title: Single nucleus RNA-seq data from the nucleus accumbens of female and male prairie voles

first: Zoe

last: Donaldson

address: 1945 Colorado Ave

department: MCDB

institute: University of Colorado Boulder

summary: Relationships are shaped by reciprocal interaction and feedback between individuals, where one individual acts, and the other interprets their actions to respond in turn. As relationships mature, pairs share common goals, improve their ability to work together, and experience coordinated emotions. However, the neural underpinnings responsible for this unique, pair-specific experience remain largely unexplored. Here, we examined the transcriptional landscape of the nucleus accumbens (NAc), a brain region extensively implicated in social bonding, in socially monogamous prairie voles in long-term peer or mating-based relationships. We show cell type-specific transcriptional differences between relationship types, as well as pair-wise transcription-based synchrony that exists at the level of individual cells regardless of relationship type. We found that, compared to peer-paired females, mate-paired females have a higher proportion of dopamine receptor D1 neurons expressing prodynorphin (Pdyn) and dopamine receptor D2 neurons expressing proenkephalin (Penk), but lower expression of gene modules related to microglial activation and neuron development. Using gene module analysis, support vector machines, and bootstrapped gene correlations, we also show that, regardless of relationship type, prairie voles exhibit transcription-based synchrony with their partner. Together, our results demonstrate that relationship type and a pair-specific social environment both shape the transcriptional landscape in the NAc. Our work reveals the emergent cellular properties of social bonds, providing a potential biological mechanism by which shared social experience reinforces and strengthens relationships.

overall_design: Female and male prairie voles were paired with a novel peer (same-sex) or mate (opposite-sex) partner for 16 days prior to sacrifice. Brain tissue was frozen at -80C and later the nucleus accumbens was dissected from each brain separately. Nuclei were dissociated from each animal separately; therefore, each sample is from one animal.

first: Liza

last: Brusman


title: Restoration of LAT signaling through the expression of a novel Adjunctive LAT-Activating CAR (ALA-CART) enhances the antigen-sensitivity and persistence of CAR T cells

status: Public on Feb 04 2025

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

country: USA

institute: University of Colorado, Denver - Anschutz Medical Campus

type: Expression profiling by high throughput sequencing

summary: Chimeric antigen receptor (CAR) T cell therapy have demonstrated remarkable success in treating B-cell malignancies that are refractory to standard therapies; however, preclinical and clinical studies have demonstrated that CAR T cell efficacy is greatly reduced against antigen-low tumors. This was exemplified in a clinical trial of CD22-directed CAR T cells where post-CAR relapses were driven by a decrease in the surface expression of the CD22 antigen. To address the poor response of CAR T cells to antigen-low tumor cells, we performed global phosphoproteomics using a SILAC/mass spectrometry approach to examine signal transduction events within CAR T cells in response to high- and low-levels of CD22 antigen. Stimulation with low levels of CD22 antigen resulted in decreased activation of several canonical T cell signaling pathways in CAR T cells, suggesting poor utilization of LAT. To overcome this inefficiency of LAT activation, we designed a bicistronic construct consisting of a clinically active 2nd generation CD22-BBz CAR along with a novel Adjunctive LAT Activating CAR incorporating the intracellular signaling domain of LAT (ALA-CART). ALA-CART cells demonstrated enhanced phosphorylation of LAT and restored downstream signaling in response to low levels of CD22. In xenograft models, ALA-CART cells completely eradicated CD22-low leukemia, significantly extending survival of mice in comparison to the clinically-active, standard CD22-BBz CAR T cells. Compared to the standard CD22-BBz CAR T cells, ALA-CART cells exhibited transcriptional differences in the resting state reflecting a less differentiated state, which corresponded to an enrichment of T stem cell memory cells and enhanced in vivo persistence. Thus, through the identification of CAR signaling deficits, we rationally designed the ALA-CART platform which improves the sensitivity and persistence of CAR T cells to target antigen-low cells, overcoming a mechanism of resistance to standard CAR therapies.

overall_design: To investigate transcriptional differences between the clinically active CD22-BBz CAR and the ALA-CART, we isolated CD4+ (by negative magnetic bead separation) and CD8+ CAR-T cells (by positive magnetic bead separation) of purified CD22-BBz and 22ALA-CART cells. CAR T cells were added to wells of 6-well tissue culture plates that were either uncoated (unstimulated CAR T cells) or wells coated with 3 ug/mL 22Fc-antigen (stimulated CAR T cells). CAR T cells were incubated at 37C for 30 mins and lysed using buffer RLT followed by extraction using RNeasy kit (Qiagen). Comparative gene expression analysis was performed on CD4 and CD8 CAR T cells with and without stimulation.

first: Catherine

last: Pham-Danis

first: M

middle: E

last: Kohler


title: Genome assembly of silkworm BmN4 cells

status: Public on Feb 03 2025

city: Tokyo

first: Yurika

last: Namba

state: --- Select a state ---

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biological Sciences, Graduate School of Science

country: Japan

institute: The University of Tokyo

type: Non-coding RNA profiling by high throughput sequencing

summary: BmN4 cells are cultured cells derived from Bombyx mori ovaries and widely used to study transposon silencing by PIWI-interacting RNAs (piRNAs). A high-accurate genome sequence of BmN4 cells is required to analyze the piRNA pathway using RNA-seq. The genome sequence of BmN4 cells was assembled using Pacific Biosciences (PacBio) HiFi and Oxford Nanopore technology Ultralong (ONT-UL) reads. Microscopic observation and image analysis showed that BmN4 cells were octoploid on average, and the number of chromosomes per cell was highly variable. We concluded the haplotype-resolved assembly of such a complex genome would be difficult; therefore, we assembled a consensus genome sequence. RNA-seq analysis of Siwi knockdown cells also revealed that Siwi-piRISC may target Countdown (Cd), an LTR retrotransposon. By comparing the consensus genome sequence with the reads, we identified differences between haplotypes, particulary structural variants, suggesting that some transposons, including Countdown, increased their copy number in BmN4 cells.

overall_design:
Siwi- or AGO3-loaded small RNA-seq profiling from BmN4 cells
Total RNA-seq profiling from BmN4 cells with either control or Siwi knockdown

first: Yukiteru

last: Ono

first: Yuka

middle: W

last: Iwasaki

first: Junichi

last: Iwakiri

first: Toshitaka

last: Kumagai

first: Goro

last: Terai

first: Kazumichi

middle: M

last: Nishida

first: Chie

last: Owa

first: Haruka

last: Kobayashi

first: Shinichi

last: Morishita

first: Mikiko

middle: C

last: Siomi

first: Kiyoshi

last: Asai


title: Dendritic cells regulate the innate-adaptive balance in lymph nodes for optimal host defense

city: Seattle

first: Jessica

last: Huang

state: WA

address: 750 Republican St

department: Immunology

institute: University of Washington

summary: Lymph nodes (LNs) enable innate defense to limit pathogen dissemination while also driving adaptive immunity. Yet, certain innate responses can restrict adaptive processes, suggesting that these must be tightly regulated. Here, we report that after infection or immunization, LN architecture is rapidly altered, with large-scale, polarized recruitment of neutrophils and monocytes from inflamed blood vessels, and intranodal repositioning of NK cells. Mechanistically, dendritic cells (DCs) promote this process through expression of inflammatory chemokines and integrin ligands. While necessary for efficient pathogen containment, DC-driven innate cell responses paradoxically limit early adaptive immunity, with infiltrating neutrophils displacing lymphocytes and reducing the LN area available for T cell priming. Upon threat secession however, DCs and DC-recruited monocytes phagocytose the neutrophils, restoring tissue architecture and generating polarized domains for downstream adaptive immune cell activation. Thus, DCs orchestrate innate cell organization during inflammation, serving as rheostats of innate versus adaptive functions of the LN.

overall_design: RNA sequencing was performed to identify genes upregulated by DCs during early inflammation. Resident DC1s and DC2s were sorted from LNs at steady state as well as 6 hours post-CpG administration. We also performed intravascular staining with fluorescent anti-CD11c antibody to further sort on vasculature-associated and non-associated populations, to ask whether there were differences based on proximity to blood vessels.

middle: Y

first: Michael

last: Gerner


title: Curcumin reverses irinotecan-acquired resistance in colorectal cancer cells: insights from whole transcriptomic data

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

summary: To investigate the key mechanisms underlying the acquisition of irinotecan resistance in colorectal cancer cells and the reversal of this resistance by curcumin, we utilized whole-genome microarray expression profiling as a discovery tool to identify the signaling networks involved. Resistance acquisition led to dysregulation of genes associated with irinotecan resistance, including TOP1, drug-metabolizing enzymes (CYPs and UGTs), and efflux transporters (ABCs), while also affecting the extression of 53 genes involed in proliferation and 33 in cell motility. Curcumin treatment significantly modulated 3,901 genes (FC >|±2|), inducing apoptosis, reducing proliferation, and inhibiting migration. Curcumin also enhanced sensitivity to irinotecan, by upregulating TOP1 and inhibiting 18 CYPs, 4 UGTs, and 20 ABCs, including those upregulated in irinotecan-resistant cells.

overall_design: An irinotecan-resistant CRC cell line (DLD1_IRI-R) was established by exposing DLD1 cells to increasing irinotecan concentrations, until cells would survive and proliferate in culture medium containing 20 μM irinotecan. The whole transcriptome analysis  was implemented in four biological replicas of DLD1_IRI-R cells and the resistant cells treated for 48h with curcumin at IC50 concentration.

first: Laura

last: Gavrilas

first: Oana

last: Sava

first: Loredana

last: Balacescu

first: Stefan

last: Miron

first: Doina

last: Miere

first: Ovidiu

first: Cruceriu

last: Daniel


title: Disease-associated astrocyte epigenetic memory promotes CNS pathology [sgEp300, sgACLY astrocytes bulk RNA-Seq dataset]

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Disease-associated astrocyte subsets contribute to the pathology of neurologic diseases, including multiple sclerosis and experimental autoimmune encephalomyelitis1,2,3,4,5,6,7,8 (EAE), an experimental model for multiple sclerosis. However, little is known about the stability of these astrocyte subsets and their ability to integrate past stimulation events. Here we report the identification of an epigenetically controlled memory astrocyte subset that exhibits exacerbated pro-inflammatory responses upon rechallenge. Specifically, using a combination of single-cell RNA sequencing, assay for transposase-accessible chromatin with sequencing, chromatin immunoprecipitation with sequencing, focused interrogation of cells by nucleic acid detection and sequencing, and cell-specific in vivo CRISPR–Cas9-based genetic perturbation studies we established that astrocyte memory is controlled by the metabolic enzyme ATP-citrate lyase (ACLY), which produces acetyl coenzyme A (acetyl-CoA) that is used by histone acetyltransferase p300 to control chromatin accessibility. The number of ACLY+p300+ memory astrocytes is increased in acute and chronic EAE models, and their genetic inactivation ameliorated EAE. We also detected the pro-inflammatory memory phenotype in human astrocytes in vitro; single-cell RNA sequencing and immunohistochemistry studies detected increased numbers of ACLY+p300+ astrocytes in chronic multiple sclerosis lesions. In summary, these studies define an epigenetically controlled memory astrocyte subset that promotes CNS pathology in EAE and, potentially, multiple sclerosis. These findings may guide novel therapeutic approaches for multiple sclerosis and other neurologic diseases.

overall_design: In this experiment there are three bulk RNA-Seq datasets. The first one includes sgEp300 (n=3) EAE astrocytes and sgScramble (n=3) EAE astrocytes. The second one includes sgAcly (n=4) EAE astrocytes and sgScramble (n=4) EAE astrocytes. The third one includes EAE astrocytes expressing Acly-Ep300-, Acly-Ep300+, Acly+Ep300-, and Acly+Ep300+ based on FIND-seq.

first: Hong-Gyun

last: Lee

last: Wheeler

first: Francisco

last: Quintana


title: Single-cell RNA Sequencing for CD248 cKO Mouse hearts at myocardial infarction model

city: Hangzhou

first: Mo

address: Jiefang road 88

department: Department of Cardiology of The Second Affiliated Hospital, School of Medicine

country: China

institute: Zhejiang University

summary: Post-injury remodeling is a complex process involving temporal specific cellular interactions in the injured tissue where the resident fibroblasts play multiple roles, including inflammation induction and tissue remodeling.   To dissect the molecular basis of these interactions, we performed single-cell and spatial transcriptome analysis in human and mouse hearts after myocardial infarction.  A subset of fibroblasts identified by unique high expression of CD248 was strongly correlated with collagen synthesis and remodeling, and genetic deletion of CD248 in fibroblast ameliorated cardiac fibrosis and dysfunction following ischemia/reperfusion, highlighting the functional importance of CD248 positive fibroblasts in post-injury pathological remodeling. CD248 stabilizes TGF-βR Ⅰ protein and activates ACKR3 expression in fibroblast, leading to enhanced T cell adhesion and retention. This CD248 mediated fibroblast-T cell interaction is required to sustain fibroblast activation and scar expansion in injured heart. Disruption of this interaction using monoclonal antibody or Chimeric antigen receptor T cell reduces T cell infiltration, ameliorates ischemia/reperfusion-induced cardiac fibrosis and improves heart function.  Therefore, single cell molecular profiling in post-injury heart has uncovered a CD248 specific subclass of fibroblast with a critical role in fibroblast-T cell interaction and a new potential therapy to treat tissue fibrosis.

overall_design: We generated fibroblast specific CD248 knockout mice by crossbreeding the Cd248fl/fl mice with the Postn-CreER mice, and then constructed cardiac myocardial infarction (MI) model. Cd248fl/fl littermate mice served as the control group.

first: Guohua

first: Xinyang

last: Hu


title: Genome-wide analysis of plasma exosomal microRNA in lung cancer

city: xi'an

first: qian

last: zhang

address: Xinsi Road

institute: Tangdu Hospital

summary: Purpose: To identify a panel of plasma exosomal miRNAs as potential biomarkers for lung cancer from the genome-wide set of currently known human miRNAs. Methods: Plasma samples from 4 lung cancer patients and 4 patients with benign lung disease were collected, and plasma exosomes were extracted by ultracentrifugation. Exosomal miRNA profiles were generated by deep sequencing based on Illumina NextSeq 500 platform. And differentially expressed exosomal miRNAs between lung cancer and benign lung disease were identified by edgeR with the default threshold of |log2 (fold change) | ≥ 1.5 and P-value < 0.05. Results: A total of 983 detectable exosomal miRNAs were analyzed to identify differentially expressed miRNAs between two groups. There were 6 significantly up-regulated miRNAs and 63 significantly down-regulated miRNAs in lung cancer cases when compared with benign lung disease. Conclusion: The comparative analysis of plasma exosomal miRNAs between lung cancer and benign lung diseases  provided a reference for exploring potential biomarkers of lung cancer. And the clinical value of candidate exosomal miRNAs needs to be further verified in lung cancer clinical trials.

overall_design: Expression levels of 983 exosomal miRNAs were investigated in plasma samples from 4 lung cancer cases and 4 patients with benign lung disease.

first: Zhang

last: Qian

first: Zheng

last: Kaifu

first: Jin

last: Faguang


title: DAPsequencing data in "A doublesex-dependent transcriptional control model for Nasonia parasitoid wasps' sex differentiation"

city: Wageningen

first: Filippo

last: Guerra

address: Droevendaalsesteeg 1, 107/W0.Aa.081

country: Netherlands

institute: Wageningen University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In insects, sexual differentiation is orchestrated by one transcription factor, Doublesex (DSX). DSX affects Drosophila melanogaster male and female transcriptome, yet how DSX regulates gene expression in other species is unknown. We investigated sex-biased gene expression during juvenile development in the parasitoid wasp Nasonia vitripennis, finding that more than three-quarters of its genes are sex-biased at a certain point in development. Moreover, we transiently knocked down dsx expression to infer its role in sex-specific transcriptome regulation, revealing thousands of affected genes in males and a more subtle effect in females. Finally, we performed an in vitro DNA-protein interaction assay to identify DSX binding sites and primary DSX target genes. By integrating these three datasets, we defined DSX's regulatory function for all genes in N. vitripennis, revealing that DSX acts mainly in males as both an activator and a repressor. This male-centric model for DSX-mediated regulation is likely to apply to many other insect species.

overall_design: The experiment consists of producing in vitro a transcription factor (Doublesex) and a control protein known not to interact with DNA (Luciferase), immobilising it on a matrix, and using it to enrich a DNA library. The enriched library is sequenced (raw data) and aligned to Nasonia vitripennis genome. Coverage peaks present in the Transcription factor subject but not in the control are scanned via MEME to find the binding sequence of the transcription factor.

first: Julien

last: Rougeot

first: Eveline C.

last: Verhulst


title: CACNA1A loss-of-function mutations affect neurogenesis in different ways in human iPSC-derived neural models

city: Genoa

first: Davide

last: Cangelosi

address: Via 5 maggio,5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

summary: CACNA1A encodes the pore-forming α1A subunit of CaV2.1 calcium channel, whose altered function is associated with different neurological disorders including variable forms of ataxia, epilepsy, and migraine. In this study, we generated isogenic iPSC-derived neural cultures carrying two CACNA1A loss-of-function variants differently affecting CaV2.1 isoforms. Morphological, molecular, and functional assays highlighted distinct neurodevelopmental defects. F1491S mutation, which is located in a constitutive domain of the channel, impaired neural induction at very early stages, as demonstrated by changes in migratory capacity and single-cell transcriptomic signatures in neural progenitors, and by defective polarization in neurons. Instead, cells carrying Y1854X mutation, which selectively affects the [EFa] isoform, behaved normally in terms of neural induction but showed altered neuronal network composition and lack of synchronized activity. Our findings highlighted important roles of CACNA1A in mechanisms underlying early neural induction, neuronal maturation, and neural network dynamics.

overall_design: The molecular signatures of isogenic iPSC-derived neural cultures carrying two CACNA1A loss-of-function variants were investigated by scRNA-seq to gain insight into the mechanism underlying these early neurodevelopmental defects.

first: Ilaria

last: Musante

first: Lorenzo

last: Muzzi

first: Marco

last: Di Duca

first: Sara

last: Guerrisi

first: Yeraldin Chiquinquira Castillo

last: de Spelorzi

last: Cingolani

first: Federico

last: Zara

first: Paolo

last: Scudieri


title: Cardiac Transcriptional Enhancer is Repurposed During Regeneration to Activate an Anti-proliferative Program

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

summary: Zebrafish have a high capacity to regenerate their hearts post-injury.Several studies have surveyed transcriptional enhancers to understand how the dynamics of gene expression are controlled during heart regeneration. We have identified a cardiac transcriptional enhancer that is activated at the site of injury called the runx1 enhancer or REN since it regulates the expression of nearby gene runx1. REN is usually active in cardiomyocytes (CMs) and epicardial tissues surrounding the cardiac valves of uninjured zebrafish hearts.  However, when REN is activated in regenerating CM and epicardial tissues at the injury site, it is concurrently downregulated around the distal heart valve.  Deletion of REN (ΔREN) results in excess Collagen around uninjured zebrafish cardiac valves.  This ΔREN Collagen phenotype is rescued with a runx1 deletion (Δrunx1), suggesting that REN and runx1 function in different genetic pathways in uninjured hearts.  A different nearby gene that does change expression around valves in ΔREN mutant hearts is adamts1 which encodes a metalloproteinase that degrades Collagen.  Taken together, this suggests that in uninjured hearts REN regulates adamts1 independently of runx1.  However, during regeneration, CM proliferation at the site of injury is enhanced in both ΔREN and Δrunx1 mutants, suggesting that REN is rewired to runx1 to stimulate its transcription.  There are two previous descriptions for how enhancers are activated during regeneration.  First, cis-regulatory sequences are reactivated from embryogenesis and second that active adult enhancers are further invigorated during regeneration.  Our data point to a third and previously unappreciated mechanism for gene control during zebrafish heart regeneration.  We report that an enhancer is repurposed both from one gene and cardiac domain to activate a different nearby gene in regenerating cardiac tissue.

overall_design: Comparitive gene expression analysis of REN mutant and Wildtype hearts under uninjured and regenerating (7dpi) conditions using bulk RNA sequencing.

first: Anupama

last: Rao

first: Andy

last: Russell

first: Jose

last: Segura-Bermudez

first: Charles

last: Franz

first: Joseph

last: Goldman


title: Restoration of the Tumor Suppressor Function of Y220C-Mutant p53 in vivo by Rezatapopt (PC14586), a Small Molecule Reactivator [in vivo]

city: Princeton

first: Lizhong

last: Xu

state: NJ

address: 400 Alexander Park Drive, Suite 301

institute: PMV Pharmaceuticals, Inc.

summary: Restoration of the tumor suppressor function of tumor-associated p53 mutants, including tumors harboring the TP53 Y220C mutation, has posed a significant challenge and remains an attractive target for therapeutic discovery. Here, we describe a clinical candidate Rezatapopt (PC14586) designed to stabilize the p53 Y220C mutant protein and restore wild-type (WT) p53 function. Extensive transcriptomics analysis of NUGC-3 xenografted tumors harboring the TP53 Y220C mutation following PC14586 treatment revealed the induction of p53 direct target genes, including protein-coding genes and long non-coding RNAs (lncRNAs), and repression of cell cycle progression-associated genes in a distinct temporal pattern. Our data demonstrate that PC14586 administration inhibited tumor growth in vivo via the induction of WT p53 transcriptional signatures, including a sustained transcriptional repression of genes involved in cell cycle regulation. Following these investigations, rezatapopt (PC14586) was identified as a clinical candidate and is currently being evaluated in the registrational Phase 2 PYNNACLE study.

overall_design:
To investigate the selectivity and robustness of PC14586 in reactivating the p53 Y220C mutant protein to p53 WT function in tumors, we treated xenografted human tumors carrying TP53 Y220C mutation (NUGC-3) in nude mice with PC14586 (100 mg/kg) and vehicle controls in 4 biological repeats for each.
We performed comparative gene expression profiling analysis of RNA-seq data from NUGC-3 xenografted tumors with PC14586 treatments at different time points (n=4 each) versus consolidated vehicle treatments (n=12).

first: Amy

last: Wiebesiek

first: Alexander

last: Solovyov

first: Benjamin

middle: D

last: Greenbaum

first: Melissa

middle: L

last: Dumble

first: Thomas

last: Davis

first: Binh

middle: T

last: Vu

first: Arnold

middle: J

last: Levine

first: Masha

middle: V

last: Poyurovsky


title: Restoration of the Tumor Suppressor Function of Y220C-Mutant p53 in vitro by Rezatapopt (PC14586), a Small Molecule Reactivator [in vitro]

summary: Restoration of the tumor suppressor function of tumor-associated p53 mutants, including tumors harboring the TP53 Y220C mutation, has posed a significant challenge and remains an attractive target for therapeutic discovery. Here, we describe a clinical candidate Rezatapopt (PC14586) designed to stabilize the p53 Y220C mutant protein and restore wild-type (WT) p53 function. PC14586 induced global gene expression changes in the cell lines harboring the TP53 Y220C mutation (NUGC-3 and T3M-4) but not in cells lacking p53 Y220C-mutant protein (NUGC-3 KO and SJSA-1). Extensive transcriptomics analysis of cells harboring the TP53 Y220C mutation following PC14586 treatment revealed the induction of p53 direct target genes, including protein-coding genes and long non-coding RNAs (lncRNAs), and repression of cell cycle progression-associated genes in a distinct temporal pattern. Our data demonstrate that PC14586 administration inhibited cell proliferation in vitro via the induction of WT p53 transcriptional signatures, including a sustained transcriptional repression of genes involved in cell cycle regulation. Following these investigations and additional in vivo studies, rezatapopt (PC14586) was identified as a clinical candidate and is currently being evaluated in the registrational Phase 2 PYNNACLE study.

overall_design:
To investigate the selectivity and robustness of PC14586 in reactivating the p53 Y220C mutant protein to p53 WT function in cells, we treated 4 different cells lines - NUGC-3 (TP53 Y220C), T3M-4 (TP53 Y220C), NUGC-3 KO (TP53 KO), and SJSA-1 (TP53 WT) – with PC14586 (5 µM) versus DMSO at two time points (5h and 16h) in 3 biological repeats for each.
We performed comparative gene expression profiling analysis of RNA-seq data from each of 4 cell lines with PC14586 versus DMSO treatments (n=3 each).

first: Dafydd

middle: H

last: Thomas


title: Effect of MS-275 and CXD101 on gene expression of M-MDSCs and PMN-MDSCs [RNA-Seq]

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: To elucidate the molecular mechanisms of HDAC1-3 inhibitors in inhibiting M-MDSCs, RNA-seq analysis of M-MDSCs and PMN-MDSCs isolated from Hepa 1-6 tumor-bearing mice treated with MS-275 or CXD101 were performed.

overall_design: M-MDSCs (CD11b+Ly-6ChiLy-6G-) and PMN-MDSCs (CD11b+Ly-6CintLy-6G+) were sorted by JSAN (KS-Techno, Japan) from tumor isolated. Total RNA was extracted from M-MDSCs or PMN-MDSCs using miRNeasy Micro Kit (Qiagen). RNA libraries were prepared using TruSeq stranded mRNA sample prep kit (Illumina, USA) and sequenced on Illumina NovaSeq 6000 platform platform (101-base single-end mode).

first: Zhiqi

last: Xie

last: Okuzaki

first: Masashi

last: Tachibana


title: Cholesterol mobilization regulates dendritic cell maturation and the immunogenic response to cancer

city: New York

first: MATTHEW

middle: Dae-Young

last: PARK

state: NY

address: 50 East 98th Street, 6A-1

institute: Icahn School of Medicine at Mount Sinai

summary: Maturation of conventional dendritic cells (cDCs) is crucial for maintaining tolerogenic safeguards against auto-immunity and for promoting immunogenic responses to pathogens and cancer. The subcellular mechanism for cDC maturation remains poorly defined. We show that cDCs mature by leveraging an internal reservoir of cholesterol – generated by de novo synthesis and recycled from extracellular cell debris – to assemble lipid nanodomains on cell surfaces of maturing cDCs, enhance expression of maturation markers, and stabilize immune receptor signaling. This process is dependent on cholesterol transport through Niemann-Pick disease type C1 (NPC1) and mediates homeostatic and TLR-induced maturation. Importantly, we identified the receptor tyrosine kinase AXL as a regulator of the NPC1-dependent construction of lipid nanodomains. Deleting AXL from cDCs enhances their maturation, thus improving antitumor immunity. Altogether, our study presents novel insights into cholesterol mobilization as a fundamental basis for cDC maturation and highlights AXL as a therapeutic target for modulating cDCs.

overall_design: Sample preparation for single-cell RNA sequencing. Single-cell suspensions from lung tissues were obtained, as described above. For scRNAseq, these cells were suspended and stained in 100μL of multiplex hashing antibodies at 4°C for 20 minutes. Stained cells were washed three times in PBS+0.5% BSA to remove unbound antibodies. Washed cells were resuspended in 150μL of wash buffer and counted using a Nexcelom Cellometer Auto2000. Hashed samples were pooled in equal amounts of live cells. Volume was adjusted to achieve a target of 2x106 cells/mL. Hashed samples were loaded onto 10X Genomics NextGen 5’ v1.1 assay, as per the manufacturer’s instructions, for a target cell recovery of 20,000 cells/lane. Libraries were constructed, as per the manufacturer’s instructions. During cDNA amplification, hashtag oligonucleotides (HTO) were enriched during cDNA amplification with the addition of 3 pmol of HTO Additive primer (5’GTGACTGGAGTTCAGACGTGTGCTC). This PCR product was isolated from the mRNA-derived cDNA via SPRISelect size selection, and libraries were made as per the New York Genome Center Hashing protocol. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer and KAPA library quantification kit (Roche, Cat. No. 0796014001.) Gene expression libraries were sequenced at a targeted depth of 25,000 reads per cells, and HTO libraries were sequenced at a targeted read depth of 1,000 reads per cell. All libraries were sequenced on the Illumina NovaSeq S2 100 cycle kit with run parameters set to 28x8x0x60 (R1xi7xi5xR2).  scRNAseq analysis. After library demultiplexing, gene-expression libraries were aligned to the mm10 reference transcriptome and count matrices were generated using the default Cell Ranger 2.1 workflow, using the ‘raw’ matrix output. Where applicable, doublets were removed based on co-staining of distinct sample-barcoding (‘Hashing’) antibodies (maximum staining antibody counts/second-most staining antibody counts = less than 5). Following alignment, cell barcodes corresponding to cells that contained more than 500 UMIs were extracted. From among these, cells whose transcripts constituted more than 25% mitochondrial genes were filtered from downstream analyses. The R package Seurat was used to scale the data, transform via a log normalization method, adjust for batch correction, cluster cells based on shared nearest neighbors, and perform dimensionality reduction based on the first 15 principal components. Gene module analyses were performed, based on the identification of groups of highly correlated genes, according to the Pearson correlation matrix of the most variable genes. This was done using the R package scDissector. Differentially expressed genes were identified using the FindMarkers function in Seurat. Mean UMI expression values were imputed to determine log fold change differences between cell types to further the analysis of markers of interest.

first: Matthew

last: Park

first: Meriem

last: Belabed

first: Miriam

last: Merad


title: Metastatic signature for Ewing’s sarcoma

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: Ewing sarcoma (ES) is the second most common bone tumor affecting children and young adults, with dismal outcomes for patients with metastasis at diagnosis. Mechanisms leading to metastasis remain poorly understood. To deepen our knowledge on ES progression, we have profiled tumors and metastases from a spontaneous metastasis mouse model using a multi-omics approach. Combining transcriptomics, proteomics and methylomics analyses, we identified signaling cascades and targets enriched in metastases that could be modulating aggressiveness in ES. Phenotypical validation of two of these targets, CREB1 and LOXHD1, showed an association with migration and clonogenicity ability. Moreover, previously described CREB1 targets were present amongst the metastatic-enriched results. Combining the different omics datasets, we identified targets as FGD4 that interconnect the different ES biological layers (RNA, protein and methylation status) and are associated to clinical outcome. Further studies will provide insight into ES metastasis mechanisms and ultimately improve survival rates for ES patients.

overall_design: Transcriptomics analysis (Clariom D) on Ewing sarcoma samples included a total of 21 samples. Established cell lines (n=4), primary tumors obtained from a spontaneous derived mouse model (n=5) and lung metastases from this same mouse model (n=12).

first: Òscar

last: Tirado

first: Mariona

last: Chicón-Bosch


title: Effect of MS-275 and CXD101 on open chromatin regions of M-MDSCs [ATAC-seq]

summary: To elucidate the molecular mechanisms of HDAC1-3 inhibitors in inhibiting M-MDSCs, ATAC-seq analysis of M-MDSCs isolated from Hepa 1-6 tumor-bearing mice treated with MS-275 or CXD101 were performed.

overall_design: M-MDSCs (CD11b+Ly-6ChiLy-6G-) were sorted by JSAN (KS-Techno, Japan) from tumor isolated. ATAC-seq libraries were prepared using ATAC-seq Kit (Active Motif, USA) according to the manufacturer’s protocol. Briefly, 1 × 105 M-MDSCs were lysed with ATAC lysis buffer and nuclei were isolated by centrifugation at 500 × g, 4°C for 10 min. Nuclei were then suspended in 50 µL of Tagmentation Master Mix and incubated at 37°C for 30 min with shaking. DNA was purified using DNA purification column and PCR amplification was performed for 10 cycles to introduce sequencing adapters to open chromatin regions. Library DNA was finally purified using Solid Phase Reversible Immobilization beads. Molecular weight was checked and libraries were quantified using Bioanalyzer and submitted for NGS analysis.


title: DNA methylation-based age prediction and sex-specific epigenetic aging in a lizard with female-biased longevity

city: Aiken

first: Ethan

middle: P

last: Shealy

state: SC

address: Bldg 737-A Savannah River Site

department: Savannah River Ecology Lab

institute: University of Georgia

type: Methylation profiling by high throughput sequencing

summary: Sex differences in lifespan are widespread across animal taxa, but their causes remain unresolved. Alterations to the epigenome are hypothesized to contribute to vertebrate aging, and DNA methylation-based aging clocks allow for quantitative estimation of biological aging trajectories. Here, we investigate the influence of age, sex, and their interaction on genome-wide DNA methylation patterns in the brown anole (Anolis sagrei), a lizard with pronounced female-biased survival and longevity. We develop a series of age predictor models and find that, contrary to our predictions, rates of epigenetic aging were not slower in female lizards. However, methylation states at loci acquiring age-associated changes appear to be more “youthful” in young females, suggesting that female DNA methylomes are preemptively fortified in early life in opposition to the direction of age-related drift. Collectively, our findings provide insights into epigenetic aging in reptiles and suggest that early-life epigenetic profiles may be more informative than rates of change over time for predicting sex biases in longevity.

overall_design: Genome-wide enzymatic methylation sequencing data from 40 individual Anolis sagrei were sequenced to a target coverage depth on 5x. Sampled individuals included representation from both sexes across six distinct ages, ranging from one month to five years. The resuting methylation data was used to examine how age and sex interact to pattern the sagrei methylome.

first: Tonia

middle: S

last: Schwartz

first: Robert

last: Cox

first: Aaron

last: Reedy

first: Benjamin

middle: B

last: Parrott


title: Short term perturbation of mouse embryonic stem cells with morphogens and small molecule compounds

first: Mariano

middle: Javier

last: Alvarez

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

summary: Two strains of mouse embryonic stem cells were perturbed for 30h with 24 distinct small molecule compounds and for 24h with 5 differentiation morphogens.

overall_design: Mouse embryonic stem cells (strains R1 and JM8.N4) were perturbed for 24h with 5 different morphogens (Activin A, bFGF, BMP4, N2B27 and Retinoic acid) and for 30h with 24 different small molecule compounds. Expression profile was obtained by RNA-Seq.


title: Effect of MS-275 and CXD101 on MDSCs

last: Motooka

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

overall_design: Refer to individual Series


title: Perturbed mouse Epiblast Stem Cells (EpiSC)

overall_design: Two different strains of mouse EpiSC were perturbed for 36h with 33 distinct small molecule compounds, and for 24h with 7 different differentiation morphogens or control culture conditions. Total Rna was biotinilated and hibridized to mouseWG-6 v2 BeadArrays (Illumina). Slides are scanned using an iScan (Illumina, SY-101-1001). Data were pre-processed by variance stabilization and robust spline normalization implemented in the lumi package for the R-System (PMID: 18467348).

first: Bo

last: Li


title: Perturbed mouse Epiblast Stem Cells (EpiSC) with Retinoic acid and small molecule compounds at different time points

summary: EpiSC were perturbed for 24h or 36h with Retinoic acid and 10 distinct small molecule compounds, mouse embryonic fibroblasts conditioned media (CM) or control basal media (Mock)

overall_design: Mouse EpiSC were perturbed for 24h or 36h with Retinoic acid and for 24h or 36h with 10 different small molecule compounds, mouse embryonic fibroblasts conditioned media (CM)  or basal media (Mock). Total RNA was biotinylated and hibridized to mouseWG-6 v2 BeadArrays (Illumina). Slides were scanned using an iScan (Illumina, SY-101-1001). Data were pre-processed by variance stabilization and robust spline normalization implemented in the lumi package for the R-System (PMID: 18467348).


title: Integrated detection and quantification of aberrant transcripts with novel splicing events

status: Public on Feb 02 2025

city: Singapore

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

summary: Splicing misregulation, such as the inclusion of previously unknown cryptic exons, is implicated in numerous diseases. Recent methods have increased accurate and efficient detection of such splicing alterations occurring in disease phenotypes. However, the quantification and differential analyses of non-canonical splicing alterations remains focused at a splice event level, thus preventing a complete view of the effects on the downstream transcriptomic landscape. Here, we present a novel and integrated pipeline, SpliCeAT, that (1) detects and quantifies differential non-canonical splicing events from short-read bulk RNA-seq data, (2) augments the canonical transcriptome with novel transcripts containing these non-canonical splicing events, and (3) performs transcript-level differential analysis to identify and quantify aberrant cryptic exon-containing transcripts based on this augmented transcriptome. Using TDP-43, an ALS/FTD-associated RNA-binding protein as an example, we identified and catalogued aberrant splicing events in embryonic mouse brains. The accuracy of our integrated pipeline was further confirmed and validated with long-read isoform sequencing. Furthermore, by comparing neuronal TDP-43 knockouts in mice with a publicly available human dataset with TDP-43 pathology, we identified and validated 4 common genes, namely, Kalrn/KALRN, Poldip3/POLDIP3, Rnf144a/RNF144A, and Unc13a/UNC13A, with cryptic exons. In summary, our integrated pipeline, novel splice events are identified, incorporated and quantified at the transcript level, thereby enabling more complete transcriptome profiling of well-annotated genomes in in the case of pathological splicing misregulation.

overall_design: Bulk RNA-seq of cortex and thalamus tissue of e14.5-day old mouse embryos with TDP-43 deleted under Nestin-Cre promotor (nervous system and other tissues)

first: Ira

last: Agrawal

first: Yong Shan

last: Lim

first: Emma

last: Sanford

first: Wan Yun

last: Ho

first: Greg

last: Tucker-Kellogg


title: Predictive modeling of chromatin features underlying replication timing

city: San Francisco

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: UCSF

first: Deniz

last: Goekbuget

first: Liana

last: Goehring

first: Ryan

last: Boileau

first: Tony

last: Huang


title: Genomic landscape of DNA methylation following m6A demethylation

city: Guangzhou

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

type: Methylation profiling by genome tiling array

summary:
ALKBH5 has been recognized as a major RNA m6A demethylase in human cells. Here, we show that genomic DNA methylation is reshaped following the transcriptomic m6a demethylation.
ALKBH5-KD human colon cancer cell line HCT116 was constructed. The genomic DNA was extracted to profile the genome-wide methylation.

overall_design: ALKBH5-knock down human colon cancer cell line HCT116 was constructed. The genomic DNA was extracted to profile the genome-wide methylation.

first: Dingcheng

last: Shen


title: Single cell RNA seq analysis of microglia from aged wild-type, NLRP3-/-, APP/PS1 and APP/PS1.NLRP3-/- mice.

city: Utrecht

first: Nathalie

last: Groen

address: Varrolaan 100

institute: Single cell discoveries

summary: NLRP3 inflammasome activation is involved in the progression of Alzheimer's disease. To unravel the unique cell populations and clusters regulated by NLRP3 in the brain, we enriched CD11b+ cells from the brains of 18 month old wild-type,  NLRP3-/-, APP/PS1 and APP/PS1.NLRP3-/- mice for single cell RNAseq.

overall_design: The brains from wild-type,  NLRP3-/-, APP/PS1 and APP/PS1.NLRP3-/- mice were isolated and dissociated using the Neural Tissue Dissociation kit (P) (Miltenyi Biotec), and using MACS isolation the myelin was labelled and removed magnetically before the enrichment of CD11b+ microglia following the manufacturer’s guidelines (Miltenyi Biotec). Single, live, CD11b+ cells were FACS sorted at 4°C (BD FACS Aria III) into 384-well plates containing 384 primers and Mineral oil (Sigma). After sorting, plates were snap-frozen on dry ice and stored at -80°C

first: Róisín

last: McManus

first: Michael

last: Heneka


title: V. cholerae transcriptome of WT and vchM deletion mutant with sub-MIC tobramycin

city: paris

first: Zeynep

last: Baharoglu

address: 25 rue du dr roux

country: France

institute: Institut Pasteur

summary: We study gene expression levels of V. cholerae N16961 hapR+ corrected strain in exponential phase with tobramycin.

overall_design: Bacterial cells were grown to OD 0,25 and RNAseq was performed.

first: Andre

last: Carvalho


title: Bile acid receptor FXR promotes intestinal epithelial ferroptosis and subsequent ILC3 dysfunction in neonatal necrotizing enterocolitis [SI bulk RNA-seq]

city: Tianjin

first: yuchao

last: Jing

address: No.22, Meteorological Tai Road, Tianjin

institute: Tianjin Medical University

summary: Necrotizing enterocolitis (NEC) is a prevalent pediatric emergency characterized by the sudden onset of intestinal ischemia and necrosis resulting from hyperinflammation.The interactions between the bile acid receptor FXR with gut microbiota and mucosal immunity in early postnatal life, and its exact role in the pathogenesis of NEC, are unknown.Here we analyze the role of FXR in IECs under NEC.

overall_design: small intestine  from Fxrfl/fl naïve, FxrΔIEC naïve, Fxrfl/fl NEC and FxrΔIEC NEC pups were were subjeted to bulk RNA-seq

first: Yuxin

last: Zhang

first: Yuchao

first: Juan

last: He


title: Genomic landscape of DNA methylation following APOBEC3A-induced mutation

summary: APOBEC-induced genomic mutation a major driver of cancer evolution. Here, we show that genomic DNA methylation is reshaped following the APOBEC-induced genomic mutation.

overall_design: APOBEC3A-overexpressed human colon cancer cell line DLD1 was constructed. The genomic DNA was extracted to profile the genome-wide methylation.

first: Zenghong


title: Differentiation time course for Mouse Epiblast Stem Cells

first: Mariano

last: Alvarez

summary: A time course with 5 differentiation arms was performed, including retinoic acid, BMP4, SB431542, mesoderm and endoderm. RNA-Seq expression profile performed in EpiSC-5 cells at 3h, 6h, 12h, 18h, 24h, 36h, 48h and 72h after treatment.

overall_design: EpiSC-5 mouse epiblast stem cells were perturbed with retinoic acid; BMP4; SB431542; WAFB (Wnt3a, Activin A, FGF2, and BMP4); and WA (Wnt3a and Activin A). Expression profiles were obtained at 3h, 6h, 12h, 18h, 24h, 36h, 48h and 72h

first: Bo

last: Li


title: Modeling long QT syndrome using gene-edited pigs

city: hangzhou

first: jiuxiao

last: zhao

state: zhejiang

address: Yuhangtang Road, Hangzhou 310058

institute: zhejiang university

summary: To date, KCNH2 mutations identified in LQT2 patients have been heavily studied by heterologous expression systems, allowing for pathogenicity evaluation of a certain hERG mutation by overexpressing mutant channels. However, they fall short in mimicking the full spectrum of electrophysiological changes and ion channel remodeling that occur in cardiomyocytes under physiological conditions in the context of LQT. Due to the marked differences in the lifespan, size, anatomy and physiology from humans, current zebrafish and rodent models cannot fully mimic the abnormal QT interval diseases 2. For instance, rodents exhibit an extremely higher heart rate and a much shorter action potential duration (APD) compared to humans. IKr is the predominant repolarizing current in human ventricles while inhibition of IKr in rodents has no significant effect on ventricular repolarization, making it infeasible to study LQT2 by genetic mouse model 3. Hence, there is a crucial need to construct an animal model capable of mimicking human inherited arrhythmia conditions. To address the above scientific question, we chose to create a miniature pig model. Given many physiological similarities with humans, and breeding and genome editing advantages (when compared to non-human primates), To explore the mechanism underlying mutation of KCNH2 caused LQT, we compared the transcriptomes of KCNH2-mut pigs and WT controls

overall_design: mRNA profiles of pig Left ventricle tissue from KCNH2-mut pigs and WT controls


title: Atovaquone-induced oxidative stress activates pentose phosphate pathway and immunogenic cell death in ovarian cancer

city: Madison

first: Alexander

last: Fagan

state: WI

address: 1300 University Ave Room 1220

department: Department of Statistics

institute: UW-Madison

summary: Atovaquone, an FDA-approved oxidative phosphorylation (OXPHOS) inhibitor, has shown promise in treating epithelial ovarian cancer (EOC), the deadliest gynecologic malignancy. However, the precise mechanisms underlying its antitumorigenic effects remain unclear. We employed a longitudinal transcriptomic approach to characterize the molecular effects of atovaquone on EOC cells. Our findings demonstrate that atovaquone disrupts cellular homeostasis and metabolism, activates stress responses, and primes immune recognition. We observed temporal downregulation of genes and pathways involved in key cellular processes, such as cell cycle and DNA replication, correlating with reduced proliferative capacity. Atovaquone also downregulated both OXPHOS and glycolysis, while upregulating the pentose phosphate pathway, suggesting a metabolic shift toward redox homeostasis restoration in response to severe oxidative stress. Consistent with oxidative stress, we found that atovaquone activated endoplasmic reticulum (ER) stress, which is linked to immunogenic cell death. During ER stress, calreticulin, a Damage-Associated Molecular Pattern (DAMP), translocates to the plasma membrane, where it promotes immune recognition. We observed that calreticulin was upregulated on the plasma membrane of atovaquone-treated EOC cells. Additionally, we detected increased levels of other DAMPs, such as High Mobility Group Box 1 (HMGB1) and Mitochondrial Transcription Factor A (TFAM), in the supernatant of atovaquone-treated cells, indicating the release of immunogenic molecules. Moreover, increased expression of ligands for activating receptors of NK cells was observed and co-culture experiments showed enhanced NK cell activity toward atovaquone-treated cells. These results highlight atovaquone’s potential as an adjuvant therapy that activates immune responses, offering a new avenue for combination therapies in EOC treatment.

overall_design: Bulk RNA-seq profiling of OVCAR3 cancer cells in the presence of DMSO, 30μM Atovaquone, and 45μM Atovaquone at 1, 8, 24, and 48 hours, as well as untreated OVCAR3 cells at 24 hours. Samples were sent in three batches at different times. All observations at 48 hours were in the third batch, batch C, and all samples in batch C were taken at 48 hours. This batch had 3 replicates each of DMSO-, 30μM-, and 45μM-treated samples. The first and second batch, A and B respectively, contained each of 1, 8, and 24 hours combined with each of 30μM, 45μM, and DMSO, as well as untreated cells observed at only 24 hours. For each such experimental condition, batch A had one biological replicate, and batch B had two.

first: Mayra

middle: A

last: Betancourt Ponce

first: Nicha

last: Boonpattrawong

last: Newton

first: Manish

last: Patankar

first: Lisa

last: Barroilhet


title: Neurobehavioral phenotypes in the pan-neuronal GAL4 zebrafish line Tg(elavl3:KalTA4)

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

summary: The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish, the Tg(elavl3:KalTA4) (HuC) line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tg(elavl3:KalTA4) zebrafish larvae compared to wildtype siblings, which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tg(elavl3:KalTA4) larvae showed alterations in brain activity, brain morphology, and behavior, including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA-seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis, we used economical low-pass whole genome sequencing to map the Tol2-mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga, a known cell cycle regulator, is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan-neuronal lines include the length of the elavl3 (HuC) promoter (9 kb) and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines, we cloned five neuronal promoters (atp6v0cb, elavl3, rtn1a, sncb, and stmn1b) ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase-based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines.

overall_design: RNA-sequencing of dissected heads of larval zebrafish of the TG(elavl3:KalTA4) zebrafish versus wildtype siblings.


title: shRNA-mediated silencing of candidate pluripotency regulators in mouse epibladst stem cells

summary: EpiSC-5 mouse epiblast stem cells were transduced with lentiviral vectors carrying shRNA for MR candidate genes or non-targeting controls. Expression profile was obtained 72h after transduccion.

overall_design: EpiSC-5 mouse epiblast stem cells were transduced with lentiviral vectors carrying shRNA for candidate pluripotency regulators on on-targeting controls. mRNA was isolated 72h after transduccion and profiled using PLATE-Seq (PMID 28740083).


title: Heat Shock Transcription Factor 4 Promotes Malignant Biological Behavior in Colorectal Cancer Through Stiffness Rather Than Collagen Content.

city: Changsha

first: kangtao

last: wang

state: Hunan

address: No. 87 Xiangya Road

department: Department of General and Vascular Surgery

institute: Xiangya Hospital, Central South University

summary: Background Colorectal cancer (CRC), a malignancy with high incidence and mortality rates, presents particularly severe prognoses at the stages of invasion and metastasis despite significant advancements in diagnostic and therapeutic technologies. The tumour microenvironment, especially the extracellular matrix (ECM) stiffness, has garnered considerable attention for its impact on CRC progression and metastasis. However, the precise relationship and molecular mechanisms between ECM stiffness and CRC prognosis remain unclear.  Methods This study included 107 CRC patients. Tumor stiffness was assessed using magnetic resonance elastography (MRE), and collagen content was analysed with Masson staining. CRC cell lines SW480 and HCT116 were cultured on matrices of varying stiffness, followed by transcriptome sequencing to identify stiffness-related differential genes and investigate their functions and signalling pathways. Additionally, an HSF4 knockout CRC cell model was constructed to evaluate the effects of HSF4 on cell proliferation, migration, and invasion through both in vitro and in vivo experiments, exploring its role in tumour growth and metastasis.  Results The study found that CRC tumour stiffness was significantly higher than normal tissue and positively correlated with collagen content and TNM staging. Transcriptome analysis revealed that high-stiffness matrices significantly regulated cell functions and signalling pathways. High expression of HSF4 was strongly associated with tumour stiffness and poor prognosis. HSF4 expression increased with higher TNM stages in CRC tissues, and its knockout significantly inhibited cell proliferation, migration, and invasion, particularly on high-stiffness matrices. In vivo experiments further confirmed that HSF4 promoted tumour growth and metastasis, independent of collagen protein increase.  Conclusion This study reveals a close relationship between tumour stiffness and CRC prognosis, identifying HSF4 as a critical player in CRC progression. HSF4 promotes tumour proliferation and metastasis by regulating EMT-related signalling pathways, with its high expression closely linked to tumour stiffness. Although LOXL1 increased collagen content and a-SMA expression, HSF4's role in promoting tumour growth and metastasis was independent of collagen protein. HSF4 holds potential as a target for CRC prognosis evaluation and treatment. Future research should further explore the regulatory mechanisms of HSF4 and its potential for clinical application.

overall_design: SW480 cells were cultured on 6-well plates coated with 2 kPa or 25 kPa hydrogels (MATRIGEN, USA). Plates were washed with PBS, and 2 ml of cell suspension at 1×10^6 cells/ml was added to each well. Each stiffness condition was tested in triplicate, and cells were incubated at 37°C in a CO2-free incubator for 72 hours. Cells were harvested by scraping, and the reaction was stopped with a complete medium. The cell suspension was centrifuged, washed with PBS, and treated with TRIzol reagent (Life Technologies) for RNA extraction. The RNA was sent to BGI Genomics, where it was reverse-transcribed into cDNA, and libraries were constructed for deep sequencing at a depth of 200×. RNA was quantified using a NanoDrop and Agilent 2100 bioanalyser (Thermo Fisher Scientific). Libraries were prepared from 1 μg of total RNA per sample, and small RNA (18-30 nt) was purified via PAGE gel electrophoresis, reverse-transcribed, and amplified by PCR. Enriched cDNA fragments were selected, purified, and assessed for quality and quantity using an Agilent 2100 bioanalyser and real-time qPCR with TaqMan probes. Sequencing was performed on the Illumina HiSeq platform (BGI, Shenzhen).

first: Kangtao

last: Wang

first: Shuai

first: Mingming

last: Jiang

first: Yan

last: Huang

first: Haiping

last: Pei

first: Ming

first: Fengbo

last: Tan


title: Effect of Notch1 signaling on muscle engraftment and maturation from pluripotent stem cells

city: Minneapolis

first: Aline Miyoko

last: Sakaguchi Yamashita

state: Minnesota

address: 2231 6th St SE

department: Department of Medicine

institute: University of Minnesota

summary: Pluripotent stem cell-derived iPax3 myogenic progenitors display an embryonic molecular signature but become postnatal upon transplantation. Because this correlates with upregulation of Notch signaling, here we probed whether Notch1 is required for in vivo maturation by performing gain- and loss-of-function studies in iPax3 myogenic progenitors. Transplantation studies revealed comparable myofiber engraftment. However, assessment of fiber type composition revealed more mature myofiber grafts in the overexpression cohort, as shown by the lower expression of embryonic MHC and increased levels of type IIX MHC. Surprisingly, more mature myofiber were also observed in the absence of Notch1, suggesting its dispensability for in vivo maturation.  Donor-derived Pax7+ cells were detected in all transplants, however, in the absence of Notch1, secondary grafts exhibited a high fraction of these cells in the interstitial space. RNA-sequencing showed changes in extracellular matrix organization, cell cycle, and metabolism, suggesting that Notch1 is required for satellite cell homing.

overall_design:
To investigated the effect of Notch1 GOF and LOF in iPax3 myogenic progenitors, we overexpress NICD1 (iPax3-N1OE) or knocking-out (KO) Notch1 (iPax3-N1KO) in PSC-derived iPax3 myogenic progenitors.
To determine the molecular changes underlying Notch1 GOF in iPax3 myogenic progenitors in an unbiased manner, we next performed RNA sequencing.
To elucidate the molecular determinants underlining the differences in satellite cell engraftment between iPax3-N1OE, iPax3-N1KO and iPax3 cohorts, we performed RNA sequencing analysis in donor-derived satellite cells.

first: Aline

last: Yamashita

first: Bayardo

middle: I

last: Garay

first: Juan

middle: E

last: Abrahante

first: Rita

middle: R

last: Perlingeiro

first: Hyunkee

last: Kim

first: Darko

last: Bosnakovski

first: Phablo

last: Abreu

first: Aaron

last: Ahlquist

first: Karim

last: Azzag


title: Insulin-like growth factor signalling regulates zebrafish lymphatic vessel development

city: Auckland

first: Jonathan

last: Astin

state: Region

address: 85 Park Road

department: Molecular Medicine and Pathology

country: New Zealand

institute: University of Auckland

summary: RNA-Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF-signalling gene - pappa2

overall_design: Differential gene expression analysis from RNA-seq data comparing WT zebrafish chondrocytes to kat6a-deficient chondrocytes in biological quadruplet.

middle: W


title: Targeting redox-sensitive MBD2-NuRD condensate for  tumor therapy [ATAC-seq]

city: shanghai

first: heyang

last: wei

address: 131 Dongan Road, Xuhui District

institute: Fudan University

summary: Transcriptional silencing of hypermethylated tumor suppressor genes is a hallmark of tumorigenesis, though the underlying mechanism remains enigmatic. In this study, we find Methyl-CpG-binding domain protein 2 (MBD2) forms nuclear condensate in diverse cancer cells, where it	 assembles and navigates the chromatin remodeler NuRD complex to these gene loci for transcriptional suppression, thus fueling tumor growth. Disturbance of MBD2 condensate reduces the level of NuRD complex-specific proteins, destabilizes heterochromatin foci, facilitates chromatin relaxation, and consequently impedes tumor progression. We demonstrate that MBD2 condensate is redox sensitive mediated by Cys359. Prooxidative interventions disperse MBD2-NuRD condensate, thereby alleviating the transcriptional repression of tumor suppressor genes. Our findings illuminate a hitherto unappreciated function of MBD2 condensate in sustaining a repressive chromatin state essential for cancer cell proliferation and suggest an oxidative stress targeting approach for malignancies with excessive MBD2 condensate.

overall_design: ATAC-seq for shCtrl, shMBD2, shMBD2+MBD2WT and shMBD2+MBD2KRR/E HeLa cells


title: Targeting redox-sensitive MBD2-NuRD condensate for  tumo therapy [RNA-Seq]

overall_design: RNA-seq for shCtrl, shMBD2, shMBD2+MBD2WT and shMBD2+MBD2KRR/E HeLa cells


title: Targeting redox-sensitive MBD2-NuRD condensate for  tumor therapy [CUT&Tag]

overall_design: FLAG-MBD2 and FLAG-GATAD2A CUT&TAG in HeLa cells


title: Gene expression profile at single cell level of C2C12 myoblasts bearing human LMNA gene with mutations WT, R482L

city: Saint Petersburg

first: Oksana

last: Ivanova

address: 2 Akkuratova street

department: Institute of Molecular Biology and Genetics

country: Russia

institute: Almazov National Medical Research Centre

summary: LMNA mutation R482L cause classical familial partial lipodystrophy of Dunnigan type (FPLD2). FPLD is a severe metabolic disorder that often leads to cardiovascular and skeletal muscle complications. How LMNA mutations affect functional properties of skeletal muscles is still not understood. In the present project we investigated the LMNA-R482L mutation-specific alterations in mouse C2C12 line of myoblasts using single cell RNA sequencing (scRNA-seq). We showed the heterogeneity of C2C12 myoblasts cell line  prior the differentiation, and compositional and transcriptional changes in LMNA-R482L C2C12 myoblasts comparing to LMNA-WT.

overall_design: C2C12 mouse myoblast cell line was genetically modified by the lentivirus with human LMNA gene of wild-type (WT) or bearing mutation R482L. 1 sample of LMNA-WT and 2 samples of LMNA-R482L C2C12 myoblasts were taken for scRNA-seq library preparation using 10X Single Cell 3' Gene Expression protocol and sequenced with NextSeq 2000 resulting in 3000 cells per sample. Data was analysed using Cell Ranger v6.1.2 (with pre-built mouse reference refdata-gex-mm10-2020-A), Seurat package v4.3.0. Supplementary file contains raw and filtered feature_bc_matrixes (.h5 format) for each sample.

first: Renata

last: Dmitrieva

first: Aleksandr

last: Predeus


title: Targeting redox-sensitive MBD2-NuRD condensate for  tumor therapy [ChIP-Seq]

overall_design: ChIP-seq for shCtrl, shMBD2, shMBD2+MBD2WT and shMBD2+MBD2KRR/E HeLa cells


title: ZRSR2-loss causes aberrant splicing in a JAK2V617F-driven myeloproliferative neoplasm but is not sufficient to drive disease progression II.

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

summary: Myeloproliferative neoplasms (MPN), including polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF), are clonal disorders driven by mutations in hematopoietic stem cells (HSCs). JAK2V617F is the most recurrent driver mutation in MPN and results in the constitutive activation of the JAK-STAT pathway. ZRSR2-loss is reported to cause mis-splicing of U12-type introns in myelodysplastic syndromes (MDS). Loss of function mutations in ZRSR2 have been found in a JAK2V617F-driven MPNs and are associated with disease progression and poor prognosis. However, the functional contribution of ZRSR2-loss to the pathogenesis and disease progression of MPN remains unknown. Using CRISPR-Cas9, we generated concomitant ZRSR2-loss in a JAK2V617F-driven human cell line and mouse model of MPN. RNA-Seq data demonstrates that ZRSR2-loss causes aberrant splicing in both human and murine cells, with the affect being more subtle in the murine context. Gene expression analysis in murine HSCs indicates that Zrsr2-loss biases lineage differentiation priming to megakaryocytes. However, Zrsr2-loss did not alter the severity or phenotype of the MPN in Jak2V617F mice. These results indicate that Zrsr2 mutations have limited impact on disease progression of Jak2V617F -driven MPN in vivo. Consistent with this, we find that ZRSR2 mutations are more frequently identified in genetically complex MPN patients carrying other high molecular risk mutations. In total, our findings demonstrate that ZRSR2-loss causes subtle mis-splicing in JAK2V617F-driven MPN that is not sufficient to drive disease progression in the absence of other high-risk mutations.

overall_design: SET-2 cells were transduced with PLKO5 GFP virus containing sgRNAs targeting human ZRSR2 (sg1: TGACGTTTCCCGAGAAACCA, sg2: ACAGTTCCTAGACTTCTATG, sg3: CTTCCAGCCACAAAAAGTAC) and non-targeting sgRNAs control (NTG1: GACGGAGGCTAAGCGTCGCAA, NTG2: GCGCTTCCGCGGCCCGTTCAA) and subjected to RNA-sequencing.

first: Anna

last: Marneth

first: Charles

last: Laurore

first: Ann

last: Mullally


title: ZRSR2-loss causes aberrant splicing in a JAK2V617F-driven myeloproliferative neoplasm but is not sufficient to drive disease progression I.

overall_design: At terminal time point, GFP and mCherry double positive LSK (Lineage- Sca1+ Kit+) cells from bone marrow of mouse expressing either Jak2V617F alone or in combination with Zrsr2 loss were enriched and sorted by BD FACS ARIA IIIu.

first: Ranran

last: Zhang

first: Megan

last: Bywater

first: Steven

last: Lane


title: ZRSR2-loss causes aberrant splicing in a JAK2V617F-driven myeloproliferative neoplasm but is not sufficient to drive disease progression

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: TDP-43 directly inhibits RNA accumulation in neurites through modulation of RNA stability

status: Public on Feb 01 2025

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

summary: The subcellular localization of hundreds of RNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for the vast majority of these RNAs, the mechanisms that govern their localization are unknown. Here we demonstrate that the ALS-associated RNA binding protein TDP-43 primarily acts to keep RNAs out of neuronal projections. Using subcellular fractionation and single molecule FISH we find that TDP-43 loss results in the increased neurite accumulation of hundreds of RNAs. These RNAs were highly enriched for known TDP-43 binding sites, suggesting that TDP-43 directly binds them to regulate their localization. We then identified precise regions within them that mediate their TDP-43-dependent localization and interaction with TDP-43 using high-throughput functional assays in cells and high-throughput binding assays in vitro. We found that these regions also mediated TDP-43-dependent RNA instability, identifying the mechanism by which TDP-43 regulates RNA localization. ALS-associated mutations in TDP-43 resulted in similar RNA mislocalization phenotypes as did TDP-43 loss in human iPS-derived motor neurons. These findings establish TDP-43 as a direct negative regulator of RNA abundance in neurites and suggest that mislocalization of specific transcripts may occur in ALS patients.

overall_design: We profiled subcellular transcriptomes of neuronal cells with and without TDP-43 and used high-throughput techniques to identify cis-elements within transcripts that mediate their TDP-43-dependent RNA localization patterns.


title: RNA-seq data from tomato young inflorescence segregating for fruit weight QTL fw2.3

city: Athens

first: Esther

last: van der Knaap

state: GA

address: 111 Riverbend Rd

institute: UNIVERSITY OF GEORGIA

summary: A novol fruit weight QTL fw2.3 was identified in tomato populaiton developed from a cross between two semi-domesticated SLC accession: BGV006768 and BGV007931. The effect of fw2.3 was observed in ovaries at anthesis stage, before fruit development. So young infloresences from F3 progenies with contrasting genotype of fw2.3 were used in RNA-seq experiment. Differentially expressed genes in the fw2.3 interval may help us to locate causal genes of this fruit weight QTL.

overall_design: RNA-seq profiling of young inflorescence from F3 tomato progenies carrying wild type or derived allele of fw2.3

first: Lei


title: Learning and actioning general principles of cancer cell drug sensitivity

city: San Giuliano Terme

first: Paolo

last: Aretini

state: Pisa

address: Via Ferruccio Giovannini 13

institute: Fondazione Pisana per la Scienza

summary: High-throughput screening platforms for the profiling of drug sensitivity of hundreds of cancer cell lines (CCLs) have generated large datasets that hold the potential to unlock targeted, anti-tumor therapies. In this study, we leveraged these datasets to create predictive models of cancer cells drug sensitivity. To this aim we trained explainable machine learning algorithms by employing cell line transcriptomics to predict the growth inhibitory potential of drugs. We used large language models (LLMs) to expand descriptions of the mechanisms of action (MOA) for each drug starting from available annotations, which were matched to the semantically closest pathways from reference knowledge bases. By leveraging this AI-curated resource, and the interpretability of our model, we demonstrated that pathways enriched for genes crucial for prediction often matched known drug-MOAs and essential genes, suggesting that our models learned the molecular determinants of drug response. Furthermore, we demonstrated that by incorporating only LLM-curated genes associated with MOAs, we enhanced the predictive accuracy of our drug models. To enhance translatability to a clinical setting, we employed a pipeline to align bulk RNAseq from CCLs, used for training the models, to those from patient samples, used for inference. We proved the effectiveness of our approach on TCGA samples, where patients’ best scoring drugs matched those prescribed for their cancer type. We further showed its usefulness by predicting and experimentally validating effective drugs for the patients of two highly lethal solid tumors, i.e. pancreatic cancer and glioblastoma. In summary, our method facilitates the inference and interpretation of cancer cell line drug sensitivity and holds potential to effectively translate them into new cancer therapeutics.

overall_design: Development of interpretable machine learning framework for the prediction of drug sensitivity of cancer cell lines by using the latest version of the Genomics of Drug Sensitivity in Cancer (GDSC) dataset

first: Francesco

last: Carli

first: Pierluigi

last: Di Chiaro

first: Mariangela

last: Morelli Mariangela

first: Chakit

last: Arora

first: Luisa

last: Bisceglia

first: Natalia

last: De Oliveira Rosa

first: Alice

last: Cortesi

first: Sara

last: Franceschi

first: Francesca

last: Lessi

first: Anna Luisa

last: Di Stefano

first: Orazio

last: Santonocito

last: Pasqualetti

first: Pasquale

last: Miglionico

first: Giuseppe R.

last: Diaferia

first: Fosca

last: Giannotti

first: Pietro

last: Liò

first: Miquel

last: Duran-Frigola

first: Chiara M

last: Mazzanti

first: Gioacchino

last: Natoli

last: Raimondi


title: Expression studies of FGFR1 knockdown in lymphoma

city: columbus

first: Lalit

last: Sehgal

state: Ohio

department: Hematology

institute: The Ohio State University

summary: To identify the differential regulated genes among cell types

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Granta-519 cells with KD derivatives (shFGFR1).


title: Gene expression profile at single cell level of alveolar bone  during orthodontic tooth movement

city: Beijing

first: Jiayi

last: Wang

state: Beijing

address: No.22 Zhongguancun south Rd., Haidian district, Beijing, China

institute: Peking university school and hospital of stomatology

summary: We used single cell RNA sequencing (SCRNA-seq) to analyze the diffenrence in cell population in the alveolar bone before and after orthodntic tooth movement

overall_design: Healthy C57BL/6J mice (6-8 weeks old) weighing 20-25g were used. A nickel-titanium coil spring was attached to the maxillary right first molar and maxillary incisors via a 0.020-inch stainless steel ligature in order to provide mesial orthodontic force on the first molar. The constant force was maintained at 25g. For the control group, no force was applied after spring attachment.Twelve mice were randomly divided into the orthodontic tooth movement group and control group for scRNA-seq. On day 7 after force application, the upper right maxillary first molar was extracted following the removal of the orthodontic appliance. Alveolar bone within 1mm of the extraction socket was immediately collected and cleansed with ice-cold PBS containing 1% FBS. Alveolar bone was pooled from 6 mice per group. Tissue was minced into 1–2 mm size and digested with 2 ml GEXSCOPE® Bone Tissue Dissociation Solution for 60min at 37℃. Samples were then filtered and centrifuged. Single-cell suspensions were obtained after removal of red cells with 2 mL GEXSCOPE® red blood cell lysis buﬀer  at 25°C for 10 min and later analyzed using scRNAseq.

first: Changyu

last: Tao

first: Yiping

last: Huang

first: Weiran

last: Li


title: TL1A deficiency attenuates osteoarthritis by regulating oxidative stress-induced senescence in articular chondrocytes [II]

city: shenyang

first: juntan

address: huaxiang street

institute: Shengjing hospital of China Medical University

summary: Osteoarthritis (OA) is a prevalent degenerative joint disease characterized by progressive cartilage degradation, chronic inflammation, and chondrocyte senescence. Tumor necrosis factor-like cytokine 1A (TL1A), a member of the TNF superfamily, has recently been implicated in regulating inflammatory processes and tissue remodeling. However, its precise role in OA pathogenesis remains incompletely understood. In this study, we investigated the impact of TL1A deficiency on OA progression and its underlying mechanism with a focus on oxidative stress-induced chondrocyte senescence.

overall_design: Clinical sample collection in this study was reviewed and approved by the Institutional Review Board (IRB) of the First Hospital of China Medical University (EC-2021-HS-004). All patients involved in this study gave informed consent. Paired smooth and damaged cartilage was obtained from the same OA patients undergoing total knee arthroplasty (n = 8). The difference between the smooth (relatively healthy area) and damaged (severely damaged area) articular surfaces was distinguished using the Mankin scoring system[33]. Detailed patients’ information is listed in Table S2.

first: Xiang

last: Gao

first: Juntan

first: Xu

first: Xun

last: Sun


title: TL1A deficiency attenuates osteoarthritis by regulating oxidative stress-induced senescence in articular chondrocytes [I]

overall_design: To investigate the transcriptional changes in human primary chondrocytes upon silencing of the TL1A gene, human primary chondrocytes were divided into two groups: the control group (siNC), transfected with non-targeting siRNA, and the experimental group (siTL1A), transfected with siRNA targeting TL1A, each with three biological replicates (siNC1, siNC2, siNC3; siTL1A1, siTL1A2, siTL1A3). After 48-72 hours of transfection, total RNA was extracted, and its quality assessed before preparing RNA-Seq libraries. Transcriptome sequencing was performed on the Illumina NovaSeq 6000 platform to identify differentially expressed genes (DEGs) between the siNC and siTL1A groups.


title: A gut-brain-body circuit mediates immune evasion in viral infection

city: Shanghai

first: Yihua

last: Zhang

state: Shanghai

address: Fudan University

summary: The gut–brain axis plays an important role in regulating antiviral immunity through multiple pathways. However, the mechanisms by which these pathways respond to viral infections remain unclear. In this study, we found that mice without TRPV1+ neurons exhibited a diminished antiviral immune response. TRPV1+ neurons in the mediodorsal thalamic nucleus (MD) enhanced antiviral immune response. In addition, the administration of a TRPV1 agonist enhanced the antiviral immune response in mice, whereas a TRPV1 inhibitor suppressed such a response. Moreover, VGLUT2+TRPV1+ neurons rather than VGAT+TRPV1+ neurons played the pivotal role in antiviral immunity. We identified the bed nucleus of the stria terminalis (BST) and the dorsomedial hypothalamic nucleus (DMH) as downstream targets of the MD. Moreover, MD–BST axis facilitated the release of substance P (SP) and calcitonin gene-related peptide (CGRP) from the brain into the cerebrospinal fluid, which then entered the bloodstream to potentiate the antiviral response in macrophages. Mechanistically, SP and CGRP enhanced the type-I interferon production via the PKA-STING and PKC-IRF3 pathways, respectively. Furthermore, viral infection triggered the production of gut microbiota–derived desthiobiotin, which reduced TRPV1 expression in the MD, thereby promoting immune evasion. Notably, the desthiobiotin inhibitor ML406 enhanced antiviral immunity and blocked immune evasion. These findings provide new insights into the mechanism by which viruses regulate the gut–brain–body axis and unveil a novel immune evasion strategy with substantial implications for developing antiviral therapies.

overall_design: RNA-seq profiling of brains from wild-type (WT) mice, treated with PBS, VSV, or HSV-1 for 48 hours.

first: Wenbo

last: Liu

first: Yijun

first: Bowen

last: Xin

first: Chenglong

first: Shuai

first: Hui

first: Xuejing

last: Lv

first: Xuhui

last: Bao

first: Qingjian

last: Han

first: Yuqiu

first: Chunmei

last: Xia

first: Dapeng

last: Yan


title: MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia [SLAM-seq]

city: Rotterdam

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

institute: Erasmus MC

summary: The transcription factor MECOM, located at 3q26, is essential for hematopoietic stem cells (HSCs) in healthy individuals. Enhancer translocations, due to 3q26 rearrangements, drive out-of-context MECOM expression in an aggressive subtype of acute myeloid leukemia (AML). Aberrantly expressed MECOM is essential for the survival and immature phenotype of these leukemia cells. Direct depletion of MECOM using an endogenous auxin-inducible degron immediately upregulates expression of myeloid differentiation factor CEBPA. MECOM depletion is also accompanied by a severe loss of CD34 expression and gain of mature myeloid cell surface marker CD15. MECOM exerts its inhibitory effect on differentiation by binding to the +42kb CEBPA enhancer, which is required for neutrophil development. This is partially dependent on the interaction between MECOM and its essential co-repressor CTBP2, a potential target in this type of AML. We demonstrate that CEBPA overexpression can bypass the MECOM-mediated block of differentiation. In addition, AML patients with MECOM overexpression through enhancer hijacking show significantly reduced CEBPA. Our study provides insight into the mechanism by which MECOM maintains the stem cell state in AML. Furthermore, CEBPA levels are an important read-out for successful targeting of MECOM in 3q26-rearranged AML.

overall_design: We introduced an auxin-inducible degron (AID) (V5-AID-T2A-eGFP) 3’ of MECOM in inv(3) cell line MUTZ3. Next, we performed Thiol(SH)–linked alkylation for the metabolic sequencing of RNA (SLAM-seq) experiments in MUTZ3 cells with and without auxin treatment, enabling the detection of nascent transcripts upon MECOM degradation.

first: Dorien

last: Pastoors

first: Marije

last: Havermans

first: Roger

last: Mulet-Lazaro

first: Leonie

last: Smeenk


title: Cell-type-specific efferocytosis determines functional plasticity of alveolar macrophages

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: Acid aspiration of gastric contents leads to aspiration pneumonitis, and as such predisposes to severe secondary bacterial infections. Alveolar macrophages are key sentinel cells in the lung, which initiate and resolve an inflammatory process. We found that after acid aspiration resident alveolar macrophages are impaired in their capacity to eliminate the clinically relevant bacterium Pseudomonas aeruginosa ex vivo and in vivo. Reduced bacterial killing peaked around 24 hours after the hit with acid, was detected up to 4 days later, and returned to normal 7 days after acid aspiration. We therefore want to characterize the capacity of avleolar macrophages after acid aspiration over time to respond to Pseudomonas aeruginosa. We expect a pro-resolving M2-like differentiation, which we aim to characterize in more detail: which inflammatory pathways are differentially regulated, are genes associated with bactericidal functions affected, is there a difference in the metabolic response.

overall_design: Two-factorial: infection (uninfected or infected with Pseudomonas aeruginosa) and time (HCl treatment for 0, 1, 4, or 7 days), n=4 in each combination, n = 32 in total from 32 animals.

first: Ulrich

last: Matt


title: KMT2D promotes castration-resistant prostate cancer progerssion by reactivating AR via FOXA1 [ChIP-seq, Cut & Tag]

city: guangzhou

first: Mayao

last: Luo

state: guangdong

address: No. 106, Zhongshan 2nd Road

institute: Guangdong Provincial People’s Hospital

summary: Histone methyltransferase KMT2D is epigenetic modifier mediates histone H3 lysine 4 methylation (H3K4me) with distinct roles across different cancer types. We previous found that KMT2D promotes growth and metastasis in Androgen receptor (AR)-negative prostate cancer (PCa). However, the functions of KMT2D and the relationship with AR in AR-positive prostate cancer remain unclear. Here, we showed that inhibition of KMT2D reduced AR-positive PCa cell survival and the sensitivity to dihydrotestosterone, a ligand for AR. RNA-Seq analysis revealed that KMT2D suppression significantly attenuated AR signaling pathway. Through multiple-omics analysis, we revealed that KMT2D recruits pioneering transcription factor Forkhead box A1 (FOXA1) to AR-specific enhancer sites, induces open chromatin conformations, and facilitates AR binding at enhancers to activate downstream gene expression, ultimately leading to AR reactivation. KMT2D knockout by CRISPR/Cas9 reduced CRPC tumor growth and AR signaling pathway activation in vivo. KMT2D-FOXA1-AR axis also mediates ketone metabolic reprogramming by regulating the expression of the key enzyme HMGCS2 to promote PCa progression. Finally, targeting UTX, a member of complex of proteins associated with SET1 (COMPASS) in which KMT2D involved, suppressed PCa cell survival and tumor growth by impairing H3K4me1 modification via KMT2D. These findings demonstrate the oncogenic role of KMT2D in PCa, suggesting that blocking COMPASS to inhibition KMT2D’s function may be a promising strategy to treat PCa.

overall_design:
ChIP-Seq of androgen receptor (AR) with siRNA-induced silencing of KMT2D in LNCaP and C4-2 cells with 10nM DHT
CUT&Tag of FOXA1, H3K4me1, H3K27ac in LNCaP and C4-2 cells. CUT&Tag of Flag in C4-2 expressing FOXA1(D226G) and FOXA1(M253K) cells


title: MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia [ATAC-seq]

overall_design: We introduced an auxin-inducible degron (AID) (V5-AID-T2A-eGFP) 3’ of MECOM in inv(3) cell line MUTZ3. Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) was performed in these cells, with or without auxin treatment, which induced MECOM degradation, to study the effects of this intervention on open chromatin.


title: MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia [4C-Seq]

overall_design: We introduced an auxin-inducible degron (AID) (V5-AID-T2A-eGFP) 3’ of MECOM in inv(3) cell line MUTZ3. Next, circular chromosome conformation capture coupled to high-throughput sequencing (4C-seq) was performed in cells with or without auxin treatment to investigate the effect on MECOM degradation on chromatin contacts.


title: KMT2D promotes castration-resistant prostate cancer progerssion by reactivating AR via FOXA1 [RNA-Seq]

overall_design: Expression profiling by high throughput sequencing. Genome binding/occupancy profiling by high throughput sequencing


title: MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia [ChIP-seq]

overall_design: We introduced an auxin-inducible degron (AID) (V5-AID-T2A-eGFP) 3’ of MECOM in inv(3) cell line MUTZ3. Next, chromatin immunoprecipitation followed by sequencing (ChIP-Seq) for EVI1, CTBP2, various transcription factors (p300, RUNX1) and histone modifications (H3K27ac, H3K27me3, H3k9me3) was performed in this cell line, either after auxin-induced MECOM degradation or in the absence of treatment.


title: KMT2D promotes castration-resistant prostate cancer progerssion by reactivating AR via FOXA1 [ATAC-Seq]

overall_design: ATAC-Seq  in LNCaP and C4-2 cells treated with siRNA-induced silencing of KMT2D


title: KLF7 regluate migration and cancer stemness in OSCC [RNA-seq]

city: Hangzhou

first: Jiong

last: Lyu

state: Zhejiang

address: Rd.Yuhangtang  866

institute: Zhejiang University

summary: In this study, we aim to analyze the role and mechanism of transcription factor KLF7 in oral cancer. We used CHIP-seq to analyze the binding sites of KLF7 on the genome of oral cancer cell line CAL27 Meanwhile, we also analyzed the changes in gene expression after CAL27 overexpression of KLF7 using transcriptome sequencing

overall_design: Chip-seq of myc-tag in CAL27 transfected with myc-tag KLF7; RNA seq profiling of CAL27 transfected with KLF7 or control vector

first: Yuwen

last: Miao

first: Jiaxiong

last: Wang

first: Xin

last: Qi

first: Huiyong

last: Zhu


title: KLF7 regluate migration and cancer stemness in OSCC [ChIP-seq]


title: HHIP protein interactions in lung cells provide insight into COPD pathogenesis

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

institute: Brigham and Women's Hospital

summary: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide. The primary causes of COPD are environmental, including cigarette smoking; however, genetic susceptibility also contributes to COPD risk. Genome-Wide Association Studies (GWASes) have revealed more than 80 genetic loci associated with COPD, leading to the identification of multiple COPD GWAS genes. However, the biological relationships between the identified COPD susceptibility genes are largely unknown. Genes associated with a complex disease are often in close network proximity, i.e. their protein products often interact directly with each other and/or similar proteins. In this study, we use affinity purification mass spectrometry (AP-MS) to identify protein interactions with HHIP, a well-established COPD GWAS gene which is part of the sonic hedgehog pathway, in two disease-relevant lung cell lines (IMR90 and 16HBE). To better understand the network neighborhood of HHIP, its proximity to the protein products of other COPD GWAS genes, and its functional role in COPD pathogenesis, we create HUBRIS, a protein-protein interaction network compiled from 8 publicly available databases. We identified both common and cell type-specific protein-protein interactors of HHIP. We find that our newly identified interactions shorten the network distance between HHIP and the protein products of several COPD GWAS genes, including DSP, MFAP2, TET2, and FBLN5. These new shorter paths include proteins that are encoded by genes involved in extracellular matrix and tissue organization. We found and validated interactions to proteins that provide new insights into COPD pathobiology, including CAVIN1 (IMR90) and TP53 (16HBE). The newly discovered HHIP interactions with CAVIN1 and TP53 implicate HHIP in response to oxidative stress.

overall_design: The purpose of the data generated in the GEO submission was to determine which genes are expressed (or not) in various experimental cell lines. These data were then used to update protein network representations.

first: Dávid

last: Deritei

first: Hiroyuki

last: Inuzuka

first: Jeong

last: Yun

first: Zhonghui

last: Xu

first: Wardatul

last: Anamika

first: John

middle: M

last: Asara

first: Feng

last: Guo

first: Xiaobo

last: Zhou

first: Kimberly

last: Glass

first: Wenyi

last: Wei

first: Edwin

middle: K

last: Silverman


title: Sequential Transcriptome Profiling: Comparative Analysis of Normal and Canine Lymphoma Preceding Detailed T-Cell and B-Cell Subtype

city: Gwangju

first: Ha-Jung

last: Kim

address: 77, Yongbong-ro, Buk-gu

country: South Korea

institute: Chonnam National University

summary:
This study aimed to delineate genes and functional pathways related to canine lymphoma pathogenesis, treatment response, and prognosis through transcriptional profiling.
By comparing different lymphoma subtypes, the study aimed to identify genes with potential applicability to the clinical characteristics of T-cell lymphoma (TCL) compared to B-cell type, which is characterized by low treatment response and poor prognosis.

overall_design: A total of 20 samples were analyzed in this study, consisting of 13 samples from dogs diagnosed with multicentric lymphoma and 7 samples from dogs without lymphoma, serving as controls. Among the lymphoma samples, three were excluded due to insufficient RNA yield, resulting in 10 lymphoma samples analyzed for transcriptome profiling. The control group provided a reference baseline for differential gene expression and functional analysis. These samples were subjected to consistent RNA extraction, quality assessment, and transcriptome analysis protocols to ensure comparability.


title: Natural killer cells regulate distinct CD8+ T cell differentiation program in cancer and contribute to resistance against immune checkpoint blockers

city: Columbus

first: Zihai

last: Li

address: 2255 Kenny Rd

summary: Immune checkpoint blockers (ICBs) targeting the PD-1/PD-L1 axis represent established therapies for many cancers. However, resistance occurs in most patients due to multiple complex immune-suppressive mechanisms in the tumor microenvironment (TME). Natural killer (NK) cells can play effector roles in tumor control, but their impact on T cell dysfunction and ICB efficacy remains controversial. Through genetic and antibody-mediated NK cell depletion, we found that NK cells play negative roles in ICB sensitivity; they further impede CD8+ T cell differentiation toward CD69+ BCL2+ EOMES+ GZMB+ TIM3- GITR- CTLA4- phenotype. Mechanistically, we identified that the retinoic acid receptor alpha (RARα)-dependent differentiation program in CD8+ T cells is hindered due to cytokine competition with NK cells. Finally, we observed that lower frequencies of NK cells correlate with better clinical response to ICBs in cancer patients. These findings suggest a potential avenue for enhancing CD8+ T cell-centered immunotherapy by targeting NK cells.

overall_design: We conducted single-cell sequencing using the 10x Genomics platform to investigate the impact of NK cells on the differentiation program of CD8+ T cells. The MC38 tumor model was utilized, and CD8+ T cells were isolated from tumors of both control and NK cell-depleted mice. Our findings demonstrate that NK cells significantly influence the differentiation trajectory of CD8+ T cells.

first: No-Joon

last: Song

first: Juan

last: Xie

first: Kyeong Joo

last: Jung

first: Yi

first: Joanna

last: Pozniak

first: Niccolò

last: Roda

first: Jean-Christophe

last: Marine

first: Brian

last: Riesenberg

first: Hyeongseon

last: Jeon

first: Anjun

last: Ma

first: Nathanael

last: Cox

first: Darren

last: Wethington

first: Kelsi

last: Reynolds

first: Tong

last: Xiao

first: Anqi

first: Parker

last: Kronen

first: Nicholas

middle: C

last: Denko

first: David

last: Carbone

first: Qin

first: William

last: Carson

first: Bethany

last: Mundy-Bosse

first: Christin

last: Burd

first: Jayajit

last: Das

first: Dongjun

last: Chung


title: RNA sequencing data of mouse intestinal epithelial cells following different dietary treatments and Trichuris muris infection

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: Mice were fed either a synthetic control diet or an inulin-enriched diet for 14 days prior to infection. Half of the mice in each dietary group were infected with 300 T. muris eggs, and euthanised 72 hours post-infection.

overall_design: Mice (n=5 per group) were rnadomly allocated to groups. Diets were fed ad libitum. IEC were isolated from colon tissue using EDTA digestion.


title: Comparative transcriptomic rhythms in the mouse and human prefrontal cortex

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

address: 450 Technology Drive

institute: University of Pittsburgh

summary: Alterations in multiple subregions of the human prefrontal cortex (PFC) have been heavily implicated in psychiatric diseases. Moreover, emerging evidence suggests that circadian rhythms in gene expression are present across the brain, including in the PFC, and that these rhythms are altered in disease. However, investigation into the potential circadian mechanisms underlying these diseases in animal models must contend with the fact that the human PFC is highly evolved and specialized relative to that of rodents. Here, we use RNA sequencing to lay the groundwork for translational studies of molecular rhythms through a sex-specific, cross species comparison of transcriptomic rhythms between the mouse medial PFC (mPFC) and two subregions of the human PFC, the anterior cingulate cortex (ACC) and the dorsolateral PFC (DLPFC). We find that while circadian rhythm signaling is conserved across species and subregions, there is a phase shift in the expression of core clock genes between the mouse mPFC and human PFC subregions that differs by sex. Furthermore, we find that the identity of rhythmic transcripts is largely unique between the mouse mPFC and human PFC subregions, with the most overlap (20%, 236 transcripts) between the mouse mPFC and the human ACC in females. Nevertheless, we find that basic biological processes are enriched for rhythmic transcripts across species, with key differences between regions and sexes. Together, this work highlights both the evolutionary conservation of transcriptomic rhythms and the advancement of the human PFC, underscoring the importance of considering cross-species differences when using animal models.

overall_design: Wildtype mouse (C57BL/6J) RNA-sequencing data. Homogenate medial prefrontal cortex from adult male and female mice sacrificed at 4 hour intervals over 24 hours.

first: Jennifer

middle: N

last: Burns

first: Aaron

last: Jenkins

first: Xiangning

last: Xue

first: Kaitlyn

last: Petersen

first: Kyle

middle: D

last: Ketchesin

first: Megan

last: Perez

first: Chelsea

last: Vadnie

first: Madeline

last: Scott

first: Marianne

middle: L

last: Seney

first: George

last: Tseng