle from different molting stages by combining ATAC-seq and RNA-seq.

overall_design: Muscle of healthy crabs in molt stage (D stage) were collected and used for ATAC-seq and RNA-seq analysis.in each stages, three muscle samples were collected as the experimental replications. ATAC-seq was performed with Illumina Hiseq platform with E. sinensis genome (accession number PRJNA555707) as the reference genome.RNA-seq was performed with Illumina novaseq platform with E. sinensis genome (accession number PRJNA555707) as the reference genome.

first: Jingjing

last: Li

first: Jinsheng

last: Sun


title: Rice Ethylene Receptors Define a Novel Plant Hormone Receptor-Ion Channel with Calcium/Cation Permeability

city: Beijing

first: 刘

last: 硕

address: 北京市海淀区西三环北路105号

institute: capital normal university

summary: The gaseous phytohormone ethylene regulates pivotal plant processes from development, productivity to resistance, yet how its signaling intersects with calcium (Ca²⁺) second messengers remains elusive. Here, we identify a calcium-dependent antagonism of ethylene response (CAER) regulating root elongation in the model cereal Oryza sativa. Unexpectedly, we show that the ethylene receptor OsERS1 acts as a Ca²⁺-permeable, non-selective cation channel, mediating permeation of both mono- and divalent cations. Mutagenesis analyses reveal that OsERS1 channel activity relies on homomeric assembly sites (C4/C6) rather than its ethylene-binding domain (C65), indicating decoupled regulatory modules for receptor and channel functions. Genetic data demonstrate that, unlike wild-type plants, both the loss-of-function mutant Osers1 and gain-of-function line Osers2d fail to exhibit CAER phenotypes, establishing that CAER depends on ethylene receptors of OsERS1 and OsERS2. Our findings reveal a previously unrecognized ion-channel function of ethylene receptors, establishing a novel paradigm of "hormone receptor-type ion channel (HRIC)" in plants. This discovery carries broad implications for redefining signal transduction networks across plant biology.

overall_design: Rice grow in low calciumor normal calcium were treated with air or ethylene

first: Ye

last: ZhangLi


title: Rescuing mitochondrial dysfunction in macrophages prevents osteonecrosis of the jaw in anti-resorptive therapy

city: 南京

first: XINXI

last: YUAN

state: 江苏省

address: 峨嵋岭20号

department: School of Stomatology

institute: Nanjing Medical University

summary: Mitochondria-driven macrophage dysregulation plays a crucial role in the progression of various inflammatory diseases, yet its exact mechanism in the pathogenesis of bisphosphonate-related osteonecrosis of the jaw (BRONJ) remains poorly understood. Here, we demonstrate that zoledronic acid (ZA) impairs mitochondrial bioenergetic function in macrophages, resulting in elevated mitochondrial membrane potential, accumulated mitochondrial reactive oxygen species, and increased expression of HIF-1α, which subsequently promotes a pro-inflammatory transition in macrophages. Importantly, ZA inhibits autophagy-initiating complex via activation of the TLR4-MyD88/PI3K-AKT-mTOR pathway, thereby impeding clearance of dysfunctional mitochondria to sustain superoxide production.

overall_design: Total RNA of BMDMs treated with or without ZA was extracted using Trizol reagent (ThermoFisher, 15596018CN) following the manufacturer’s procedure. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Then the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The libraries were then sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. The transcriptome sequencing and analysis were conducted by OE Biotech.

first: Hang

last: Zhang

first: Xin

last: Shen

first: Xinxi

last: Yuan


title: Genetic mapping identifies Homer1 as a developmental modifier of attention [scRNA-seq]

city: New York

first: Priya

last: Rajasethupathy

state: NY

address: 1230 York Ave

country: USA

institute: The Rockefeller University

summary: Attention is the process of directing cognitive resources toward specific stimuli and is required for most higher-order cognitive functions. The genetic factors and resulting neural circuit physiology that drive variation in this trait are not well understood. Here we took an unbiased forward genetics approach to identify genes of large effect on attention. We performed genetic mapping on 200 genetically diverse mice and identified a small locus on chromosome 13 that is significantly associated with pre-attentive processing. Further characterization of the locus revealed Homer1, encoding a synaptic protein, as a potential driver gene that merited further investigation. Strikingly, down-regulation of specifically the short isoforms of Homer1 in prefrontal cortex (PFC) during an early developmental window led to improvements in multiple measures of attention in the adult. An important functional consequence of low Homer1 is a resulting upscaling of GABAergic receptors and enhanced inhibitory tone in PFC. These Homer1-dependent changes to inhibitory tone led to overall improvements in neural signal-to-noise, cue detection, and fast latency correct choices. We thus identify a single locus of large effect on attention and propose Homer1-dependent inhibitory tone, sculpted during a developmental sensitive period, as a key regulator of adult attentional performance.

overall_design: Cells from mouse prefrontal cortext (PFC) were isolated and processed using scRNA-seq, from different Collaborative Cross (CC) lines (CC025 and CC083) as well as from Homer1a/Ania3 developmental knockdown and scramble control mice. At least 2 samples of 3 pooled biological replicates were included per CC line and knockdown condition.

first: Zachary

last: Gershon

first: Alessandra

last: Bonito-Oliva

first: Matt

last: Kanke

first: Andrea

last: Terceros

first: Praveen

last: Sethupathy


title: Time-Resolved Analysis Reveals FEN1 as a Crucial Factor of Circadian Transcriptome Dynamics and Core Cellular Homeostasis in HEK 293T cell

city: Suzhou

first: Tao

state: Jiangsu

address: No.28 Kehua Road

institute: Suzhou Vocational Health College

summary: Circadian rhythms orchestrate genome-wide transcriptional oscillations to coordinate cellular homeostasis. While the core clock machinery has been extensively characterized, its integration with other critical biological processes, such as the DNA damage response and cell cycle control, remains incompletely understood. Here, we identify the DNA replication and repair nuclease FEN1 as a critical modulator of circadian transcriptome dynamics in human cells. Time-series RNA-seq across six circadian time points in synchronized HEK293T cells revealed that FEN1 depletion induces widespread reprogramming of rhythmic gene expression, with over 30% of oscillatory transcripts exhibiting loss or gain of rhythmicity, phase shifts, or amplitude changes. Notably, reprogrammed genes were enriched in cell cycle, DNA damage response, and cellular senescence pathways. Systematic phase set enrichment analysis uncovered coordinated delays and inversions in G1/S checkpoint regulators and metabolic genes, disrupting temporal coherence. Despite retention of rhythmicity in core clock genes, amplitude attenuation and phase advances were observed, indicating compromised oscillatory stability. Functional validation demonstrated reduced S phase entry, G1 accumulation, and accelerated senescence in FEN1 knockdown cells, in line with transcriptomic predictions. qPCR analysis confirmed altered expression of representative target genes. These findings uncover an unrecognized role for FEN1 in sustaining circadian transcriptional architecture and reveal its broader impact on cell cycle control and aging programs.

overall_design: Wild-type (WT) and FEN1 KD cells were harvested at 4-hour intervals throughout 24 h for transcriptomic profiling via RNA sequencing (six time points: 0, 4, 8, 12, 16, and 20 hours).

first: Songbai

last: Liu

first: Fei

last: Ge

first: Yuling

first: Ying

last: Zhao


title: Genetic mapping identifies Homer1 as a developmental modifier of attention

overall_design:
RNA-seq profiling of medialdorsal thalamus (mdTH), prefrontal cortex (PFC), and ventral tegmentl area (VTA) from Diversity Outbred (DO) mice with high and low PPI performance as well as PFC from Collaborative Cross (CC) mouse lines with high (CC083) and low (CC025) PPI performance. For each DO performance group and CC line, 3 biological replicates were used. GSM4745192 was used as PFC DO High Performer #2 and GSM4745207 was used as mdTH DO High Performer #2, both from GSE156836. For differential expression analysis, different batches of RNAseq were included as a covariate in the DESeq2 model.

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The table below lists GEO accessions reused/reanalyzed for this study.
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title: Discovery of a Novel DNMT1 Inhibitor with Improved Efficacy in Treating β-Thalassemia [ATAC-seq]

city: Shanghai

first: Yijie

last: SHEN

address: 130 Dong'an Road

institute: Fudan University

summary: The β-thalassemia is a recessively inherited disease affecting millions around the world. Pharmacological induction of fetal hemoglobin (HbF) is an effective therapeutic strategy for the management of β-thalassemia. DNA methyltransferase inhibitors are effective HbF inducers, however was not currently approved for β-thalassemia treatments. Here we report that the newly developed non-nucleoside DNMT1 inhibitor DMT207 strongly reactivates the expression of HbF in HUDEP-2 cells and adult primary erythroblasts with minimal toxicity. Moreover, in a mouse model of β-thalassemia, the administration of DMT207 effectively induces the expression of mouse fetal- and embryonic-type hemoglobin, promotes the maturation of erythroid cells, and alleviates the splenomegaly of mice. Further multi-omics studies expose γ-globin as one of the most sensitive genes in response to DMT207 treatment. Mechanistically, DMT207 inhibits DNMT1 enzymatic activity through trapping DNMT1 into an open conformation and meanwhile enhances interactions between the conformationally-kinked DNMT1 and UHRF1, partially contributing to specific degradation of DNMT1. Thus, we conclude that DMT207 is a promising novel DNMT1 inhibitor that could benefit patients with β-thalassemia.

overall_design: HUDEP-2 cells and human erythroid progenitor cells were cultred with drug treatment and subjected to RNA-seq, ATAC-seq, and WGBS analysis.

first: Jiale

last: Wei

first: Shibing

last: Tang

first: Dongliang

last: Wu

first: Liangyi

last: Zong

first: Shuyuan

last: Ma

first: Ruijie

last: Gong

first: Siyuan

last: Xu

first: Chuxuan

last: Peng

first: Qin

last: Feng

first: Songchen

first: Qitong

first: Yuhua

last: Ye

first: Quan

first: Cheng

last: Luo

first: Zhihai

last: Li

first: Xiangqian

last: Kong

first: Xianjiang

last: Lan


title: Discovery of a Novel DNMT1 Inhibitor with Improved Efficacy in Treating β-Thalassemia [WGBS]

first: Yijie

type: Methylation profiling by high throughput sequencing

last: Shen

first: Jiale

last: Liu


title: Discovery of a Novel DNMT1 Inhibitor with Improved Efficacy in Treating β-Thalassemia [RNA-seq]

last: SHEN

first: Shibing

first: Dongliang

last: Zhao


title: Clonal dynamics reveal cancer resistance arises from adaptive programs [scRNA-Seq]

city: Philadelphia

first: Yeqing

last: Chen

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Most advanced cancers initially respond to targeted therapies but eventually relapse1. Rather than acquiring new mutations, resistance is driven by drug-tolerant persister cells (DTP) that enter a reversible drug-refractory state and sustain minimal residual disease2. Here, we developed MeRLin, a high-resolution barcoding platform combining single-cell RNA sequencing, RNA fluorescence in situ hybridization, and computational analyses to track clonal and transcriptional dynamics of melanoma cells during targeted therapy. Clonal tracking reveals that dominant resistant clones arise from minor pre-treatment subpopulations. The pre-treatment melanoma populations diversify into phenotypically distinct DTP subpopulations, marked by stress-like, lipid metabolism, PI3K signaling, and extracellular matrix remodeling programs associated with adaptive resistance. Spatial transcriptomics revealed the co-localization of lipid metabolism and PI3K signaling programs near the tumor boundaries, and a complex network of autocrine and paracrine interactions among DTP subpopulations. Using barcoded RNA fluorescence in situ hybridization, we identified a dominant persister subpopulation in resistant tumors marked by SLC2A1 expression. Thus, MeRLin provides a robust framework to dissect melanoma heterogeneity and uncover vulnerabilities in persister populations to improve long-term treatment efficacy.

overall_design: WM4237-1 cells were spinfected with a lentiviral barcode library in the presence of polybrene (8 μg/mL). mNeptune2.5-positive cells were sorted by flow cytometry to ensure a multiplicity of infection (MOI) below 40%. Barcoded cells were then expanded and split into replicate populations, with one aliquot preserved as the original control. Replicates of barcoded WM4237-1 cells or non-barcoded, dissociated WM4007 PDX cells were subcutaneously injected into immunodeficient mice and monitored for tumor growth. Once tumors were established, mice were treated with BRAFi/MEKi, and tumor samples were collected longitudinally throughout treatment until relapse.

first: Haiyin

first: Jessica

last: Kaster

first: Maggie

last: Dunne

first: Min

last: Xiao

first: Ling

first: Monzy

last: Thomas

first: Nazifa

last: Promi

first: Dylan

last: Fingerman

first: Gregory

middle: S

last: Brown

first: Xingyue

last: Zhu

first: Meenhard

last: Herlyn


title: Exosomal miRNA Profiling in Plasma and Cerebrospinal Fluid of DOCA-Salt-Induced Hypertensive and Control Mice

city: NEW ORLEANS

first: Vahideh

last: Tarhriz

state: LA

address: Perdido,

department: Cardiovascular Research Center of Excellence

institute: Louisiana State University Health Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aimed to profile exosomal miRNAs in both plasma and cerebrospinal fluid (CSF) from male and female mice subjected to DOCA-salt treatment—a widely used model for inducing hypertension—and from their respective baseline controls. Exosomes were isolated using size exclusion chromatography (SEC), followed by small RNA extraction and quality control. Exosomal miRNAs were sequenced using the QIAseq miRNA Library Kit (Qiagen) on the Illumina NovaSeq 6000 platform. Libraries incorporated unique molecular identifiers (UMIs) to mitigate PCR bias. High-throughput sequencing data were analyzed for quality, aligned to multiple databases (miRBase, piRNABank, and Rfam), and normalized using CPM values. Differentially expressed miRNAs were identified and subjected to target prediction and pathway analysis using miRTarBase, GO, and KEGG. These findings may provide insight into the molecular signatures associated with hypertension and sex-specific responses in extracellular vesicle-derived miRNAs.

overall_design: Eight exosomal RNA samples were isolated from plasma and CSF of mice (n=8), divided into four experimental groups: Female Baseline (FB), Female DOCA-salt (FD), Male Baseline (MB), Male DOCA-salt (MD); Each group included both plasma-derived and CSF-derived exosomes. Total RNA was extracted using the miRNeasy Micro Kit (Qiagen), and library preparation was performed with QIAseq miRNA Library Kit (Qiagen), which includes UMI incorporation to reduce amplification bias. Libraries were sequenced with single-end 150 bp reads on an Illumina NovaSeq 6000 platform, with a target depth of 10 million reads per sample. Post-sequencing, data were processed using Cutadapt for quality filtering, and aligned using Bowtie to miRBase, piRNABank, and Rfam. UMI-based read quantification was followed by normalization with the edgeR package. Differentially expressed miRNAs were further analyzed for target prediction and enrichment using the miRTarBase database, Gene Ontology (GO), and KEGG pathway enrichment tools.

first: Eric

last: Lazartigues

first: Huijing

last: Xia

first: Mortaza

last: Eivazi

first: Ayushi

last: Patel

first: Stacey

last: Miller


title: Ligature-induced periodontitis (LIP) induces rapid alveolar bone loss followed by gingival immunosuppressive conditions

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

overall_design: LIP was induced in male B6 mice, and in part of the mice, the ligature was removed on day 3

first: Netanely

last: Yasmin

first: Hovav

last: Avi-Hai


title: Derivation and analysis of human somatic sensory neuron subtypes facilitated through fluorescent hPSC reporters

first: Joriene

middle: C

last: de Nooij

address: 650 West 168th Street

department: Neurology

institute: Columbia University

summary: Peripheral sensory neuropathy (PSN) is associated with several devastating neurological conditions, yet effective strategies to prevent or alleviate the consequences of PSN are nearly non-existent. A major challenge in the development of better therapeutic interventions is the lack of appropriate human model systems. Human induced pluripotent stem cell (hiPSC)-derived somatosensory neurons present a promising strategy to overcome this issue but remain of limited translational utility, in part due to the low efficiency and lack of sensory subtype selectivity of the existing sensory neuron derivation protocols. To improve upon iPSC-based somatosensory disease models, we here describe the generation and validation of a genetic toolset to fluorescently label all or distinct (nociceptor, low threshold mechanoreceptor, and proprioceptor) somatosensory subtypes. These new resources will be transformative for hPSC-based approaches in PSN disease modeling - a critical step towards translating new findings into clinically relevant therapeutic strategies.

overall_design: Gene edited (AVIL:tdT) Rues2 hESCs were subjected to three different sensory differentiation protocols to bias neurons to either a 'nociceptor', 'low threshold mechanoreceptor', or 'proprioceptor' phenotype. Neurons were matured to days in vitro (DIV)60 and RNA was isolated for 10x genomics.


title: A Multi-Gene Signature Predicting 1-Year Survival in Stage I Liver Cancer: Integration of Preclinical and TCGA Data

city: Washington

first: Rabindra

last: Roy

state: District Of Columbia

address: 3900 Reservoir Rd NW, Preclinical Science Building, Room# LF05

department: Oncology/Lombardi Comprehensive Cancer Center

institute: Georgetown University

summary:
This study used the Long Evans Cinnamon (LEC) rat model of Wilson's Disease and Hepatocellular Carcinoma (HCC), along with data from The Cancer Genome Atlas (TCGA) human database, to create a novel biomarker panel.  We generated and analyzed a rat microarray gene expression profile by comparing liver tumor tissues with adjacent normal tissues from the same animals, covering approximately 30,000 genes. The microarray results were translated into a five-gene panel that predicts 1-year survival probability in Stage I liver cancer patients using TCGA data in combination with machine learning and bioinformatics approaches.
The 5-year panel of five genes demonstrated robust performance throughout validation, particularly in predicting 1-year survival in Stage I patients.

overall_design: To understand the difference in gene expression between the tumor and the adjacent normal tissue, we performed a gene expression microarray using total RNA. Total RNA was isolated from the 84-week adjacent normal and 84-week tumor LEC liver tissue and analyzed by Affymetrix Rat microarray.

first: Ritam

last: Adhikari

first: Bhaskar

last: Kallakury

first: Chiranjeev

last: Dash


title: Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes

city: Singapore

first: Yue

last: Wan

address: 60 Biopolis Street, Genome

country: Singapore

institute: Genome Institute of Singapore

summary: Alternative splicing patterns have diverged rapidly during vertebrate evolution, yet the mechanisms and functional consequences of species-dependent splice isoform differences are not well understood. Through an integrative analysis of genome-wide predictions of highly stable RNA duplexes, alternative splicing profiles, and proximity ligation-detection of RNA-RNA interactions in vivo, we observe evidence that the majority of long-range intronic RNA duplexes are mediated by inverted Alu-repeat elements, and that these structures are associated with widespread exon skipping in primates. Our results further reveal evidence that Alu-derived RNA duplexes have contributed to divergence in alternative splicing patterns during mammalian evolution.

overall_design: We applied SPLASH (Sequencing of Psoralen crosslinked, Ligated, and Selected Hybrids) to capture RNA secondary structures and RNA–RNA interactions in human nascent transcripts. Briefly, cultured human K562 cells were crosslinked in vivo at RNA base-paired regions. Following crosslinking, chromatin fractionation was performed to enrich chromatin-attached nascent RNA. Genomic DNA and ribosomal RNA were depleted to further enrich for the nascent RNA population. The crosslinked RNA base-paired regions were then biotin-labeled, and the RNA was fragmented before streptavidin affinity purification. The resulting double-stranded RNA molecules were proximity-ligated to form chimeric molecules, followed by reverse crosslinking. These molecules then underwent standard RNA-seq workflows, including reverse transcription, library preparation, and high-throughput sequencing.

first: Hyunbeen

last: Lee

first: Xinang

last: Cao

first: Guillermo

last: Parada

first: Ira

middle: A

last: Iosub

first: Jernej

last: Ule

first: Benjamin

middle: J

last: Blencowe


title: Constitutive AMPK activation prevents HCC through inhibition of HNF4a

city: Houston

first: Jeanine

middle: L

last: Van Nostrand

state: TX

address: One Baylor Plaza M502C Van Nostrand

department: Molecular and Cellular Biology

institute: Baylor College of Medicine, Houston

summary: Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality and is largely driven by metabolic disorders such as obesity and Type 2 Diabetes. The AMP-activated protein kinase (AMPK) is a master regulator of metabolism, and its activation has been proposed as a therapeutic strategy for treating metabolic disorders. However, while AMPK activity is downregulated in HCC, the precise role of AMPK in HCC development has not been clearly delineated. Here, we investigated the ability of constitutive AMPK activation to prevent HCC development using a constitutively active AMPK transgenic mouse model and a pharmacological AMPK activator. We observed that AMPK activation significantly reduced tumor formation in both diethylnitrosamine (DEN)-induced and streptozocin-induced (STAM) models of HCC via altered bile acid metabolism and inhibition of hepatic nuclear factor alpha (HNF4) signaling. These findings provide mechanistic insights into AMPK biology and highlight the potential of AMPK as a therapeutic target, emphasizing the intricate interplay between metabolic dysregulation and cancer development.

overall_design: ChIP-seq of HNF4a from livers of wild-type and AMPK constitutively active mice following 14 days of exposure to high fat diet and doxycycline.

first: Zhen

last: Sun

first: Bernard

last: Linares

first: Cassidy

last: Urdiales

first: Fiyad

last: Al-sarmi

first: Boyuan

last: Sang

first: Nagireddy

last: Putluri

first: Jeanine L


title: PROTECTION OF TELOMERES 1b safeguards the Arabidopsis genome by regulating ROS homeostasis

city: College Station

first: Dorothy

middle: E

last: Shippen

address: 300 Olsen Blvd

department: Department of Biochemistry & Biophysics

institute: Texas A&M University

summary: Telomeres safeguard the genome, acting as sentinels of oxidative stress and preventing chromosome ends from eliciting a DNA damage response. PROTECTION OF TELOMERES 1 (POT1) is a highly conserved telomere protein, essential for chromosome integrity and telomeric DNA replication. Arabidopsis thaliana encodes two divergent POT1 paralogs: AtPOT1a stimulates telomerase activity, but AtPOT1b function is unknown. Here we show that AtPOT1b modulates reactive oxygen species (ROS) homeostasis. Oxidative stress induces AtPOT1b expression and telomeric accumulation, while AtPOT1b inactivation elevates ROS, increases telomeric and genome-wide oxidation, and causes stochastic telomere length changes. To address how AtPOT1b controls ROS, we report its localization in nuclei and peroxisomes, and association with catalases and peroxidases that enhance ROS scavenging. Impairing AtPOT1b-CAT2 interaction increases ROS accumulation and telomeric oxidation. Moss or human POT1 rescues ROS overaccumulation in Arabidopsis pot1b mutants, but not telomere deficiency in pot1a pot1b mutants, supporting a conserved role for POT1 in modulating ROS homeostasis and genome stability, distinct from canonical telomeric functions.

overall_design: RNA-seq profiling of Arabidopsis wild-type and pot1b mutant seedlings under Zeocin and mock treatment

first: Ji-Hee

last: Min

first: Claudia

last: Castillo-González

first: Borja

last: Barbero Barcenilla

first: In-Cheol

last: Yeo

first: Xiaoyuan

last: Xie

first: Sreyashree

last: Bose

first: Fausto

last: Andres Ortiz-Morea

first: Di

last: Liu

first: Eli

last: Canal

first: David

last: Curtis

first: Monisha

last: Yerram

first: Joonyoung

last: Shin

first: Pavel

last: Ulianich

first: Chinmay

last: Phadke

first: Ping

last: He

first: Andrzej

middle: T

last: Wierzbicki

first: Junjie

last: Zhang

first: Eugene

middle: V

last: Shakirov

first: Thomas

last: Juenger


title: A hierarchy of luminal transcription factors defines AR cistrome and is lost in neuroendocrine prostate cancer

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: Androgen receptor (AR) is a hormonal transcription factor (TF) that binds to cis-regulatory elements of prostate lineage-specific genes to govern androgen response and progression of prostate cancer (PCa). This AR cistrome has been reported to be controlled by multiple chromatin-pioneering factors such as FOXA1, HOXB13, and GATA2. However, how these pioneer factors cooperate to regulate the AR cistrome remains unclear. Here, through comparative ChIP-seq analyses, we found that FOXA1 alone was sufficient to recruit AR to its binding sites regardless of H3K4me1. FOXA1 further enlisted HOXB13 and/or GATA2 to augment AR binding and enhancer activation, while HOXB13 and/or GATA2 alone were unable to recruit each other, nor AR. Moreover, HOXB13 knockdown attenuated AR and GATA2 expression and chromatin binding but failed to reprogram their cistromes, suggesting a role as a cofactor rather than a pioneer factor.

overall_design: ChIP-seq of control and knockdown of various transcription factors and histone modifications were performed in LNCaP cells to understand the hierarchy. Some ChIP-seq and all RNA-Seq and RRMS were previously published at GSE69045 and GSE239278.

first: Viriya

last: Keo

first: Xiaodong

last: Lu

first: Lourdes

last: Brea

first: Xianglin

last: Shi

first: Jonathan

last: Zhao


title: A dopamine D1-like receptor agonist ameliorates stab wound-induced brain injury through its immunosuppressive effect

city: Toon

first: Mohammed

last: Choudhury

state: Ehime

address: 454 Shitsukawa

department: Anesthesia and Perioperative Medicine

country: Japan

institute: Ehime University Graduate School of Medicine

summary: Traumatic brain injury (TBI) causes progressive nervous tissue degeneration long after the initial injury due to secondary neuroinflammatory reactions. G protein-coupled dopamine D1-like receptors, which elevate intracellular cAMP levels, have been shown to mediate the suppressive effects on lipopolysaccharide (LPS)-induced proinflammatory activation of microglia and macrophages. The present study investigated whether or not the D1-like receptor-specific agonist SKF-81297 (SKF) administered intraperitoneally once daily for 3 days starting 1 h after TBI could ameliorate TBI in a rat model of stab wounds in the forebrain. SKF reduced the volume of TBI-induced brain tissue loss, increased mobile activity, and ameliorated cognitive dysfunction two months after TBI. A single dose of SKF suppressed the expression of IL-1β and TNFα in brain tissue by reducing oxidative injury 24 h post-TBI. SKF decreased the energy metabolism of microglia, macrophages, and neutrophils in TBI brain. SKF prevented LPS-induced translocation of NFκB into the nuclei of primary cultured microglia. The agonist clenbuterol (CLB) for adrenergic β2 receptor, another Gs-linked GPCR, exerted comparable ameliorative effects in TBI model rats by suppressing neuroinflammation. In summary, SKF may exert anti-inflammatory effects by suppressing the NFB pathway through increasing cAMP similarly to CLB and also by decreasing energy metabolism of inflammatory cells, leading to amelioration of TBI-induced brain degeneration.

first: MohammedE

first: Ayane

last: Takenaga

first: Haruto

last: Yamamoto

first: Hiroto

last: Yamauchi

first: Emiri

last: Koga

first: Naoki

last: Abe

first: Noriyuki

last: Miyaue

first: Shirabe

last: Matsumoto

first: Keisuke

last: Sekiya

first: Akari

last: Kusakawa

first: Naohito

last: Tokunaga

first: Koichi

last: Tanaka

first: Takeharu

last: Kunieda

first: Masahiro

last: Nagai

first: Junya

last: Junya

first: Tasuku

last: Nishihara


title: Beyond dormancy: organ-specific gene regulatory networks control winter development in peach buds

city: Legnaro

first: Giovanni Battista

last: Tornielli

state: Padova

address: Viale dell'Università, 16

department: DAFNAE

country: Italy

institute: University of Padova

summary: Bud dormancy in temperate perennials is traditionally conceptualized as a stereotyped state of developmental repression triggered by environmental cues. However, whether this model applies uniformly to different bud types remains unclear. Here, we investigate the development of vegetative and flower buds in Prunus persica under the same winter conditions, integrating anatomical, hormonal, and transcriptomic data with network inference and interaction assays. Vegetative buds, though assumed to be quiescent, show progressive histological differentiation and sustained transcriptional activity during chilling accumulation, akin to flower buds. Despite similar ABA/GA profiles, divergent transcriptional outputs suggest bud-specific hormone integration. Co-expression analysis identifies jasmonate-linked modules responsive to photoperiod in vegetative buds, while chilling-responsive modules centered on SVP1 characterize floral buds. A subset of SVP–DAM interactions was confirmed via BiFC, revealing physical associations between SVP1 and DAM3, DAM5, and DAM6. Additional DAM/SVP regulatory combinations were inferred from GRN analysis. These networks reveal distinct regulatory architectures: DAM5/6 homodimers prevail in vegetative buds, while DAM–SVP heterodimers, especially involving DAM4 and SVP1/2, dominate in floral buds. Together, these findings challenge the dormancy paradigm and support a revised model in which cold-season development is orchestrated by bud-specific regulatory programs shaped by organ identity and environmental cues.

overall_design: Transcriptomic data from peach vegetative and flower buds sampled during various stages of chilling accumulation during winter development.

first: Joseph

last: Justin

first: Perrella

last: Giorgio

first: Aiese Cigliano

last: Riccardo

first: di Marisco

last: Marco

first: Canton

last: Monica

first: Carrera

last: Esther

first: Conti

last: Lucio

first: Bonghi

last: Claudio

first: Varotto

last: Serena


title: m6A RNA methylation in the maintenance of X-chromosome inactivation and X to autosome dosage compensation in early embryogenesis [RNA-Seq]

city: Bangalore

first: SRIMONTA

last: GAYEN

state: Karnataka

address: GE14, new biological science building, Indian institute of Science

department: Department of Developmental biology and Genetics

country: India

institute: Indian Institute of Science, Bangalore, India

summary: In females, inactivation of one X-chromosome balances the dosage of X-linked genes similar to males. In addition, transcriptional upregulation balances the dosage of genes expressed from the single active-X  to the double copy of autosomes in both sexes. However, the factors and mechanisms involved in the maintenance  of X-chromosome inactivation (XCI) and X to autosome dosage compensation remain poorly understood. In this study, we report the contribution of m6A RNA methylation in maintenance of XCI and X to autosome dosage compensation in early embryonic and extraembryonic lineages. In the study, we find that m6A RNA methylation has a minimal role to play in maintenance of silencing of the inactivated-X chromsoome in TSC, XEN and EpiSC .  Moreover, we also show that the X-linked transcripts are less enriched with m6A than the autosomal transcripts suggesting its role in increased X-transcript stability and hence upregulation.  In addition, surprisingly  we observed that X-linked transcripts without m6A are fully dosage compensated than the transcripts with m6A which undergo partial X to autosome dosage compensation in TSC, XEN and EpiSC. Further, we also found that global depletion of m6A level in TSC, XEN and EpiSC has a minor effect on the  X to autosome dosage balance implicating the minor contribution of m6A RNA methylation during early embryogenesis.

overall_design: Allelic RNA-seq analysis in DMSO and STM2457 (METTL3 inhibitor) treated TSC, XEN, and EpiSC cell lines upon 12 hours of inhibition.

first: Runumi

last: Baro

first: Hemant

last: Naik

first: Amritesh

last: Sarkar

first: Srimonta

last: Gayen


title: TNF-α Deficiency Underlies NK Cell Dysfunction in Colorectal Cancer

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

institute: La Sapienza University of Rome

summary: Natural killer (NK) cells are central to innate antitumor immunity, yet their function is systemically compromised in colorectal cancer (CRC). We show that CRC patients exhibit early and pronounced alterations in peripheral blood NK cells, marked by a reduced frequency of total CD56⁺ cells, a shift toward CD56lowCD16⁺ subset, and impaired cytotoxic and cytokine responses. Notably, plasma from CRC patients, particularly those with advanced disease, induces similar dysfunction in healthy donor (HD) NK cells, suppressing mTORC1 signaling and effector activity. Transcriptomic profiling of HD NK cells exposed to CRC plasma revealed downregulation of TNF-α signaling components, concordant with reduced systemic and intracellular TNF-α levels in patients. Additionally, CRC plasma suppressed the JAK-STAT pathway and upregulated SOCS family genes, further dampening NK cell responsiveness. Inhibition of TNF-α in HD NK cells recapitulated the CRC plasma–induced defects, while exogenous TNF-α partially restored NK cell function, including STAT5 and S6 phosphorylation. These findings uncover TNF-α signaling deficiency as a systemic mechanism of NK cell suppression in CRC, linking impaired metabolism to immune evasion. Targeting this axis may offer a novel strategy to reinvigorate NK cell–mediated antitumor immunity in CRC.

overall_design: For bulk RNA sequencing experiments, 10⁶ NK cells were isolated by fluorescence-activated cell sorting (FACS) using a FACSAria III cell sorter (BD Biosciences, San Jose, CA, USA). NK cells were defined as lineage-negative (CD3⁻CD14⁻CD19⁻CD5⁻CD4⁻), CD45⁺CD7⁺CD56⁺ cells and were sorted from the PB of three independent healthy HDs. Sorted NK cells were then co-cultured for 48 hours with 3% plasma obtained from either three different stage IV colorectal cancer (CRC) patients or matched HD controls. Following incubation, NK cells were harvested, and total RNA was extracted.

first: Helena

last: Stabile

first: Cinzia

last: Fionda

first: Laura

last: Beltrame

first: Giuseppe

last: Sciumé

first: Silvia

last: Ruggieri


title: Defining mechanism of action and resistance of novel Mycobacterium abscessus MmpL3 inhibitors

city: East Lansing

first: Robert

last: Abramovitch

state: MI

address: 2215 Biomedical And Physical Sciences

institute: Michigan State University

summary: Defining impact of two MmpL3 inhibitors, MSU-43085 and MSU-45683 on  M. abscessus gene expression

overall_design: M. abscessus was grown to mid-log phase (OD600 of ~0.5 to 1), diluted to an OD of 0.5, and aliquoted in T25 flasks, 20 mL each. In duplicates, flasks were treated with 5 x the MIC of two MmpL3 inhibitors (MSU-43085, MSU-45683) or equivalent volume DMSO as the negative control and incubated standing at 37°C for 24 hours. Total bacterial RNA was then extracted as described by Baker, Johnson, and Abramovitch, and RNA-seq data was analyzed using the QIAGEN CLC genomics workbench software. Differentially expressed genes were defined as those with at least a 1.5-fold change from the control and an FDR p-value <0.05.

first: Bassel

last: Abdalla


title: IgA autoantibodies trigger pro-inflammatory, pro-fibrotic and type I interferon responses in Hidradenitis suppurativa skin lesion

city: Bethesda

first: Kan

last: Jiang

state: MD

address: 9000 Rockville Pike

institute: NIAMS/NIH

summary: Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease with complex immune dysregulation. While previous studies have reported tertiary lymphoid structures (TLS) and IgA-producing B cells in HS lesions, the pathogenic role of IgA autoantibodies remains poorly understood. Here, we demonstrate that lesional HS skin exhibits elevated expression of IGHA1, IGHA2, and J chain, as confirmed by qPCR, immunofluorescence, and western blot analyses. Single-cell RNA sequencing identified local plasma and B cells as the primary source of IgA. Autoantigen profiling revealed a diverse repertoire of IgA autoantibodies targeting nuclear, cytoplasmic, and membrane antigens, including MDA5, complement C3/C4, NLRP1, and ACE, with levels correlating with disease severity. We identified IgA autoantibodies targeting CD68⁺ macrophages, which induced secretion of TNF, IL-6, and IL-1β, and upregulated inflammasome and fibrotic pathways. Anti-NET IgA was elevated in HS and promoted NET formation, establishing a pathogenic feedback loop. NET–IgA immune complexes activated M2 macrophages to secrete CCL18, driving collagen production by fibroblasts and promoting a type I IFN signature. IgA immune complexes presented by myeloid dendritic cells activated CD4⁺ T cells, triggering IFN-γ production, further amplifying local inflammation. Direct exposure of fibroblasts to NET–IgA complexes triggered expression of adhesion molecules, chemokines, and regulators of adaptive immunity. Together, these findings uncover a novel role for IgA autoantibodies in HS, implicating them as central drivers of chronic inflammation, fibrosis, and immune crosstalk across neutrophils, macrophages, fibroblasts, and T cells.

overall_design: M2 macrophages treated with control IgA or HS IgA purified from skin tissue using protein M, skin fibroblasts incubated with NETs or NET + IgA, or skin fibroblasts incubated with supernatants of macrophages exposed to NETs or NET + IgA

first: Carmelo

last: Carmona-Rivera

first: Liam

last: O’Neil

first: Eduardo

last: Patino-Martinez

first: William

last: Ambler

first: Mariana

last: Kaplan


title: Effects of topological domain disruption on transcriptional regulation are chromatin context dependent

city: Mexico City

first: Angel

middle: Josue

last: Cerecedo-Castillo

state: Coyoacan

address: Circuito Exterior s/n Ciudad Universitaria

department: Molecular Genetics

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: The three-dimensional (3D) chromatin organization within the nucleus is essential for regulating gene expression by facilitating interactions between cis-regulatory elements while insulating domains to restrict non-specific interactions. CTCF and cohesin, key architectural proteins, form topologically associated domains (TADs) that play a significant role in this spatial organization. While previous studies have demonstrated that TAD boundaries function to insulate genes from inappropriate interactions with distal enhancers or silencers, the functional impact of these boundaries on gene expression remains highly complex and context dependent. Here, we investigate the topological organization of the Notch1 locus, a gene involved in cell fate determination and cancer, to understand the regulatory impact of TAD boundaries on gene expression. We identified a highly conserved topological domain surrounding Notch1, with CTCF and cohesin binding at both 5' and 3' boundaries. Deletion of these boundary elements via CRISPR-Cas9 led to a significant increase in Notch1 expression, as well as enhanced expression of neighboring non-coding RNAs (Nalt1 and Linc01451) within the domain. Disruption of these boundaries also resulted in altered cell proliferation and colony formation. These effects correlated with altered enhancer-promoter interactions within the domain, especially involving a key enhancer located within the Linc01451 gene. Cross-species analyses revealed that the Notch1 domain and its boundary organization are conserved in mice, where perturbations similarly influenced Notch1 expression and cellular phenotypes in mouse embryonic stem cells (mESCs) but had minimal effects in murine erythroleukemia (MEL) cells. Together, these findings suggest that CTCF-dependent topological boundaries play a critical role in insulating the Notch1 locus and maintaining precise expression levels in a chromatin context- dependent manner, highlighting a regulatory mechanism that may extend to other lineage-specific and disease-relevant genes.

overall_design: 4C-seq Profiling of K562 Wild-Type and Mutant Cells at CTCF-Depleted Sites in the Notch1 Locus

first: Diana

middle: I

last: Mojica-Santamaría

first: Hober

middle: N

last: Núñez-Martínez

first: Carlos

last: Perlata-Alvarez

first: Gustavo

last: Tapia-Urzúa

first: Georgina

last: Guerrero

first: Rodrigo

middle: G

last: Arzate-Mejía

first: Félix

last: Recillas-Targa


title: Low intensity proton beam irradiation downregulates antioxidative protection in Aspergillus nidulans

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: The effect of a simulated solar particle event on the fungus Aspergillus nidulans was investigated by exposing surface cultures to a low intensity proton beam (10 pA) and comparing their transcriptomes with those of untreated cultures. Results showed upregulation of DNA repair, ribosome biogenesis, and protein ubiquitination genes, while glycolysis, and respiration genes were downregulated. Surprisingly, antioxidative enzyme genes were bulk-downregulated, increasing susceptibility to oxidative stress induced by menadione sodium bisulfite (MSB). Experiments with an oxidative stress-sensitive mutant and MSB-pretreated cultures suggested that oxidative stress protection was crucial for surviving proton radiation. Therefore, down-regulation of antioxidant enzyme genes was not an adaptive response, but probably a consequence of a disturbance in redox sensing caused by reductive pre-hydrated electrons from water radiolysis. These results shed light on the complex interaction between radiation stress and fungal responses, which could lead to the potential exploitation of the underlying mechanisms in real space environments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mycelia of Aspergillus nidulans reference strain under proton irradiated and untreated conditions with three biological replicates.

first: Tamás

first: Barnabás Cs.

last: Gila

first: Károly

last: Antal

first: István

last: Pócsi


title: Chronic ER Stress Induced of Cell-surface Chaperones as the Therapeutic Targets of CAR Cells in Acute Myeloid Leukemia

city: Kunming

first: ZHENFEI

last: ZHONG

state: Yunnan

address: East Outer Ring Road,Chenggong District

institute: Institute of Biomedical Research, Yunnan University

summary: Acute myeloid leukemia (AML) is a heterogeneous disease characterized by a clonal expansion of myeloid progenitors that affects the bone marrow. Despite advancements, survival rates of the treatments for AML remain still low, due to the heterogeneity and lack of specific targets, necessitating new precision therapies. Through integrative cell surface proteomes and cell biology analyses, we identified various potential neoantigens including endoplasmic reticulum (ER) chaperone proteins forced by chronically oncogenic stress, translocated to cell surfaces of AML subtype (e.g., FLT3-ITD+ AMLs), making them as promising diagnostic markers and therapeutic targets. As proof-of-concept, we then engineered chimeric antigen receptor (CAR) natural killer (NK) cells to target cell surface localized HSP90B1, a representative ER resided chaperone protein, showing selective killing of csHSP90B1-positive AML cells in vitro and in animal models. Single-cell transcriptional analyses further revealed heterogeneous landscapes of myeloid lineage differentiation and uncovered a therapeutic window targeting the identified AML cell cluster with novel characteristics of adaptive oncogenic stress to eradicate these malignant cells via immunotherapeutic interventions. Collectively, our findings not only identify several neoantigens as the specific biomarkers for refining AML patient classification, but also hold a significant promise for AML precision treatment through using immunotherapy approaches.

overall_design: We generated multiple RNA-seq datasets from MV4-11, Molm13, RS4;11 cell lines and peripheral blood mononuclear cells (PMBCs) from healthy donors and FLT3-ITD+ AML patients. Additionally, we also created RNA-seq datasets from MV4-11 and Molm13 cells treated with quizartinib, one tyrosine kinase inhibitor (TKI), and HEK293-T cells treated with thapsigargin (TG), an ER stressor, serving as a reference for ER stress conditions.


title: JUN is a master mediator of resistance to MAPK pathway inhibition in KRAS-mutant pancreatic ductal adenocarcinoma.

city: Amsterdam

first: Astrid

last: Bosma

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

summary: Pancreatic ductal adenocarcinoma (PDAC) is often driven by KRAS mutations, but inhibitors targeting the most frequent KRAS substitutions in PDAC are not yet approved in the clinic. We previously discovered that KRAS-mutant PDAC are sensitive to the combination of SHP2 and ERK inhibitors, recently investigated in the Phase I/Ib clinical trial NCT04916236. Lately, RAS(ON) multi-selective inhibitors have entered clinical development, representing a promise for mono or combination therapies in PDAC. However, resistance may arise even for combination therapies. Here, we aimed at anticipating mechanisms of resistance to SHP2 plus ERK or RAS(ON) multi-selective inhibitors. Through unbiased CRISPR-based screenings, we identified mTOR and JUN hyperactivation as interconnected mechanisms that overcome MAPK suppression. Functional genetic and pharmacological experiments pointed at JUN as the most downstream resistance mediator, and indirect therapeutic target, using MAP2K4 inhibitors. Alterations in the PI3K/AKT/mTOR and JUN pathways may serve as biomarkers for sensitivity/resistance in clinical trials testing MAPK inhibitors combinations in KRAS-mutant PDAC.

overall_design: RNAseq profiling of Panc 10.05 cells wild type and PTEN KO (clones 2.6.2 and 2.1.4) either untreated or treated with the combination of SHP2 and ERK inhibitors for 24 or 72 hours.

first: Sara

last: Mainardi


title: Eukaryotic chaperone CCT5 or CCT7: a novel target for the regulation of embryonic stem cell state transition

city: Yangzhou

first: Jiali

last: Jiang

address: 98 Nantong West Road, Yangzhou City

institute: Northern Jiangsu People's Hospital Affiliated to Yangzhou University

summary: A deeper understanding of the molecular mechanisms underlying the transition to the totipotent state will broaden the foundations of developmental biology, and the underlying mechanisms of early cell fate decisions have been an important topic of investigation. Based on the previous sequencing data of different mouse early embryonic development, 236 and 267 factors were identified to be continuously up-regulated at stages of mouse early embryonic development (with at least two-fold change in the next stage compared with the previous stage), and the core key factors CCT5 and CCT7 were selected. CCT5 and CCT7, as important members of the CCT family of chaperone proteins, are key regulators of telomerase transport, and their depletion will lead to the loss of TCAB1 protein and impair telomere maintenance. However, their role in the state transition of embryonic stem cells (ESCs) needs further investigation. Here, we show that defects in CCT5 or CCT7 affect the maintenance of telomere length, which in turn activates DNA damage pathways, induces epigenetic reprogramming, promotes cells into a state of enhanced plasticity and promotes the activation of repeat sequences and 2C gene programs to generate universal 2-cell-like cells. Thus, CCT5 and CCT7 may be epigenetic barriers to the transition from pluripotency to the totipotent state. At the same time, CCT5 or CCT7 may activate WNT signaling pathway by promoting β-catenin nuclear translocation, promote the expression of specific factors such as Esrrb, and regulate the pluripotent state of ESCs.

overall_design: To further explore whether CCT5/7 is a barrier to the transition from pluripotency to totipotency, mESCs with knockdown of Cct5 or Cct7 (Cct5 KD, Cct7 KD) were generated.   Mouse ESCs were infected with virus solution containing pLKO-Tet on-Puro vector as control cells, and mESCs were infected with virus solution prepared with pLKO-Tet on-shRNA Cct5-puro or pLKO-Tet on-shRNA Cct7-puro plasmid as target gene knockdown cell lines.   The cells were cultured with puromycin (0.5 μg/ml) for 14 days and positive clones were selected for identification.   The expression of the transgene was induced by 2 μg/mL doxycycline (Dox) for 2 days, and the control group was treated with the same concentration of Dox for the same time.   Dox was induced continuously and could be stably knock down. Cell cultures were mainly serum + Lif cultures.  We further performed RNA-seq on Cct5 KD, Cct7 KD and their control cells.


title: Heterologous Prime-Boost Immunization of AAV-based Neoantigen Cancer Vaccine Induces Anti-Tumor Immunity to Inhibit Tumor Growth and Relapse

city: Taichung

first: ChihYang

last: H

address: No.2 Rude Rd

country: Taiwan

institute: China Medical University Hospital

summary: Therapeutic cancer vaccines, which induce anti-tumor immunity by targeting specific antigens, constitute a promising approach to cancer therapy. Our previous work developed a novel engineered adenovirus-associated virus (AAV)-based tumor-specific (neoantigen) cancer vaccine to boost antitumor immunity in combination with radiotherapy, resulting in tumor regression and less distant metastasis. However, the therapeutic efficacy of constitutive vector-based vaccination may be limited by poor immunogenicity, pre-existing vector-specific immunity, and vaccine-induced vector-specific immunity. Here, we examined the combinational therapeutic efficacy of AAV-based cancer vaccine, local radiotherapy and immune checkpoint blockade (ICB) in two poor immunogenic cancer animal models. We found that administration with AAV-based neoantigen vaccine significantly increased the response to radiotherapy and ICB, and decreased the risk of distant metastasis. Furthermore, we evaluated a heterologous prime-boost immunization strategy using two optimized AAV serotype vaccines to amplify tumor-specific immunity to neoantigens. These optimized AAV2/AAV6 neoantigen vaccine displayed strong immunogenicity with potent induction of CD8+ T cells. As combined with local radiotherapy, the prime-boost vaccine induced superior tumor clearance and survival compared with other groups. Remarkably, optimized AAV2/AAV6 vaccination promoted CD8+ T-cell infiltration in the tumors, and elicited the enrichment of T cell clones. Furthermore, exhausted T cell marker expression was significantly decreased in the tumor-infiltrating CD8+ T cells. Taken together, these results highlight the synergistic potency of engineered AAV2/AAV6 vaccines combined with local radiotherapy for poor immunogenic cancers.

overall_design: 1. AAV2-Vec and AAV6-Vec; 2. AAV2-neoAg and AAV6-neoAg; 3 AAV2-neoAg and optimized AAV6-neoAg; 4. AAV2-Vec and AAV6-Vec+ RT; 5. AAV2-neoAg and AAV6-neoAg+ RT; 6. AAV2-neoAg and optimized AAV6-neoAg+RT

first: Chi-Hsien

last: Huang

first: Hsin-Yu

last: Chang

first: Jhen-Yu

last: Chen

first: Wei-Ze

last: Hong

first: Yi-Wen

first: Chien-Yueh

last: Lee

first: Chia-Hsin

last: Wu

first: Chia-Hisn

first: Yu-Sen

last: Lin

first: Yuan-Yao

last: Tsai

first: Wei-Ling

last: Kao

first: K. S. Clifford

last: Chao

first: Kevin Chih-Yang


title: The long noncoding RNA lnc13 restrains inflammatory responses to maintain oral tolerance to gluten

city: New York

first: Ruxiao

last: Yang-Fischer

institute: Columbia University

summary: Celiac disease (CeD) is an autoimmune disorder triggered by dietary gluten. While HLA-DQ2/8-mediated presentation of gliadin peptides is required for disease, the mechanisms that underlie the loss of oral tolerance to gluten remain incompletely understood. Long noncoding RNAs (lncRNAs) have been increasingly recognized as regulators of immune function, yet their role in oral tolerance has not been previously explored. Using a screen designed to identify lncRNAs responsive to T  cell activation and enriched for CeD-associated GWAS variants, we identified lnc13 as a top candidate. In HLA-DQ8 transgenic mice lacking lnc13, unmanipulated gluten ingestion led to hallmark features of loss of oral tolerance to gluten:  reduced regulatory T cells, and increased IFN-γ⁺ lymphocytes, IL-12⁺ myeloid cells, cytotoxic intraepithelial immune cells and crypt hyperplasia in the small intestine. Mechanistically, lnc13 binds specific DNA regulatory regions and limits inflammatory responses to pro-inflammatory signals. In particular, lnc13 restrains IL-15-driven differentiation of CD8⁺ NK-like lymphokine-activated killer cells—an IL-15–dependent pathway strongly implicated in CeD. These findings establish lnc13 as a critical noncoding modulator of oral gluten tolerance.

overall_design: data include: gluten challenged lnc13-KO-DQ8 and lnc13-WT-DQ8 mice whole tissue, LPLs or IELs subjected for RNA-seq;IEL CD8ab+ T cells post gluten challenge are also subjected to RNA-seq; lnc13 RAP-DNA-seq; and lnc13 WT and KO CD8a+ IELs after 48h cultured in IL-15.

first: Sankar

last: Ghosh


title: Single-cell sequencing of human PBMCs are exposure to CPMV

city: La Jolla

first: Nicole

last: Steinmetz

state: CA

address: 9500 Gilman Drive

institute: UCSD

summary: Cowpea mosaic virus (CPMV) is a potent immunomodulator with anti-tumor function. CPMV is being developed as an intratumoral immunotherapy candidate for clinical translation. A fundamental question is understanding how CPMV modulates the immune system through genetic/transcriptomic changes. This experiment outlines how CPMV exposure reprograms immune cells toward anti-neoplastic functions.

overall_design: Human PBMCs were isolated from three deidentified donors. These PBMCs were incubated with CPMV (a nontreated group was included) before RNA isolation and processing.

middle: F

first: Marina

last: Dobrovolskaia

first: Bao

last: Tran

first: Yongmei

last: Zhao

first: Shaojun

last: Xie


title: Novel Stem Cell Model Uncovers Macrophage-Mediated Antiviral Immunity and Repair in Human Type 2 Alveolar Epithelial Cells

city: Parkville

first: Michael

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

summary: The lung alveoli are constantly exposed to inhaled pathogens and inorganic hazards, relying on robust defence mechanisms to maintain homeostasis. Alveolar macrophages and type 2 alveolar epithelial cells (AT2s) collaborate to orchestrate protection. Compromised defence can dysregulate immunity and repair, leading to acute and chronic respiratory diseases. To better understand these processes and drive therapeutic discovery, human model systems that capture key cell interactions are essential. Here, we develop the first induced pluripotent stem cell (iPSC)-derived platform that integrates AT2 cells and macrophages in an air-liquid interface. Coculture enhanced AT2-specific gene expression and lipid synthesis, while macrophages actively metabolised surfactant. iPSC-derived AT2s supported macrophage survival by producing M-CSF, promoting an alveolar macrophage-like phenotype. Additionally, macrophages played a crucial role in modulating proinflammatory signalling, enhancing antiviral immunity, and restricting viral replication during respiratory infections. Furthermore, we identify a role for iPSC-derived macrophages in epithelial repair, a process disrupted by VEGF signalling. We present an iPSC-derived platform to study AT2-macrophage interactions in homeostasis, infection, and repair, offering valuable insights into their roles in respiratory disease initiation and progression.

overall_design: Monocultured iAT2s and iMacs, iAT2-iMac co-cultures, as well as RSV infected iAT2s, iMacs and iAT2-iMac cocultures were captured and sequences for scRNA-seq using 10X Flex workflow (10X-1000475) at 48 hours post infection.

first: Declan

last: Turner

first: Hannah

last: Baric

first: Katelyn

last: Patatsos

first: Sahel

last: Amoozadeh

first: Kathleen

last: Strumila

first: Jack

last: Murphy

first: Liam

last: Gubbels

first: Melanie

last: Neeland

first: Shivanthan

last: Shanthikumar

first: Sarah

last: Londrigan

first: Mirana

last: Ramialison

first: Fernando

last: Rossello

first: Ed

last: Stanley

first: Rhiannon

middle: B

last: Werder


title: Acute high-dose irradiation disrupts cell adhesion and Silk-Ovarioid formation in human primary ovarian cells

city: Solna

first: Tianyi

last: Li

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary:
Background
Radiotherapy is a cornerstone of cancer treatment; however, its effects on healthy ovarian somatic cells remain largely unexplored. This study addresses this gap by investigating how human cortical and medullary primary ovarian cells (cPOCs and mPOCs, respectively) respond to acute, high-dose X-ray exposure in vitro.

Methods
Ovarian tissue was obtained from eight patients (aged 23–36 years) undergoing gender-affirming surgery at Karolinska University Hospital in Huddinge, Sweden. The tissue was separated into cortex and medulla and dissociated into cPOCs and mPOCs. Monolayer cultures of cPOCs and mPOCs were exposed to 10 Gy X-rays upon reaching confluency, or left unexposed as paired controls. Following irradiation, cells were assessed for ATP content and mitochondrial dehydrogenase activity, followed by immunofluorescence staining, bulk RNA sequencing (Illumina Stranded mRNA Prep Ligation protocol; sequencing on the Illumina NovaSeq 6000 platform), bulk proteomic analysis (liquid chromatography–tandem mass spectrometry), and a functional assay for assessing their ability to form 3D Silk-Ovarioids.

Results
While irradiation did not significantly affect cell viability, immunofluorescence analyses revealed alterations in DNA damage response, apoptosis, and cell cycle regulation. Transcriptomic analysis showed minimal changes at 1 h post-irradiation in both cPOCs and mPOCs. However, marked shifts in transcriptomic profiles were observed at 4 h (2,810 and 2,540 DEGs in cPOCs and mPOCs, respectively) and at 24 h (2,462 and 2,802 DEGs, respectively), including upregulation of the p53 pathway and downregulation of MYC targets, E2F targets, the G2/M checkpoint, and the mTORC1 pathway. At the proteomic level, differentially expressed proteins associated with cell adhesion, focal adhesion, and cadherin binding were detected at 24 h post-irradiation. Functionally, irradiated cells demonstrated an impaired capacity to self-organize into 3D Silk-Ovarioids, indicating compromised cell–cell adhesion.

Conclusion
These findings reveal a novel mechanism by which radiotherapy may damage ovarian tissue independently of follicular loss, underscoring the need for targeted strategies to preserve somatic cell function in fertility preservation protocols.

overall_design:
In total 50 samples collected from 5 patients were sequenced. Samples were derived from primary ovarian cells and 5 groups (i.e.,control_t1, control_t24, irradiated_t1, irradiated_t4, irradiated_t24) were included in the study. Two types (i.e., cortex and medulla) were used.

***************************************************************
Raw files for human/patient samples are being made available in Swedish National Data Service (SND) (DOI: [https://doi.org/10.48723/ya3w-an36]) for controlled access to the personally identifiable sequence data.
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first: Spyridon

last: Panagiotis  Deligiannis

first: Elisabeth

last: Moussaud-Lamodière

first: Akos

last: Végvári

first: Anastasios

last: Damdimopoulos

first: Darja

last: Lavogina

first: Kiriaki

last: Papaikonomou

first: Roman

last: Zubarev

first: Ganesh

last: Acharya

first: Agne

last: Velthut-Meikas

first: Pauliina

last: Damdimopoulou

first: Andres

last: Salumets

first: Valentina

last: Di Nisio


title: Comparative analyses of the Pacific oyster larvae exposed to the retiniic acid and its inhibitor Ro-41-5232

city: Exeter

first: Paul

middle: Andrew

last: O'Neill

state: --- Select a state ---

address: Stocker Road

country: United Kingdom

institute: University of Exeter

summary: Pacific oyster larvae were cultured at 22'C with or without 1uM retiniic acid or the 1uM retiniic acid receptor inhibitor,  Ro-41-5232 with triplicate. At 9hpf, RNAs were isolated, cDNA libraries were prepared and sequenced using Illumina HiSeq2500, 100bp paird end reading.

first: Kudoh

last: Tetsuhiro

first: Shimizu

last: Keisuke

first: Endo

last: Kazuyoshi


title: High resolution multi-scale profiling of embryonic germ cell-like cell derivation reveals pluripotent state transitions in humans [low_pass_karyotyping]

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: Primordial germ cells (PGCs) are the embryonic precursors of the gametes. In mice and rats, PGCs can readily acquire pluripotency in vitro by forming embryonic germ cells (EGCs). To date, a comparable in vitro system has not been established in humans, despite the fact that human PGCs (hPGCs) readily undergo pluripotent conversion in the context of germ cell tumorigenesis. Here we report that hPGC-like cells (hPGCLCs) undergo conversion to human embryonic germ-like cells (hEGCLCs) upon exposure to the same inductive signals previously used to derive mouse EGCs. This defined, feeder-free culture system allows efficient derivation of human EGCLCs which  can be expanded and maintained in standard human pluripotent stem cell medium. This new in vitro model captures the transition from the pluripotent stem cell state to a germ cell identity and back again, and therefore represents a highly tractable system to study pluripotent and epigenetic transitions, including those which occur during human germ cell tumorigenesis.

overall_design: We established a definer and feeder free protocol to reprogram hPGCLCs to EGCLCs. We then performed gene expression profiling analysis (bulk RNA-seq, scRNA-seq) but also DNA methlyation profiles on hiPSCs, iMeLCs, hPGCLCs and hEGCLCs at different time points.

first: Sarah

last: Stucchi

first: Lessly

middle: P

last: Sepulveda-Rincon

first: Camille

last: Dion

first: Giuseppe

last: Testa

first: Harry

last: Leitch


title: Senescent-like myofibers contribute to anti-regenerative cytokine signaling in Duchenne muscular dystrophy

city: Bunkyo-ku

first: Masanari

last: Ikeda

state: Tokyo

address: Yayoi 1-1-1

institute: the University of Tokyo

summary: Duchenne muscular dystrophy (DMD) is a genetic muscular disease characterized by progressive muscle degeneration. p16 is expressed in skeletal muscles and induces cellular senescence in a rat model of DMD, whereas its ablation enhances muscle regeneration. However, the mechanism underlying this phenomenon remains unclear. This study aimed to elucidate the mechanism for p16-induced DMD exacerbation. RNA-seq analysis revealed p16-dependent upregulation of cytokine gene expression in DMD rat skeletal muscles, which also altered the systemic blood cytokine profile. Furthermore, the effect of an altered humoral environment on muscle regeneration was assessed using the transplanted extensor digitorum longus muscle. Regeneration of grafted muscles from wildtype rats was suppressed in DMD rats but was significantly improved by p16 ablation. Notably, p16 was expressed in the myofibers of DMD rats, and enzymatically isolated myofibers from DMD rats also showed p16-dependent cytokine expression. Thus, cytokines secreted by senescent-like myofibers mediate the anti-regenerative niche in DMD rats, uncovering a novel mechanism for disease progression and potential therapeutic targets.

overall_design: The gene expression profile in the tibialis anterior muscle was compared between 9-month-old wild-type, DMD, and p16-null DMD rats (n=3, 3, 6) and between 3-month-old and 18-month-old wild-type rats (n=3, 3).

first: Yukie

last: Tanaka

first: Hidetoshi

last: Sugihara

first: Takashi

last: Matsuwaki

first: Keitaro

last: Yamanouchi


title: m6A RNA methylation in the maintenance of X-chromosome inactivation and X to autosome dosage compensation in early embryogenesis [MeRIP-Seq]

city: Bangalore

first: SRIMONTA

last: GAYEN

institute: Indian Institute of Science, Bangalore, India

summary: In females, inactivation of one X-chromosome balances the dosage of X-linked genes similar to males. In addition, transcriptional upregulation balances the dosage of genes expressed from the single active-X  to the double copy of autosomes in both sexes. However, the factors and mechanisms involved in the maintenance  of X-chromosome inactivation (XCI) and X to autosome dosage compensation remain poorly understood. In this study, we report the contribution of m6A RNA methylation in maintenance of XCI and X to autosome dosage compensation in early embryonic and extraembryonic lineages. In the study, we find that m6A RNA methylation has a minimal role to play in maintenance of silencing of the inactivated-X chromsoome in TSC, XEN and EpiSC .  Moreover, we also show that the X-linked transcripts are less enriched with m6A than the autosomal transcripts suggesting its role in increased X-transcript stability and hence upregulation.  In addition, surprisingly  we observed that X-linked transcripts without m6A are fully dosage compensated than the transcripts with m6A which undergo partial X to autosome dosage compensation in TSC, XEN and EpiSC. Further, we also found that global depletion of m6A level in TSC, XEN and EpiSC has a minor effect on the  X to autosome dosage balance implicating the minor contribution of m6A RNA methylation during early embryogenesis.

overall_design: MeRIP-seq was performed on total RNA isolated from female TSC, XEN and EpiSC cells.

first: Runumi

last: Baro

first: Hemant

last: Naik

first: Amritesh

last: Sarkar

first: Srimonta

last: Gayen


title: Dissecting the Role of Myf6 in Facilitating Fibroblast Conversion into Myogenic Progenitor and Differentiated Cells [ATAC-Seq]

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Conversion of fibroblasts into skeletal muscle cells by overexpression of the transcription factor MyoD has been widely employed over past decades in a multitude of experimental settings. However, the potential of additional myogenic regulatory factors such as Myf5, Myf6 and Myog to elicit a myogenic conversion has been significantly less studied. To address this disparity, we set out to investigate the role of MRFs in fibroblast conversion into skeletal muscle stem and differentiated cells. Surprisingly, we found that Myf6, a transcription factor associated with postnatal late-stage myogenesis, efficiently converted fibroblasts into myotubes alone, or alternatively into expandable Pax7-expressing induced myogenic progenitor cells (iMPCs) in the presence of defined small molecules. To investigate reprogramming dynamics in a tightly regulated system, we generated an inducible Myf6 overexpression transgenic mouse model, which enabled dissection of transcription and epigenetic dynamics unique to iMPC formation. Mechanistically, we characterized the chromatin binding of Myf6, as well as its protein binding partners, during iMPC reprogramming and conventional transdifferentiation, revealing shared and different targets and binding partners. To further investigate its role, we surprisingly found that endogenous Myf6 is dispensable for iMPC formation by MyoD and small molecules. In accordance with this observation, we demonstrated that subjecting MyoD-KO fibroblasts to reprogramming with Myf6 and small molecules gave rise to expandable MyoD-KO iMPCs, indicating that MyoD is similarly dispensable for iMPC formation and self-renewal. Multi-omics analyses of Myf6-derived MyoD-KO iMPCs uncovered upregulated genes that compensated for the lack of MyoD, whose downregulation during iMPC production mitigated Pax7 expression, highlighting their roles as reprogramming regulators. Collectively, these results illustrate a redundancy between MRFs’ function in myogenic cellular conversions, highlighting an unexpected potency for Myf6 in the induction of a muscle stem cell fate in vitro.

overall_design: TetO-Myf6 mouse embryonic fibroblasts (MEFs) were treated with doxycycline (dox) to induce Myf6 overexpression and/or Forskolin/RepSox/CHIR99021 (F/R/C) for 24h and subjected to ATAC-Seq to investigate chromatin accessibility changes

first: Giada

last: Bacchin

first: João

last: Agostinho de Sousa

first: Adhideb

last: Ghosh

first: Falko

last: Noé

first: Ori

last: Bar-Nur


title: Transient SUMOylation Inhibition In Human Pre-adipocytes Stably Imprints a Transcriptional Beiging Fate

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

summary: Adaptive thermogenesis, or beiging, involves the conversion of energy-storing white adipocytes into energy-dissipating beige adipocytes, enabling physiological adaptation to environmental stressors such as hypothermia. While white and beige adipocytes share a largely similar transcriptome, this identity shift requires significant transcriptional and epigenetic reprogramming. However, the molecular mechanisms governing this transition remain incompletely understood.  Here, we identify SUMOylation as a critical repressor of adipocyte beiging. Using the small-molecule SUMOylation inhibitor TAK-981, we demonstrate that transient SUMOylation inhibition primes human adipocytes to express beiging genes including UCP1 and induce mitochondrial uncoupling in a rosiglitazone-dependent manner. Furthermore, SUMOylation suppresses both the de novo differentiation of human adipose stem cells into beige adipocytes and the transdifferentiation of mature white adipocytes into beige cells. Mechanistically, TAK-981 modulates the cAMP-PKA-p38 signaling axis, ultimately affecting downstream transcriptional programs under the control of PPARG and PPARA enhancers.  Our findings establish SUMOylation as a fundamental barrier to white-to-beige adipocyte reprogramming and suggest that the pharmacological combination of PPARG partial agonists with TAK-981 could promote metabolically beneficial adipose tissue remodeling in clinical settings.

overall_design: RNA sequencing of differentiated immortalized human white adipocytes that have been treated transiently with TAK-981 and/or Rosiglitazone.


title: Innovative cancer-targeting antibody production strategy by using cancer-derived small Extracellular Vesicles (sEV)

city: Oklahoma City

first: Dongin

last: Kim

state: Oklahoma

address: 1110 N Stonewall Ave

department: Pharmaceutical Sciences

institute: University of Oklahoma Health Sciences Center

summary: Abstract Introduction: With all the advancements in the development of tumor-targeting agents, most of the research has showed that only less than 0.7% of targeted therapy arrives at the tumor site, suggesting high levels of off-target adverse reactions [1-3]. Therefore, developing a new tumor-targeting ligand that could enhance tumor-targeting efficacy seems inevitable. Here, we designed a novel tumor-targeting antibody production method using cancer-derived small Extracellular Vesicles (sEVs). Since sEVs inherit their structure and function from their parent cells [4] , the antibodies produced against sEVs could target both cancer cells and sEVs. Using this approach, antibody-decorated targeted systems may achieve superior tumor-targeting efficiency, potentially overcoming the suboptimal drug concentration in the tumor. Methods: The sEVs (150 ~200 nm) from ovarian cancer cell (OVCAR-8) were isolated and injected into mice. Once the specificity of the collected plasma from mice to the OVCAR-8 cells was confirmed, hybridoma cells were generated by fusing the mice’s B cells as the antibody-producing part and the myeloma cells. Among various monoclonal antibodies (mAbs) produced by different hybridoma cells, the best OVCAR-8-targeting mAb was isolated and purified. Next, the selected mAb was decorated to the surface of paclitaxel-encapsulated CD8+ T cell sEVs (AB-TSEV/P). Then the formulations including AB-TSEV/P were treated to the OVCAR-8-bearing mice and the changes in tumor volume and body weight was measured for 80 days. An in vivo biodistribution study of AB-TSEV loaded with IR-780 dye (AB-TSEV/IR) was then conducted using an IVIS Spectrum Imaging System to evaluate the accumulation of AB-TSEV/IR in the tumor site. Results: Based on the characterization results, the size of OVCAR-8-derived sEVs and CD8+ T cell sEVs were 150-200 nm. The plasma from mice after injection of sEVs showed specificity to OVCAR-8 cells through multifold cell killing efficacy over non-parent cancer and non-cancer cells. Based on our results from immunocytochemistry analysis, the selected monoclonal antibody had a significantly higher affinity to OVCAR-8 cells compared to non-cancerous cells. AB-TSEV/P decreased the tumor growth compared to formulations without mAb. Mice’s body weight was not changed significantly during the study. Also, in vivo biodistribution study showed that compared to control, AB-TSEV preferred a higher accumulation in the tumor. Conclusions: We developed a new strategy for antibody production using cancer cell sEVs. This antibody could target the sEV’s parent cells. Thus, a significant amount of the targeted formulation decorated with this antibody will potentially arrive at the tumor, overcoming the current suboptimal dose of cancer therapy. Although we only used ovarian cancer sEVs for this study, considering the potential of this approach, this technology can be applied to not only different cancers but also other diseases, where we can culture their cells and subsequently produce their sEVs.

overall_design: We Treated the OVCAR-8 cells with different conditions. We had 5 groups. First groups was untreated group (Untreated_1_S29, Untreated_2_S30 and Untreated_6_S27). Second was the cells that were treated with Antibody only (AB_1_S7, AB_2_S8 and AB_4_S9). Third group were the cells treated with antibody conjugated to a spacer (PEG) and anchor (BODIPY) (ASAB_1_S4, ASAB_3_S5 and  ASAB_6_S6). Fouth group was the cells treated with CD8+ T cell sEVs (TSEV_1_S1, TSEV_2_S2 and TSEV_3_S3). Fifth group was the cells treated with antibody decorated on CD8+ T cell sEVs. (AB-TSEV_1_S28 and AB-TSEV_4_S31) Since our antibody has targetting affinity to OVCAR-8 cells, we wanted to see the effect of this teratment on the RNA profile of the cells.


title: Single-cell multi-omics provide insights into molecular drivers of CAR T Cell Persistence and Function in Multiple Myeloma

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

country: Spain

institute: CIMA

summary: The underpinning mechanisms driving chimeric antigen receptor (CAR) T cell function and persistence after infusion, and their correlation with clinical outcome, remains poorly understood. Here, we applied single-cell multiomics, coupled with gene regulatory network analyses, to evaluate CAR-T cell transcriptional heterogeneity, dynamics and clonal evolution, in longitudinal bone marrow (BM) and peripheral blood (PB) paired samples, collected from MM patients treated with BCMA CAR T cells. We identify several regulons with increased activity, within CAR T cell infiltrating the BM, as key drivers of the more activated and exhausted phenotype observed in those cells compared to their PB counterparts. Interestingly, regulatory dysfunctions in the effector-to-memory axis promoted higher presence of terminally differentiated cells, leading to a lack of CAR T cell persistence. Moreover, we identified a hyperexpanded CAR T clone in the BM of a patient with partial response. Deeper characterization showed increased IL10 expression in that clone, that was associated to transcription factors related to exhausted CAR T cells, like PRDM1. Overall, our analyses provide insights into the regulatory mechanisms that could promote lack of CAR T cell persistence and dysfunction, representing potential targets to be modulated for the development of improved CAR T therapies for MM.

overall_design: CAR T cells isolated from BM and PB samples of three R/R MM patients and their paired infusion product were subjected to single cell RNA and TCR sequencing.

first: Lorea

last: Jordana-Urriza

first: Maria E

last: Calleja-Cervantes

first: Felipe

last: Prosper


title: mTORC1 promotes adipose tissue ILC2 homeostasis through upregulation of PPARγ

city: 黄浦区

first: Lin

last: Hu

state: 上海市

address: 重庆南路280号

country: China

institute: 基础医学院

summary: The disruption of adipose tissue group 2 innate lymphoid cells (ILC2s) is associated with obesity-induced insulin resistance. However, the molecular mechanisms underlying the impaired ILC2 function in obesity remain unclear. In this study, we show that obesity-induced lipid accumulation suppresses mechanistic target of rapamycin complex 1 (mTORC1) activity in ILC2s. Deletion of Rptor, a critical adaptor protein in mTORC1, results in reduced numbers of ILC2 and diminished type 2 cytokine production in ILC2s, leading to enhanced adipose tissue inflammation and insulin resistance. Mechanistically, mTORC1 signal facilitates the expression of PPARγ, which promotes mitochondrial biogenesis and ST2 expression to sustain ILC2 metabolic and functional fitness. Together, our data identify mTORC1 as a crucial regulator of adipose tissue ILC2 homeostasis and highlight mTORC1-PPARγ axis as a potential therapeutic target for obesity-related metabolic diseases.

overall_design: To investigate the molecular mechanisms underlying the impaired ILC2 function,we conditional knock out rptor gene to delete mTORC1 signaling in adipose tissue ILC2s,we generated Il5RFP-cre (R5/+) Rptorf/f mice to specifically delete mTORC1 signaling in ILC2s (designated as R5/+ Rptorf/f mice for knockout [KO] and R5/+ for wildtype [WT]),then to explore the function of mTORC1 signaling in ILC2s from the mice.

first: Dongdi

last: Wang

first: Yue

last: Chen

first: Jinxin

last: Qiu

first: Hongdong

first: Youqin

last: Zhang

first: Ju

first: Jiping

last: Sun

first: Lei

last: Shen


title: Dissecting the Role of Myf6 in Facilitating Fibroblast Conversion into Myogenic Progenitor and Differentiated Cells [RNA-Seq]

first: Genome

last: Informatics

overall_design: We characterized the transcriptome of the Myf6-induced conversion of mouse embryonic fibroblasts (MEFs) into iMPCs via bulk RNA-Seq in 3 different experiments: 1. in a lentiviral-induced expression system, where rtTA3-expressing MEFs were transduced with lentiviruses encoding for dox-inducible Myf6 overexpression (LV[TetOn]-Puro-TRE3G>mMyf6[NM_008657.3]) 2. in a defined transgenic mouse model enabling dox-inducible Myf6 overexpression (Teto-Myf6) 3. in MEFs lacking endogenous MyoD, compared them to their WT counterparts upon lentiviral-induced dox-inducible Myf6 overexpression In all these systems, MEFs were cultured with iMPC medium either alone or with doxyxyxline (dox) and/or small molecules (F/R/C) to induce reprogramming and collected at different time points during the reprogramming, as well as at the established iMPC clone stage (on F/R/C only and dox-indipendent). They were also compared to untreated MEFs cultured in 1:1 MEF:iMPC media.

first: Giada

last: Bacchin

first: Adhideb

first: Falko


title: Single-Tubule RNA-Seq Reveals Signaling regulated by phosphorylated T551/S552 on beta-catenin

city: Bethesda

first: Shuo-Ming

last: Ou

address: 10 Center Dr

country: USA

institute: NHLBI

summary: Purpose: Experiments were done in WT mice and Mutant (T551A/S552A at beta-catenin) mice. Cortical collecting ducts (CCD) were manually micro-dissected and utilized for transcriptomic analysis by single-tubule small sample RNA-Seq Methods: We carried out RNA-sequencing in cortical collecting duct (CCD) from WT and MUT mice. Results and conclusion: RNA-Seq in microdissected CCD showed that cell cycle related genes were significanlty changed in the mutant (T551A/S552A) mice.

overall_design: cDNAs from microdissected cortical collecting ducts were generated and sequenced using Illumina Novaseq 6000.

first: Hiroaki

last: Kikuchi

first: Euijung

last: Park

first: Chin-Rang

last: Yang

first: Viswanathan

last: Raghuram

first: Shaza

last: Khan

first: Adrian

middle: R

last: Murillo de Ozores

first: Lihe

first: Chung-Lin

last: Chou

first: Mark

last: Knepper


title: Ablation of PKCα phosphorylation cascades by CRISPR-Cas9 Base Editing Rescues Heart Failure

city: Dallas

last: Guo

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

summary:
BACKGROUND:
The global prevalence of heart failure is increasing significantly, and the prognosis for patients with heart failure remains poor, highlighting the urgent need for novel therapeutic strategies. Protein kinase C alpha (PKCα) plays a central role in heart failure progression. Phosphorylation of PRKCA at T497 triggers a series of phosphorylation cascades, leading to its activation. Ablation of T497 phosphorylation leads to reduced protein stability and activity. However, there is no therapeutic strategy for heart failure targeting PKCα T497.
METHODS:
We employed CRISPR-Cas9 adenine base editing to ablate the phosphorylation site T497 of PKCα. We generated mice harboring a PKCα phosphoresistant T497A mutation in the germline and administered adeno-associated virus 9 (AAV9) harboring base editor of PrkcaT497A to postnatal wild-type (WT) mice to explore its clinical feasibility. To model for heart failure, mice were subjected to transverse aortic constriction (TAC). Cardiac function, hypertrophy, fibrosis, and transcriptional changes were evaluated by echocardiography, wheat germ agglutinin staining, Masson’s trichrome staining, and RNA sequencing, respectively. The editing efficiency of PrkcaT497A was assessed using Sanger sequencing and deep amplicon sequencing. Cellular Ca2+ homeostasis was analyzed using epifluorescence microscopy in Fura-2–loaded human induced pluripotent stem cells-derived cardiomyocytes (iPSC-CMs) carrying the PRKCAT497A mutation under chronic angiotensin II (AngII) stimulation.
RESULTS:
The T497A mutation in PKCα prevented subsequent phosphorylation and led to PKCα degradation. Four weeks after TAC surgery, WT mice showed dramatically impaired cardiac function, cardiac remodeling, and increased lung weight, whereas PKCα phosphoresistant mice were protected from these effects. PKCα phosphoresistant mice also showed protection against heart failure-related aberrant changes in cardiac gene expression, cardiac hypertrophy, and fibrosis. Likewise, mice administrated with AAV9-base editors exhibited similar cardioprotective effects against TAC-induced heart failure. In vitro, PKCα-edited iPSC-CMs were protected from AngII-induced impairments in contractility and Ca2+ transients observed in WT iPSC-CMs.
CONCLUSIONS:
The editing of PRKCAT497A through adenine base editing may potentially provide a promising therapeutic approach for human cardiac diseases.

overall_design: RNA-seq profiling of hearts from 10-week-old wild-type and Prkca T497A mutant mice subjected to Sham or TAC surgery. Tissue was collected 5 weeks post-surgery.

first: Tomonori

last: Tadokoro

first: Hui

last: Li

first: Yoon-Jung

last: Kim

first: Lin

last: Xu


title: Monocytes provoke breast cancer cells to express PD-L1 via a cell-to-cell interaction involving CD44 and Moesin

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

institute: Kyoto Prefectural University of Medicine

summary: In recent years, immunotherapy using immune checkpoint inhibitors has been conducted for TNBC patients. While a limited proportion of patients show excellent response, about a half of the patients do not significantly respond to the immunotherapy. Monocytes are the progenitors of macrophages that are most abundantly seen in the tumor microenvironment (TME), but the influence of monocytes on BCCs has not been fully clarified. Thus, we examined whether monocytes prompted BCCs to express PD-L1. As a result, PD-L1 expression in BCCs was upregulated by co-culturing them with monocytes. RNA sequencing analysis revealed overexpression of Moesin mRNA in the BCCs co-cultured with monocytes. These findings may suggest a novel machinery of tumor escape from anti-tumor immunity, potentially providing a way to improve immunotherapy against TNBCs that are resistant to current immune-checkpoint blockade therapy.

overall_design: Two biological replicates were analyzed for each of 2 conditions (control MDAMB-231, MDAMB-231 co-cultured with human monocytes)

first: Saya

last: Matsumoto


title: Psmd13, a proteosome regulatory subunit for co-transcriptional miR-29a processing during neurogenesis

city: Melbourne

first: Diji

last: Kuriakose

address: Clayton

institute: Monash University

summary: miR-29a plays a critical role in neuronal development and is associated with neurodegenerative diseases, but its regulatory mechanisms remain unclear. To identify genes that influence miR-29a expression, we utilized the genetically diverse Collaborative Cross (CC) mouse strains and conducted expression profiling and Quantitative Trait Loci (QTL) analysis. A significant QTL on chromosome 7 was identified, and ten candidate genes were mapped within this region. RNAi-mediated knockdown experiments revealed that Psmd13 and Nap1l4 significantly increased miR-29a expression, implicating these genes as upstream regulators. Further investigation in mouse neural precursor cells (mNPCs) demonstrated that Psmd13 knockdown enhanced neuronal differentiation, as indicated by increased βIII-tubulin-positive cells, and miR-29a inhibition also promoted this process. Co-immunoprecipitation experiments showed that Psmd13 interacts with Dicer, modulating miR-29a levels through a differentiation-dependent mechanism. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed co-binding of Psmd13 and Dicer at key genomic loci, including miR-29a, influencing chromatin accessibility and transcriptional regulation. Notably, proteasome inhibition using MG132 decreased Psmd13 and Dicer levels, leading to downregulation of miR-29a and impaired neuronal differentiation. These findings suggest that Psmd13 and Dicer coordinate to regulate miR-29a biogenesis and neuronal differentiation, highlighting the proteasome's essential role in maintaining neurodevelopmental homeostasis.

overall_design: Genome-wide co-localization of Psmd13 and Dicer at active miR loci during neurogenesis.


title: Desulfovibrio Vulgaris Flagellin Induces Epithelial-Mesenchymal Transition of Colorectal Cancer through LRRC19/TRAF6/TAK1 Pathway

city: Tianjin

first: Yue

last: Dong

address: 154 Anshan Road, Heping District, Tianjin

institute: Tianjin Medical University General Hospital

summary: Dysbiosis of microbiota derived from mucosa and feces indicated the inseparable relationship between gut microbiota and colorectal cancer (CRC). However, the specific mechanisms underlying remain incompletely understood. We found that Desulfovibrio vulgaris (DSV) was upregulated in CRC animal models and patient databases. We aimed to further investigate the role of DSV and detected a high level in the feces and tissues of CRC patients. Moreover, DSV gavage administration promoted colonocyte proliferation in germ-free mice. Subsequently, we identified, synthesized, and purified the Desulfovibrio vulgaris flagellin (DVF) to explore the underlying mechanisms of DSV pathogenicity in CRC. DVF promoted proliferation, migration, and invasion in CRC cells. Transcriptome sequencing uncovered that epithelial-mesenchymal transition (EMT)-associated genes and tumor-related signaling pathways were enriched in the DVF-treated group. DVF could induce EMT in CRC cells and xenograft models separately, specifically manifested by downregulation of E-cadherin and upregulation of N-cadherin and Vimentin. Mechanistically, DVF-dependent EMT required a novel functional transmembrane receptor called leucine-rich repeat containing 19 (LRRC19). The interaction between DVF and LRRC19 regulated the ubiquitination of TRAF6 instead of TRAF2, further promoting the ubiquitination of transforming growth factor-β-activated kinase 1 (TAK1) for autophosphorylation. The phosphorylation of TAK1 further facilitated the EMT. Collectively, DVF promotes EMT dependent on the LRRC19/TRAF6/TAK1 pathway in CRC. Our research offers new insights into the mechanism of gut microbiota participating in the CRC and establishes a promising clinical therapy target.

overall_design: RNA-seq was performed in the Caco-2 cells with or without Desulfovibrio Vulgaris flagellin

first: Jingyi

last: Wang

first: Jingge

last: Wei


title: Feeding Time Altered Intestinal Microbiota and SCFA Potentially Induce Diurnal Oscillations of Ovarian IL-17 and Influence Follicular Development in Puberty Growing Rabbits

city: Beijing

first: Mengqi

last: Zhu

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

summary: Lifestyle factors of modern societies (i.e., disrupted feeding times and sleep) can affect microbiota and metabolic rhythms, leading to low fertility and infertility in adult females. This study investigated the crucial role of feeding time regulated rhythms of gut microbes and metabolites in pubertal follicular development in rabbits. Results demonstrated that night-restricted feeding (NRF) accelerated puberty onset, increased antral follicle, and enhanced granulosa cell proliferation while reducing apoptosis. Further ovarian transcriptome analysis revealed that feeding time regulated the IL-17 signaling pathway, with IL-17 protein exhibiting a diurnal oscillation of low during the day and high at night in the NRF group. The rhythmic IL-17 that mimics NRF stimulated the proliferation of granulosa cells and upregulated the expression of clock genes (BMAL1, CLOCK) and proliferation-related genes (WEE1) in vitro. Similar diurnal IL-17 fluctuations low during the day and high at night were observed in the colon of NRF group, along with increased concentrations of short-chain fatty acids (acetate, propionate, and butyrate acid) and higher abundance of associated microorganisms (Akkermansia and NK4A214_group) in the cecum. Our findings indicate that night-restricted feeding promotes pubertal follicular development and granulosa cell proliferation, which is associated with the diurnal oscillation of ovarian IL-17. The oscillation of IL-17 in both the ovary and colon may be linked to changes in the gut microbiota and short-chain fatty acids (SCFA) resulting from altered feeding times.

overall_design: RNA-seq profiles of rabbit ovaries collected at 11:00 am and 11:00 pm at 144 days of age from daytime feding and night-restricted feeding.

first: Zhong-Hong

last: Wu

first: Meng-Qi

first: Jian-Xiang

last: Cheng

first: Chun-Hua

last: Shan

first: Jie

last: Huang

first: Ke-Hao

last: Zhang

first: Yao

first: Peng

last: Liu

first: Zhong-Ying


title: Dissecting the Role of Myf6 in Facilitating Fibroblast Conversion into Myogenic Progenitor and Differentiated Cells [scRNA-Seq]

first: Genome

last: Informatics

overall_design: MyoD-KO and WT MEFs were reprogrammed into iMPCs via Myf6 overexpression and Forskolin/RepSox/CHIR99021 treatment. After reprogramming, Myf6-independent iMPC colonies were picked and expanded for 4 passages. One established MyoD-KO and one WT iMPC clone were harvested and analyzed with scRNA-Seq.

first: Giada

last: Bacchin

first: Adhideb

last: Ghosh

first: Falko

last: Noé

first: Ori

last: Bar-Nur


title: High resolution multi-scale profiling of embryonic germ cell-like cell derivation reveals pluripotent state transitions in humans

first: LMS

last: Bioinformatics Core

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

overall_design: Refer to individual Series


title: Pim1 exacerbates inflammatory arthritis by mediating Th17 differentiation

city: 深圳市

first: su

last: zepeng

address: 深南中路3025号

institute: 中山大学附属第八医院（深圳福田）

summary: The present study demonstrated that pim1-promoted mito-Ca2+ influx enhanced the activity of mitochondrial OXPHOS, bringing about the differentiation of Th17 and driving the pathogenic progression of inflammatory arthritis. Targeting pim1 impeded Th17 differentiation and alleviated collagen-induced arthritis (CIA) and SKG arthritis, suggesting that Pim1 is a target for the treatment of inflammatory arthritis.

overall_design: Naïve CD4+ T cells, cells under Th17 polarlization condition and cells treated with Pim1 inhibitor AZD1208

first: Zhongyu

last: Xie

first: Zepeng

last: Su

first: Huiyong

last: Shen