title: Genomewide analysis of S6K1-depleted human dorsal forebrain organoids [RNA-seq]

city: Macau

first: Ning-Yi

last: Shao

address: University of Macau

department: Faculty of Health Sciences

institute: University of Macau

summary: To elucidate the role of S6K1 in human brain development, we performed next-generation sequencing-based genomweide analysis of S6K1 knockout (KO) human embryonic stem cells (ESCs) and brain organoids. Development/differentiation-related genes were highly enriched in DEGs of S6K1 KO hESCs compared to WT hESCs. Single cell transcriptomic analysis showed unusual retinal cell development in S6K1-depleted brain organoids, thereby reducing neural populations. Furthermore, we generated brain organoids containing both WT and S6K1 KO cells and then isolated them after completing differentiation to compare the feature of each portion grown in mixed condition. ATAC sequencing analysis of each portion in mixed brain organoids displayed no significant differences in retinal cell marker gene transcriptomes between WT and S6K1 KO portions, while chromatin accessibility of neural-specific genes were lower in S6K1 KO portion than WT. Collectively, this study revealed that S6K1 plays dual role in human brain development; suppression of retinal lineage specification and production of mature neurons through non-cell autonomous and cell autonomous action, respectively.

overall_design: Bulk RNA sequencing of three replicates of WT and three replicates of S6K1-depleted human embryonic stem cells line (H7)

first: Ki

middle: H

last: Nam

first: Sang

last: Yi

first: Lin-Fan

last: Xiao

first: Jaecheol

first: Jeung-Whan

last: Han


title: Genomewide analysis of S6K1-depleted human dorsal forebrain organoids

status: Public on Sep 25 2025

country: China

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Construction and validation of a scoring system for perineural invasion-mediated inflammation in gastric cancer

city: Guangzhou

first: xunjun

last: li

state: China

address: Guangzhou 510515, Guangdong Province, Ch

institute: Nanfang Hospital

summary: To validate the performance of scoring system for perineural invasion-mediated inflammation in gastric cancer,we sequenced the tumor tissues and adjacent normal tissues from patients with gastric cancer.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 subgroups,including perineural invasion and non perineural invasion.
Based on gene expression profiling analysis of RNA-seq data,we calculated the ICI score of each patients and comepared their scores between perineural invasion and non perineural invasion subgroups.

first: Xunjun

last: Li

first: Yiyun

last: Wang


title: Genomewide analysis of S6K1-depleted human dorsal forebrain organoids [ATAC-seq]

overall_design: ATAC sequencing of GFP-positive (S6K1 knockout) and GFP-negative (WT) cells sorted from human dorsal forebrain organoids (week 5) containing mixed cells (WT+S6K1 knockout)

middle: A

last: Lee


title: The Integrated Stress Response Suppresses Antiviral RNA Interference by Autophagy-mediated Degradation of RNA-induced Silencing Complex

status: Public on Sep 24 2025

city: Shenzhen

first: Zhaowei

state: Guangdong

address: No.66, Gongchang Road, Guangming District

department: School of Ecology

institute: Sun Yat-sen University

summary: The small interfering RNA (siRNA) pathway is a highly conserved antiviral defense mechanism in vertebrates and invertebrates. Although the core components of this pathway are well characterized, its upstream regulatory networks remain poorly understood. Here, we identify the integrated stress response (ISR) as a negative regulator of the siRNA pathway, and demonstrate that the picorna-like virus CrPV (Cricket Paralysis Virus) exploits this mechanism for immune evasion. Mechanistically, the picorna-like virus triggers the ISR through transcriptional suppression of ppp1r15, a key regulator of eukaryotic initiation factor 2α (eIF2α) dephosphorylation. ISR activation subsequently induces the autophagy-lysosomal pathway by up-regulating Atg1 transcription in an ATF4-dependent manner. This process leads to selective degradation of Argonaute 2 (Ago2) and other core components of the RNA-induced silencing complex (RISC), thereby suppressing the host RNA interference (RNAi) machinery and enhancing viral replication. Our findings uncover an unconventional immune evasion strategy employed by a picorna-like virus and establish a previously unrecognized crosstalk between the ISR and siRNA pathways.

overall_design: This RNA-sequencing aims to analyze the effect of ppp1r15 gene knockdown on transcription in Drosophila S2 cells. We transfected Drosophila S2 cells with dsRNA targeting GFP (as a control,labeled as dsGFP) and two dsRNAs targeting the ppp1r15 gene (labeled as dsppp1r15#1 and dsppp1r15#2), respectively. Each experiment was performed with three biological replicates (labeled as _1, _2, and _3). Total RNA was extracted from cells using the RNA isolater Total RNA Extraction Reagent (Vazyme, Cat #R401-01). The mRNA was then enriched and reverse-transcribed to construct a cDNA library. The cDNA libraries were sequenced using the Illumina NovaSeq 6000 (Illumina, San Diego, USA). mRNA enrichment, reverse transcription, cDNA library construction, quality control, and sequencing were performed by Biomarker Technologies (Biomarker Technologies Ltd, Beijing, China). The analysis of transcriptomic sequencing data was performed on the Secevo HPC cluster of the School of Ecology, Sun Yat-sen University (Shenzhen, China).

first: Qiyu

first: Lingyue

last: Chen

first: Jiayin

first: Zhijian

first: Zixian

last: Ma

first: Xuan

last: Xie

first: Xiaohui

last: Zeng

first: Yuanyuan

last: Bie


title: Stem Cell Engineering for the Generation of Allogeneic CAR-Directed Natural Killer T Cells Targeting Endometrial Carcinoma

city: Los Angeles

first: Lili

last: Yang

state: California

address: 610 Charles E. Young Dr. East

department: Microbiology Immunology & Molecular Genetics

country: USA

institute: University of California, Los Angeles

summary: Aggressive subtypes of uterine endometrial carcinoma (UEC) often result in mortality due to recurrence of disease with chemoresistant tumor cells surrounded by an immune suppressive microenvironment. Current CAR-T cell therapies have shown limited efficacy in solid tumors, largely constrained by poor tumor infiltration, immune suppression, and the logistical limitations of autologous cell production, which hinder broad patient access. In this study, we conducted comprehensive immunophenotyping of primary UEC patient samples and identified a therapeutic opportunity for CAR-engineered invariant natural killer T (CAR-NKT) cells capable of targeting both tumor cells and the immunosuppressive TME. Using a hematopoietic stem and progenitor cell (HSPC) engineering platform coupled with ex vivo differentiation culture, we generated allogeneic mesothelin-targeting CAR-NKT cells (AlloMCAR-NKT) with high purity and yield. AlloMCAR-NKT cells exhibited potent cytotoxic activity against UEC tumor cells and CD1d⁺ tumor-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs). Importantly, compared to conventional CAR-T cells, AlloMCAR-NKT cells demonstrated an improved safety profile, showing no evidence of graft-versus-host disease (GvHD) and minimal cytokine release syndrome (CRS)-related toxicity. These findings highlight the potential of AlloMCAR-NKT cells as a safe and effective off-the-shelf cellular immunotherapy for the treatment of UEC and potentially other solid tumors characterized by an immunosuppressive microenvironment.

overall_design: Gene expression profiling of therapeutic cells products for UEC treatment

first: Yan-Ruide


title: Chemotherapy-driven de novo Wnt pathway activation dictates a dynamic shift to a drug-tolerant state in breast cancer cells

city: Leuven

first: Frederic

last: Lluis

state: Leuven

address: Herestraat 49

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

summary: Triple-negative breast cancer (TNBC) initially exhibits a robust response to chemotherapy; however paradoxically, the treatment enriches a population of drug-tolerant persister (DTP) cells, which are known to drive therapy resistance. Therefore, it is crucial to, foremost, identify and subsequently target the signaling pathways implicated in therapy-induced drug resistance and the emergence of DTP cells.  In this study, by combining the use of human TNBC cell lines, 3D patient-derived organoid models, and in vivo xenograft models, we identified activation of the Wnt/β-catenin signaling pathway as a common mechanism underlying early DTP cell(s) enrichment in response to different chemotherapeutic agents. Live-cell imaging using Wnt-reporter TNBC cell lines validated diverse patterns of Wnt-transcriptional enrichment, encompassing both intrinsic selection and acquired de novo activation in response to chemotherapy treatment. Purification of differential Wnt-transcriptional populations revealed that post-treatment WntLow cells succumb to apoptosis, while, in contrast, chemotherapy-treated Wnt-active (WntHigh) cells adopt stem cell-like traits, exhibit reduced proliferation, and are, in turn, refractory to treatment. The transition to a post-treatment WntHigh state is orchestrated by increased expression of Wnt ligands, R-spondins, and factors facilitating Wnt ligand secretion, such as PORCN. Consequently, genetic or concomitant - but not sequential - pharmacological inhibition of Wnt ligand secretion alongside chemotherapy prevents treatment-induced WntHigh enrichment and sensitizes TNBC tumors to chemotherapy. Taken together, these observations provide a strong rationale for testing dual treatment comprising chemotherapy and Wnt ligand secretion inhibitors in clinical trials, extending to all TNBC patients.

overall_design: MDA-MB-231 TNBC cell line treated with different chemotherapeutic agents (Docetaxel and Carboplatin) for 72 hours.

first: Youssef

last: El Laithy

middle: L

last: Vinas


title: CRISPRi Screening of Enhancers in Human Primary Astrocytes Identifies Regulatory Circuitry Disrupted in Alzheimer’s Disease

city: Kensington

first: Irina

last: Voineagu

state: NSW

address: High St

department: Biotechnology and Biomolecular Sciences

country: Australia

institute: The University of New South Wales

summary: We used CROP-seq to perform a high-throughput, parallel screen of 979 candidate enhancer perturbations in normal human astrocytes (NHAs), a primary cell-line. We identified the target gene(s) for 145 of these candidates, which were enriched for transcription with eRNA, transcription factor footprinting, and superenhancer annotation. Most regulatory interactions were <50kb, targeting the nearest gene in ~50% of cases, but were not typically captured by eQTL or in silico predictions. These data elucidate the regulatory network of an understudied-but-crucial brain cell-type.

overall_design: To identify regions of open chromatin, ATAC-seq was performed on Normal Human Astrocytes (NHA; Lonza) stably expressing dCas9-KRAB-Blast

first: Nicole

middle: O

last: Green

first: Gavin

middle: J

last: Sutton

first: Samuel

last: Bagot

first: Hannah

last: Danon

first: Juli

first: Akira

last: Gokool

first: Samantha

last: Miles

first: Charles

last: Herring

first: Hamid

last: Alinejad-Rokny

first: Ryan

last: Lister

first: Joseph

last: Rosenbluh

first: Johann

last: Gagnon Bartsch


title: Secreted β-helix protein YjbI controls bimodal antibiotic susceptibilities from an asymmetric surface disposition

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

summary: While cytoplasmic pentapeptide repeat proteins (PRPs) protect DNA gyrase from cytotoxic quinolones, the function of secreted (s)PRPs remains unknown. We show that a YjbI-type sPRP regulates antibiotic sensitivity, bimodally for small or large molecules, from the Caulobacter crescentus outer membrane (OM). YjbI silences two converging envelope stress pathways that globally reprogram the OM proteome via TonB-dependent receptors (TBDRs), periplasmic proteases and AcrAB-NodT, a multidrug efflux pump whose induction by small molecules and antibiotics is lethal to yjbI mutant cells. Loss of YjbI also confers sensitivity to vancomycin and bacitracin, two large peptidoglycan-targeting and zinc-binding antibiotics that permeate the OM via the uncharacterized TBDR BugA and orthologs. Zinc stress triggers YjbI’s rapid proteolytic removal and transcriptionally activates BugA, other TBDRs, and (ultimately replenishes) YjbI. Molecular dynamics simulations and reactive thiol-probing imply an asymmetric surface disposition of YjbI, explaining the differential accessibility of its conserved cysteine pairs that flank the quadrilateral β-helix.

overall_design: Examination of HA-ChvI and HA-UzcR whole genome binding/occupancy (ChIP-Seq) in Caulobacter crescentus NA1000 (WT and yjbI::Tn mutant)

first: Jordan

last: Costafrolaz

first: Laurence

last: Degeorges

first: Gaël

last: Panis

first: Simon-Ulysse

last: Vallet

first: Manuel

last: Velasco Gomariz

first: Fernando

last: Teixeira Pinto Meireles

first: Matteo

last: Dal Peraro

first: Kathrin

middle: S

last: Fröhlich


title: Gene expression profiling of PBMC from normal individuals, chronic hepatitis B patients

city: Chongqing

first: Li

last: Zhou

state: Chongqing

address: 61 Middle University Road，Huxi Street

department: College of Public Health

institute: Chongqing Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Aberrant gene expression analysis between peripheral blood mononuclear cell (PBMC) samples from healthy individuals and patients with chronic hepatitis B were identified using Agilent gene arrays.

overall_design: Peripheral blood mononuclear cells (PBMCs) from 5 healthy individuals and 5 patients with chronic hepatitis B were isolated and total RNA was extracted for Agilent gene microarray analysis.


title: CRISPRi Screening of Enhancers in Human Primary Astrocytes Identifies Regulatory Circuitry Disrupted in Alzheimer’s Disease [RNA-seq]

first: Irina

last: Voineagu

overall_design:
To investigate basal gene and eRNA expression, RNA sequencing was performed on Normal Human Astrocytes (NHA; Lonza) stably expressing dCas9-KRAB-Blast
Three distinct libraries were prepared; mRNA-seq (to compare to scRNA-seq), ribo-depleted RNA-seq (to compare to TT-seq), and ribo-depleted RNA-seq of transient transcriptome sequencing (TT-seq) samples.
Please note that the 'TTseq_RiboDep.csv' contains processed data for both 'ribo-depleted RNA-seq' and 'TT-seq' samples, and is linked to the 'ribo-depleted RNA-seq' sample records.

first: Nicole

middle: F

last: Green

first: Gavin

last: Sutton

first: Samuel

last: Bagot

first: Hannah

last: Danon

first: Juli

last: Wang

first: Akira

last: Gokool


title: Genomewide analysis of S6K1-depleted human dorsal forebrain organoids [single-cell RNA-seq]

first: Ning-Yi

last: Shao

overall_design: Single cell RNA sequencing of WT and S6K1-depleted human dorsal forebrain organoids (week 5, week 14)

first: Ki

last: Nam

first: Sang

last: Yi

first: Lin-Fan

last: Xiao

first: Jaecheol

last: Lee

first: Jeung-Whan

last: Han


title: RNA-sequencing assay to Identify changed gene expression in stomach adenocarcinoma  (STAD) cells with SMYD3 knockdown

city: Fujian

first: Yi

last: Zeng

address: Fu Ma Road 420,Fuzhou,Fujian

institute: Fujian Medical University Cancer Hospital, Fujian Cancer Hospital

summary: Purpose: To elucidate how SMYD3 influenced the expression profile in STAD cells, SMYD3 expression was reduced using one shRNA in STAD HGC-27 and SGC-7901 cells. Then, transcriptional profiling of cells with SMYD3 knockdown (shSMYD3) and the control cells (shNC) was performed to characterize differentially expressed genes (DEG).Methods: When shNC and shSMYD3 cells grew to approximately 80% confluence, these cells were washed twice using pre-chilled PBS. Total RNAs were harvested using Trizol reagents (Thermo Fisher Scientific).  Poly(A) mRNA was isolated and enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. The mRNA was then recovered for library generation with NEBNext ® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, E7420S) following the manufacturer’s instructions. The cDNA libraries were sequenced at WuXiNextCODE (China). FastQC was used to examine the quality of raw reads. Read alignment was conducted using STAR (v2.5.1b),  and R package edgeR (v3.8.5) was used to determine relative transcript abundances and differentially expressed genes (DEGs) between sample pairs. Results: Generally, 248 genes  were increased and 112 genes decreased in HGC-27 shSMYD3 cells, compared with shNC cells (FDR<0.05, Fold Change>2). Additionally, 135 genes (FDR<0.05, Fold Change>2) were increased and 97 genes decreased in SGC-7901 shSMYD3 cells, relative to shNC cells. GO analysis showed that these changed genes were significantly enriched in signal pathways related to cancer. Conclusions: Reduced SMYD3 expression alters multiple cancer-related signal pathways.

overall_design: Two biological replicates for each group shNC and shSMYD3 - were subjected to RNA-sequencing analysis respectively, among which shNC acted as the reference sample for shSMYD3.

first: Jingyu

last: Deng

first: Yong

last: Liu

first: Gang

last: Ma


title: miRNA expression profiles of garlic-derived exosomes

city: ChongqingPR China

first: Li

last: Yin

address: 69 Hongguang Road Huaxi Street, Banan District

department: College of Pharmacy and Biological Engineering

institute: Chongqing University of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we investigated the miRNA profiling of garlic-derived exosomes and screened the miRNAs associated with the expression of 6-phosphofructo-2-kinase/fructose-2, 6-biphosphatase 3 (PFKFB3), one of the critical glycolytic enzymes, which shape the metabolic reprograming of macrophage induced by lipopolysaccharide (LPS) and mitigate the inflammatory response in adipocytes.

overall_design: Ultracentrifugation combined with PEG precipitation was used to isolate exosomes from garlic purchased from a local market. After total RNAs were extracted from GDE, and the quality and concentration of the RNAs were checked using an Agilent 2200 UV spectrophotometer. And then, reverse-transcription-PCR amplification, small-RNA libraries were prepared and sequenced, with raw reads being collected using an Illumina Hiseq 2500 platform.

first: Yangping

last: Bian

first: Jianhui


title: Temporal dynamics of collateral RNA cleavage by LbuCas13a in human cells

city: Leiden

first: Niels

last: Geijsen

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: LUMC

summary: We have found that LbuCas13a exhibits collateral RNA cleavage activity in human cells after activation by the target RNA. Here we use total RNA sequencing to explore which RNAs are depleted by the collateral activity of LbuCas13a. ERCC spike-in RNAs were used for normalization between samples. This revealed near global depletion of mRNAs at 50 and 200 minutes after Cas13 protein and guide delivery. Mitochondrial and nuclear transcripts were not affected.

overall_design: Total RNA sequencing of HAP1-dEGFP cells with ERCC spike-in control RNAs. Cells were either left untreated, transfected with an empty iTOP transfection, transfected with LbuCas13a and a non-targeting gRNA by iTOP, or transfected with LbuCas13a and a dEGFP targeting gRNA by iTOP. Cells were harvested at 50, 200 and 1440 minutes after transfection.

first: Jorik

last: Bot

first: Zhihan

last: Zhao

first: Mengyuan

last: Li

first: Darnell

last: Kammeron

first: Peng

last: Shang


title: The differentially expressed genes after treatment of 5-AZA-CdR in OSCC cell lines

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: This study aimed to explore the candidate genes activated by the DNA methylation transferase inihibitor (DNMTi) 5-AZA-CdR.

overall_design: The OSCC cell lines were seeded into 6-well plates and were treased with 10 μM 5-AZA-CdR or DMSO for 48 hours. The differentally expressed genes by 5-AZA-CdR treatment were screened by RNA sequencing. The transcriptome sequencing studies were performed by deep sequencing, using Illumina NovaSeq 6000.

first: Shanshan

last: Qin

first: Dandan


title: A versatile one-shot high-multiplex base editing strategy enables the generation of 20-plex knockout CAR T cells with enhanced anti-tumor efficacy

city: Philadelphia

first: Regina

middle: M.

last: Young

state: Pennsylvania

address: 3400 Civic Center BLVD

department: CCI

institute: University of Pennsylvania

summary: Advances in genomic editing have expanded the therapeutic potential of cell therapies such as chimeric antigen receptor (CAR) T cells, and integrating multifunctional enhancements and allogeneic properties into next-generation therapeutic products requires high-multiplex gene editing strategies that minimize editing-associated toxicity. Here, we pioneered a viral vector-free, one-shot adenine base editing (ABE) approach to enable the simultaneous high-multiplex knockout of at least 20 distinct genes in primary human T cells. The incorporation of this strategy into CAR T cells produced cells with a hyperfunctional phenotype based on a rationally selected 20-plex knockout gene-set. Refinement of this gene-set attenuated initial in vivo toxicity, revealing superior in vivo tumor control of 20-plex edited CAR T cells compared to mock-edited controls in a mouse model of pancreatic ductal adenocarcinoma. We further extended this approach to primary human hematopoietic stem cells (HSCs) and natural killer (NK) cells, demonstrating the method’s broad utility for ex vivo gene editing at unprecedented multiplexity levels across diverse cell types of translational relevance.

overall_design: RNA-seq profiling of primary human T cells with or without high-multiplex editing of 20 distinct genes (CD3E, B2M, CIITA, PVR, CD52, ICAM1, CD58, PDCD1, CTLA4, CD5, RASA2, MED12, ZC3H12A, RC3H1, TET2, ARID1A, SMARCC1, SMARCA4, SMYD3, ADORA2) 48hrs after electroporationrealized by 2 different gene editing strategies (wildtype Cas9 mRNA or ABE8e mRNA).

first: Nils

middle: W

last: Engel

first: Kusala

last: Anupindi

last: Wellhausen

first: Abdulla

last: Berjis

first: Michael

last: Bowman

first: Shreeya

last: Gounder

first: Shirley

last: Sun

first: Olga

last: Shestova

first: Maksim

last: Shestov

first: Daniel

last: Baker

first: Dongdong

last: Yan

first: Donna

last: Gonzales

last: Zhu

first: Philipp

middle: C

last: Rommel

first: Saar

last: Gill

first: Robert

middle: M

first: Carl

last: June


title: YAP-driven stemness and TEAD-induced neuroendocrine cells drive resistance to KRASG12C therapies in metastatic colorectal cancer [Xenium Spatial Transcriptomics]

city: Houston

first: Oluwadara

last: Coker

state: Texas

address: 6767 Bertner Ave

department: GI Medical Oncology

institute: MD Anderson Cancer Center

summary: KRAS mutations are a predominant driver of metastatic colorectal cancer (mCRC), with approximately 10% of patients harboring the KRAS p.G12C variant. Despite the development of KRASG12C (G12Ci) and EGFR (EGFRi) inhibitors such as sotorasib and panitumumab, therapeutic resistance remains a major limitation. To define resistance mechanisms, we analyzed tissue biopsies from patients treated with G12Ci+EGFRi and employed Xenium spatial transcriptomics (Xenium ST), along with comprehensive multi-omics profiling of patient-derived xenograft (PDX) models. Known genomic alterations including NRAS p. Q61K mutations and KRASG12C amplifications were observed; however, non-genomic resistance was strongly associated with activation of the YAP-TEAD pathway. Xenium ST data revealed two key tumor subpopulations: tumor intestinal stem cells (TISCs), marked by upregulation of KRAS and YAP, and neuroendocrine-like (NE) cells, which showed KRAS upregulation alone. G12Ci+EGFRi-resistant PDX models were enriched for TISCs and associated stemness programs. The addition of a TEAD inhibitor (TEADi; IAG-933) to dual therapy induced deep tumor regression and suppressed KRAS, YAP, stemness pathways; however, NE-like cells were enriched following triple therapy. These findings suggest that TEADi enhances the efficacy of KRASG12C + EGFR inhibition by targeting TISCs but may not eliminate NE-like subpopulations, which could mediate TEAD-independent resistance and represent a therapeutic challenge.

overall_design: FFPE tissue sections from pre- and post-progression biopsies of three patients with KRAS p.G12C mutation that received G12Ci+EGFRi during clinical trials were analyzed using spatial transcriptomics.

first: Alexey

last: Sorokin

first: Neal

last: Akhave

first: Kelsey

last: Pan

first: Veena

last: Kochat

first: Fengqin

last: Gao

first: Zhensheng

last: Liu

first: Carrie

last: Davis

first: Liying

last: Jiang

first: Antonio

last: Scamardo

first: Chi Wut

last: Wong

first: Yixin

last: Xu

first: Preeti

last: Kanikarla

first: William

last: Israel

first: Hey Min

last: Lee

first: Oscar

last: Villarreal

first: Haoqiang

last: Ying

first: Wantong

last: Yao

first: Jumanah

last: Alshenaifi

first: Amanda

last: Anderson

first: Natalie

last: Fowlkes

first: David

last: Menter

first: Saikat

last: Chowdury

first: Kunal

last: Rai

last: Hong

first: Scott

last: Kopetz


title: Engineered 3D Immuno-Glial-Neurovascular Human miBrain Model

city: Cambridge

first: Benjamin

last: James

state: MA

address: 32 Vassar St

institute: Massachusetts Institute of Technology

summary: Patient- specific, human-based cellular models integrating a biomimetic blood–brain barrier, immune, and myelinated neuron components are critically needed to enable accelerated, translationally relevant discovery of neurological disease mechanisms and interventions. To construct a human cell-based model that includes these features and all six major brain cell types needed to mimic disease and dissect pathological mechanisms, we have constructed, characterized, and utilized a multicellular integrated brain (miBrain) immuno-glial-neurovascular model by engineering a brain-inspired 3D hydrogel and identifying conditions to coculture these six brain cell types, all differentiated from patient induced pluripotent stem cells. miBrains recapitulate in vivo–like hallmarks inclusive of neuronal activity, functional connectivity, barrier function, myelin-producing oligodendrocyte engagement with neurons, multicellular interactions, and transcriptomic profiles. We implemented the model to study Alzheimer’s Disease pathologies associated with APOE4 genetic risk. APOE4 miBrains differentially exhibit amyloid aggregation, tau phosphorylation, and astrocytic glial fibrillary acidic protein. Unlike the coemergent fate specification of glia and neurons in other organoid approaches, miBrains integrate independently differentiated cell types, a feature we harnessed to identify that APOE4 in astrocytes promotes neuronal tau pathogenesis and dysregulation through crosstalk with microglia.

overall_design: This study profiled RNA expression from multiple cell types isolated from human iPSC-derived ‘miBrains’ and matched monocultures. Neurons, astrocytes, oligodendroglia, and microglia were differentiated from the same iPSC batches, cultured in miBrains for two weeks (plus an additional 4 days for iMG), and isolated by FACS based on fluorescent reporters or CD45 expression. Parallel monocultures of each cell type were maintained under matched conditions. Triplicate biological replicates were collected per condition. The design enables comparison of gene expression between organoid-incorporated versus monoculture conditions across multiple neural cell types

first: Alice

last: E. Stanton

first: Adele

last: Bubnys

first: Emre

last: Agbas

first: Dong

last: Park

first: Alan

last: Jiang

first: Rebecca

last: Pinals

first: Liwang

last: Liu

first: Nhat

last: Truong

first: Anjanet

last: Loon

first: Colin

last: Staab

first: Oyku

last: Cerit

first: Hsin-Lan

last: Wen

last: Mankis

first: Margaret

middle: E

last: Bisher

first: Abigail

middle: K

last: Lytton-Jean

first: Manolis

last: Kellis

first: Joel

last: Blanchard

first: Robert

last: Langer

first: Li-Huei

last: Tsai


title: Astrocytic CREB regulates transcriptomic, neuronal, and behavioral responses to cocaine

city: New York

first: Molly

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Emerging evidence increasingly indicates that astrocytes are involved in neuropsychiatric disorders, including addiction, but the cocaine-induced astrocyte transcriptome has yet to be investigated. We performed RNA-sequencing on whole-cell sorted astrocytes from the nucleus accumbens and bioinformatically characterized the astrocyte transcriptome following cocaine self-administration in male mice. We found that astrocytes exhibit robust and contextually-specific transcriptional signatures that implicate CREB as a cocaine-induced transcriptional regulator in astrocytes. CUT&RUN-sequencing revealed increased astrocytic CREB DNA binding in response to cocaine. Viral-mediated manipulation of NAc astrocytic CREB activity in combination with addiction-related behaviors revealed that astrocytic CREB increases the rewarding and reinforcing properties of cocaine. Furthermore, we identified potential molecular mechanisms of astrocytic CREB’s influence through modulating astrocytic calcium dynamics and selectively increasing D1-type medium spiny neuronal activity.

overall_design: Wildtype C57BL/6J male mice were intraperitoneally (I.P.) injected with saline or cocaine (20 mg/kg) for 7 consecutive days in their homecage and astrocytes were  isolated following 24 hr withdrawal. CUT&RUN was subsequently performed for CREB or IGG control.

first: Leanne

last: Holt

first: Angelica

last: Miner-Toribio

first: Rita

last: Futamura

first: Caleb

last: Browne

first: Freddyson

last: Martínez-Rivera

first: Tamara

last: Markovic

first: Trevonn

last: Gyles

first: Szu-ying

last: Yeh

first: Eric

last: Parise

first: Matthew

last: Rivera

first: Corrine

last: Azizian

first: Yun Young

last: Yim

first: Veronika

last: Kondev

first: Shi

last: Yan

first: Alexa

last: Labanca

first: Giselle

last: Rojas

first: Li

last: Shen

first: Yan

last: Dong

last: Nestler


title: Regulation of an lncRNA irf8 by the Ikzf1/Myb complex drives neutrophil development

first: he

last: yuepeng

address: No.266 Fangzheng Avenue,Shuitu Hi-tech Industrial Park, Shuitu Town, Beibei District, Chongqing

institute: Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences

summary: As critical executors of the immune system, neutrophils provide an immediate inflammatory response for the clearance of debris and microbes, which is essential for the protection of health. Developmentally, neutrophils and macrophages share common progenitors, whose fate is tightly controlled by transcriptional programs. Dysregulation of these programs causes severe hematological disorders, including neutropenia, neutrophilia, leukemia, and inflammatory disorders. However, the mechanisms underlying the generation of neutrophils through these programs are poorly understood. Here, we revealed that Ikzf1 and Myb were enriched in neutrophils. Overactivation of Ikzf1 promoted neutrophil generation while suppressing macrophage emergence. Conversely, the simultaneous loss of Ikzf1 and Myb, but not the individual mutations, drastically impaired neutrophil production and enlarged the macrophage pool in both zebrafish and mice. Mechanistically, Ikzf1 and Myb formed a complex that targeted irf8 and induced the expression of a long non-coding RNA (lncRNA), irf8-2, through a novel regulatory element. LncRNA irf8-2 biased neutrophil commitment by modulating irf8 dosage via Zfp36l1. The deletion of irf8-2 resulted in defective neutrophil development and enhanced macrophage production.  However, a partial ratio of neutrophils and macrophages was restored when Ikzf1, Myb, and Irf8 were all compromised. Overall, our study reveals that Ikzf1 and Myb cooperatively bias neutrophil development against Irf8 via the lncRNA irf8-2 and Zfp36l. This study provides novel insights into the conserved molecular balance between neutrophil and macrophage development during myelopoiesis, with potential implications for understanding and treating myeloid disorders.

overall_design: Tg(coro1a:DsRed) embryos from WT and ikzf1D4+3/D4+3; mybhkz3/hkz3 (DM) embryos at 30 hours post fertilization (hpf) were collected and dissociated using a 1 U mL-1 Papain Dissociation Kit (Worthington) in Dulbeccos phosphate buffered saline (DPBS) at 37 C for 20-30 minutes. Single cell suspensions were generated by gentle trituration, passed through a 40 um cell strainer, and subjected to fluorescence activated cell sorting (FACS). The sorted cells were subsequently processed for Smart seq. Tg(coro1a:DsRed) embryos from WT, Tg(coro1a:HA-ikzf1), Tg(coro1a:FLAG-myb), ikzf1+/+; myb+/+ (WT), and ikzf1D4+3/D4+3; mybhkz3/hkz3 (DM) embryos at 30 hpf were collected and dissociated using a 1 U mL-1 Papain Dissociation Kit (Worthington) in DPBS at 37 C for 20-30 minutes. Single cell suspensions were generated by gentle trituration, passed through a 40 um cell strainer, and subjected to FACS. Approximately 5000 sorted cells were subsequently processed for ATAC seq. Single cell suspensions of FACS sorted coro1a-DsRed cells from more than 30 embryos at 24 hpf were resuspended in DPBS as described in a previous study. The cell suspensions were filtered through a 70 um cell strainer before sorting. The collected coro1a-DsRed positive cells were loaded onto the channels of Single Cell G Chip (v3.1 chemistry, PN1000120).

first: Yuepeng

last: He

first: Yang

last: Li

first: Yibo

last: Shao

first: Xue

last: Huang

first: Jiangyong

first: Shengnan

last: Liu

first: Yalan

last: Xiao


title: Seasonal divergence in reproductive timing on the verge of spring: comparing hypothalamic transcriptome of two seasonally sympatric North American songbird populations.

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

state: IN

address: 1001 E Third St

department: Biology

institute: Center for Genomics and Bioinformatics

summary: Every year as spring approaches and day length increases, many birds begin to reproduce, an annual expression of seasonal phenology that requires physiological preparation. In species distributed over a broad geographic range, populations that breed at higher latitudes are often migratory and delay reproduction until later in the year as compared to those breeding at lower latitudes. Dark-eyed Juncos serve as an excellent model for understanding the timing mechanisms regulating population-level variation in seasonal reproductive responses. We compared two seasonally sympatric dark-eyed junco populations in early spring. One migrates (Junco hyemalis hyemalis) and breeds in Alaska and Canada, while the other remains resident (Junco hyemalis carolinensis) and breeds in the Appalachian Mountains of Virginia USA. These populations exhibit different photoperiodic responses to the same environment with respect to activation of the HPG axis, leading to earlier gonadal recrudescence in the resident population. We caught co-wintering sympatric male migrant (n=6) and resident (n=7) juncos from the field in March and collected the hypothalamic tissues. We also collected blood samples to determine circulating testosterone and a wing feather to determine stable isotope ratios (dH) as estimate of breeding latitude. We found three differentially expressed genes, among which gonadotropin releasing hormone 1 (GnRH1) showed significantly higher expression in early breeding residents as compared to migrant juncos. The dH showed a positive linear correlation with testosterone levels and GnRH1 mRNA, providing strong evidence for latitudinal variation in breeding phenology. This study provides insight into the underlying neuroendocrine response giving rise to a population-level difference in the timing of reproduction observed in a seasonally sympatric (co-wintering) population of resident and migrant juncos.

overall_design: A total of 6 migrant and 7 resident junco hypothalamii were punched and homogenized in RLT buffer containig 1% 2-Mercaptoethanol on ice. Total RNA was prepared using AllPrep DNA/RNA Universal Kit (Qiagen, Cat. # 80224). RNA integrity and concentration were determined using Agilent 2200 Tapestation System. RNA library was prepared and Illumina Nexseq 500 used for sequencing.

first: Devraj

last: Singh

first: Adam

last: Fudickar

first: Ellen

last: Ketterson


title: Drug tolerant persisters and immunotherapy persister cells exhibit cross-resistance and share common survival mechanisms

city: Brookline

first: Maria

last: Davern

state: Massachusetts

address: 440 Brookline avenue / Mayer Building

institute: Dana-Farber Cancer Institute

summary: Persisters are a rare sub-population of tumor cells that survive anti-cancer therapy and are thought to be a major cause of recurrence. These cells have been identified following both drug- and immune-therapy but are generally considered to be distinct entities. Since both pharmacological agents and immune cells often kill via apoptosis, we tested a hypothesis that both types of cells survive based on reduced mitochondrial apoptotic sensitivity, which in turn would yield a similar and reciprocal multi-agent resistant phenotype. Supporting this hypothesis, we indeed observed that IPCs acquired a reduced sensitivity to multiple drug classes and radiotherapy, suggesting non-immune mechanisms are important in the survival of cancer cells after immunotherapy. Likewise, DTPs developed not only a reduced sensitivity to multiple drug classes and radiotherapy, but also acquired a reduced sensitivity to T cell killing. Both IPCs and DTPs developed a decreased sensitivity to mitochondrial apoptosis. A sub-population of IPCs downregulated  antigen and upregulated PD-L1. Intriguingly, in the IPCs that didn’t employ these mechanisms of resistance, a greater decrease in sensitivity to mitochondrial apoptosis was observed, suggesting that the presence or absence of a resistance mechanism can exert selective pressures over the emergence of others. Targeting anti-apoptotic dependencies in persisters increased sensitivity to chemotherapy or CAR T therapy. These results suggest that common biological mechanisms underly survival of persisters, whether derived from immune or drug therapy, and offer an explanation for the acquired cross-resistance to these two types of therapies often observed in the clinic.

overall_design: RNA was extracted from parental HeLa cells, selected HeLa immune persister cells (IPC) and 3 different HeLa drug tolerant persister (DTP) cells following respective treatment with IC90 concentrations of 5-FU, Oxaliplatin and Etopiside for 7 days. RNA was extracted using the RNeasy Mini Kit (Qiagen). Prior to RNA sequencing, RNA was treated with DNase using RNase-Free DNase Set (Qiagen). rRNA depletion was performed from 100ng of purified RNA using QIAseq FastSelect rRNA HMR reagents according to manufacturer’s protocol. Libraries were prepared using Roche Kapa Biosystems RNA HyperPrep sample preparation reagents on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced with paired-end 150bp reads on an Illumina NovaSeq 6000at the Dana-Farber Cancer Institute Molecular Biology Core Facilities. Sequenced reads were aligned to the UCSC hg38 reference genome assembly and gene counts were quantified using STAR (v2.7.3a).

first: Davern

last: Maria

first: Letai

last: Anthony


title: CYP450-Mediated Detoxification and NF-κB/NLRP3-Driven Mechanisms in Emodin-Induced Hepatotoxicity in vitro and in vivo

city: fuzhou

first: qiyuan

last: Yang

state: Fujian Province

address: The First Affiliated Hospital of Fujian Medical University, Taijiang District, Fuzhou City, Fujian Province

summary: Emodin, a bioactive compound abundant in Chinese medicinal herbs, possesses broad therapeutic potential but raises safety concerns due to conflicting reports of hepatotoxicity. This study investigated the toxicological mechanisms underlying emodin-induced liver injury. We showed that emodin induced dose-dependent cytotoxicity and hepatic injury in HepG2 cells. Moreover, emodin (400 mg/kg) induced hepatotoxicity in mice after administered for three weeks.This study delineates the metabolic detoxification pathways of emodin and elucidates its toxicological mechanisms.

overall_design: RNA sequencing was performed on liver tissue from wild-type C57BL/6 mice with and without emodin.

first: Lili

last: Wu

first: Zhikun

last: Zhan

first: Siyu

last: Chen

first: Runzhi

last: Wang

first: Qiyuan

first: Xing


title: The KAP1 chromatin regulator and Paupar long non-coding RNA control subventricular zone neural stem cell maintenance and neurogenesis [shPaupar]

city: Oxford

first: Farah

last: Alammari

address: Sherrington road

country: United Kingdom

institute: Oxford University

summary: Neural stem cells (NSCs) in the subventricular zone (SVZ) produce functional neurons throughout life and are an accessible and robust system to understand neurodevelopmental mechanisms. Elucidating the properties of NSCs will also provide insights for their use in the treatment of neurodevelopmental disorders and brain injuries. However, the epigenetic mechanisms that maintain NSCs and control neurogenesis remain unclear. We previously showed that Paupar, a CNS-expressed long non-coding RNA (lncRNA), controls neuroblastoma cell growth by binding and modulating the activity of the KAP1 transcription co-factor. We interrogated the last stages of olfactory bulb (OB) neurogenesis and showed that depletion of these two molecules in vivo reduced the number of newborn neurons and delayed their morphological differentiation. Here we investigated upstream functions of these two epigenetic regulators in SVZ NSCs self-renewal and neurogenesis. We combined studies using inducible knockout and in vivo knockdown electroporation, with molecular analysis. Our results demonstrate that KAP1 and Paupar are broadly expressed in the normal postnatal/adult SVZ neurogenic lineage, that they physically interact in SVZ cells and regulate NSC behaviour in the SVZ. KAP1 directly maintains the neural stem cell pool and regulates the expression of genes involved in the cell cycle. Paupar, in turn maintains stem cell quiescence by restricting lineage progression from stem cells to transit amplifying progenitors (TAPs). These results suggest important roles for a KAP1-Paupar containing chromatin regulatory complex in the control of SVZ NSC and SVZ-OB neurogenesis.

overall_design: RNA-sequencing of Paupaar loss-of-function in neural stem cells generated from the SVZ and controls

first: Jemima

last: Becker

first: Bin

last: Sun

first: Anna

last: Hoerder-Suabedissen

first: Keith

last: Vance

first: Francis

last: G. Szelee


title: YAP-driven stemness and TEAD-induced neuroendocrine cells drive resistance to KRASG12C therapies in metastatic colorectal cancer

first: Oluwadara

last: Coker

overall_design: RNA-seq profiling of a) mCRC PDX models treated with G12Ci/G12Ci+EGFRi until no response was achieved as observed by persistent tumor growth, b) mCRC PDX models treated with TEADi monotherapy and in combination with G12Ci+EGFRi for 21 days.

first: Alexey

last: Sorokin

first: Neal

last: Akhave

first: Kelsey

last: Pan

first: Veena

last: Kochat

first: Fengqin

last: Gao

first: Zhensheng

last: Liu

first: Carrie

last: Davis

first: Liying

last: Jiang

first: Antonio

last: Scamardo

first: Chi Wut

last: Wong

first: Yixin

last: Xu

first: Preeti

last: Kanikarla

first: William

last: Israel

first: Hey Min

last: Lee

first: Oscar

last: Villarreal

first: Haoqiang

last: Ying

first: Wantong

last: Yao

first: Jumanah

last: Alshenaifi

first: Amanda

last: Anderson

first: Natalie

last: Fowlkes

first: David

last: Menter

first: Saikat

last: Chowdury

first: Kunal

last: Rai

last: Hong

first: Scott

last: Kopetz


title: Erianin induces apoptosis and pyroptosis via MAPK/ERK and PI3K/Akt pathways and synergizes with anlotinib in anaplastic thyroid carcinoma

city: Tianjin

first: Minghan

last: Qiu

state: Tianjin

address: Department of Oncology, Tianjin Union Medical Center of Nankai Univercity, 190 Jieyuan Street, Hongqiao District, Tianjin, China.

department: Department of Oncology

summary: Anaplastic thyroid carcinoma (ATC) is an aggressive thyroid malignancy characterized by rapid progression, resistance to conventional therapies, and poor patient prognosis. There is an urgent need for innovative therapeutic strategies. Erianin, a natural compound derived from Dendrobium, has demonstrated significant anti-tumor effects in various cancers, yet its role in ATC remains unexplored.In this study, we confirmed the significant anticancer effects of erianin on ATC through both in vitro and in vivo models, including the induction of apoptosis and GSDME-dependent pyroptosis in ATC cells.

overall_design: CAL62 cells after treating with 50nM Erianin or DMSO for 48h，in three replicate experiments.

first: Qiaonan

last: Zhang

first: Ming

last: Gao

first: Jie

last: Hao


title: Kdm6b-mediated epigenetic choreography of temporal precision during motor neuron differentiation

city: hefei

first: wenxian

last: wang

address: No. 81, Meishan Road, Shushan District, Hefei City, Anhui Province

institute: Anhui Medical University

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

overall_design: Refer to individual Series


title: Role for NF-kB in herpes encephalitis pathology in mice genocopying an inborn error of IRF3-IFN immunity

city: Aarhus

first: Soren

last: Paludan

address: CF Møllers Alle 6, Building 1115

department: Biomedicine

country: Denmark

institute: Aarhus university

summary: Herpes simplex encephalitis (HSE) is a devastating disease with high mortality and serious sequelae. Genetic defects in the interferon (IFN-I) pathway predispose individuals to HSE, but underlying mechanisms remain unclear. Using transgenic mice with the IRF3 R278Q mutation, orthologue to HSE-associated IRF3 R285Q, and iPSC-derived CNS cells from a pediatric patient carrying the variant, we investigated mechanisms in HSE. IRF3 R278Q transgenic mice exhibited aggravated HSV-1 brain disease and elevated CNS viral loads. Accordingly, microglia from the IRF3 R278Q mice showed reduced HSV-1-induced IFN-I expression. Surprisingly, unaltered Ifnb levels along with elevated levels of inflammatory cytokines were detected in infected transgenic mouse brains, correlating with higher viral load. This was successfully modelled in patient microglia. Multiomics-based immune profiling revealed an inflammatory monocyte population in the infected IRF3 R278Q mouse brain, which was enriched for NF-κB activation. NF-κB inhibition improved disease outcomes, surpassing the effect of acyclovir. These findings suggest that IFN-I defects lead to elevated levels of HSV-1 replication in the brain, which subsequently enables NF-κB-driven immunopathology, offering insights with therapeutic potential.

overall_design: Brain stems from IRF3 full knockout mice, transgenic mice homozygous for an IRF3 R278Q aminoacid substitution and WT mice were harvested on day 5 post ocular HSV-1 infection. Two to three brain stems were pooled per sample. Single-cell suspensions were used to generate barcoded single-cell RNA-seq libraries according to the manufacturer’s protocol. Library quality control was performed, and sequencing was carried out on a high-throughput sequencer.


title: Stage-specific Kdm6b-transcription factor partnerships orchestrate temporal precision during stepwise motor neuron differentiation [CutRun_CutTag]

summary: Histone modifiers instruct cellular differentiation, yet how they achieve temporal precision remains enigmatic. Here we demonstrate that the H3K27 demethylase Kdm6b acts as a master epigenetic conductor and achieves timed gene activation by sequentially partnering with stage-specific transcription factors (TFs) in motor neuron (MN) differentiation. Genome-wide profiling revealed Kdm6b occupancy progressively shifted from proximal promoters to distal enhancers, along with increasing regulatory elements during maturation. At occupied sites, Kdm6b triggered rapid H3K27me3 loss with concurrent H3K27ac/H3K4me1 gain, establishing activation-competent chromatin. By integrating developmental TFs and histone modification landscapes, Kdm6b builds up the dynamic epigenetic choreography to precisely regulate MN developmental programs from early MN fate specification, intermediate cell differentiation and growth to later maturation. The ordered expression of developmental genes was compromised by stage-specific Kdm6b inhibition. Our work resolves how a single epigenetic regulator achieves temporal precision in driving stepwise MN development, with broad implications for neurodevelopment and diseases.

overall_design: Cut&Run-seq of Kdm6b, Neurod1 and Cux1/2, and Cut&Tag-seq of H3K27me3, H3K27ac, H3K4me1 and H3K4me3 within in vitro differentiated motor neurons from mouse embryonic stem cells at stages D4, D4H8, D5 and D6.

first: Wenxian

last: Wang

first: Haihan

last: Ren

first: Bing

last: Pan


title: The KAP1 chromatin regulator and Paupar long non-coding RNA control subventricular zone neural stem cell maintenance and neurogenesis

first: Farah

last: Alammari

overall_design: RNA-sequencing of KAP1 loss-of-function in neural stem cells generated from the SVZ and controls

first: Jemima

last: Becker

first: Bin

last: Sun

first: Anna

last: Hoerder-Suabedissen

first: Keith

last: Vance

first: Francis

last: G. Szelee


title: Stage-specific Kdm6b-transcription factor partnerships orchestrate temporal precision during stepwise motor neuron differentiation [RNA-seq]

overall_design: RNA-seq profiling within in vitro differentiated motor neurons from mouse embryonic stem cells at stages D4, D4H8, D5 and D6.

first: Jun-Ma

last: Yu


title: Investigations into the basal neural-like properties of dental pulp stem cells reveals they possess a functional type 2 muscarinic receptor which regulates quiescence

city: Sakaka

first: Saeed

last: Alqahtani

country: Saudi Arabia

institute: Jouf University-College of Dentistry

summary: Dental pulp stem cells (DPSCs) are a population of mesenchyme-derived cells residing within the dental pulp known for their multipotent differentiation potential and neural-like properties. While a functional cholinergic system has been described in various mesenchymal stem cell (MSC) populations, its presence and role in DPSCs remain unexplored. This study investigated the neurotransmitter-associated gene expression profile of human DPSCs using a targeted array panel and immunocytochemistry. The functionality of acetylcholine receptors (AChRs) was assessed through pharmacological activation and inhibition using receptor-specific agonists and antagonists. Cellular responses to cholinergic modulation, including effects on viability and proliferation, were evaluated via LDH release, CCK-8, and annexin V/PI staining assays. Among the 92 neurotransmitter-associated genes profiled, 43 were expressed, including multiple muscarinic receptors and nicotinic receptor subunits. Protein level expression of the m2, m3, and m5 muscarinic receptors was confirmed. Furthermore, activation of the m2AChR, using arecaidine propargyl ester hydrobromide (APE), led to a reversible reduction in DPSC proliferation without compromising cell viability. The findings demonstrate that DPSCs exhibit cholinoceptive properties and identify the m2AChR as a key modulator of cell cycle arrest. This receptor may serve as a therapeutic target for regulating DPSC behaviour and maintaining stem cell quiescence in regenerative applications.

overall_design: RNA-Seq profiling of untreated DPSCs and DPSCs stiumulatied with 100 μM arecaidine propargyl ester hydrobromide (APE) for 4 and 24 hours.

first: Christopher

last: Nile


title: Chronic Intermittent Hypoxia Drives M1 Macrophage Polarization in Dorsal Root Ganglia

city: San Antonio

first: Nathaniel

last: Jeske

state: TX

address: 7703 Floyd Curl Dr

department: OMS

institute: UTHSA

summary: Immune cells play a crucial role in maintaining the health of all body tissues. When chemical signals are released into the local environment form injured or infected cells, tissue-specific immune cells become attracted and migrate to that area. Upon arrival, they begin releasing their own signals that produce a cascade of effects, including pain modulation. However, little is known about how systemic hypoxia influences immune modulation of pain in the peripheral nervous system.  We sought to identify the unique role of macrophages in peripheral sensory ganglia by using a translational model of sleep apnea.  Mice were exposed to chronic intermittent hypoxia (CIH) for 14 days and L4-L6 dorsal root ganglia were removed for analyses of macrophage content.  Immunofluorescence histochemistry and fluorescence-activated cell sorting indicate a prevalence of M1 macrophage markers and a reduction of M2 macrophage markers in DRG tissues taken from CIH mice.  Total RNA-seq identified multiple genes upregulated in DRG macrophages following CIH exposure, including toll-like receptor 9 (TLR9).  In vitro treatment of primary macrophage cultures with the FDA-approved TLR9 antagonist hydroxychloroquine (HCQ) inhibited M1 macrophage polarization.  Calcium imaging of DRG neurons taken from CIH-exposed mice revealed hypersensitivity to KCL that was prevented by HCQ co-treatment.  Furthermore, HCQ acutely abated hyperalgesic priming behavior in mice exposed to CIH.  Together, these results identify TLR9 as a druggable target capable of reducing nociceptor sensitization in CIH, with implications for exaggerated pain sensitivity in patients with sleep apnea.

overall_design: RNA-seq profiling of dorsal root ganglion macrophages from mice undergoing 14 day normoxic or chronic intermittent hypoxia treatment

first: Samuel

last: B. Chivers

first: Mary Ann

last: Andrade

first: Cassandra

last: L. McLay

first: Kristopher

last: L. Weiland

first: Pankil

last: K. Shah

first: Glenn

last: M. Toney

last: A. Jeske


title: Transcriptomic profiles of susceptibility and resilience to stress in the amygdala and hippocampus of male rats

city: Berkeley

first: Daniela

last: Kaufer

address: 430E LKS, Univ of California - Berkeley

department: Integrative Biology, Neuroscience

institute: University of California, Berkeley

summary: Traumatic experiences elicit a wide range of cognitive responses in both humans and animals, leading to diverse outcomes such as enhanced performance, cognitive impairment, or the development of mood and anxiety disorders like posttraumatic stress disorder (PTSD). A key challenge in understanding these varied responses is to decipher the underlying biological mechanisms that contribute to individual variability in trauma resilience or susceptibility. The purpose of this study was to elucidate the molecular bases for these differences, focusing on the amygdala and hippocampus—brain regions integral to stress responses. We exposed adult, male rats to an acute, severe stressor and profiled persistent anxiety-like behavior outcomes 7 days later. We investigated the transcriptional signatures in the basolateral amygdala and hippocampal dentate gyrus via bulk RNA sequencing from animals with behavioral outcomes indicative of stress resilience or vulnerability. Our results suggest that the basolateral amygdala and dentate gyrus display distinct transcriptomic changes following acute, severe stress. Furthermore, we identified specific region-dependent genes related to insulin signaling, neural plasticity, and stress responses that correlate with each phenotype. Notably, a larger number of genes separated stress-resilient animals from both control and stress-susceptible animals, underscoring that an active molecular response, particularly in the hippocampus, facilitates protection from the long-term consequences of severe stress. These findings provide novel insight into the mechanisms that engender individual variability in the behavioral responses to stress and offer new targets for the advancement of therapies for stress-induced neuropsychiatric disorders.

overall_design: This dataset contains RNA-seq data from the hippocampus (dentate gyrus, DG) and amygdala (basolateral amygdala, BLA) from adult male rats exposed to 3 h immobilization with predator scent stress or control conditions and phenotyped for anxiety-like behavior (avoidance, acoustic startle).

first: Kimberly L.P.

last: Long

first: Sandra E.

last: Muroy

first: Siamak K.

last: Sorooshyari

first: MeeJung

last: Ko

first: Yanabah

last: Jaques

first: Kishant

last: Mohan

first: Peter

last: Sudmant


title: Transcriptomic profiling of liver tissue from control, DHT-induced PCOS-NAFLD model, and baicalin-treated mice using RNA-seq

city: Hangzhou

first: BIhui

last: Jin

address: 158#, Shangtang road

institute: zhejiang provincal people's hospital

summary: This study aimed to characterize the liver transcriptomic changes in a mouse model of polycystic ovary syndrome (PCOS)–related non-alcoholic fatty liver disease (NAFLD) and to assess the therapeutic effects of baicalin (BA). Female C57BL/6J mice were implanted subcutaneously with dihydrotestosterone (DHT) pellets to induce PCOS-NAFLD. Liver tissues from control, model, and BA-treated mice were collected for RNA sequencing (RNA-seq). Differential gene expression and functional enrichment analyses were performed to identify biological processes and pathways associated with disease progression and BA intervention.

overall_design: Liver RNA-seq was performed on female C57BL/6J mice divided into three groups: control, PCOS-NAFLD model, and BA-treated at a dose of 200 mg/kg/day (n = 4 per group).

first: Bihui

first: Lingbo

last: Qian


title: A novel in vitro model of trauma-induced endotheliopathy provides a platform for studying mechanisms of coagulopathy

first: Jeries

last: Abu-Hanna

address: Oxford Haemophilia and Thrombosis Centre, Windmill Road

institute: University of Oxford

summary: Trauma-induced coagulopathy (TIC) significantly contributes to trauma-related mortality, driven by dysregulated coagulation and fibrinolysis. Endotheliopathy of trauma (EoT) is central to TIC, yet its underlying mechanisms remain unclear. Current in vitro models fail to replicate the complex trauma environment, including haemorrhagic shock, tissue injury, and inflammation. This study aimed to develop a novel in vitro model of EoT that mimics key TIC features, enabling the investigation of endothelial contributions to TIC. Endothelial colony-forming cells (ECFCs) were exposed to trauma-relevant factors, including epinephrine, TNF-α, IL-6, HMGB1, hydrogen peroxide, and hypoxia. Endothelial injury markers (syndecan-1, thrombomodulin), haemostatic protein expression, coagulation, and fibrinolysis were analysed using ELISA, immunofluorescence, global haemostasis assays, and RNA sequencing. Plasma from healthy donors and trauma patients was used to assess clinical relevance. Traumatised ECFCs exhibited progressive dysfunction, with early surface damage and sustained fibrinolytic dysregulation. Transcriptomic analysis showed activation of inflammatory pathways, metabolic shifts, and epigenetic changes. Surface expression of anticoagulant proteins decreased, while procoagulant tissue factor increased, heightening thrombogenic potential. Initially, traumatised ECFCs promoted fibrinolysis via thrombomodulin shedding but later secreted antifibrinolytic PAI-1, mimicking the biphasic TIC phenotype. Plasma assays revealed thrombin generation and clot lysis changes similar to trauma patients. This in vitro model successfully replicates EoT and TIC-associated haemostatic imbalances, capturing the time-dependent evolution of endothelial dysfunction. It provides mechanistic insights into TIC and serves as a platform for testing targeted interventions to mitigate endothelial-driven coagulopathy in trauma.

overall_design: RNAseq profiling of endothelial colony-forming cells (ECFCs) from 6 healthy donors treated with a cocktail simulating systemic traumatic injury conditions to induce endotheliopathy.


title: Brassinosteroids mediate proper coordination of sepal elongation

city: Villa Park

first: Byron

last: Rusnak

state: IL

address: 128 E Division st

department: Plant Biology

institute: Cornell University

summary: Arabidopsis sepals must grow in a coordinated and robust fashion to a consistent size and shape to close and protect the developing flower bud. To understand how this robust coordination occurs, we use the loss of robustness mutant development related myb-like1 (drmy1), which exhibits variable sepal initiation and growth, causing failure of the sepals to close the flower bud. Specifically, drmy1 has overgrown outer (abaxial) sepals and undergrown inner (adaxial) sepals, leading to a large discrepancy in the sizes of different sepals within individual flower buds. Using single cell and spatial RNA-seq, we found changes in expression of key genes related to brassinosteroid (BR) signaling in drmy1, particularly in cell types important to young flower bud development such as epidermal cells, boundary cells, and meristematic cells. Confocal imaging of a BRI1-EMS-SUPPRESSOR1 (BES1) ratiometric reporter confirms that BR signaling is upregulated and more variable in young drmy1 sepals. Subsequently, we found that altering BR signaling in drmy1 by crossing with BR mutants or adding brassinolide (a potent brassinosteroid) or brassinazole (a brassinosteroid biosynthesis inhibitor) can partially rescue this elongation defect by differentially altering the relative growth of the inner and outer sepals. Increasing BR signaling rescues by increasing the growth of the inner sepal but not the outer sepal, while decreasing BR signaling rescues by decreasing the growth of the outer sepal but not the inner sepal. These results suggest that brassinosteroids mediate the robust coordination of the growth rates between inner and outer sepals during early development, ensuring proper flower bud closure.

overall_design: 108 hours after induction with dexamethasone, WT and drmy1 in the ap1cal 35S::AP1-GR background was harvested by cutting off the cauliflower-like clusters of flower buds and protoplasted for scRNAseq

last: Rusank

first: Lilijana

last: Oliver

first: Kyle

last: Procopio

first: Adrienne

last: Roeder


title: Transcriptome profile of naive CD8 T cells from WT and CD103 deficient mice

city: Bethesda

first: Can

last: Li

state: Maryland

address: 9000 Rockville Pike

institute: NIH

summary: The Ly6C–CXCR3– naïve CD8 T cells highly express CD103. To understand the biological significance of CD103 expression on naïve CD8 T cells, we performed RNA sequencing on sorted naïve CD8 T cells from WT and CD103-dificient (Itgae–/–) mice to elucidate the function of CD103 expressed on naïve CD8 T cells.

overall_design: Transcriptome analysis of Ly6C–CXCR3– naïve CD8 T cells sorted from lymph node of WT (C57BL/6) and Itgae–/– mice.

first: Jung-Hyun

last: Park


title: Exploring the dendritic cell subset regulating naïve CD8 T cell homeostasis

summary: The maintenance of naïve CD8 T cells within lymphoid organs is a finely tuned process involving multiple factors provided by stromal cells and antigen-presenting cells, particularly dendritic cells (DCs). In this study, we employed Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-Seq) to comprehensively profile dendritic cell subsets and their potential roles in supporting naïve CD8 T cell homeostasis. By integrating transcriptomic and surface protein expression data, we identified distinct dendritic cell populations with specialized gene expression signatures and immunological features. These findings provide novel insights into the cellular and molecular mechanisms governing CD8 T cell maintenance, with implications for immune regulation and potential therapeutic strategies.

overall_design: Peripheral lymph nodes (pLNs; comprising axillary, brachial, inguinal, and submandibular lymph nodes) from 16-week-old female C57BL/6 mice were harvested and utilized for DC isolation by collagenase D digestion. Cells were depleted with T and B cells, and CD11c+I-A/I-E+ cells were sorted for the staining of CITE-Seq antibodies (ADTs) by following the TotalSeq protocol (BioLegend).


title: Effects of Amino Acid Restriction on Decidualization of Human Endometrial Stromal Cells

city: London

first: Chloe

middle: Emily

last: Jang

state: Ontario

address: 1151 Richmond St

country: Canada

institute: Western University

summary: This study aimed to evaluate the effects of amino acid restriction, as mimicked by Halofuginone (HF), and amino acid supplementation on decidualization of human endometrial stromal cells (HESCs). When HESCs were exposed to decidualization agents, distinct morphological changes and increased insulin-like growth factor binding protein 1 (IGFBP-1) production were observed, indicative of successful decidualization.  HF treatment inhibited IGFBP-1 secretion and expression of key decidualization markers in a dose-dependent manner. Supplementation with proline, but not leucine, rescued the inhibitory effects of HF on decidualization of HESCs. RNA-sequencing analysis revealed that several growth factors crucial for decidualization were inhibited by HF, suggesting their sensitivity to amino acid availability. HF disrupted transforming growth factor β (TGFβ)-SMAD signaling, which was restored by proline supplementation.

overall_design: To assess the effect of amino acid restriction on the process of decidualization, immortalized human endometrial stromal cells were treated with decidualization agents, cyclic AMP and medroxyprogesterone acetate, in the presence or absence of Halofuginone (HF).

first: Cristiana

last: Iosef

first: Stephen

last: Renaud

first: Victor

last: Han


title: Transcriptome profile of memory phenotype CD8 T cells are shaped by overexpression of CD103

summary: The CD8 T cells in the peripheral tissues maintained as a mixture of naïve and memory-phenotype in the steady state, while the mechanism how the balance of naïve and memory-phenotype CD8 T cells is controlled remains unclear. Here, we report that integrin CD103 plays critical role in this process. CD103 is differentially expressed on peripheral CD8 T cells with highest expression on naïve CD8 T cells (Ly6C–CXCR3–) and lowest expression on memory-phenotype CD8 T cells (Ly6C+CXCR3+). To understand the biological significance of CD103 downregulation on memory-phenotype CD8 T cells, we generated transgenic mice that overexpress CD103 under the control of the human CD2 promoter/enhancer so that CD103 is constitutively expressed on all T lineage cells (CD103Tg), and we found that memory-phenotype CD8 T cells are accumulated in CD103Tg mice. Therefore, we performed RNA sequencing on sorted memory-phenotype CD8 T cells from WT and CD103Tg mice to elucidate the molecular mechanism how forced expression of CD103 promotes accumulation of memory-phenotype CD8 T cells.

overall_design: Transcriptome analysis of Ly6C+CXCR3+ CD8 T cells sorted from lymph node of WT (C57BL/6) and CD103Tg mice


title: Intravenous immunoglobulin has epigenetic, ribosomal, and immune effects in Paediatric Acute-Onset Neuropsychiatric syndrome

city: Westmead

first: Brian

last: Gloss

address: 176 Hawkesbury Rd

department: Scientific Platforms

institute: Westmead Institute of Medical Research

summary: Paediatric acute-onset neuropsychiatric syndrome (PANS) is characterised by infection-provoked abrupt and dramatic onset of obsessive compulsive disorder (OCD) or eating restriction, along with neurodevelopmental regression. Although the aetiology of PANS remains uncertain, due to a prevailing neuroimmune hypothesis, some children receive the immune modulator intravenous immunoglobulin (IVIg). Using single-cell RNA sequencing of peripheral immune cells, we examined gene expression in five children with PANS (mean age 10.2 years, range 5–17, 60% male) who were receiving IVIg. Maternal autoimmunity (n=3) and familial neurodevelopmental/neuropsychiatric disorders (n=5) were present. The index PANS event occurred age 1.8–13 years, characterised by abrupt eating restriction (n=5), developmental regression (n=4), and OCD (n=3). Single-cell RNA sequencing (144,470 cells) was performed in five patients pre- and post-IVIg, and four controls (mean age 13.5 years, range 11–16, 50% male). In PANS pre-IVIg compared to controls, there were downregulated immune pathways (defense response, innate immunity, secretory granules) in most cell types. However, NK cells exhibited upregulated immune pathways (response to corticosteroid), supporting a baseline ‘immune dysregulation’. In PANS pre-IVIg compared to controls, ribosomal pathways were upregulated in neutrophils and CD8 T cells, but downregulated in NK cells. Post-IVIg, the previously downregulated immune pathways were upregulated in most cell types, and the baseline ribosomal pathway abnormalities were reversed.  Histone modification pathways (histone methyltransferase, chromatin) were downregulated in neutrophils and NK cells post-IVIg. We propose PANS is an epigenetic immune-brain disorder with cellular epigenetic, ribosomal, and immune dysregulation. Therefore, epigenetic and immune-modulating therapies, such as IVIg, may have a critical role in treating this disabling disorder.

overall_design: Single-cell RNA sequencing in children with Paediatric Acute-Onset Neuropsychiatric syndrome before and after IVIg treatment and healthy controls

first: Velda

middle: X

first: Hiroya

last: Nishida

first: Brooke

last: Keating

first: Xianzhong

last: Lau

first: Ruwani

last: Dissanayake

first: Jessica

last: Hayes

first: Shekeeb

last: Mohammad

first: Shrujna

last: Patel

first: Russell

last: Dale


title: Single-Cell RNA Sequencing Reveals Cellular Heterogeneity and Reparative Mechanisms in Cystic Change of Osteonecrosis of the Femoral Head

city: Guangzhou

first: Xiaoqiang

last: YANG

address: 12,Jichang Road

institute: Guangzhou University of Chinese Medicine

summary:
Aims:
Steroid-induced osteonecrosis of the femoral head (SIONFH) is a debilitating condition often accompanied by cystic change in the affected bone. Previous studies and our clinical observation have suggested the potential for tissue repair within the cystic change, but the underlying cellular mechanisms remain unclear. This study aims to investigate the heterogeneity of cells in the cystic change region, focusing on chondrocytes and endothelial cells, using single-cell RNA sequencing (scRNA-seq) and subsequent histological validation.
Method:
Cystic change tissues were obtained from patients undergoing total hip arthroplasty. Single-cell RNA sequencing was performed to identify distinct cell populations, particularly chondrocytes and endothelial cells. Alcian blue staining was employed to detect chondrocytes, while immunohistochemistry (IHC) was used to verify the presence of repair-associated chondrocytes. Additionally, HE staining was performed to further analyze tissue architecture like blood vessels.
Results:
ScRNA-seq analysis identified two major cell types in the cystic change region: endothelial cells involved in angiogenesis and chondrocytes, which included subpopulations associated with cartilage repair. Alcian blue staining showed strong cartilage matrix staining within the cystic change. Immunohistochemistry further validated the expression of repair-associated markers in the chondrocyte population, suggesting active cartilage repair. Cellular communication analysis revealed intercellular interactions between reparative chondrocyte via matrix proteins (FN1, COL1A1) and integrin receptors on angiogenic endothelial cell, suggesting their potential collaboration in the repair process.
Conclusion:
This study highlights the positive effects of cystic change region of SIONFH in the process of repair based on clinical observations and single-cell RNA sequencing technology. The presence of functionally distinct cell populations, including angiogenic endothelial cells and repair-associated chondrocytes, within cystic change region of SIONFH. The findings suggest a biological basis for repair in the cystic change tissue, providing insights that may inform future therapeutic strategies targeting bone and cartilage regeneration in osteonecrosis.

overall_design: Single-cell sequencing analysis was conducted from four cystic change samples from SIONFH patients.


title: Effect of Ref-1 redox inhibition with APX2009 on gene expression in human retinal endothelial cells

city: Indianapolis

first: Kelley

last: Mark

state: Indiana

institute: Herman B Wells Center for Pediatric Research

summary: Ischemic retinopathies, such as proliferative diabetic retinopathy (PDR) and retinopathy of prematurity (ROP), are characterized by abnormal retinal neovascularization. Current therapeutic interventions for these diseases include intravitreal injections of anti-VEGF biologics, which face multiple limitations due to variable patient response and utilization of alternative pathways to promote angiogenesis. APE1/Ref-1, a protein with both DNA endonuclease and redox regulatory functions, may be a novel therpautic target for proliferative retinopathies, because the redox function of Ref-1 modulates multiple signaling pathways involved in angiogenesis and inflammation. Here, we aimed to identify novel signaling pathways regulated by Ref-1 redox activity using RNA sequencing of human retinal endothelial cells treated with Ref-1 redox inhibitor APX2009.

overall_design: RNA-seq profiling of human retinal endothelial cells after 6 hour treatment with 1% DMSO under normoxic conditions or 10mM APX2009 treatment under normoxic conditions.

first: Mark

middle: R

last: Kelley

first: Timothy

last: Corson

first: Kamakshi

last: Sishtla

first: Gabriella

middle: D

last: Hartman

first: Jun

last: Wan

first: Sheng

last: Liu


title: In situ programming of tumor microenvironment to alleviate immunosuppression for pancreatic cancer immunotherapy

city: changchun

first: Man

last: Sun

address: No. 2699, Qianjin Street, Chaoyang District, Changchun City, Jilin Province, China

institute: jilin university

summary: Recent studies have highlighted the pivotal role of the cGAS-STING pathway in cancer immunotherapy. However, clinical trials with cGAS-STING pathway agonists have faced setbacks thanks to their short biological half-life, lack of specificity, and potential to promote tumor immune evasion. To address these challenges, we developed a novel drug delivery platform, termed cmExoaCD11b, designed to precisely target and reprogram the tumor microenvironment (TME) in situ for pancreatic cancer immunotherapy. cmExoaCD11b was engineered to encapsulate high copy numbers of cGAMP and IL-12 mRNA using cellular nanoporation technology and was functionalized with anti-CD11b antibodies for targeted delivery to macrophages. Notably, cmExoaCD11b facilitates the repolarization of M2 macrophages to M1 phenotype, thereby reprograming the TME and enhancing the release of pro-inflammatory cytokines. cmExoaCD11b successfully reversed the immunosuppressive status in the TME and suppressed tumor growth. More importantly, cmExoaCD11b has demonstrated significant therapeutic efficacy in both murine pancreatic cancer models and patient-derived xenograft models. These results suggest that cmExoaCD11b represents a promising approach to overcoming immunosuppression in pancreatic cancer, paving the way for its potential application in cancer immunotherapy.

overall_design: Single-cell sequencing analysis of mouse pancreatic cancer immune cells after treatment with administered drugs.

first: Huan

last: Zhang


title: Reprogramming SREBP1-dependent lipogenesis and inflammation in high-risk breast with licochalcone A: a novel path to cancer prevention

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

summary: Anti-estrogens have had a limited impact on breast cancer (BC) prevention. Novel agents with better tolerability, and efficacy beyond estrogen receptor (ER) positive BC are needed. We studied licochalcone A (LicA) for ER-agnostic BC prevention. We demonstrated that LicA significantly reduced proliferation in seven human breast cell lines and suppressed ER+ and ER- xenograft tumors in mice. We confirmed these observations ex vivo in contralateral unaffected breast (CUB) of women with unilateral sporadic BC, and breast cancer cell lines using RNA sequencing, metabolism flux modeling, confirmatory NanoString metabolic pathway panel analysis in independent sets of specimens, proteomics, and western blots. We found that LicA targets sterol regulatory element binding protein 1 (SREBP1) with subsequent metabolic-inflammatory changes, lowering spatiotemporally resolved cholesterol levels inside malignant cells to the levels in normal mammary cells. Mechanistically, in CUBs we observed that LicA downregulated PI3K-AKT-SREBP1-dependent lipogenesis, NF-kB-dependent inflammation, and de novo nucleotide biosynthesis, stalling proliferation. Studies in cell lines showed suppression of PI3K and AKT phosphorylation, SREBP1 protein expression, and the SREBP1-dependent enzymes such as ACAT2, ACLY, FASN, SCD, consistent with reduced NEDD8 required for SREBP1 stabilization. We found significant reduction in NF-kB expression, its nuclear translocation mediator karyopherin β1, and prostaglandin E2 synthesis. We demonstrated a reduction in PRPS1-catalyzed de novo nucleotide biosynthesis, and downregulation of proliferative markers MKI67, RRM2, and the survival marker BCL2.  LicA reduces pro-tumorigenic aberrations in lipid homeostasis and inflammation through SREBP1. It is a promising non-endocrine candidate for BC prevention. Future studies in immunocompetent BC prevention models are warranted.

overall_design: Surgical tissues of the contralateral unaffected breast of women with unilateral breast cancer was processed to microstructures and treated with LicA (5 uM) or DMSO for 24 h. RNA was extracted. It was quantified by Qubit and qualified by Bioanalyzer, prior to library preparation and RNa sequencing.

first: Atieh

last: Hajirahimkhan

middle: T

first: Carolina

middle: H

last: Chung

first: Xingyu

last: Guo

first: Kyli

last: Berkley

first: Raymond

last: Moellering

first: Oukseub

last: Lee

first: Ruohui

last: Chen

first: Wonhwa

last: Cho

first: Sriram

last: Chandrasekaran

first: Susan

last: Clare

first: Seema

middle: A

last: Khan


title: Enhanced Production of HCV E1E2 Subunit Vaccine Candidates via Protein-Protein Interaction Identification in Glyco-engineered CHO cells

city: La Jolla

first: Nathan

middle: E.

last: Lewis

state: CA

address: 9500 Gilman Dr. IBRFII, 5220E

department: Bioengineering; Pediatrics

institute: University of California, San Diego

summary: Hepatitis C Virus (HCV) is a bloodborne virus that affects 70 million people globally with infections that can often go unnoticed, thus motivating the development of an HCV vaccine. While prior work has developed secreted E1E2 (sE1E2) protein vaccines, efforts to express it recombinantly have  resulted in very low titers. To address this challenge, here we employed a multi-omics approach to identify protein interactors that enhance the secretion of sE1E2. By detecting Protein-Protein Interactions (PPIs) using Biotinylation by Antibody Recognition (BAR) and integrating the data with RNA-Seq, we identified proteins within the secretory pathway that interact with sE1E2 and validated their impact by overexpressing the interacting proteins. Among these, CUL4A and YWHAH significantly enhanced sE1E2 secretion in geCHO cells. The integration of omics techniques and genetic engineering in this study provides valuable insights into improving protein secretion in CHO cells, paving the way for the development of more affordable and accessible biotherapeutics.

overall_design: RNA-seq profiling of glyco-engineered CHO cells expressing the subunit HCV vaccine, E1E2

first: Mina Ying Min

last: Wu

first: Frances

last: Rocamora

first: Caressa

last: Robinson

first: Thomas

last: Fuerst

first: Eric

last: Toth

first: Svetlana

last: Maurya

first: Nathan E.


title: Infection and herbicide exposure implicate c-Abl kinase in α-synuclein serine 129 phosphorylation

city: Kiel

middle: F.

last: Meyer

address: Schwanenweg 20, Haus U27, 2 OG

department: Infektion Onkologie

country: Germany

institute: IKMB

summary: Parkinson's disease is a complex multifactorial neurodegenerative disorder characterized by α-synuclein aggregation in Lewy bodies, with phosphorylation at serine 129 (pSer129) being a critical pathological hallmark. However, the exact mechanisms linking the diverse triggers to a unified disease phenotype remain poorly understood. In this study we aim to investigate the common effects of infection and pesticide exposure on accumulation of pSer129 α-synuclein, focusing on the involvement of c-Abl in this process. The functional analysis of RNA sequencing results demonstrated that both H. pylori and rotenone induce oxidative stress, neuroinflammation and neurodegenerative pathways. Rotenone and H. pylori activated c-Abl, perhaps through the induced oxidative stress and promote α-synuclein phosphorylation. The kinase inhibitors ponatinib, nilotinib, and asciminib effectively rescued pSer129 α-synuclein and reversed associated gene expression changes induced by rotenone or H. pylori. Moreover, GSK3β is involved in the induction of pSer129 by c-Abl. Furthermore, H. pylori’s vacuolating cytotoxin play a crucial role in phosphorylation of pSer129 α-synuclein through c-Abl.

overall_design: SH-SY5Y cells (ATCC, CRL-2266, RRID: CVCL_0019) were infected with Helicobacter pylori WT P12 strain (Hpy) or treated with 10µM of Rotenone in the presence or absence of 50nM of the ABL1 inhibitor Ponatinib. 6 hours after treatment, transcriptional responses were studied by RNAseq. Vehicle only (DMSO) controls were also included.

first: Marzieh

last: Ehsani

first: Zeyang

last: Sun

first: Alvaro

last: Quevedo Olmos

first: Gesa

last: Roesler

first: Mahdi

last: Rasa

first: David

last: Holthaus

first: Saskia

last: F. Erttmann


title: Acetate derived from metabolism of ethanol affects gene expression in bone and delays chondrogenic differentiation

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: Alcohol intake is a risk factor for development of osteopenia. Ethanol perturbs gene expression in osteoblasts and osteoclasts and disrupts growth plate morphology. Hepatic metabolism of ethanol to acetate elevates concentrations of acetate in the circulation.  We investigated whether acetate could mediate the toxicity of ethanol on gene expression in bone and on chondrocyte differentiation. When ethanol and acetate were compared by gavage for four consecutive days, none of eleven genes involved in bone homeostasis  showed expression significantly affected by acetate, but the acetate responses significantly correlated with ethanol responses. Intraperitoneal injection with acetate to transiently elevate serum acetate for four consecutive days significantly increased expression of two markers of osteoclast differentiation, calcitonin receptor (Calcr) and Ocstamp. Early chondrogenic differentiation of ATDC5 cells for 7 days in vitro characterized by aggrecan (Acan) and collagen 2a1 (Col2a1) mRNA expression and proteoglycan production was inhibited by both 50 mM ethanol and 5 mM acetate. Ethanol effects were not blocked by the alcohol dehydrogenase inhibitor 4-methylpyrazole. 50 mM ethanol retarded both ATDC5 cell growth and culture medium acidification. Inhibition of chondrogenic differentiation by 5 mM acetate was associated with elevated phosphorylation of Erk1 and Erk2 and decreased expression of transcription factors Sox9 and Runx2. In acetate-exposed cells, blocking of Erk1 and Erk2 phosphorylation with Trametinib prevented further reduction of Acan and Col2a1 mRNA expression. We conclude that ethanol-derived acetate mediates at least part of the induction of Calcr and Ocstamp expression, and that acetate mimics effects of ethanol on early chondrogenic differentiation.

overall_design: Alcohol intake is a risk factor for development of osteopenia. We investigated whether acetate could mediate the toxicity of ethanol on gene expression in bone and on chondrocyte differentiation.

first: Kim

middle: B

last: Pedersen

first: Cheyleann

last: Del Valle-Ponce de Leon

first: Hardy

last: Hang

first: Jin-Ran

last: Chen

first: Christopher

last: Taylor

first: Meng

last: Luo

first: Alexandra

last: Denys

first: Martin

middle: J

last: Ronis


title: Distinct roles of the corepressors NCOR and SMRT in shaping the macrophage epigenome and transcriptome linked to metabolic and inflammatory pathways

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

summary: The NCOR/SMRT corepressor complex is a fundamental coregulator of these mechanisms. However, the individual roles and the relative importance of the two major subunits NCOR and SMRT remain poorly understood. Here, we assessed the genome-wide roles of NCOR and SMRT in mouse macrophages by integrative analysis of cistrome, epigenome, and transcriptome. Although both corepressors exhibit genome-wide cooccupancy, their depletion revealed that SMRT primarily represses inflammation-related genes, whereas NCOR primarily represses metabolism-related genes. NCOR also activates inflammatory genes, some characteristic of tumor-associated macrophages. Corepressor depletion selectively alters chromatin accessibility, acetylation at enhancers, and the interplay with transcription factors. Both corepressors influence each other at chromatin, with SMRT superior to NCOR.

overall_design: We used different methods to deplete NCOR and SMRT in macrophages and compared the resulting transcriptional changes. Using multi-omics tools, we summarized the priority and dependency relationships among different proteins within the corepressor complex in macrophages.

first: Astradeni

last: Efthymiadou

first: Eckardt

last: Treuter


title: Hepatic acetyl-CoA metabolism modulates neuroinflammation and depression susceptibility via acetate

city: wuhan

first: yu

last: cao

address: Qiaokou District

institute: Huazhong University of Science and Technology

summary: Extensive research highlights impaired brain energy metabolism in neuropsychiatric disorders, whereas much less is known about the role of peripheral metabolic state. Liver is the metabolic hub, and herein, we demonstrated that hepatic hydrolysis of acetyl-coenzyme A, a central metabolic intermediate, signals the brain and helps buffer stress. Using a chronic social defeat stress paradigm in male mice, we observed a hepatic glucose-to-acetate metabolic switch followed by a glucocorticoid-repressed transcription of the acetyl-coenzyme A hydrolase, acetyl-coenzyme A thioesterase 12, to confer stress vulnerability. Hepatic overexpression of acetyl-coenzyme A thioesterase 12 alleviated depression-like phenotypes via increasing acetate output to promote histone acetylation in the ventral hippocampus, which bolstered the expression of programmed cell death ligand 1 in astrocytes, limiting neuroinflammation and rescuing inhibitory synaptic transmission dysfunction. Our findings demonstrate hepatic acetyl-coenzyme A hydrolysis serves as a key liver-brain axis component that regulates depression susceptibility.

overall_design: We used RNA sequencing to analyze differentially expressed genes in the vHip of control mice, CSDS-exposed, AAV8-eGFP mice exposed to SSDS and hepatic ACOT12 gene knockdown mice exposed to SSDS.

first: Yu

last: Cao

first: Fang

last: Wang

first: Pengfei

last: Wu

first: Jianguo


title: High phosphorus and low protein mediate medial artery calcification and calcific uremic arteriolopathy in CKD mice: Significance of p38 MAPK signaling

city: New Haven

first: Yujun

last: Cai

address: 310 Cedar St.

institute: Yale University

summary: Medial artery calcification and calcific uremic arteriolopathy (CUA) are observed in patients with chronic kidney disease (CKD). They are strongly associated with increased morbidity and mortality, yet the underlying mechanisms are poorly understood, and no effective drug targets have been developed. Herein, we observed that a high phosphate, low protein (HPi-Lp) diet induced medial artery and skin arteriolar calcification in 5/6 nephrectomy (5/6 Nx) CKD mice. We further determined that p38 MAPK signaling was critical in this vasculopathy. Calcification was examined using a micro-CT scan, Alizarin Red staining, Von Kossa staining, and calcium assay. Additionally, we found that the HPi-Lp diet feeding aggravated glomerulus impairment and renal fibrosis in 5/6 Nx mice. Using RNA-Seq analysis, we identified that p38 MAPK signaling was specifically activated in the 5/6 Nx-HPi-Lp mice. Inactivation of p38 MAPK signaling using a pharmacological inhibitor SB203580 significantly reduced medial artery calcification, skin arteriolar calcium deposits, and kidney fibrosis. Collectively, our data suggest that 5/6 Nx mice fed a HPi-Lp diet can be used as a reliable mouse model for studying medial artery and CUA arteriolar calcification. Additionally, targeting p38 MAPK signaling could be a promising therapeutic strategy to mitigate these vascular disorders in patients with CKD.

overall_design: RNA-Seq of the aorta of 5/6 Nx mice fed different phosphorus and protein diet

first: Raul

last: Guzman

first: Ying

last: Jin


title: Sexually dimorphic changes in liver and muscle transcriptome of 4-month-old dairy calves derived from artificial insemination or the transfer of a frozen-thawed in vitro produced embryo

city: Dublin

first: Laura

last: Thompson

address: Belfield

country: Ireland

institute: University College Dublin

summary: More than 1.2 million in vitro produced (IVP) bovine embryos are transferred annually worldwide, significantly outnumbering those from traditional superovulation, but there are limited reports on the birth and postnatal development of such calves. The conditions imposed during in vitro embryo culture may cause modifications of the embryo genome, including the transcriptome, potentially affecting postnatal organ function. This study compared the liver and muscle transcriptome in 4-month-old male and female dairy calves conceived by artificial insemination (AI) or IVP (n = 4 per sex per treatment). Biopsy tissue samples were collected and processed for RNA sequencing. Analysis of the RNAseq data revealed a distinct separation between the liver transcriptomes of female and male calves, regardless of method of production. Moreover, within the cohort of female calves, a strong separation between female calves derived from IVP vs AI was observed. Analysis of differentially expressed genes (DEGs) indicated downregulation of oxidative phosphorylation pathways and upregulation of pathways strongly enriching immune system processes, specifically Th17 cell differentiation and antigen processing and presentation. For the muscle transcriptome, the separation between male and female calves was less apparent compared with liver transcriptome, but there was still a clear separation between female calves derived from IVP vs AI, with downregulated genes enriching the p53 signalling pathway and upregulated genes enriching muscle structure development pathways. These results suggest that female embryos derived from IVP vs AI have developmental differences that manifest as differential transcriptomic profiles postnatally. In conclusion, these findings demonstrate that the IVP process induces significant alterations in the liver and muscle transcriptome of female postnatal calves. Further exploration is necessary to understand the potential implications for lifetime growth, health and production characteristics.

overall_design: Heifers were randomly assigned to one of the two groups; those receiving timed AI with frozen thawed semen (AI, n=8) and those transferred a single frozen-thawed Grade 1 Day 7 or Day 8 in vitro produced embryo (IVP, n=8). Resulting calves were divided into two groups based on their origin, AI (n=8; 4 male, 4 female) or IVP (n=8; 4 male, 4 female). Calves in both groups were raised in similar conditions up to 4 months of age, at which point biopsies were taken from the liver and muscle using a percutaneous punch technique. RNA extraction, quality control, library preparation, and sequencing was performed on the liver and muscle tissue samples. The subsequent read count files were employed to determine the differentially expressed genes (DEG) with the edgeR package for the R software and the gene expression counts were normalized by library size with edgeR methods. The DEG between groups were defined as those with false discovery rate (FDR) <0.05. The EntrezID corresponding to the DEG, was interrogated for enriched Gene Ontology and KEGG pathways using ShinyGO V0.77.

first: Alan

last: Crowe

first: Maria

last: Rabaglino

first: Stephen

last: Butler

first: Pat

last: Lonergan


title: Profiling RNA subcellular localization in situ by TATA-seq

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Membranelles organelles, dynamic subcellular structures formed by RNA and RNA-binding proteins (RBPs) undergoing liquid-liquid phase separation (LLPS), play key roles in biological processes such as RNA degradation in P bodies, translation inhibition in stress granules, and RNA splicing in nuclear speckles. However, the study of RNA species within these organelles has been hindered by the absence of simple, sensitive, and specific methodologies. Here, we introduce Target Transcript Amplification and Sequencing (TATA-seq), a novel strategy for precisely profiling RNA in membranelles organelles via in situ targeted transcription and linear amplification. TATA-seq uses a primary antibody against a marker protein of the target organelle to recruit a secondary antibody conjugated with streptavidin, which binds an oligonucleotide with a ds-T7 promoter. This initiates in situ transcription of RNA transcripts, followed by amplification with T7 RNA polymerase to generate sufficient material for sequencing. An IgG control is used to subtract background noise during data analysis. We demonstrate the method’s utility by profiling RNA in stress granules induced by sodium arsenite in HeLa cells, with validation through FISH and immunofluorescence. TATA-seq offers a simple, highly sensitive, and precise tool for studying RNA dynamics within membranelles organelles, expanding the capabilities of RNA research.

overall_design:
We performed TATA-Seq on sodium arsenite-treated HeLa cells to detect RNAs within stress granules.
Both the AS-IgG and Ctrl-IgG groups employed the IgG antibody homologous to G3BP1 (the marker protein of stress granules) to help filter out background signals from non-specific binding.
Both the KO-IgG and WT-IgG groups employed the IgG antibody homologous to TNRC6A to help filter out background signals from non-specific binding.

first: Chu

last: Xu

first: Junjie

last: Li


title: Differentially expressed transcripts associated with depressive symptoms during pregnancy and postpartum

city: Uppsala

first: Alkistis

last: Skalkidou

address: Dag Hammarskjölds väg 14 B

department: Women's and Children's Health

country: Sweden

institute: Uppsala university

summary: Peripartum depression can have severe impact on the mother’s and the infant’s health. Yet, its biological underpinnings are largely unknown. The present study sought to identify transcriptomic signatures of depressive symptoms  during pregnancy and postpartum. Blood samples were collected during late pregnancy or early postpartum for mRNA isolation and sequencing, while depressive symptoms were assessed using the Edinburgh Postnatal Depression Scale. Stratifying according to the timepoint samples were collected, differentially expressed genes (DEGs) were identified by (1) comparing mRNA levels between the symptom trajectory groups, and (2) correlating with EPDS scores. DEGs for samples collected late pregnancy, but not postpartum, were associated with depressive symptoms occurring only during pregnancy or persisting postpartum, compared with controls. There were 16 upregulated and 109 downregulated DEGs significantly associated with changes in EPDS score at week 32 among samples collected late pregnancy. Gene Set Enrichment Analysis identified immune response and cell motility as processes linked to these DEGs. Hypothesis-based analysis on previously identified postpartum depressive symptoms-related DEGs, replicated a positive association between expression of immune-related genes ISG15 and RSAD2 with postpartum-onset depressive symptoms, both at samples taken during late pregnancy and postpartum. The present findings point to transcriptomic signatures associated with depressive symptoms, mostly related to immune system dysregulation.

overall_design: Nested case-control study; blood samples were collected in late pregnancy or postparum from women with of without depressive symptomes.

first: Richelle

last: Björvang

last: Vrettou

first: Xabier

last: Bujanda Cundin

first: Eugenio

last: Del Prete

first: Joëlle

last: Rüegg

first: Susanne

last: Lager

first: Diego

last: di Bernardo

first: Erika

last: Comasco