title: Structure-Dependent Developmental Toxicity of Alkyl-Substituted Naphthalenes

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: Oregon

address: 28645 east hwy 34

department: Environmental and Molecular Toxicology

institute: Oregon State University

summary: Naphthalene and its alkyl-substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons (PAHs) in environmental and human exposure studies, yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi-volatile compounds. This study developed a vial based high through-put method to effectively assess the activity of naphthalenes and a set of 24 alkyl-substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical (0-50 µM) in rotating sealed glass vials to minimize volatilization. Benchmark concentration (BMC50) values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96-well plate exposures. LogKow and body burden were poor predictors of toxicity, suggesting a non-narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes, with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets (e.g., CYP1A2, NT5E, FOLR1) that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi-volatile compounds, reveals structure-dependent toxicity among alkyl-substituted naphthalenes, and provides a foundation for further mechanistic studies and improved risk assessment of alkyl-substituted PAHs.

overall_design: Zebrafish were exposed to 25 chemicals, naphthalene and 24 alkyl-sustituted naphthalenes, using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from 6 hours post fertiliation (hpf) to 24 hpf. RNA was collected at at 48 hpf. Exposures, collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO-seq platform.

first: Mackenzie

last: Morshead

first: Lisa

last: Truong

first: Steven

last: Carrell

first: Richard

last: Scott

first: Kim

middle: A

last: Anderson


title: Endothelial KLF15/VASN axis inhibits angiogenesis via activation of Notch1 signaling [ChIP-Seq]

status: Public on May 24 2025

city: Shanghai

first: jia

last: zhang

address: Ruijin 2nd Road 197

country: China

institute: Shanghai Jiao Tong University School of Medicine Department of Hypertension

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Kruppel like factors (KLFs) are a subfamily of zinc finger proteins. As one of the family members, KLF15 can specifically bind to GC rich sequences on the promoter, thereby exerting transcriptional regulatory effects. Here we found that KLF15 negatively regulates angiogenesis in endothelial cells. KLF15 induces an increase in vasorin (VASN) expression, thereby activating the Notch signaling pathway and leading to a decrease in angiogenesis. These findings point to an KLF15/VASN axis as critical determinants of Notch signaling activation.

overall_design: ChIP-seq of FLAG-tag in endothelial cells transfected with adenovirus carrying KLF15 gene

first: Xiao-Dong

last: Li

first: Ping-Jin

last: Gao

first: Ji-Guang

last: Wang

first: Jia

last: Zhang

first: Jia-Jia

last: Zhao


title: Transcriptional differences in suspended breast cancer cells exposed to hypoxia.

status: Public on May 23 2025

city: guangzhou

first: jingyi

last: long

address: The Third Affiliated Hospital of Southern Medical University

institute: The southern medical university

type: Expression profiling by high throughput sequencing

summary: We report the transcriptional differences of suspended MCF-7 and MDA-MB-231 breast cancer cells after exposure to hypoxia.

overall_design: MCF-7 cells (1*106 cells/well) and MDA-MB-231 cells (1*106 cells/well) were suspended in high-glucose DMEM containing 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C, 5%CO2 and seeded in individual wells of ultra-low attachment 6-well culture plates (Corning® Costar®, CLS3471). To simulate a hypoxic environment, we placed suspension-cultured tumor cells in a sealed Rectangular jar(MITSUBISHI GAS CHEMICAL, JAR-25) with hypoxia indicator with AnaeroPack™- Anaero(MITSUBISHI GAS CHEMICAL) and incubated for 6hrs hrs. RNA was extracted and submitted for library preparation, RNA sequencing and preliminary analysis.

first: Lyu

last: Xiaoming

first: Long

last: jingyi


title: Interlocking core regulatory circuits enable viral hijacking in Merkel cell carcinoma

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

country: USA

institute: NCI, NIH

summary: Merkel Cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer. The conditions and cell type(s) of MCC are unknown. Virus positive MCC (VP-MCC) is driven by T antigens expressed from integrated Merkel cell polyomavirus (MCPyV). We found that VP-MCC required lineage-specific neuroendocrine transcription factors (TFs), including ATOH1, INSM1, ISL1, LHX3, POU4F3, and SOX2 that were central to core regulatory (CR) transcriptional circuitry. MCPyV small T antigen and host CR TFs co-bound VP-MCC super enhancers while T antigen expression was directly regulated by LHX3 and ISL1, establishing an interlocking network between host CR circuitry and the oncovirus. Moreover, MCPyV integration sites were enriched near VP- MCC super enhancers, further suggesting a functional relationship between viral oncogenesis and core neuroendocrine circuitry.

overall_design: Genome-wide profiles for histone marks, DNase hypersensitivity, transcription factors, and 3D loops of active chromatin (AQuA-HiChIP).

first: Berkley

middle: E

last: Gryder

first: Xinyu

last: Wen


title: Direct Reprogramming of Human Fibroblasts into Retinal Progenitor Cells by Small Molecules to Treat Photoreceptor Degeneration

status: Public on May 22 2025

city: Taipei

first: Yueh-Chang

last: Lee

address: No.128, Sec. 2, Academia Rd.

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: Retinal progenitor cells (RPCs) hold promise for restoring vision in advanced stages of photoreceptor degeneration. We have developed a technique to directly reprogram human Tenon's fibroblasts (HTFs) into induced RPC-like cells (iRPCs) using small molecules. To explore the transcriptomic profile of iRPCs, we performed bulk RNA-seq analysis of HTFs and FACS-sorted iRPCs. The Gene Ontology (GO) enrichment analysis demonstrated significantly highly enriched GO terms include Proteinaceous Extracellular Matrix, Axon and Dendrite, Synaptic Membrane and Transport Vesicle, Presynapse and Postsynapse, Basement Membrane and Collagen Trimer, Platelet Alpha Granule and ER Lumen. The significantly down-regulated GOs were Spindle and Chromosomal Structures, Sarcomere and Muscle Fiber Components, Cell Adhesion Complexes.

overall_design: RNA-seq profilling of HTFs and their derivatives (iRPCs) at day0 and day6 of chemical reprogramming

first: Pei-Lun

last: Lai

first: Chien-Ying

first: Fang-Ling

last: Chang

first: Shang-Yen

last: Wu

first: Po-Yu

last: Lin

first: Chi-Hsuan

last: Chuang

first: Yu-Xin

last: Chou

first: Zhao-Feng

last: Chen

first: Chih-Lun

last: Cheng

first: Hsuan

first: Chi-Hou

last: Ng

first: Shang-Chih

last: Yang

first: Shang-Fu

first: Wei-Ju

first: Yu-Chieh

last: Ho

first: Kishan

last: Kapupara

first: Cheng-En

last: Zou

first: Yao-Tseng

first: Jean

last: Lu


title: Folliculin deletion in the mouse kidney results in cystogenesis of the loops of Henle via aberrant TFEB activation

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

summary: The mammalian kidney contains numerous nephrons connected to the collecting ducts, and each nephron consists of a glomerulus, a proximal tubule, the loop of Henle (LoH), and a distal tubule. Folliculin (Flcn) is a causative gene for Birt-Hogg-Dube (BHD) syndrome, which is characterized by a variety of symptoms including renal cysts and cancers. Although deletion of Flcn in the mouse collecting duct has been reported to result in cyst formation, its precise role in the nephron remains unclear. We report here that nephron-specific Flcn knockout mice exhibit cystogenesis along the entire nephron segments, most prominent in the LoH, preceded by an irregularly shaped lumen lined by enlarged epithelia. Single-cell RNA sequencing revealed many upregulated genes, especially in the mutant LoH. These genes include those related to lysosomal activity and mTORC1 activation and are likely targets of TFE3/TFEB. While the double Flcn/Tfe3 knockout only ameliorates the glomerular cysts, the double Flcn/Tfeb knockout dramatically reverses most of the phenotypes along the entire nephron. Thus, Flcn deletion leads to cystogenesis via aberrant TFEB activation. Our findings reveal the essential role of the Flcn-TFEB-mTORC1 signaling pathway in nephron development, particularly in LoH, and shed light on the initial disease state of BHD syndrome.

overall_design: To investigate the gene expression profiles upon Flcn deletion in all nephron lineages, scRNA-seq analysis were performed using Flcn heterozygous (Six2Cre; Flcn flox/+) and Flcn homozygous (Six2Cre; Flcn flox/flox) neonatal kidneys (P0).

first: Ola

last: Shalaby

first: Koichiro

last: Miike

first: Masaya

last: Baba

first: Ryuichi

last: Nishinakamura


title: Dissecting the effects of sequence on transcription attenuation by the Restrictor complex [INSERT-Seq]

city: Boston

first: Claudia

last: Mimoso

state: MA

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

summary: The eukaryotic genome is actively transcribed by RNA Polymerase II (RNAPII) to produce both messenger RNAs (mRNAs) and a repertoire of non-coding RNAs (ncRNAs). For genome integrity, RNAPII elongation and termination is tightly regulated to enable the full-length synthesis of mRNAs and the rapid turnover of many ncRNAs. The Restrictor Complex has recently been implicated in attenuating the expression of many ncRNAs, however the mechanism by which Restrictor suppresses gene expression remains unclear. Here, we address central questions regarding the specificity of Restrictor-mediated transcription attenuation.

overall_design: INSERT-seq with steady-state-RNA-level read-out was performed for 9 samples: 3 biological replicate sets of siNT, siWDR82 and siZC3H4 treated cells.

first: Hanneke

last: Vlaming

first: Nathalie

middle: P

last: de Wagenaar

first: Karen

last: Adelman


title: Dissecting the effects of sequence on transcription attenuation by the Restrictor complex [RNA-Seq]

overall_design: Examination of 6 samples by RNA-seq; 3 biological replicate sets of siZC3H4 and siNT treated cells


title: Dissecting the effects of sequence on transcription attenuation by the Restrictor complex

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

overall_design: Refer to individual Series


title: Dissecting the effects of sequence on transcription attenuation by the Restrictor complex [TT-Seq]

overall_design: Examination of 11 samples by TT-seq; 3 biological replicate sets of DMSO and dTAG-13 treated cells. 2 biological replicate sets of siZC3H4 and 3 biological replicates of siNT treated cells


title: Dissecting the effects of sequence on transcription attenuation by the Restrictor complex [PRO-Seq]

overall_design: Examination of 6 samples by PRO-seq; 3 biological replicate sets of DMSO and dTAG-13 treated cells.


title: Tumor CD45+ cells and spleen LY6G+ PMNs isolated from Hdc-GFP mice with subcutaneous ACKP syngeneic GC line-established tumors and treated with TFF2-MSA and/or anti-PD-1 therapies.

city: Sydney

first: Chenkai

last: Ma

state: NSW

address: 11 Julius Avenue

country: Australia

institute: CSIRO

summary: We designed a novel TFF2-MSA peptide as a CXCR4 partial agonist, and used it either alone or in combination with anti-PD-1 to treat established ACKP tumors. PMNs are known to be highly heterogenous, thus these tumors are grown in Hdc-GFP host mice to trace Hdc+ PMN subsets. We then used single cell-RNA sequencing (scRNA-seq) to elucidate the effect of TFF2-MSA on tumor and spleen PMNs, and more broadly the tumor microenvironment.

overall_design: The CD45+ cells were isolated with subcutaneous syngeneic ACKP tumors following 3 cycles of treatment with vehicle, TFF2-MSA, anti-PD-1, or their combination. To detect the systemic effect of TFF2-MSA on PMNs, LY6G+ PMNs were isolated from the spleens of ACKP tumor-bearing mice following the vehicle, TFF2-MSA, and TFF2-MSA plus anti-PD-1 treatments. A spleen PMN sample from tumor-free mice was included to identify tumor-induced effects on PMNs. To increase the visibility of PMNs in scRNA-seq, given their low RNA content, we employed a strategy of mixing Ly6G+ tumor PMNs with total CD45+ cells isolated from the same tumors at a 1:2 ratio during sample preparation for scRNA-seq analysis.

first: Jin

last: Qian

first: Timothy

last: Wang


title: HIF-1α binding in suspended MDA-MB-231 breast cancer cells

first: jingyi

last: long

summary: We report the transcriptional differences of suspended MCF-7 and MDA-MB-231 breast cancer cells after treated with CoCl2 100uM for 24 hours.

overall_design: CUT&Tag technology represents a cutting-edge method for investigating protein-DNA interactions. Utilizing a hyperactive novel fusion enzyme (Hyperactive pG-Tn5 / pA-Tn5 Transposase), this technique, under antibody guidance, specifically targets and cleaves DNA sequences near target proteins. It boasts several advantages over traditional ChIP-Seq, including lower cell input requirements, enhanced signal-to-noise ratio, and improved repeatability. MDA-MB-231 cells treated with 100uM CoCl2 for 24 hours were used. The CUT&Tag assay and subsequent DNA library construction were performed by following the manufacturer’s instructions for the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-01). An anti-HIF1-a monoclonal antibody (Affinity, BF8002) is used as the primary antibody. Paired-end sequencing was performed on an Illumina Novaseq 6000 system. Paired-end reads (150 bp) were aligned using Bowtie2 version 2.2.5. Macs2 peak calling software was used for peak calling.

first: Lyu

last: Xiaoming

first: Long

last: jingyi


title: Gene expression in NSCLC cancer cell with EGFR-TKI resistance after statin treatment

city: Tainan

first: Kuan-Chung

last: Hsiao

address: 367 shengli road

institute: NHRI

summary: We have established a Genfitnib resistant lung cancer cell line, Ire. RNA-sequencing analysis was performed to analyze the diffreential gene expression in Ire cells with or without statin treatment.

overall_design: Total RNA was extracted from  Ire cells with or without statin treatment and the differential gene expression was determined by using RNA-sequencing analysis


title: RNA seq for HLECs transfected with siIFITM1

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

summary: To understand the role of IFITM1 in HLECs, HLECs were transfected with siIFITM1 or sicontrol . RNAs isolated from these cells were subjected to RNA seq analysis. DOI: 10.1096/fj.202500783R

overall_design: HLECs were transfected with a 5 nM siRNA pool against IFITM1 (Invitrogen, Carlsbad, CA, USA) or nontarget control (Invitrogen, Carlsbad, CA, USA) as previously described for 3 days. Then, cells were processed for total RNA isolation using miRNeasy kit (Qiagen, Hilden, Germany). Expression profiling was conducted using a Next-Generation Sequencing platform at Northwestern University Center for Genetic Medicine core. Gene differential expression profiles obtained from RNA-seq analysis were subjected to gene ontology analysis using DAVID.

first: Huimin

last: Jiang

first: Seyedeh

last: Parisa Foroozandehasl

first: Robert

middle: M

last: Lavker


title: Osr2Cre-mediated deletion of Hnf4a in the mouse kidney

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: This study aims to identify genes regulated by Hnf4a in developing nephrons. In the mouse kidney, Osr2Cre efficiently deletes the Hnf4a flox allele and targets all nephron tubules except distal tubules. To investigate gene expression changes, we performed bulk RNA-seq on Osr2Cre-targeted cells from Hnf4a mutant and control kidneys.

overall_design: Osr2Cre activated Rosa26 Ai3 reporter and deleted Hnf4a in the developing mouse kidney. Rosa26-Ai3 reporter-positive cells from the mouse kidney at E18.5 were FACS-isolated and subjected to bulk RNA-seq

first: Joo-Seop

last: Park

first: Eunah

last: Chung

first: Christopher

last: Ahn


title: Evaluation of novel computational methods that identify RNA-binding protein footprints from structural data

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

summary: RNA binding proteins (RBP) play diverse roles in mRNA processing and function. However, from over 1,000 RBPs encoded in the human genome, a detailed molecular understanding of their interactions with RNA is available only for a small fraction. In most cases, our knowledge of the combination of RNA sequence and structure required for specific binding is insufficient for enabling exhaustive prediction of binding sites transcriptome-wide. In that context, the rapidly expanding collection of transcriptomic datasets that map distinct, yet intertwined post-transcriptional marks, such as RNA structure and RBP binding, presents an opportunity to integratively analyze them in order to better characterize binding. A grand challenge faced by our community is that relatively little information on the structural context of RNA-protein interactions has been gleaned from integrating such datasets, partially due to lack of suitable methods. To engage scientists from diverse backgrounds in addressing this gap, the RNA Society organized the RBP Footprint Grand Challenge⸺an international community effort to develop new methods or leverage existing ones for predicting RBP binding sites through analysis of a growing volume of sequence, structure, and binding data and to experimentally validate select predictions. Here, we report the initiative, analyses and methods developed by the participants, validation results, and several new in vivo binding datasets generated for validation. We hope this work will inspire additional innovation in computational methods, further utilization of available data resources, and future endeavors to engage the community in collaborating towards closing other critical data analysis gaps.

overall_design: eCLIP for four RBPs in five cell types was conducted in replicates for each condition.

first: Orel

last: Mizrahi

first: Meredith

last: Coreley

first: Ori

last: Feldman

first: Thorben

last: Fröhlking

first: Lei

last: Sun

first: Alison

last: Ziesel

first: Maciej

last: Antczak

first: Mattia

last: Bernetti

first: Shaimae

last: Elhajjajy

first: Hsuan-Lin

last: Her

first: Wenze

last: Huang

first: Grady

middle: G

last: Nguyen

first: Samuel

middle: S

first: Raul

middle: I

last: Perez Martell

first: Luke

last: Trinity

first: Kui

last: Xu

first: Tomasz

last: Zok

first: Giovanni

last: Bussi

first: Hosna

last: Jabbari

first: Yaron

last: Orenstein

first: Sharon

last: Aviran

first: Michelle

last: Meyer

first: Gene

middle: W

last: Yeo


title: Gene expression in roots or shoots (wild-type, tga7)

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

institute: The University of Tokyo

summary: To examine differential effect of the mutation of Arabidopsis TGA7 on the gene expressions, we performed microarray analysis using the shoots or the root of wild-type and tga7 mutant.

overall_design: shoot part and root part from WT and tga7 seedlings grown on 1/2 MS plates for 5 days and on nitrogen-sufficient and nitrogen-defficient agar plates for 5 days.

first: Jia

middle: Y

last: Ye

first: Shuichi

last: Yanagisawa


title: Blunted CD40-responsive enhancer activation in CREBBP-mutant lymphomas can be restored by enforced CD4 T-cell engagement

city: Houston

first: Haopeng

last: Yang

state: TX

address: 7455 Fannin ST

department: Lymphoma and Myeloma

institute: The University of Texas MD Anderson Cancer Center

summary: The CREBBP lysine acetyltransferase (KAT) is frequently mutated in follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) and has been studied using gene knock-out (KO) in murine and human cells. However, the majority of CREBBP mutations encode amino acid substitutions within the catalytic KAT domain (CREBBP KAT-PM) that retain an inactive protein and have not been extensively characterized. Using CRISPR gene editing and extensive epigenomic characterization of lymphoma cell-lines, we found that CREBBP KAT-PM lead to unloading of CREBBP from chromatin, loss of enhancer acetylation and prevention of EP300 compensation. These enhancers were enriched for those that are dynamically loaded by CREBBP in the normal centroblast-to-centrocyte transition in the germinal center, including enhancers activated in response to CD40 signaling, leading to blunted molecular response to CD40 ligand in lymphoma cells. We provide evidence that CREBBP KAT-PM inhibits EP300 function by binding limiting quantities nuclear transcription factor, thereby preventing its compensatory activity. This effect can be experimentally overcome by expressing saturating quantities of transcription factor, or biologically attenuated by strong stimulation of CD40 signaling that increases nuclear transcription factor abundance. Importantly, epigenetic responses to CD40 signaling can be induced by enforcing CD4 T-cell engagement using a bispecific antibody, leading to CD40-dependent restoration of antigen presentation machinery in CREBBP KAT-PM cells and cell death. We therefore provide a mechanistic basis for enhancer deregulation by CREBBP KAT-PM and highlight enforced CD4 T-cell engagement as a potential approach for overcoming these effects.

overall_design: CUT&RUN ATAC-seq,and mint-ChIP-seq experiment to understand chromatin loading change across different CREBBP mutants, and their repsonse to CD40 stimulation or T-cell engagement. RNA-seq experiment to understand gene expression changes across different CREBBP mutants, and their reponse to CD40 stimulation or T-cell engagement.

first: Wenchao

last: Zhang

first: Vida

last: Ravanmehr

first: Guiling

last: Cui

first: Kevin

middle: J

last: Bowman

first: Ruidong

last: Chen

first: Jared

last: Henderson

first: Shyanne

middle: R

last: Lockman

first: Estela

last: Rojas

first: Ashley

middle: L

last: Wilson

first: Sydney

last: Parsons

first: Ariel

last: Mechaly

first: Leslie

last: Regad

first: Ahmed

last: Haouz

first: Christopher

last: Flowers

first: Sattva

last: Neelapu

first: Loretta

last: Nastoupil

first: Richard

last: Davis

first: Qing

last: Deng

first: Fernando

last: Rodrigues-Lima

first: Michael

last: Green


title: Analysis of iECM Immunomodulatory Capacities in an Animal Model of Systemic Inflammation

first: Maria

last: Karkanitsa

address: 9100 Regents Rd, Apt G

department: Shu Chien Gene Lay Department of Bioengineering

institute: University of California San Diego

summary: Immunomodulatory effects of an infusible extracellular matrix (iECM) material were evaluated by a 547 mouse immunology panel using the nanostring nCounter mouse immunology panel (n=547 genes)

overall_design: Female C57 bl/6 were treated with a dual dose of lipopolysaccharide (LPS) to induce severe systemic inflammation leading to a Multiple Organ Dysfunction Syndrome (MODS) phenotype over a 30 hour period. Animals were treated with an infusible extracellular matrix (iECM) material or saline 10 hours post initial LPS dosage. Animals were sacrificed 30 hours post initial LPS dosage and RNA from blood, heart, lung, kidney, and brain tissue were isolated and transcriptional differences due to iECM treatment  were analyzed using nanostring nCounter analysis.

first: Anne

last: Lyons

first: Raymond

last: Wang


title: Effect of knockdown of CENPU on gene expression of Huh-7 and MHCC-97H hepatoma cells

city: Wuhan

first: Yingyi

last: Liu

address: #169, East Lake Road, Wuchang District, Wuhan

department: Department of Hepatobiliary and Pancreatic Surgery

institute: Zhongnan Hospital of Wuhan University

summary: To investigate the function of CENPU in the regulation of  hepatocellular carcinoma tumorigenesis , we established Huh-7 and MHCC-97H cell lines in which CENPU gene has been knocked down by siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Huh-7/MHCC-97H cells and its KD derivatives (siCENPU).

first: Ye

last: Yao

first: Bo

last: Liao

first: Xi

last: Chen


title: The protein deacetylase HDAC10 controls DNA replication in malignant lymphoid cells

city: Mainz

first: Giuseppe

last: Petrosino

state: --- Select a state ---

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

summary: Histone deacetylases (HDACs) are a family of 18 epigenetic modifiers. Targets and cancer-relevant functions of HDAC10 in leukemia cells are enigmatic. We used flow cytometry, confocal immunofluorescence, single-cell DNA electrophoresis, global RNA-sequencing, mass spectrometry-based proteomics, and quantitative measurement of protein acetylation sites to evaluate how HDAC10 controls cancer-relevant signaling pathways in leukemia cells. We demonstrate that a subset of human cultured and primary acute B-cell/T-cell leukemia and lymphoma cells require HDAC10 for their survival. In such cells, HDAC10 controls a MYC-dependent transcriptional induction of the DNA polymerase subunit POLD1. Consequently, inhibition of HDAC10 halts cells in the S and G2/M phases of the cell cycle and causes DNA breaks, and an accumulation of poly-ADP-ribose chains indicating unresolved DNA damage. These processes culminate in caspase-dependent apoptosis. We reveal that HDAC10 has a nuclear function controlling the MYC-POLD1 axis. HDAC10 maintains the processivity of DNA replication and genome integrity in leukemic cell subtypes. This mechanistically defined HDAC10ness could prospectively be exploited as treatment option.

overall_design: We performed gene expression profiling to investigate the impact of inhibition of HDAC10 by PZ48 in RS4-11 cells.

first: Andreas

middle: O

last: Mieland

first: Mario

last: Dejung

first: Jia-Xuan

first: Amitkumar

last: Fulzele

first: Fereshteh

last: Mahmoudi

first: Jia-Wey

last: Tu

first: AI-Hassan

last: Mustafa

first: Yanira

last: Zeyn

first: Christoph

last: Hieber

first: Matthias

last: Bros

first: Tina

last: Schnöder

first: Florian

middle: H

last: Heidel

first: Sara

last: Najafi

first: Ina

last: Oehme

first: Ilse

last: Hofmann

first: Mike

last: Schutkowski

first: Sebastian

last: Hilscher

first: Christian

last: Kosan

first: Falk

last: Butter

first: Sanil

last: Bhatia

first: Wolfgang

last: Sippi

first: Oliver

last: Krämer


title: The dynamic change of microRNA expression profile in endometrium and peripheral blood during the peri-implantation window

city: Zhubei City, Hsinchu County

first: An

last: Hsu

address: 7F-6, No. 66, Shengyi 5th Road

institute: INTI Labs

type: Non-coding RNA profiling by high throughput sequencing

summary: Previous studies have shown that microRNAs (miRNAs) play a crucial role in human embryo implantation by regulating the expression of genes involved in the process. While dynamic changes in plasma miRNA during the peri-implantation period have been established, systematic and comprehensive studies on miRNA expression changes in both endometrial tissue and blood during this period are lacking. A total of 62 subjects, including 62 endometrial tissue samples and 62 paired peripheral blood samples, were collected from participants undergoing hormone treatment cycles between day P+3 to P+7. Next-generation sequencing (NGS) assay was used to profile miRNA expression levels, and the results were annotated using miRBase. To identify the dynamic differentially expressed (DE) miRNAs between day P+3 to P+7, we compared the following group pairs: P+3 and P+4, P+4 and P+5, P+5 and P+6, and P+6 and P+7. We then perform functional miRNA-target interaction (MTI) and pathway enrichment analyses to understand the biological functions of dynamic DE miRNAs. We identified 76 and 48 dynamic DE miRNAs in endometrial tissue and peripheral blood samples, respectively. Functional MTI and pathway enrichment analyses revealed that these DE miRNAs influence numerous biological pathways and functions related to implantation, such as cell senescence, cell growth, apoptosis, focal adhesion, autophagy, platelet activation and signaling. Although only 10 DE miRNAs overlapped between endometrial tissue and peripheral blood, 7 of these showed consistent dynamic expression changes. Further analysis revealed a high similarity in the biological pathways and functions involving the target genes of DE miRNAs in both endometrial tissue and peripheral blood. 76 and 48 dynamic DE miRNAs were identified in endometrial tissue and peripheral blood samples, respectively. These miRNAs influence numerous biological pathways and functions related to implantation.

overall_design: miRNA-seq profiling of 62 endometrial tissue samples and 62 peripheral blood samples at day P+3 to P+7 after progesterone treatment

first: Chun-I

last: Lee

first: Eric Pok

last: Yang

first: Tsung-Hsien

first: Maw-Sheng


title: Neocortical temporal patterning by a two-layered regulatory structure

city: Beijing

first: Zhe

last: Zhao

state: Beijing

address: Tsinghua university, Beijing

department: The IDG/McGovern Institute for Brain Research

institute: Tsinghua university

summary: In the developing neocortex, a diverse array of neurons with defined types and abundances are systematically generated by a limited population of radial glial progenitors (RGPs) as they undergo successive fate changes. How this temporal patterning is regulated at the molecular level remains largely unknown. Here we present an in-depth single-cell multi-omics assay for deep characterization of regulatory programs, along with an analytical framework that integrates joint dynamics in single-cell transcription and chromatin structure to interrogate the regulation of temporal identities and fate progression of RGPs. We found that RGP temporal patterning is governed by a two-layered regulatory structure consisting of global regulators acting upon a cascade of transcription factor (TF) hubs. This cascade proceeds not by confining cascaded TF expression to specific temporal windows, but through synergistic transcriptional and epigenetic dynamics that temporally modulate TF regulatory activity. Furthermore, global regulators exhibit a progressively increasing expression pattern, and our computational modeling analysis found that the gradient of this pattern specifies the duration of each cascading stage and, subsequently, the abundance of specific progeny output. Together, this two-layered regulatory structure offers a mechanistic control of temporal patterning and emphasizes the importance of global regulators in managing temporal programs.

overall_design: Hi-C experiment in mouse cortical development (E10-E11, E12-E13, E14-E15, E12-E15). H3K27me3 and H3K27ac ChIP-seq in mouse cortical development (E10, E12). H3K27me3 and H3K27ac CUT&Tag in mouse cortical development (E12-E13, E14-E15).

first: Guohua

last: Yuan

first: Yinqing

last: Li


title: Single-Cell Profiling of Neutrophil Gene Expression in the Mouse Colon following TNBS-induced Colitis

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

country: Ireland

institute: NIBRT

summary: Neutrophil infiltration is hallmark of chemically induced colitis and inflammatory bowel disease (IBD). We used single-cell RNA sequencing to analyze heterogenity in infiltrated colonic neutrophil population in presence and absence of microbiota, or when DUOX2 in inactivated in neutrophils.

overall_design: Mice were treated with 2.5% TNBS intrarectally, and colon was collected after 48 h (day2). Viable neutrophils were purified using FACS (CD11b+, Ly6G+, DRAQ7-) followed by scRNA analysis.

first: Ashish

middle: K

last: Singh

first: Ulla

last: Knaus


title: Identifying brain-penetrant small-molecule modulators of human microglia using a cellular model of synaptic pruning

city: Medford

first: rebecca

last: batorsky

address: 177 College Ave

department: Tufts Institute of Artificial Intelligence

institute: Tufts University

summary: Microglia dysregulation is implicated across a range of neurodevelopmental and neurodegenerative disorders, making their modulation a promising therapeutic target. Using PBMC-derived induced microglia-like cells (piMGLCs) in a scalable assay, we screened 489 CNS-penetrant compounds for modulation of microglial phagocytosis of human synaptosomes in a validated assay for microglia-mediated synaptic pruning. Compounds from the library that reduced phagocytosis by ≥2 standard deviations across the library without cytotoxicity were validated in secondary screens, with 28 of them further confirmed to reduce phagocytosis by 50% or more. These compounds comprise a wide range of therapeutic classes with different mechanisms of action, including immunosuppressants, kinase inhibitors, antipsychotics, and epigenetic modulators. Image-based morphological measurements were calculated to measure the degree of ramified vs. ameboid morphotypes as an indicator of activation state. Additionally, transcriptomic profiling indicated divergent effects on cell signaling, metabolism, activation, and actin dynamics across confirmed compounds. In particular, multiple CNS-penetrant small molecules with prior FDA approval or demonstration of safety in vivo demonstrated modulatory effects on microglia. For example, identified drugs such as the tyrosine kinase inhibitors lapatinib, alectinib, and lazertinib and the epigenetic modulator vorinostat have been approved for various cancer treatments and are being investigated for other indications; however, they have not been extensively studied in patients for neurodevelopmental and neurodegenerative disorders. These potential disease-modifying agents represent high-priority candidates for repositioning studies in neurodevelopmental, neuroinflammatory, or neurodegenerative disorders. https://www.nature.com/articles/s41386-025-02123-1

overall_design: RNA-seq profiling of PBMC-derived induced microglia-like cell response to multiple compounds to study modulation of phagocytic response

first: Liam

last: McCrea

first: Rebecca

last: Batorsky

first: Joshua

last: Bowen

first: Hana

last: Yeh

first: Jessica

last: Thanos

first: Ting

last: Fu

first: Roy

last: Perlis

first: Steven

last: Sheridan


title: Light and sex modify Snord116 genotype effects on metabolism, behavior, and imprinted gene networks following circadian entrainment

city: Davis

first: Aron Judd

middle: Perez

last: Mendiola

state: CA California

address: 1 Shields Avenue

department: Medical Microbiology and Immunology

institute: University of California - Davis

summary: Mammals utilize imprinted and X-linked epigenetic mechanisms in development, metabolism, and behavior. Imprinted genes, including Prader-Willi syndrome Snord116 noncoding RNAs, are implicated in the regulation of sleep and circadian rhythms through poorly understood mechanisms. Utilizing mouse models of Snord116 deficiency and overexpression, we performed an integrated, sex-stratified analysis of free running behaviors, indirect calorimetry, and cortical transcriptomes following entrainment to a 22 hour light:dark T-cycle. We observed significant interactions of sex, entrainment, and Snord116 genotype in period length at baseline and after-effects of post-entrainment. Snord116 deletion’s effect on respiratory exchange ratio was light sensitive, with sex and entrainment effects dominant under total darkness. Snord116 genotype impacted both rhythmic and non-rhythmic cortical gene networks that integrated sex, light, and entrainment effects with genotype-phenotype correlations. A co-expressed gene network enriched for imprinted, Snord116-target, and Xist-proximal long noncoding RNAs was identified as a light-sensitive regulatory hub of sexual dimorphic responses to a dynamic environment.

overall_design: RNA-seq profiling of pre-frontal cortex male and female wild-type mice collected at circadian timepoints (ZT0, ZT3, ZT6, ZT9, ZT12, ZT15, ZT18, and ZT21) and pre-frontal cortex male and female experimental mice collected from metabolic studies through indirect calorimetry (CLAMS) (D:D) and behavior and activity through Running Wheel (RW) (L:D) at timepoint ZT6.

first: Jennifer

last: Rutkowsky

first: Kari

last: Neier

first: Sophia

last: Hakam

first: Osman

last: Sharifi

first: Callum

last: Donnelly

first: Christina

last: Torres

first: Cielo

last: Hernandez

first: Dag

last: Yasui

first: Jon

last: Ramsey

first: Janine

last: LaSalle


title: Single cell RNAseq of human macrophage polarization states

city: Los Angeles

first: Alexander

last: Hoffmann

state: California

address: 570 Boyer Hall

department: MIMG

institute: University of California, Los Angeles

summary: We employed the BD Rhapsody scRNAseq platform to identify human macrophage polarization states and their response to various stimulaiton conditions. Using a select panel of genes (BD Immune Response Panel Hs) we were able to identify unique transcriptomes for naive, IFNy, IFNb, IL-4, IL-10, and IL-13 polarized macrophages under unstimulated conditions and in response to 3 hours of acute stimulation with LPS, polyIC and TNF.

overall_design: Human blood was obtained from a deidentified donor from the UCLA CFAR Centralized Laboratory Support Core in accordance with UCLA IRB 11-000443. Peripheral blood mononuclear cells were isolated from blood by Ficoll (Cytiva, 17-1440-03) density centrifugation. Monocytes were isolated using CD14+ bead selection (Milltenyi, 130-050-201), plated on 6-well tissue culture plates at a density of 5x105 cells/well, and cultured in RPMI (Gibco, 11875-093) supplemented with 10% ES fetal bovine serum (Gibco, 10439-024), penicillin-streptomycin (Corning, 30-002-Cl), L-glutamine (2mM; Corning, 25-005-CI) and 20ng/ml human macrophage colony-stimulating factor (M-CSF) (R&D systems, 216-MC-100). Media was replaced at day 4, and on 6 days from isolation, the cells were polarized for 24 hours with 100 U/mL IFN-β (PBL Assay Science, 11415-1), 20 ng/mL IFN-γ (Peprotech, 300-02), 50 ng/mL IL-10 (R&D, 217-IL), 40 ng/mL IL- 13 (R&D, 213-ILB), 20 ng/mL IL-4 (R&D, 204-IL), or left naïve. After 24 hours of polarization the cells were either left unstimulated or stimulated for 3 hours with LPS 1ng/ml (Sigma-Aldrich, L6529), TNF 10ng/ml (R&D, 210-TA-020), or polyIC 50ug/ml (Invivogen-TLRL-PIC). To collect the macrophages, the plate was washed with PBS, then incubated with 1mL warm 1mM EDTA for 15 minutes. Cells were lifted with a cell scraper, multiplexed using the BD Human Single-Cell Multiplexing Kit (BD, 633781), and loaded onto the cartridge following manufacturer’s instructions (BD Rhapsody #210967). The LPS and TNF sitmulated samples were loaded on Cartridge 1 and the polyIC and unstimulated on Cartridge 2. Targeted mRNA amplification was performed utilizing the Immune Response Panel Hs primer panel (BD, 633750), with subsequent library preparation. The pooled library was sequenced with paired-end 100bp reads on an Illumina NovaSeq X Plus. After sequencing, the FASTQ files were aligned to the Immune Response Panel reference file, generating raw read counts per gene and per cell, which were then linked to cell samples of origin, with the final output being a cell by molecular matrix.

first: Sarina

last: Lowe

first: Noah

last: Yan

first: Madelaine

last: Leitman


title: Tumor-activating IL2 rejuvenates intratumoral TIM3-CD8+T cell responses through targeting TIM3+CD8+T cell

first: Xuhao

last: Zhang

state: 北京

address: 30 Shuangqing Road, Haidian District

institute: Tsinghua University

summary: TIM3, a T-cell inhibitory receptor, is expressed on exhausted T cells in tumor microenvironment (TME). Anti-TIM3 antibody therapy could alleviate the suppression of tumor-infiltrating lymphocytes (TILs) in IL-2 dependent fashion. We hypothesize that high expression of TIM3 and limited IL-2 in TME facilitate immune evasion.  To test that, we engineered anti-TIM3-pro-IL2 to selectively deliver IL-2 to TIM3high TILs by TIM3 antibody and reduce its toxicity with a cis delivery mechanism. Since IL-2 could reduce its activity at acidic pH inside TME, we also screened a low pH-selective IL-2 mutein (IL2V2) with enhanced affinity for IL-2Rβ.  We then integrated pro-IL-2 into the anti-TIM3 antibodies in two different forms: TIM3-Rα-MMPs-IL2V2 (TIM3-ProIL2V2) as IL-2 release-form vs TIM3-IL2V2-MMPs-Rα as cis-form after binding to TIM3high T cells, ensuring the need of targeted delivery to TIM3-expressing TILs. Surprisingly, released IL2V2 from TIM3-Rα-MMPs-IL2V2 proved superior in anti-tumor immunity, but not cis delivery form TIM3-IL2V2-MMPs-Rα. Mechanistically, TIM3-ProIL2V2 not only reactivated TIM3+ TILs but also facilitated the activation and expansion of TIM3- T cells which in turn supported a sustained source of TIM3+ effector. TIM3-ProIL2V2 could control multiple tumor models including human tumor in humanized mice, confirming the hypothesis. TIM3-ProIL2V2 activates and expands TIM3-CD8+ T cells to overcome current major unmet medical need: anti-PD-1/L1 resistance.  This strategy illustrates the potential of a tailored, low pH-resistant IL2 variant in invigorating both TIM3-negative and positive CD8+ T cells, offering a promising avenue for treating resistant tumors with reduced toxicity.

overall_design: Since the antitumor effect of TIM3-ProIL2V2 depended on pre-existing CD8+ T cells, we further isolated intratumoral CD8+ T cells and investigated the transcriptional signatures at the single-cell level following TIM3-ProIL2V2 monotherapy.

first: Huiping

last: Liao


title: Novel Gene expression-based Risk Stratification tool predicts recurrence in Non-muscle invasive Bladder cancer

city: Bangalore

first: Hari

last: S

state: Karnataka

address: 1st Cross, Shankara Matt Premises, Shankarapuram, Basavanagudi

country: India

institute: Sri Shankara Cancer Hospital and Research Centre

summary:
Background

Bladder cancer represents a heterogeneous disease with distinct clinical challenges. Non-muscle invasive bladder cancer (NMIBC) typically presents as indolent and slow-growing, yet a critical clinical challenge remains: identifying which patients will progress to muscle-invasive disease requiring radical interventions. Early detection of progression propensity is essential, as once muscle invasion occurs, the risk of distant metastasis increases substantially, and treatment shifts from conservative TURBT (Transurethral Resection of Bladder Tumor) to aggressive surgical interventions with significant morbidity. Current risk stratification methods fail to adequately predict this transition in approximately 30% of cases, highlighting the urgent need for more accurate prognostic tools.

Objective

This retrospective study aimed to develop and validate a transcriptomics-based mRNA score for predicting early NMIBC recurrence, comparing its performance against traditional risk stratification methods.

Methods

We analyzed mRNA expression profiles from primary retrospective NMIBC tumor specimens (n=25) collected between [2018-2022]. Traditional risk stratification tools, including EORTC scoring, were applied alongside our novel mRNA-based risk score to evaluate predictive accuracy for recurrence.

Results

The transcriptomics-based mRNA score demonstrated a median prediction accuracy of 90% across 10,000 resampling iterations for predicting early NMIBC recurrence, significantly outperforming traditional EORTC risk scores. Our comprehensive gene set identified 435 differentially expressed genes associated with recurrence. Kaplan-Meier analysis showed significantly different recurrence-free survival between high and low mRNA risk score groups (Bonferroni corrected p-value<0.0001). Conclusions This retrospective analysis confirms that mRNA expression-based risk stratification provides superior predictive accuracy compared to conventional clinicopathologic risk tools. Implementation of this gene signature could potentially reduce over-investigation and improve surveillance cost-effectiveness after TURBT in patients with primary high-risk NMIBC. These findings may transform the clinical management paradigm by enabling more personalized follow-up protocols based on molecular risk assessment.

overall_design: RNA was extracted from FFPE blocks of NMIBC tumors and subjected to RNA sequencing analysis

first: Srivatsa

last: Narasimha

last: PS

first: Rahul

last: Pappala

first: Lista

last: Paul

first: Durgadevi

last: Veeraiyan

first: Ambili

last: Narikot

first: Vidya

last: Veldore

first: Nishtha

last: Tanwar

first: Srikanth

last: Reddy

first: Hitesh

last: Goswami

first: Rekha

middle: V

last: Kumar

first: B

last: Srinath

first: Aruna

last: Korlimarla


title: Macrophage sensitivity to reprogramming by bexmarilimab is shaped by the tumor microenvironment [RNA-Seq]

city: Turku

first: Maija

last: Hollmén

address: Tykistökatu 6A 4th floor

country: Finland

institute: University of Turku

summary: Tumor-associated macrophages (TAMs) adapt to the tumor microenvironment (TME), either aiding cancer eradication or promoting tumor growth and immune evasion. To manipulate TAMs therapeutically, a deep understanding of their interaction with the TME is essential. This study exploits a breast cancer patient-derived explant culture (PDEC) model to predict TMEs responsive to bexmarilimab, a macrophage reprogramming therapy showing clinical benefit in various solid tumors. The PDEC model captured key aspects of bexmarilimab's action, validated a gene signature for predicting treatment sensitivity, and characterized responses in both tumor and adjacent cancer-free tissue. We identified three distinct treatment responses shaped by the local TME and macrophage phenotype, origin and localization. The inflammatory state of the TME was detected as the primary factor defining response to bexmarilimab. These findings emphasize the need for patient selection to maximize bexmarilimab's efficacy, particularly in immunologically cold tumors lacking late-stage activated TAMs and reveal the complexity of TAM targeting in cancer.

overall_design: RNA-seq profiling of breast cancer and adjacent cancer-free tissue patient-derived explant cultures after 48h of bexmarilimab or isotype control treatment.

first: Jenna

last: Rannikko


title: The broccoli derivative sulforaphane extends lifespan by slowing the transcriptional aging clock

city: Eugene

first: Patrick

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

institute: University of Oregon

summary: Sulforaphane (SFN), an organosulfur isothiocyanate derived from cruciferous vegetables, has been shown to inhibit inflammation, oxidative stress, and cancer cell growth; it has also been shown to increase the lifespan of the C. elegans nematode strain N2. Here, we tested the lifespan effects of SFN following the standard experimental procedures of the Caenorhabditis Intervention Testing Program (CITP). The CITP, a multi-institute research consortium, aims to identify chemical interventions that can robustly and reproducibly promote health and lifespan. To investigate the functional targets of SFN, we employed bulk RNA-Seq at a variety of ages to create a “transcriptional aging clock” using control individuals and then tested how global patterns of gene expression are altered under SFN treatment. Multi-dimensional scaling analysis of the transcriptome revealed transcriptional age under SFN treatment was similar to control individuals approximately four days younger, representing a nearly 20% shift relative to overall lifespan. These results support the idea that robust longevity-extending interventions can act via global effects across the organism, as revealed at a functional level via changes in gene expression.

overall_design: We performed differential gene expression analysis comparing SFN-treated and DMSO control samples in 2, 4, 8, 12, and 16-day old adult worms in the wildtype N2 strain.

first: Christine

middle: A

last: Sedore

first: Erik

last: Segerdell

first: Anna

last: Coleman-Hulbert

first: Stephen

last: Banse

first: Gordon

last: Lithgow

first: Monica

last: Driscoll

middle: C


title: Lymphotropic Virotherapy Engages DC and High Endothelial Venule Inflammation to Mediate Cancer In Situ Vaccination

city: Durham

first: Matthias

last: Gromeier

state: NC

address: 203 Research Dr

department: Neurosurgery

institute: Duke University

summary: Intratumor (IT) inoculation of the rhino:poliovirus chimera, PVSRIPO, yielded objective radiographic responses with long-term survival in 20% of patients with recurrent glioblastoma (rGBM). PVSRIPO infects dendritic cells (DCs) and sets up non-cytopathogenic viral (v)RNA replication, which triggers sustained type-I IFN (IFN-I) signaling and antitumor T cell priming. Here we identify IFN-I signaling in glioma-draining cervical lymph nodes (cLN) as a mediator of polio virotherapy. Transient IFN-I signaling after IT therapy was rescued by cervical perilymphatic injection (CPLI) of PVSRIPO, targeting cLN directly. Dual-site (IT+CPLI) PVSRIPO induced profound inflammatory reprogramming of cLN, enhanced vRNA replication and IFN-I signaling in DCs and High Endothelial Venules (HEV), augmented anti-glioma efficacy in mice, and was associated with T cell activation in rGBM patients. A Ph2 clinical trial of IT+CPLI PVSRIPO is ongoing (NCT06177964). This work implicates the lymphatic system as a novel virotherapy target and demonstrates the CPLI concept to complement brain tumor immunotherapy.

overall_design: hCD155tg C57BL/6 mice were implanted with CT2A glioma cells and treated with immunotherapeutic human rhinovirus-poliovirus chimera PVSRIPO in one of four combinations of mock or RIPO intratumorally (IT, 7 and 10 days post implantation) and paralymphatically (CPLI, 10 and 13 days post implantation) with deep and superficial cervical lymph nodes harvested for RNA sequencing.

first: Andrea

last: Ludwig

first: Zachary

middle: P

last: McKay

first: Griffin

last: Carter

first: Mark

last: Katz

first: Georgia

last: Howell

first: Vaibhav

last: Jain

first: Stephanie

last: Arvai

first: Dirk

last: Dittmer

first: Darell

middle: D

last: Bigner

first: David M

last: Ashley

first: Madison

last: Shoaf

first: Annick

last: Desjardins

first: Simon

last: Gregory

first: Michael

last: Brown


title: Macrophage sensitivity to reprogramming by bexmarilimab is shaped by the tumor microenvironment [scRNA-Seq]

first: Maija

last: Hollmén

overall_design: scRNA-seq analysis of paired breast cancer tumor and adjacent cancer-free tissues.

first: Akira

last: Takeda

first: Jenna

last: Rannikko


title: Variant-specific disruption to Notch signaling in PAX6 microphthalmia and aniridia patient-derived hiPSC optic vesicles [ATAC-Seq]

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

country: United Kingdom

institute: UCL

summary: The homeobox-containing transcription factor PAX6 is a key regulator of eye development. Pathogenic heterozygous PAX6 variants lead to variable ocular phenotypes. Missense variants are often associated with milder ocular conditions, although variants in the DNA-binding paired domain which alter target binding lead to severe ocular phenotypes including bilateral microphthalmia, similar to SOX2 anophthalmia syndrome. However, the variant-specific pathway disruption resulting in phenotypic heterogeneity is not well understood.

overall_design: Chromatin accessibility using ATAC-seq was carried out on Aniridia (PX and AN) and wildtype control iPSC derived 3D retinal organoids at timepoints day 35, two clonal lines per condition, two replicates per clone.

first: Nicholas

last: Owen

first: Philippa

last: Harding

first: Brian

last: Chan


title: Variant-specific disruption to Notch signaling in PAX6 microphthalmia and aniridia patient-derived hiPSC optic vesicles

overall_design: Gene expression analysis (RNA-seq) was carried out on Aniridia (PX and AN) and wildtype control iPSC derived 3D retinal organoids at timepoints day 0, 20 and  35, two clonal lines per condition, three/four replicates per clone.


title: Endothelial KLF15/VASN axis inhibits angiogenesis via activation of Notch1 signaling

city: shanghai

first: jiajia

last: zhao

address: Ruijin 2nd Road 197

institute: Shanghai Institute of Hypertension, Ruijin Hospital

summary: Angiogenesis is a dynamic process fine-tuned by transcription factors in endothelial cells. The Krüpple-like factor 15 (KLF15)-mediated transcriptional regulation mechanism is critical for cardiovascular diseases. However, the role of endothelial KLF15 in governing angiogenesis remains unknown.KLF15 and vasorin (VASN) were deleted from endothelial cells using tamoxifen-inducible Cdh5-promoter-driven Cre recombinase in EC-KLF15 KO and EC-VASN KO mice, respectively. EC-KLF15 KO, EC-VASN KO and control mice were subjected to retinal angiogenesis or tumor cell transplantation. The RNA sequencing (RNA-seq), ATAC-seq, and ChIP-seq were conducted to identify VASN as a downstream effector of KLF15. Cell proliferation, wound healing, tube formation, and sprouting assays were performed to delineate endothelial cell function. In EC-KLF15 KO mice and adenovirus-mediated KLF15 overexpression mice, we showed that KLF15 negatively regulated retinal angiogenesis, as confirmed in cultured endothelial cells. KLF15 opened chromatin, bound to the promoters of GC-rich sequences, and transactivated the expression of VASN. Subsequently, VASN suppressed endothelial angiogenic function which was essential for Dll4-induced Notch1 signaling activation. Moreover, increased expression of VASN in EC-KLF15 KO mice suppressed retinal angiogenesis, which was attenuated by γ-secretase inhibitor. EC-VASN KO mice recapitulated the promotion of retinal angiogenesis in EC-KLF15 KO mice. Finally, the EGF-like domain of VASN was essential for its interaction with Notch1, and VASN EGF-like domain-derived peptides activated Notch1 signaling and suppressed angiogenesis.The KLF15/VASN axis negatively regulates angiogenesis by activating Notch1 signaling. KLF15 and VASN in endothelial cells might represent novel therapeutic targets for the treatment of impaired angiogenesis-related diseases and tumors.

overall_design: RNA sequencing profiling of Human Umbilical Vein Endothelial Cells (HUVECs) infected with adenovirus expressing KLF15 (AdKLF15) or a control adenovirus (AdCTL) to identify differentially expressed genes and analyze the transcriptional changes induced by KLF15 expression in endothelial cells.

first: Xiao-Dong

last: Li

first: Ping-Jin

last: Gao

first: Ji-Gguang

last: Wang

first: Jia

last: Zhang

first: Jia-Jia

last: Zhao


title: Glucagon-like Peptide-2 Acts through Central GLP-2R and MC4R in Mobilizing Stored Lipids from the Intestine

city: Saskatoon

first: Kundanika

last: Mukherjee

state: Saskatchewan

address: 107 Wiggins Rd,  2D40 Health Sciences Building

department: APP

country: Canada

institute: University of Saskatchewan

summary: Dysregulated gut lipid handling contributes to atherogenic dyslipidemia, a cardiovascular disease risk factor for patients with diabetes. The gut hormone glucagon-like peptide-2 (GLP-2) plays significant roles in intestinal lipid handling. In post-absorptive state, GLP-2 mobilizes pre-formed chylomicrons that are stored in the intestine from previous meals, the mechanisms of which are not fully understood. Our previous study demonstrated the involvement of a gut-brain neural pathway in this effect, but the key components of this pathway remain unknown. Here, we evaluated central GLP-2 receptor (GLP-2R) and melanocortin 4 receptor (MC4R) as important players in the pathway. Mesenteric lymph duct cannulated rats received intracerebroventricular infusion of a GLP-2R antagonist (GLP-2(11-33)), an MC4R antagonist (SHU9119), or saline as control. Post-absorptive lipid output from the intestine in response to peripheral GLP-2 was assessed. Spatial transcriptomics analysis was performed to determine the changes in mRNA expression among treatment groups. Blockade of central GLP-2R or MC4R attenuated the effects of GLP-2 in stimulating lymph triglyceride output. Treatments differentially affected key genes in jejunal endothelial cells, smooth muscle cells and neuronal cells. These results support the critical roles of central GLP-2R and MC4R in a neural pathway for peripheral GLP-2 in mobilizing lipids stored in the intestine during post-absorptive state.

sample_organism:
Rattus
synthetic construct

platform_organism:
Rattus
synthetic construct

overall_design: Jejunum samples collected from peripherally GLP-2-treated sprague dawley rats with MC4R antagonist icv infusion (n=3; MG) or GLP-2R antagonist icv infusion (n=3; GG) or saline icv infusion (n=4; SG) were used for the analysis: MG or GG were compared to SG.  MG was compared to GG.

first: Muhammad

last: Khan

first: John

middle: G

last: Howland

first: Changting

last: Xiao


title: A novel rexinoid agonist, UAB116, decreases metastatic phenotype in hepatoblastoma by inhibiting the Wnt/β-catenin pathway via upregulation of TRIM29

city: BOYNTON BEACH

first: Swatika

last: Butey

state: Florida

address: 107 North Monterey Cir

department: Pediatric Surgery

institute: UAB Beierle Lab

summary: Hepatoblastoma (HB) is the most common pediatric primary liver tumor. About 20% of children have pulmonary metastasis at presentation. Survival rates for these children are dismal, not exceeding 25%. To study this subset of the HB population, we sequenced a metastatic HB cell line, HLM_2, and identified a downregulation in the liver X receptor (LXR)/rexinoid X receptor (RXR) pathway. LXR/RXRs are transcriptional regulators of genes involved in HB carcinogenesis including the Wnt/β-catenin signaling pathway. We assessed the effects of a novel LXR/RXR agonist, UAB116, on metastatic HB, hypothesizing  that this compound would affect genes governing the Wnt/β-catenin pathway, leading to decreased metastatic phenotype in HLM_2 metastatic HB cells. We evaluated the effects on viability, proliferation, stemness, clonogenicity, and motility, and performed RNA sequencing to study differential gene regulation. Treatment with UAB116 (0-50 µM) for 72 hours decreased HLM_2 proliferation, stemness, clonogenicity, and invasion. RNA sequencing identified an 8-fold increase in TRIM29, a gene known to inhibit β-catenin, in cells treated with UAB116. These results show that treatment with an LXR/RXR agonist, UAB116, decreases metastatic HB cell proliferation, stemness, and invasion, likely through upregulation of TRIM29, a known regulator of the Wnt/β-catenin pathway, providing support for further exploration of LXR/RXR agonism as a therapeutic strategy for metastatic HB.

overall_design: By creating two groups, we studied the effects of novel rexinoid agonist UAB116 on HLM_2 cells. Group 1 were untreated HLM_2 cells that acted as control, and group 2 HLM_2 cells were treated with 25µM of UAB 116 for 72 hours. RNA extraction was performed to obtain samples for each group, which were then submitted for RNA sequencing analysis, and one sample per condition was processed.

first: Elizabeth

last: Beierle


title: Bile acid 7a-dehydroxylating bacteria accelerate injury-induced mucosal healing in the colon

city: Lausanne

first: Antoine

last: Jalil

address: EPFL station 15

country: Switzerland

institute: Ecole Polytechnique federale de Lausanne

summary: Host-microbiome communication is frequently perturbed in gut pathologies due to microbiome dysbiosis, leading to altered production of bacterial metabolites. Among these, 7a-dehydroxylated bile acids are notably diminished in inflammatory bowel disease patients. Herein, we investigated whether restoration of 7a-dehydroxylated bile acids levels by Clostridium scindens, a human-derived 7a-dehydroxylating bacterium, can reestablish intestinal epithelium homeostasis following colon injury. Gnotobiotic and conventional mice were subjected to chemically-induced experimental colitis following administration of Clostridium scindens. Colonization enhanced the production of 7a-dehydroxylated bile acids and conferred prophylactic and therapeutic protection against colon injury through epithelial regeneration and specification. Computational analysis of human datasets confirmed defects in intestinal cell renewal and differentiation in ulcerative colitis patients while expression of genes involved in those pathways showed a robust positive correlation with 7a-dehydroxylated bile acid levels. Clostridium scindens administration could therefore be a promising biotherapeutic strategy to foster mucosal healing following colon injury by restoring bile acid homeostasis.

overall_design: BRB-seq profiling of colon from 10-week-old male wild-type (Tgr5+/+) and TGR5 knock-out (Tgr5-/-) mice were gavaged daily for 5 days with live C. scindens after 7 days of vancomycin treatment (500mg/l in drinking water) (108 CFU – Tgr5+/+ SPF-Van + C. scindens and Tgr5-/- SPF-Van + C. scindens) or vehicle (PBS - Tgr5+/+ SPF-Van and Tgr5-/- SPF-Van). Experimental colitis was induced by a 7-day treatment with DSS (2.5% in drinking water) followed by 3 days of drinking water (recovery period).


title: Dendritic cell iron overload exacerbates acetaminophen hepatotoxicity

city: Kumamoto

first: Toshiro

last: Moroishi

address: 1-1-1 Honjo, Chuo-ku

institute: Kumamoto University

summary: Liver immune homeostasis relies on the coordinated actions of various immune cells including dendritic cells (DCs), which exert regulatory roles in both innate and adaptive immunity. Various pieces of evidence demonstrate that the properties of immune cells are highly influenced by iron metabolism. However, the roles of iron metabolism on DC function remain poorly understood. Here, we show that mice with iron overload in DCs displayed worsening of liver injury and mortality in acetaminophen (APAP) -induced acute hepatitis. Enhanced neutrophil infiltration was observed in these mice during the progression of liver injury. DCs with iron overload showed increased expression of the neutrophil-attracting cytokine IL-6, thereby accelerating liver injury. Mechanistic studies revealed that iron enhanced the recruitment of NF-κB to the IL-6 promoter upon TLR4 activation. Our findings provide an insight into the regulatory mechanisms by which iron metabolism influences DC function. This study also highlights the critical role of the DC-IL-6-neutrophil axis in acute liver injury.

overall_design: RNA sequencing on whole livers from control and FBXL5ΔDC mice without APAP treatment and those treated with APAP for 6 hours.

first: Saisai

last: Liu

first: Yohei

last: Kanamori

first: Yanliang


title: Decreases in monoubiquitination of histone H2B is a critical regulator of age-related memory decline

city: Blacksburg

first: Timothy

last: Jarome

state: VA

address: 175 W Campus Dr

institute: Virginia Polytechnic Institute and State University

summary: We report a critical role of decreased monoubiquitination of H2B (H2Bubi) in age-related memory decline. We found that contextual fear conditioning in aged rats led to modest transcriptional changes in the hippocampus, which was correlated with impaired memory. Conversely, CRISPR-dCas9-mediated increases in the H2Bubi ligase, Rnf20, in the hippocampus improved memory in aged rats and resulted in a more robust transcriptome. Surprisingly, 18 genes upregulated with learning in the control group was also found in the rnf20 upregulation condition, though the later included more than 20 additional upregulated and 10 downregulated genes. These data suggest that upregulating H2Bubi in the aged hipocampus may improve memory by controlling transcriptional changes in a subset of memory critical genes

overall_design: Male 22 month old Fischer ratss were injected into dorsal hippocampus CA1 region with CRISPR gRNA targeting Rnf20 alone or with dCas9-VPR. Four weeks later, animals were trained to contextual fear conditioning and the CA1 region (dorsal) was dissected, RNA collected via columns and used for RNA-seq analysis

first: Kincaid

last: Shannon

first: Setenet

last: Gueladouan

first: Preveza

last: Natalie

first: Arndt

last: Kaiser

first: Gwin

last: Phillip

first: Lin

last: Yu

first: Xie

last: Hehuang

first: Jarome

last: Timothy


title: Investigation of the Altered Transcriptomic Dynamics of Bone Marrow Adipose Tissue Under Exogenous Stimuli in the Context of AML Pathogenesis

city: Ankara

first: Bihter

last: Muratoğlu

state: Ankara

address: Sihhiye

department: Stem Cell Sciences

country: Turkey

institute: Hacettepe University

summary: Bone marrow is a critical tissue for hematopoietic stem cell regulation, comprising various cell types, including adipose tissue, which actively contributes to hematopoietic biology. The mechanisms underlying the transcriptomic response of bone marrow adipose tissue to xenobiotic stimuli remain poorly understood, particularly its role in leukemia progression. Acute myeloid leukemia (AML) stromal cells differ significantly from healthy bone marrow stroma, with environmental pollutants and xenobiotics playing a crucial role in pathogenesis. This study investigates the transcriptomic alterations in bone marrow adipose-derived mesenchymal stem cells following aryl hydrocarbon receptor (AhR) agonist and antagonist stimulation. Comparative analyses include healthy donors, Fanconi anemia (FA), and AML samples to elucidate their contributions to leukemia development.

overall_design: The study examines the transcriptomic dynamics of bone marrow adipose tissue mesenchymal stem cells (BMAT-MSCs) derived from healthy donors (HD), Fanconi anemia (FA) patients, and acute myeloid leukemia (AML) patients using RNA-seq profiling. BMAT-MSCs were subjected to treatments with a untreated control (Control), the AhR antagonist StemRegenin 1 (SR1, 1.5 uM), the AhR agonist 6-Formylindolo(3,2-b)carbazole (FICZ, 100nM), and the pro-inflammatory cytokine tumor necrosis factor-alpha (TNF-α, 100ng/mL) for 18 hours. Prior to these treatments, all samples were synchronized using 100 nM dexamethasone (DEX) for 1 hour.

first: Cansu

last: Özdemir


title: Crosstalk with infant derived Th17 cells promotes maturation of intestinal epithelial cells in an enteroid model through IL-22 signaling

city: Vancouver

first: Pascal

last: Lavoie

state: BRITISH COLUMBIA

address: 950 West 28th Avenue

institute: BC Children's Hospital

summary: The use of 3D human intestinal organoid (HIO) models is growing in biomedical research due to their ability to mimic human tissue for studying diseases, developing biomarkers, and testing therapies. However, current models of the infant gut are limited, focusing mostly on necrotizing enterocolitis, leaving gaps in our understanding of healthy infant gut development. Additionally, achieving full differentiation and maturation of secretory cells, especially Paneth cells, remains challenging. Our studies suggest IL-22 can enhance maturation, though its effects on infant enteroids remain unexplored. In this study, infant-derived ileal enteroids were cultured with Th17 supernatant or IL-22, and their development was assessed via immunofluorescence staining and RNA sequencing. Our results showed that neonatal Th17 cell-derived IL-22 supported the growth and maturation of infant enteroids, including Paneth cell differentiation. IL-22 induced gene expression changes related to cellular identity, maturation, immune response, and barrier function, as revealed by RNAseq analysis.

overall_design: Human infant-derived ileal enteroids were cultured with recombinant IL-22. Morphological and functional changes were assessed using immunofluorescence staining and RNA sequencing, respectively, to characterize the developmental and functional profiles of intestinal epithelial cells (IECs) and to investigate the impact of IL-22 co-culture on IEC differentiation and maturation.

first: Zohreh

last: Sharafian

first: Bethany

last: Poon

first: Joannie

last: Allaire

first: Christina

last: Michalski

first: Bruce

last: Vallance

middle: M


title: SPT6 Regulates H3K14Ac Deposition in Mouse Embryonic Stem Cells [ChIP-seq-mES]

city: Shanghai

first: Daixuan

last: ZHANG

address: No. 131, Dongan Road, Xuhui District

institute: The Institutes of Biomedical Sciences

summary: SPT6 (suppressor of Ty 6) is a conserved histone chaperone that facilitates transcription elongation, nucleosome reassembly, and RNA polymerase II progression. The functions of SPT6 in regulating chromatin remain not fully understood. Here we show that SPT6 localized to H3K14Ac enriched regions and promoted H3K14Ac densities in mouse embryonic stem cells (mESCs). Loss of SPT6 results in decreased H3K14Ac and transcription. Mechanistically, we showed that SPT6 enhances the chromatin binding levels of acetyltransferases KAT7 and KAT6A/KAT6B. In addition, we showed that SPT6 also promotes H3K14Ac in a KAT7/6A/6B independent manner. Our findings identify a vital role of SPT6 in maintaining the integrity of H3K14Ac profile in mESCs, thus suggesting a crosstalk between transcription machinery and H3K14Ac in mammals.

overall_design: Examination of SPT6 binding, KAT7 binding, KAT6A binding, KAT6B binding and H3K14Ac in Parental, dTAG-SPT6 cells, AID-KAT6A cells, AID-KAT6B cells and Kat6a/Kat6b double knock out mESCs. Examination of H3 and H3K14Ac in Parental, dTAG-SPT6 mESCs.

last: Zhang


title: SPT6 Regulates H3K14Ac Deposition in Mouse Embryonic Stem Cells [RNA-seq]

overall_design: Examination of total RNA in dTAG-SPT6 mESCs treated with DMSO or 100 nM dTAG-13 for 3h.


title: SPT6 Regulates H3K14Ac Deposition in Mouse Embryonic Stem Cells [ChIP-seq-HEK293T]

overall_design: Examination of H3K14Ac in HEK293T cells.


title: Immune-related gene expression data of whole blood and spleen from immuno-competent mice implanted with C1498 leukemia cells (AML model) and treated with 5-Azacytidine or Vehicle

city: Duarte

first: Nancy

middle: Danielle

last: Ebelt

state: CA

address: 1500 E Duarte Rd

department: Immuno-Oncology

institute: Beckman Research Institute of City of Hope

summary:
Significant differences in gene expression were observed for 5-Azacytidine treated leukemic mice compared to vehicle treated mice during hematologic remission
in both spleen and blood samples

overall_design: C57Bl/6 mice were unimplanted and untreated (Healthy), or implanted with C1498 leukemia cells and treated with vehicle (DMSO in diluent) or 5-Azacytidine (AZA) for two complete cycles after which whole blood and spleens were harvested

first: Edwin

last: Manuel


title: Albiflorin Discovered from Paeoniae Rubra Radix Attenuates Liver Fibrosis and Inflammation via Regulating CXCL12/CXCR4 Axis

city: China

first: huijing

last: lv

address: Zunyi Medical University

institute: Zunyi Medical University

summary: Liver fibrosis, a common pathological feature of chronic liver injury, faces a lack of effective treatment methods. Albiflorin (ALB), a pinane-type monoterpene compound isolated from the medicinal and edible plant Paeonia lactiflora Pall, has demonstrated a variety of biological activities. Here, we reported on the hepatoprotection and potential mechanisms of ALB against liver fibrosis. The results indicated that ALB significantly alleviated the histological damage and collagen deposition caused by CCl4-induced liver fibrosis and led to a reduction in serum levels of ALT, AST, CRE, and BUN. Meanwhile, ALB downregulated the expression of liver fibrosis markers (α-SMA and Collagen I) and decreased inflammatory cytokines (IL-1β, IL-6, TNF-α, and NLRP3). According to RNA-sequencing analysis, the CXCL12/CXCR4 axis was identified as a potential signaling pathway for ALB's action against liver fibrosis. Further mechanistic data revealed that ALB exerts anti-inflammatory and antifibrotic effects through the JAK1/STAT3 and p38 MAPK pathways mediated by the CXCL12/CXCR4 axis. Notably, treatment with AMD3100 diminished the hepatoprotective effect of ALB on CCl4-induced liver fibrosis. Furthermore, we found that the combination of ALB with metformin (MET) exhibited a significant synergistic effect in the treatment of liver fibrosis, with the CXCL12/CXCR4 axis playing a crucial role in this process. Thus, the findings of this study provided theoretical data support and suggested a new possible treatment strategy for liver fibrosis.

overall_design: 1.5×105 LX-2 cells in logarithmic growth phase were seeded in 6-well cell culture plates and cultured in an incubator at 37℃ and 5%CO2 for 24 hours. The control group and the experimental group were added with 20 ng/ml TGF-β1 to induce the activation of LX-2 cells. After 24 hours of continuous culture, the experimental group was added with the prepared ALB solution, and the control group was added with the same dose of culture medium. RNA was extracted after 24 h incubation at 37 ° C in an incubator with 5%CO2.


title: A distinct mechanism of m6A methylation of mRNA in bacteria compared to eukaryotes

city: Chicago

first: Jingxuan

last: Jia

state: IL

address: 929E 57th St

institute: University of Chicago

summary: The aim of the study was to uncover the mechanism behind m6A methylation on E. coli mRNA, and to elude to its functional roles by characterising it and asessing its affects under stress. We carried out m6A sequencing under different conditions.

overall_design: m6A-RNA sequencing of wild-type E. coli MG1655 cells (2 replicates), cells from 4 Keio strains with a single gene knokcout, and from wid-type E. coli cells subjected to heat stress (2 replicates) or oxidative stress (2 replicates), to determine the mechanism behind m6A installation in E. coli and its characteristics under stress

first: Klara

last: Szydlo

first: Leonardo

last: Santos

first: Zoya

last: Ignatova

first: Yuan

last: Wu

first: Weixin

last: Tang


title: SPT6 Regulates H3K14Ac Deposition in Mouse Embryonic Stem Cells [PRO-seq]

overall_design: Examination of nascent RNA in dTAG-SPT6 mESCs treated with DMSO or 100 nM dTAG-13 for 3h.


title: FOXO4-SP6 axis controls surface epithelium commitment by mediating epigenomic remodeling [ATAC]

city: Guangzhou

first: Jiafeng

last: Liu

state: Guangdong

address: No.7 Jinsui Road, Tianhe District, Guangzhou

institute: sun yat-sen university

summary: Proper development of surface epithelium (SE) is a requisite for the normal development and function of ectodermal appendages; however, the molecular mechanisms underlying SE commitment remain largely unexplored. Here, we developed a KRT8 reporter system and utilized it to identify FOXO4 and SP6 as novel, essential regulators governing SE commitment. We found that the FOXO4-SP6 axis governs SE fate and its abrogation markedly impedes SE fate determination. Mechanistically, FOXO4 regulates SE initiation by shaping the SE chromatin accessibility landscape and regulating the deposition of H3K4me3. SP6, as a novel effector of FOXO4, activated SE-specific genes through modulating the H3K27ac deposition across their super enhancers. Our work highlights the regulatory function of the FOXO4-SP6 axis in SE development, contributing to an improved understanding of SE fate decisions and providing a research foundation for the therapeutic application of ectodermal dysplasia.

overall_design: ATAC-seq for hESCs, SE initiating cells, and differentiated SE cells that were treated with either scrambled-shRNA or shFOXO4/SP6-shRNA.

first: Huaxing

last: Huang

first: Fengjiao

last: An


title: CD8+ T Cells in Breast Cancer Tumors and Draining Lymph Nodes: PD-1 levels, Effector Functions and Prognostic Relevance.

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: We analyzed the T cell receptor (TCR) repertoire of memory CD8+ T cells (CD8+ T cells excluding CD45RA+CD27+) isolated from invaded lymph nodes (LNs), non-invaded LNs, and primary tumors of patients with luminal breast cancer. Our findings revealed shared oligoclonal TCRs between LN and tumor-infiltrating CD8+ T cells, suggesting local recirculation of tumor-enriched T cells.

overall_design: TCR-β sequencing of sorted CD8+ Tcells from breast cancer patients.CD8+ Tcells were purified and processed from matched non-invaded lymph node (N=3), invaded lymph node (N=3) and tumors (N=3).

first: Nicolas

last: Núñez

first: Jimena

last: Tosello

first: Jeremy

last: Bigot

first: Olivier

last: Lantz

first: Eliane

last: Piaggio


title: Androgens mediate sexual dimorphism in Pilarowski-Bjornsson syndrome

city: Reykjavik

first: Kimberley

last: Anderson

address: Sturlugata 8

country: Iceland

institute: University of Iceland

summary: The effect of sex on the penetrance of autosomal dominant Mendelian conditions is an understudied area of research. Variants in CHD1 have previously been identified in females with Pilarowski-Bjornsson syndrome (PILBOS), a recently described cause of developmental delay. We now demonstrate that both sexes can show signs of PILBOS, although males are more likely to display PILBOS phenotypes when carrying more severe variants. A novel mouse model carrying a human-derived missense variant in the Chd1 gene (Chd1R616Q/+) shows female-restricted disease phenotypes including growth retardation, anxiety and hypotonia. Orchiectomy of male mice unmasks a growth retardation phenotype in Chd1R616Q/+ mutants compared to orchiectomized wild type (WT) littermates. Conversely, testosterone supplementation in female Chd1R616Q/+ mice and WT littermates rescues the growth phenotype, suggesting that androgens dictate PILBOS disease penetrance. On the human population level, we demonstrate a significant overrepresentation of healthy males carrying rare missense variants in CHD1 in the gnomAD database, further supporting a male protective effect against CHD1 variants. We further identify 212 other genes that show similar missense variant overrepresentation in males. Together our data suggests androgen-regulated sexual dimorphism in Pilarowski-Bjornsson syndrome and opens up novel avenues to understand the mechanistic basis of sexual dimorphism of autosomal Mendelian disorders.

overall_design: In order to examine the functional impact of the CHD1 R616Q variant, we performed bulk RNA-sequencing (RNAseq) using E18.5 NPCs derived from mouse embryos of both mutant and wild-type genotypes. Futhermore, we treated the cells with DMSO vehicle control or dihydrotestosterone (DHT) in order to assess the impact of androgens on the gene expression of these cells.

first: Sara

middle: T

last: Halldorsdottir

first: Hans

last: Bjornsson


title: Cell type specific enhancers for primate prefrontal cortex

city: PITTSBURGH

first: William

middle: R.

last: Stauffer

state: PA

address: 3501 Fifth Ave

department: Neurobiology

institute: University of Pittsburgh

summary: Humans and nonhuman primates (NHPs) can reason, deliberate, and make causal inferences. It is now possible to study the cell types and circuits underlying these complex neural functions by using adeno-associated viral (AAV) vectors to deliver circuit-breaking tools that are driven by cell type-specific enhancers. Here, we set out to identify cell type specific enhancers for principal neurons in the dorsolateral prefrontal cortex. We used single nucleus RNA-Seq to define molecular phenotypes, and we used single nucleus ATAC-Seq to identify cell type specific open chromatin regions (OCRs). We used machine learning models that learned the regulatory vocabulary for each cell type and ranked 500nt OCRs according to their potential to drive cell type specific transgene expression – we call these 500nt sequences ‘enhancer candidates’. The top-ranked enhancer candidates for layer 3 pyramidal neurons (L3PNs) and a layer 5 pyramidal neuron extra-telencephalic (ET) subtype were packaged into AAVs with unique DNA barcodes. We use a combination of enhancer screening and one at a time validation to identify enhancers capable of driving cell type specific gene expression. The best performing ‘layer 3’ enhancer consistently restricted expression to layers 2 and 3. The performance of best performing layer 5 ET vector was titer dependent, but it demonstrates high specificity for POU3F1+ PN.  This work provides vectors for examining cell types related to NHP cognitive functions and establishes a platform for future development of more cell type and circuit-specific AAVs that function in NHP brains.

overall_design: Single nuclei RNA and ATAC profiles of rhesus macaque prefrontal cortex.

first: Jing

last: He

first: BaDoi

last: Phan

first: Willa

last: Kerkhoff

first: Aydin

last: Alikaya

first: Olivia

last: Brull

first: Megan

last: Fredericks

first: Tao

last: Hong

first: Morgan

last: Sedorovitz

first: Chaitanya

last: Srinivasan

last: Wirfel

first: Samual

last: Dauby

first: Rachel

last: Tittle

first: Meng

last: Lin

first: Andreea

last: Bostan

first: Bryan

last: Hooks

first: Omar

last: Gharbawie

first: Leah

last: Byrne

first: Andreas

last: Pfenning


title: Piezo1 initiates host immune defense against pathogenic fungi through mechanosensory recognition of Candida albicans hyphae

city: Xiamen

first: Lanfen

last: Chen

state: Fujian

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

summary: Candida albicans metamorphoses from benign yeast to a rigid hyphae , becoming an opportunistic pathogen in immunocompromised patients. The process by which immune cells discern fungal transformations remains elusive. Here we report that the mechanosensitive ion channel Piezo1 is indispensable for recognizing fungal hyphae and triggering anti-fungal innate immune responses. Hyphae-triggered Piezo1 activation increased CLRs expression in innate immune cells by inducing the expression of C/EBPb via the Piezo1/CaMKs/CREB axis. In addition, Piezo1/CaMKs signaling activated kinases NDR1/2, which augmented NLRP3 inflammasome assembly and promoted hyphae-induced inflammation. Abolishing the yeast-to-hyphae transition dampens CLR and NLRP3 activation. Piezo1-deficient mice exhibit compromised clearance of C. albicans infection, whereas Piezo1 agonist amplifies C. albicans clearance. In addition, CaMKs, CREB or NDR1/2 inhibition exacerbates hyphae infections, like Piezo1 deficiency. Therefore, we ascertain Piezo1-mediated mechanotransduction as vital for immune surveillance and control of hyphal C. albicans, heralding Piezo1 agonist as a potential remedy for fungal infections.

overall_design: RNA-seq analysis of WT and Piezo1KO BMDMs, with or without YODA1 treatment.

first: Yiran

last: Shi

first: Dawang

last: Zhou


title: FOXO4-SP6 axis controls surface epithelium commitment by mediating epigenomic remodeling [ChIP]

first: Jiafeng

last: Liu

overall_design: ChIP-seq for transcription factors (FOXO4,SP6) and histone modifications (H3K27ac, H3K4me1, H3K4me3)

first: Huaxing

last: Huang

first: Fengjiao

last: An


title: Targeting COPA to enhance erdafitinib sensitivity in FGFR-altered bladder cancer

city: WuHan

first: huayuan

last: zhao

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Fibroblast growth factor receptor (FGFR) family aberrations are common in urothelial cancer. The FGFR tyrosine kinase inhibitor erdafitinib has been approved for locally advanced or metastatic urothelial cancer with FGFR2/3 alterations. Despite the initial efficacy of erdafitinib, resistance cannot be avoided. The molecular mechanism of erdafitinib resistance has not been well investigated. Here, we performed genome-wide CRISPR screen and identified coatomer protein complex subunit α (COPA) as a key target to enhance erdafitinib sensitivity. Functionally, the deficiency of COPA reduced the proliferation of FGFR-altered bladder cancer cells upon erdafitinib treatment. Mechanistically, COPA knockout increased LRPPRC protein degradation, leading to reduced ID3 mRNA stability in an m6A-dependent manner. Collectively, these findings reveal a novel mechanism of erdafitinib resistance, providing a potential therapeutic target for FGFR-altered bladder cancer.

overall_design: To determine the target genes and downstream signaling pathways of COPA in bladder cancer cells, transcriptome analysis was performed in sg-NC and COPA-KO cells with DMSO or erdafitinib treatment.

first: Huayuan

last: Zhao

first: Guosong

last: Jiang

first: Hui

last: Zhang


title: In vivo response of the transcriptome of human immune cells to vitamin D3 supplementation in a cohort of 45 individuals

city: Olsztyn

first: Carsten

last: Carlberg

state: Warmia-Mazury

address: Tuwima 10

department: Food Technology

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

summary: In this study, we analyse the in-vivo modulation of the transcriptome of human PBMCs by a bolus of vitamin D3 (1000 IU/kg) over 24 hours.

overall_design: PBMCs of 45 healthy individuals were collected directly before and 24 h after an in-vivo intake of a single large bolus of 1000 IU/kg of vitamin D3. Analysis was performed on the cohort to identify vitamin D target genes.

first: Ranjini

last: Ghosh Dastidar


title: FOXO4-SP6 axis controls surface epithelium commitment by mediating epigenomic remodeling [RNA]

overall_design: To illustrate the function of FOXO4 and SP6 in regulating SE differentiation, we knocked down FOXO4 and SP6 in human embryonic stem cells (hESCs) by shRNAs, and then performed RNA-seq to obtain data from 4 different cells at two time points: the SE initiation stage in D3 and the maturation stage in D7.  Comparative gene expression analysis was conducted on the RNA-seq data from differentiated hESCs and their knockdown derivatives (shFOXO4 and shSP6).


title: Transcriptional study of the home-use TriPollar radiofrequency device on mice skin

city: Nanjing

first: Yuanyuan

last: Wu

state: Jiangsu

address: 138 Xianlin Avenue

institute: Nanjing University of Chinese Medicine

summary: Radiofrequency technology has shown notable efficacy in addressing skin aging. Despite its effectiveness, there is a lack of transcriptional studies exploring how radiofrequency technology enhances skin aging. This self-control study utilized ICR male mice divided into two age groups (four-month-old and one-year-old) to assess the impact of Tripollar Stop VX2 radiofrequency device on skin. The treatment was conducted every other day for one week with device set on low-range mode.

overall_design: We sacrificed six mice in four-month-old and five mice in one-year-old in this self-control studies

first: Xiaofeng

last: Li


title: Targeting VRK2 Enhances the Efficacy of Anti-PD-1 Therapy in Hepatocellular Carcinoma by Reducing Direct Phosphorylation and Stability of MYC: CUT-TAG sequencing for MYC in hepatocellular carcinoma cells

city: Wuhan

first: chen

last: su

address: No. 1095, Jiefang Avenue

institute: Huazhong University of Science and Technology

summary: VRK2–MYC axis, a transcription-dependent regulatory axis, could be a prognostic indicator and potential therapeutic target in liver cancer.

overall_design: Cleavage Under Targets and Tagmentation (CUT&TAG) sequencing was then performed on MYC in cells from different treatment groups,

first: Chen

last: Su

first: Zhibin

last: Liao

first: Jie

last: Mo

first: Furong

first: Zhanguo

first: Peng

last: Zhu

first: Bixiang


title: Transcriptome analysis of early embryonic development in a mouse model of polycystic ovary-like syndrome

city: Jinan

first: Shan

last: Han

address: Wenhua West road

institute: Shandong University

summary: Polycystic ovarian syndrome (PCOS) is the most common gynaecological endocrine disease in women of reproductive age, with a prevalence rate of more than 12%, and is characterised by sporadic ovulation or anovulation, hyperandrogenism and polycystic ovarian changes. Polycystic ovary syndrome has a complex clinical presentation and, in addition to affecting follicular development and reproductive endocrine levels in women of childbearing age, it also impairs early embryonic development, affecting pregnancy outcome and offspring health, but its pathogenesis is unclear. In this study, we constructed a mouse model of PCOS using late-gestational hyperandrogen exposure, and examined the reproductive endocrine phenotype and glycolipid metabolism phenotype in mice. We found that PCOS model mice exposed to dihydrotestosterone in late pregnancy could exhibit hyperandrogenic manifestations, presenting elevated vaginal-anal index and delayed puberty establishment, as well as disturbed estrous cycle in adulthood. Ovulation number, number of mature oocytes, fertilisation rate and number of blastocysts were significantly lower in PCOS model mice compared to control mice. Subsequently, we assessed the follicular development and embryonic development ability of the mice using superovulation and in vitro fertilisation experiments, and obtained preimplantation embryonic RNA expression profiles of PCOS mice by performing Smart-seqII RNA sequencing to explore the possible mechanisms by which PCOS affects preimplantation embryonic development and offspring health. Bioinformatics analyses showed that 160 differentially expressed genes were identified out of 12,165 genes in blastocyst samples from both groups of mice, of which calcium/calmodulin-dependent protein kinase II β (CAMK2B2), melanoma-associated antigen B2 (MAGEB2), and the ADAM metallopeptidase domain (Adam4) were significantly differentially between the polycystic ovary syndrome and control groups Expression. Functional enrichment analyses revealed that the differential genes were mainly associated with pathways such as glandular development, nephron development, organ development and receptor catabolism. Our current study highlights the deleterious effects of intrauterine exposure to hyperandrogenism on the expression of polycystic ovary syndrome in mice, as well as resulting in impaired development of their eggs and early embryos. These findings may provide valuable insights into the early prevention of polycystic ovary syndrome.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for blastula of PNA mice and its controls


title: Targeting VRK2 Enhances the Efficacy of Anti-PD-1 Therapy in Hepatocellular Carcinoma by Reducing Direct Phosphorylation and Stability of MYC，CUT-TAG sequencing for MYC in hepatocellular carcinoma cells

overall_design: Identify downstream target genes regulated by VRK2 or MYC in MHCC97H cells using whole transcriptome sequencing (RNA-Seq). The expression of MYC or VRK2 was interfered with using siRNA in MHCC97H

last: Liu


title: Id2 expression level determines the development of effector vs. exhausted tissue-resident memory CD8+ T cells during CNS chronic infection

city: Toulouse Cedex 3

first: Nicolas

last: Blanchard

address: CHU Purpan BP3028

department: Inserm UMR1291

institute: Toulouse Institute for Infectious and Inflammatory Diseases (Infinity)

summary: Tissue-resident memory T cells (Trm) play a central role in regional immunity within non lymphoid tissues to efficiently protect against reinfection as well as to control persistent pathogen infection. Although single-cell transcriptomics analysis of Trm in various diseases have uncovered a phenotypic and functional heterogeneity of Trm, the underlying molecular mechanisms directing such diversity are poorly defined. To better understand these mechanisms, we used the model of infection with the parasite Toxoplasma gondii (T. gondii), which establishes a persistent infection in the central nervous system (CNS) controlled by brain CD8+ Trm. Through single-cell transcriptomic analysis of brain CD8+ T cells from T.gondii-infected mice, we uncovered that brain Trm subsets have an heterogenous expression of the transcriptional regulator Id2, and that these differences in Id2 levels correlated with different functional states. Using mixed bone marrow chimeras, our results revealed that T-cell specific Id2-deficiency caused parasite-specific Trm to develop an aberrant phenotype in a cell-intrinsic manner, characterized by diminished effector functions and reduced expression of the tissue retention molecules CD49a and CXCR6. This phenotype was similarly observed upon overexpression of E2A, a transcription factor negatively regulated by Id2, in parasite-specific CD8+ T cells. Conversely, the loss of Id2 in brain-infiltrating CD8+ T cells led to the accumulation of exhausted PD1+ Tox+ CD8+ Trm cells, whereas Id2 overexpression repressed the acquisition of the exhaustion phenotype and promoted the accumulation of pathogen-specific CD8+ T cells in the brain. Overall, our study indicates that Id2 expression level dictates the acquisition of an effector vs. exhausted phenotype by CD8+ Trm during chronic CNS pathogen infection.

overall_design: Single-cell RNA-seq dataset (CITE-seq) was obtained from one experiment in which C57BL/6 mice were chronically infected with T.gondii.GRA6-OVA and analyzed at day 154pi.  Spleens or brains were pooled from 4 infected mice.  Cells from pooled spleens or brains were labeled with TotalSeqC CD3 and CD8 antibodies (Biolegend), and with PE-coupled dCODE Kb-OVA (SIINFEKL) and Kb-SIYRYYGL control dextramer, to enable retrospective identification of OVA-specific cells among total CD8+ T cells. CD8+ T cells were purified using MACS Miltenyi mouse CD8a+ T Cell Isolation kit (Miltenyi Biotec 130-104-075) before proceeding to single-cell emulsion with 15946 splenic CD8+ T cells and 11856 brain CD8+ T cells, respectively.  Single-cell libraries were generated with Chromium Next GEM Single Cell 5' Kit v2 and 5' Feature Barcode Kit according to the manufacturer’s protocol (10X Genomics). Library size and quality were verified on a Fragment Analyzer (Agilent). Libraries were sequenced on 1 lane of SP flowcell with Illumina NovaSeq6000 sequencer, using paired-end sequencing (2 x 150) and a single 8 bp-long index.

first: Aboubacar

last: Coulibaly

first: Marine

last: Alis

first: Frederick

last: Masson


title: Transcriptional profiling of 22Rv1 cells upon treatments of RBN-2397 and tapinarof

city: San Francisco

first: Alan

last: Ashworth

address: 1450 3rd Street, HD-271

department: Helen Diller Family Comprehensive Cancer Center

institute: University of California, San Francisco

summary: Small molecule inhibitors of the mono (ADP) ribosyl transferase PARP7 are being evaluated therapeutically as a monotherapy for tumors overexpressing PARP7 and in combination with immune checkpoint inhibitors. We previously showed that sensitivity to the PARP7 inhibitor (PARP7i) RBN-2397 could be enhanced by co-treatment with agonists of the aryl hydrocarbon receptor (AHRa) in cell lines that show strong intrinsic sensitivity to RBN-2397. Here we demonstrate that a range of tumor cell lines that are relatively insensitive to PARP7i or AHRa as individual agents are profoundly sensitive to the combination. Our data show that this synergistic response is dependent on AHR/ARNT and is associated with increased levels of nuclear AHR and increased transcription of AHR target genes. In some hormone-dependent cell lines, we find that combination treatment is associated with proteasomal turnover of the steroid hormone receptors, androgen receptor (AR) and estrogen receptor (ER). Both wildtype and therapy-resistant mutant forms of these receptors are degraded upon treatment with AHRa and PARP7i in breast and prostate cancer models. These results suggest that combining PARP7i with AHRa may extend the utility of these drugs to a wider range of tumors, including those that are refractory to hormone therapy.

overall_design: RNA-seq of 22Rv1 propstate cancer cells in hormone deprived media, -/+ DHT, RBN-2397 or tapnarof.

first: Xuxu

last: Gou

first: Morgan

middle: E

last: Diolaiti