title: Selectively expressed RNA molecules as a versatile tool for functionalized cell targeting

city: Würzburg

first: Redmond

last: Smyth

state: Bayern

address: Josef-Schneider-Straße 2, D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Exact targeting of specific mammalian cell types or diseased cells is one of the most urgently needed prerequisites for a new generation of potent pharmaceuticals. Different approaches have been pursued, failing mainly due to a lack of specific surface markers in most cases. Developing a novel RNA-based methodology, we can now ensure exact cell targeting and simultaneously combine this with selective expression of effector proteins, thereby functionalization of the target cell for therapy, diagnostics or cell steering. The specific combination of the molecular properties of antisense technology and mRNA therapy with functional RNA secondary structures based on Nano-DMS-MaP analysis allowed us to develop selectively expressed RNA molecules for medical applications. These so-called seRNAs remain inactive in non-target cells and are only activated by partial degradation to induce translation in preselected cell types of interest. Cell type specificity and type of functionalization are easily adaptable based on a simple modular system. In proof of concept in vitro and in vivo studies we used seRNAs as a highly selective platform technology for powerful cell targeting. We effectively treat breast tumor cell clusters in mixed cell systems and reduce early brain tumors of mice without detectable side effects with just a single treatment. Our data open up new potential avenues for various therapeutic applications.

overall_design: Nano-DMS-MaP analysis of seRNA. Selective and non-selective constructs we transfected into cells. RNA structure was determined by Nano-DMS-MaP probing.

first: Frederik

last: Rastfeld

first: Marco

last: Hoffmann

first: Sylvie

last: Krüger

first: Patrick

last: Bohn

first: Anne-Sophie

last: Gribling-Burrer

first: Laura

first: Carina

last: Stegmayr

first: Sven

last: Gerlach

first: Nils

last: Hersch

first: Daniel

last: Köninger

first: Christina

first: Helene

last: Walter

first: Dirk

last: Wiedermann

first: Hajaani

last: Manoharan

first: Gereon

last: Fink

first: Rudolf

last: Merkel

first: Heribert

last: Bohlen

first: Maria

last: Rueger

first: Bernd


title: TBP bookmarks and preserves neural stem cell fate memory by orchestrating local chromatin architecture (RNA-Seq)

status: Public on Dec 10 2024

city: Beijing

first: Yuying

last: Shen

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

type: Expression profiling by high throughput sequencing

summary: Mitotic bookmarking has been posited as an important strategy for cells to faithfully propagate their fate memory though cell generations. However, the physiological significance and regulatory mechanisms of mitotic bookmarking in neural development remain unexplored. Here, we identified TBP (TATA binding protein) as a crucial mitotic bookmarker for preserving fate memory of Drosophila neural stem cells (NSCs). Phosphorylation by the super elongation complex (SEC) is important for TBP to retain as discrete foci at mitotic chromosomes of NSCs to effectively transmit their fate memory. TBP depletion leads to drastic NSC loss, whereas TBP overexpression enhances the ability of SEC to induce neural progenitor dedifferentiation and tumorigenesis. Importantly, TBP achieves its mitotic retention through recruiting the chromatin remodeler EP400, which in turn increases local chromatin accessibility via depositing H2A.Z. Thus, local chromatin remodeling ensures mitotic bookmarking, which may represent a general principle underlying the preservation of cell fate memory.

overall_design: To investigate the biological function of TBP and H2A.Z in Drosophila neural stem cells, we compared the gene expression profiles of neural stem cells with shRNA knockdown of TBP, H2A.Z loss of function and control neural stem cells using RNA-seq.

first: Kun

last: Liu

first: Jie

first: Jingwen

first: Tongtong

last: Ye

first: Runxiang

last: Zhao

first: Rulan

last: Zhang

first: Yan

last: Song


title: TBP bookmarks and preserves neural stem cell fate memory by orchestrating local chromatin architecture (CUT&Tag)

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: To identify the TBP, H2A.Z, ELL and dEP400 distribution pattern, and the relationship between them, we carried out in vivo CUT&Tag assay in Drosophila type II neural stem cells. To find out the genomic loci mitotically bound by hTBP, we isolated mitosis versus interphase neural stem cells and performed anti-hTBP CUT and Tag and identified the binding sites of endogenous TBP in interphase and mitotic neural stem cells respectively. We also found out the genomic loci bound by human H2A.Z and mitotically bound by human TBP in HEK 293T cells by CUT and Tag.


title: TBP bookmarks and preserves neural stem cell fate memory by orchestrating local chromatin architecture (ATAC-Seq)

overall_design: To assess chromatin architecture of neural stem cells in mitosis, we next performed in vivo ATAC-seq with asynchronous versus mitotic neural stem cells. To investigate whether dEP400 facilitates TBP mitotic retention by increasing local chromatin accessibility, we carried out in vivo ATAC-seq assays.


title: Inhibition of Intimal CX3CR1+ Macrophages Mitigates Thoracic Aortic Aneurysm Progression in Marfan Syndrome

first: Jiaqi

last: Huang

address: Xueyuan Road 38

summary: Current understanding on the pathogenesis of thoracic aortic aneurysms (TAAs) in Marfan Syndrome (MFS) mainly focuses on vascular smooth muscle cell (VSMC) pathologies. Whether immune cell-mediated inflammation drives the progression of TAAs is still elusive. Using single-cell RNA sequencing, a subset of macrophages highly expressing CX3CR1 and mainly locating in the aortic intima was identified in aortic root and ascending aortas from Fbn1C1041G/+ mice, and further validated in MFS patients. Specific elimination of CX3CR1+ macrophages by diphtheria toxin in Cx3cr1-CreERT2iDTRF/+Fbn1C1041G/+ mice efficiently ameliorated TAA progression, suggesting their pathogenic action. Using monoclonal antibodies Adalimumab and Teprotumumab to respectively neutralize the proinflammatory cytokines TNFalpha and IGF1 produced by CX3CR1+ macrophages from MFS patients substantially suppressed CX3CR1+ macrophage-mediated inflammation in MFS patient-specific induced pluripotent stem cell (iPSC)-derived VSMCs. Furthermore, bone marrow transplantation and parabiosis using Cx3cr1GFP/+ mice revealed the intimal CX3CR1+ macrophages derived from circulating monocytes. Administration of CCR2 antagonist RS504393 to inhibit monocyte infiltration significantly reduced intimal CX3CR1+ macrophages and subsequently alleviated TAA development in Fbn1C1041G/+ mice. In conclusion, intimal CX3CR1+ macrophages mediated TAA formation through paracrinally causing VSMC inflammation. Targeting intimal CX3CR1+ macrophages would be a promising anti-inflammatory strategy in TAA therapy for MFS.

overall_design: Single cell suspensions of aortic root and ascending aortas from WT (N = 6) and Fbn1C1041G/+ (N = 6) mice

first: Zhujiang

first: Hanshi

last: Xu

first: Zhenting

last: Wang


title: SUV39H1 epigenetically modulates the MCPIP1-AURKA signaling axis to enhance neuroblastoma tumorigenesis

city: Guangzhou

first: Meng

last: Li

address: 651 East Dongfeng Road

department: Department of Pediatric Oncology

institute: Sun Yat-sen University Cancer Center

summary: Epigenetic regulation is a pivotal factor during neuroblastoma (NB) pathogenesis and investigations into cancer epigenetics are actively underway to identify novel therapeutic strategies for NB patients. SUV39H1, a member of the H3K9 methyltransferase family, contributing to tumorigenesis across multiple malignancies. However, its specific role in NB remains unexplored. In this study, we conducted a high-throughput screen utilizing a compound library containing 288 epigenetic drugs, leading to the identification of chaetocin as the most potent NB inhibitor by targeting SUV39H1. Genetic manipulation and therapeutic inhibition of SUV39H1 significantly impacted proliferation, migration, cell cycle phases, and apoptosis in NB cells. Concurrently, chaetocin demonstrated robust anti-tumor efficacy in vivo with tolerable toxicity. RNA-seq unveiled that SUV39H1 knockdown and inhibition down-regulated cell cycle pathways, impacting vital genes such as AURKA. Besides, MCPIP1 emerged as a novel tumor suppressor following SUV39H1 inhibition, which decreased AURKA expression in NB. In detail, SUV39H1 mediated the enrichment of H3K9me3 at the promoter region of MCPIP1, repressing the MCPIP1-mediated degradation of AURKA and facilitating the subsequent accumulation of AURKA, which revealed the oncogenic role of SUV39H1 via the SUV39H1-MCPIP1-AURKA signaling axis in NB. Therapeutic inhibition of SUV39H1 using chaetocin emerges as an effective and safe strategy for NB patients.

overall_design: To investigate the oncogenic role of SUV39H1 and the molecular mechanisms governed by SUV39H1 in NB cells, we performed the RNA-sequencing (RNA-seq) in the NB cell line SK-N-SH.Biological triplicate of RNA-seq analysis was performed on SK-N-SH cells of SUV39H1 inhibition: shNC-SK-N-SH cells (3 samples), shSUV39H1-SK-N-SH cells (3 samples), DMSO-SK-N-SH cells (3 samples), and chaetocin-SK-N-SH cells (50 nM, 3 samples) . The significant differentially expressed genes (DEGs) were obtained.


title: Targeting the mevalonate pathway potentiates NUAK1 inhibition-induced immunogenic cell death and antitumor immunity

city: 上海市

first: gui

last: liming

state: 上海市

address: 华山路1954号上海交通大学生物医学工程学院

institute: 上海交通大学

summary: The induction of immunogenic cell death (ICD) impedes tumor progression via both tumor cell-intrinsic and -extrinsic mechanisms, representing a robust therapeutic strategy. However, there remains a dearth of ICD-inducing targets. Employing kinome-wide CRISPR-Cas9 screening, we have identified NUAK1 as a potential target. The ICD-provoking effect of NUAK1 inhibition depends on the production of reactive oxygen species (ROS), consequent to the downregulation of NRF2-mediated antioxidant gene expression. Moreover, the mevalonate pathway/cholesterol biosynthesis, activated by XBP1s downstream of NUAK1 inhibition-induced endoplasmic reticulum stress, functions as negative feedback on ICD. Targeting the mevalonate pathway using HMGCR inhibitor statins amplifies NUAK1 inhibition-mediated ICD and antitumor activity, while cholesterol mitigates ICD by diminishing ROS. The combination of NUAK1 inhibitors and statins enhances the efficacy of anti-PD-1 therapy. Collectively, our study unveils the promise of blocking the mevalonate pathway in conjunction with ICD-targeted immunotherapies such as NUAK1 inhibition.

overall_design: MC38 tumor cell lines were treated with vehicle or HTH-01-015 for 24h, then the cells were collected for RNA-seq

first: Liming

last: Gui

first: Kaiwen

last: Chen

first: Jingjing

last: Yan

first: Ping


title: Neutrophil transcriptome in community acquired pneumonia and age matched controls

city: Birmingham

first: Frances

last: Grudzinska

address: Edgbaston

department: Institute of Inflammation and Ageing

country: United Kingdom

institute: University of Birmingham

summary: Community acquired pneumonia (CAP) is a leading cause of hospitalistion and is associated with high mortality and morbidity. Neutrophils from CAP donors display altered functions, and these altered functions are associated with adverse outcomes. We undertook an oberservational study of CAP in frail older adults and age matched controls to determine drivers of neutrophil dysfunction.

overall_design: Observational study of CAP participants with age and co-morbidity matched controls

middle: S

first: Aaron

last: Scott

first: David

middle: R

last: Thickett


title: A Conserved Switch to Less Catalytically Active Polycomb Repressive Complexes in non-dividing cells

city: Clayton

first: Evan

last: Healy

state: VIC

address: 23 Innovation Way, Building 77,, Monash University

country: Australia

institute: Monash University

summary: Characterisation of Polycomb complex assemblies in quiescent and cycling human fibroblasts

overall_design: RNA-Seq, Chip-seq (H3K27me3, H3K27me2, H3K27me1) and Chip-Rx (EZH1, EZH2, EED,CBX7, PHC1, CBX8)

first: Rachel

last: McCole

first: James

last: Nolan

middle: M

last: Reck

first: Craig

last: Monger

first: Samantha

last: Rustichelli

first: Eric

last: Conway

first: Gerard

middle: L

last: Brien

first: Cheng

first: Orla

last: Deevy

first: Hannah

middle: K

last: Neikes

last: Potjewyd

first: Aoibhinn

last: Mooney

first: Richard

last: Flavin

first: Elisabeth

last: Vandenberghe

first: Sarena

middle: F

last: Flanigan

first: Diego

last: Pasini

first: Chen

last: Davidovich

first: Michiel

last: Vermeulen

first: Lindsey

middle: I

last: James

first: Adrian

middle: P

last: Bracken


title: TBP bookmarks and preserves neural stem cell fate memory by orchestrating local chromatin architecture

first: Yuying

last: Shen

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

overall_design: Refer to individual Series


title: AKR1B1 is required for maintaining acute leukemia cell survival by epigenetic silencing of tumor suppressor genes

status: Public on Dec 09 2024

city: Harbin

first: Huitao

last: Fan

state: Heilongjiang

address: 23 Youzheng street

department: NHC Key Laboratory of Cell Transplantation

institute: The First Affiliated Hospital of Harbin Medical University

summary: In order to explore the role of AKR1B1 in gene transcription expression, we established shControl and shAKR1B1_1 in Jurkat cells to down-regulate AKR1B1 expression in Jurkat. We then analyzed gene expression using RNA-seq. Finally, 6 sets of shControl and shAKR1B1_1 data are obtained

overall_design: Comparative gene expression profiling by performing RNA-seq in 3 replicates each of control and knockdown of AKR1B1 of Jurkat cells

first: Jingyu

last: Chen

first: Lu

last: Xu

first: Wangshi

last: Li


title: Single-cell analysis reveals fibroblast heterogeneity and myofibroblast conversion in ligamentum flavum hypertrophy

city: Seoul

first: Hyun Jung

last: Kim

address: 73 Goryeodae-ro, Seongbuk-gu

department: Anatomy

country: South Korea

institute: Korea University

summary: The ligamentum flavum (LF) is a crucial structure in maintaining spinal stability; however, hypertrophy of the LF is a significant contributor to lumbar spinal canal stenosis (LSCS). However, the mechanisms linking LF hypertrophy to the exacerbation of LSCS remain incompletely understood. In this study, we investigated the cellular proportions and signaling pathways observed in the hypertrophied LF using single-cell RNA sequencing (scRNA-seq). The LF tissues were obtained from three patients undergoing decompressive surgery at the lumbar level. These patients had been diagnosed with LSCS prior to surgery and had an LF thickness exceeding 4 mm. After single-cell dissociation of the LF tissues, scRNA-seq was performed. Fibroblasts accounted  for 75% of the total cells, followed by endothelial cells, T cells, macrophages, and B cells. Among heterogeneous types of fibroblasts, we identified that a subset of fibroblasts trans-differentiated into myofibroblasts. Two types of macrophages that exhibited phenotypic plasticity akin to M1 and M2 states were observed. We also identified novel signaling pathways involved in fibroblast and immune cell interaction in the hypertrophied LF, such as GAS and GRN, as well as known signaling pathways, such as TGF-β, PDGF, CXCL, and ANGPTL. Our study highlights the transdifferentiation process from fibroblasts to myofibroblasts in the hypertrophied LF through intrinsic changes in and extrinsic influences of fibroblasts.

overall_design: Human ligamentum flavum tissues diagnosed with LSCS accompanied with Ligamentum Flavum were collected during surgery involving decompressive lumbar laminectomy. LF tissue was dissociated and cells were isolated. The suspended cells were processed through 10x Genomics and were analyzed as scRNAseq.

first: Chang

middle: H

last: Ham

first: Yiseul

first: Woo-Keun

last: Kwon

first: Woong

last: Sun

first: Joo

first: Hyun

middle: J

first: Hong

last: Moon


title: The IGF2BP1 oncogene is a druggable m6A-dependent enhancer of YAP1-driven gene expression in tumor growth

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

summary: The Hippo/YAP1 signaling pathway regulates normal development by controlling contact inhibition of growth. In cancer, YAP1 activation is often dysregulated, leading to excessive tumor growth and metastasis. We demonstrate that the RNA-binding protein IGF2BP1 impedes the repression of YAP1 by Hippo signaling in carcinomas. IGF2BP1 stabilizes YAP1 mRNA and enhances YAP1 protein synthesis through an m6A-dependent interaction with the 3’UTR of the YAP1 mRNA. This results in increased nuclear YAP1 accumulation in IGF2BP1-expressing ovarian cancer, boosting transcriptional activity and bypassing contact inhibition. Inhibiting IGF2BP1-mRNA binding using the small molecule BTYNB reduces YAP1 levels and transcriptional activity, leading to significant growth inhibition in carcinoma cells and ovarian cancer organoids. Conversely, SRC inhibition via Saracatinib only impacts epithelial-like tumor cells, suggesting that the impact of SRC is limited by the stalling of YAP1 at adherens junction. This is particularly significant in de-differentiated, rather mesenchymal carcinoma-derived cells, which exhibit high IGF2BP1 and YAP1 expression, rendering them less reliant on SRC -directed growth stimulation. In such invasive carcinoma models, the combined inhibition of SRC and IGF2BP1 or YAP1/TAZ by Verteporfin proved superior over monotherapies. These findings highlight the therapeutic potential of targeting IGF2BP1, a key regulator of oncogenic transcription networks.

overall_design: PolyA-RNA sequencing of SAS cells was performed to to demonstrate that the RNA-binding protein IGF2BP1 impedes the repression of YAP1 by Hippo signaling in carcinomas.

first: Nadine

last: Bley

first: Alexander

last: Rausch


title: Effect of host PCSK9 treatment on the gene expression of EO771 primary tumor [RNAseq_KI_tumor]

city: New York

first: Wenbin

last: Mei

address: 1230 York Ave

country: USA

institute: Rockefeller University

summary: Identifying patients at risk for metastatic relapse is a critical need in oncology. We identified a common missense germline variant in PCSK9 that associates with reduced breast cancer survival outcomes in multiple cohorts. Genetic modeling of this gain-of-function single nucleotide variant in mice revealed that it causally promoted breast cancer metastasis. Conversely, host PCSK9 deletion reduced metastatic colonization in multiple breast cancer models. Host PCSK9 promoted metastatic initiation events in lung and increased proliferative competence by targeting tumoral LRP1 receptors which repress metastasis-promoting genes. Antibody-mediated therapeutic inhibition of PCSK9 suppressed breast cancer metastasis in multiple models. This variant stratified women in a large Swedish early-stage breast cancer cohort into those with 98% versus 78% distant-metastasis-free interval at 15 years after diagnosis. Our findings reveal that a commonly inherited genetic alteration predicts breast cancer survival and governs breast cancer metastasis—uncovering a hereditary basis underlying a prevalent cause of mortality.

overall_design: To investigate how host affects breast tumor gene expression, we transplanted EO771 cells into the mammary fat pad of female human PCSK9 knockin (wildtype and V474I variant) mice. We the conducted RNASeq of the size-matched tumors.

first: Anthea

last: Lovisa


title: Y chromosome linked UTY modulates sex differences in valvular fibroblast methylation in response to nanoscale extracellular matrix cues

city: La Jolla

first: Rayyan

middle: Mohammed

last: Gorashi

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: UC San Diego

summary: Aortic valve stenosis (AVS) is a progressive disease wherein males develop valve calcification relative to females that develop valve fibrosis. Valvular interstitial cells (VICs) aberrantly activate to myofibroblasts during AVS, driving the fibrotic valve phenotype in females. Myofibroblasts further differentiate into osteoblast-like cells and secrete calcium nanoparticles, driving valve calcification in males. We hypothesized the lysine demethylase UTY (ubiquitously transcribed tetratricopeptide repeat containing, Y-linked) decreases methylation uniquely in response to nanoparticle cues in the valve extracellular matrix to promote an osteoblast-like phenotype.  Here, we describe a bioinspired hydrogel cell culture platform to interrogate how nanoscale cues modulate sex-specific methylation states in VICs activating to myofibroblasts and osteoblast-like cells. We found UTY (ubiquitously transcribed tetratricopeptide repeat containing, Y-linked) modulates VIC phenotypes in response to nanoscale cues uniquely in males. Overall, we reveal a novel role of UTY in the regulation of calcification processes in males during AVS progression.

overall_design: Porcine valvular interstitial cells were cultured on soft hydrogels and hydrogels embedded with 2000 nm polystyrene nanoparticles.

first: Talia

last: Baddour

first: Brian

middle: A

last: Aguado


title: Effect of host PCSK9 treatment on the gene expression of EO771 primary tumor

overall_design: To investigate how host affects breast tumor gene expression, we transplanted EO771 cells into the mammary fat pad of female wildtype and Pcsk9 KO mice. We the conducted RNASeq of the size-matched tumors.

first: Schayan

last: Faraj Tabrizi


title: Quorum sensing regulates virulence factors in the coral pathogen Vibrio coralliilyticus.

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street, Biology Building

department: Biology

institute: Indiana University

summary: The bacterial pathogen Vibrio coralliilyticus infects a variety of marine organisms globally and causes early onset of disease in multiple coral species. The etiology of coral disease and relative pathogenicity of V. coralliilyticus strains is well-documented, but the mechanisms of V. coralliilyticus coral colonization, virulence factor production, and interactions with coral microbiome are understudied. Many virulence factors responsible for pathogenic behaviors are controlled through a density-dependent, bacterial communication system called quorum sensing (QS). In other Vibrio species, behaviors like bioluminescence, biofilm formation, toxin secretion, and protease production are controlled via the master quorum sensing transcriptional regulator called LuxR/HapR. Comparative genomics indicated that V. coralliilyticus genomes share high sequence identity for most of the QS signaling and regulatory components identified in other Vibrio species. Here, we characterize active components of the V. coralliilyticus QS system and identify the VcpR (LuxR/HapR homolog) regulons in two strains with distinct infection etiologies. We show that VcpR transcription is dependent on signaling by autoinducer AI-2, whereas we were unable to detect production of acyl-homoserine lactone autoinducers. The VcpR regulator controls expression of >200 genes in both the type strain BAA-450 and isolate OCN008, including two genes encoding proteases (VcpA and VcpB) known to impact coral infection. In both isolates, VcpR activates the expression of Type VI Secretion System genes from both systems 1 and 2, which results in interbacterial competition and killing of prey bacteria. We conclude that the QS system in V. coralliilyticus is active and controls expression of genes involved in relevant bacterial behaviors that may influence coral infection.

overall_design: Utilizing bioinformatics, in vitro molecular assays (3 replicates for positive detection or 2 replicates for negative detection), reporter assays (three replicates per assay), and qPCR/RNA-seq (3 replicates per genotype: wild-type versus vcpR-null) to define the quorum sensing circuit and transcriptional regulation in Vibrio coralliilyticus strains, OCN008, OCN014, and BAA-450. Most assay results compared to the canonical quorum sensing control strain, Vibrio campbellii BB120.

first: Victoria

last: Lydick

first: Robert

last: Pepin

first: Emra

last: Klempic

first: Ram

last: Podicheti

first: Douglas

middle: B

last: Rusch

first: Blake

last: Ushijima

first: Laura

middle: C

last: Brown


title: Effect of recombinant PCSK9 treatment on the gene expression of EO771 cells

overall_design: To investigate how extrinsic PCSK9 affect breast cancer gene expression, we treated EO771 cells with 2ug/ml PCSK9 or BSA for 24 hours in vitro and conducted RNASeq.


title: The microbiota metabolite, phloroglucinol, confers long-term protection against inflammation

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary: Phloroglucinol is a key byproduct of gut microbial metabolism that has been widely used as a treatment for irritable bowel syndrome. Here, we demonstrate that phloroglucinol tempers macrophage responses to pro-inflammatory pathogens and stimuli. In vivo, phloroglucinol administration decreases gut and extraintestinal inflammation in murine models of inflammatory bowel disease and systemic infection. The metabolite induces modest modifications in the microbiota. However, the presence of an active microbiota is required to preserve its anti-inflammatory activity. Remarkably, the protective effect of phloroglucinol lasts partially at least 6 months. Single-cell transcriptomic analysis of bone marrow progenitors demonstrates the capacity of the metabolite to induce long-lasting innate immune training in hematopoietic lineages, at least partially through the participation of the receptor and transcription factor, aryl hydrocarbon receptor (AhR). Phloroglucinol induces alterations in metabolic and epigenetic pathways that are most prevalent in upstream progenitors as hallmarks of central trained immunity. These data identify phloroglucinol as a dietary-derived compound capable of inducing central trained immunity and modulating the response of the host to inflammatory insults.

overall_design: One month after oral administration, bone marrow was isolated from control and phloroglucinol-treated animals, and Lineage negative (Lin–) cKit positive (cKit+) hematopoietic stem and progenitor cells (HSPCs) from each group were sorted and pooled for analysis using scRNAseq.

first: Janire

last: Castelo

first: Sarai

last: Araujo

first: Diego

last: Barriales

first: Samuel

middle: T

last: Pasco

first: Iratxe

last: Seoane

first: Ainize

last: Peña-Cearra

first: Ainhoa

last: Palacios

first: Carolina

last: Simó

first: Virginia

last: Garcia-Cañas

first: Muthita

last: Khamwong

first: Itziar

last: Martín-Ruiz

first: Monika

last: Gonzalez-Lopez

last: Barcena

first: José

middle: E

last: Rodríguez

last: Lavín

first: Naiara

last: Gutiez

first: Raquel

last: Marcos

first: Estibaliz

last: Atondo

first: Arantza

last: Cobela

last: Plaza-Vinuesa

first: Adrián

last: Plata

first: Eneko

last: Santos

first: Alberto

last: Fernandez-Tejada

first: Mari

last: Villarán

last: Mancheño

first: Aize

last: Pellón

first: Blanca

last: de las Rivas

first: Rosario

last: Muñoz

first: Abelardo

last: Margolles

first: Patricia

last: Ruas-Madiedo

last: Selma

first: Mercedes

last: Gómez de Agüero

first: Leticia

last: Abecia

first: Juan

last: Anguita

first: Héctor


title: Single-Cell Gene Expression Profiling reveals distinct exhaustion and senescence signatures in T cells across various types of male infertility

city: Milano

first: Silvia

last: Gregori

state: Italy

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

summary: scRNA-seq experiment of fertile, Oligo-Astheno-Terato spermia and idiopathic non-obstructive azoospermia subjects.

overall_design: scRNA-seq was applied to CD3+ T cells negatively isolated from peripheral blood of fertile (FER, n=5), Oligo-Astheno-Terato spermia (OAT, n=4), and idiopathic non-obstructive azoospermia (NOA, n=6) subjects.

first: Giada

last: Amodio

first: Giorgia

last: Giacomini

first: Andrea

last: Salonia


title: Neuroligin-3 R451C Induces Gain-of-Function Gene Expression in Astroglia in an Astroglia-Enriched Brain Organoid Model

status: Public on Dec 08 2024

city: Piscataway

first: Ziyuan

last: Ma

state: NJ

address: 604 Allison Rd

department: Cell Biology and Neuroscience

institute: Rutgers University

summary: Astroglia are integral to brain development and the emergence of neurodevelopmental disorders. However, studying the pathophysiology of human astroglia using brain organoid models has been hindered by inefficient astrogliogenesis. In this study, we introduce a robust method for generating astroglia-enriched organoids through BMP4 treatment during the neural differentiation phase of organoid development. Our RNA sequencing analysis reveals that astroglia developed within these organoids exhibit advanced developmental characteristics and enhanced synaptic functions compared to those grown under traditional two-dimensional conditions, particularly highlighted by increased neurexin (NRXN)-neuroligin (NLGN) signaling. Cell adhesion molecules, such as NRXN and NLGN, are essential in regulating interactions between astroglia and neurons. We further discovered that brain organoids derived from human embryonic stem cells (hESCs) harboring the autism-associated NLGN3 R451C mutation exhibit increased astrogliogenesis. Notably, the NLGN3 R451C astroglia demonstrate enhanced branching, indicating a more intricate morphology. Interestingly, our RNA sequencing data suggest that these mutant astroglia significantly upregulate pathways that support neural functions when compared to isogenic wild-type astroglia. Our findings establish a novel astroglia-enriched organoid model, offering a valuable platform for probing the roles of human astroglia in brain development and related disorders.

overall_design: To assess the effects of the NLGN3 R451C mutation in human astroglia, we conducted RNA-seq experiments on WT/R451C astroglia cultured in 3D (three replicates per group) and WT astroglia cultured in 2D (three replicates).

first: Rui

last: Dang

first: Mridul

last: Dalmia

first: Mengmeng

last: Jin

first: Kushal

last: Aluru

first: Vincent

last: Mirabella

first: Ava

middle: V

last: Papetti

first: Li

last: Cai

first: Peng

last: Jiang


title: Chromobox protein homolog 7 suppresses the stem-like phenotype of glioblastoma cells by regulating the myosin heavy chain 9-NF-κB signaling pathway

city: wuxi

first: Kaixiang

last: Ni

state: jiangsu

address: No. 299 Qingyang Road

institute: Wuxi People's Hospital affiliated to the Nanjing Medical University

summary: Chromobox protein homolog 7 (CBX7) can inhibit the progression of various tumors, but its impact on the stem cell-like properties of GBM cells remains unclear. Clinically, low levels of CBX7 are associated with poor prognosis and increased distant metastasis in GBM patients, and this low expression is caused by methylation of the CBX7 promoter. In this study, through bioinformatics analysis, we found that CBX7 is the most significantly downregulated member of the CBX family in GBM and is closely associated with the stem-like phenotype of GBM cells. Subsequent research showed that CBX7 promotes the degradation of myosin heavy chain 9 (MYH9) protein through the ubiquitin-proteasome pathway via the polycomb repressive complex (PRC1) and suppresses the stem-like phenotype of GBM cells by inhibiting the nuclear factor kappa-B (NF κB) signaling pathway. Furthermore, overexpression of MYH9 in GBM cells can reverse the inhibitory effects of CBX7 on migration, proliferation, invasion, and stemness of GBM cells. In summary, CBX7 acts as a tumor suppressor by inhibiting the stem cell-like characteristics of GBM. The CBX7-MYH9-NF-κB signaling axis may serve as a potential therapeutic target for GBM.

overall_design: CBX7 overexpression group, 3 replicate biosample; CBX7 wt group, 3 replicate biosamples. All samples were subjected to transcriptome sequencing.

first: Yuankun

last: Liu

first: Jiantong

last: Jiao

first: Karrie Mei-Yee

last: Kiang

first: R

last: Damian Holsinger


title: Expression changes in Setdb1-knockdown with shRNA in Hepa1-6 cells, a mouse hepatocellular carcinoma line

city: Minato-ku

first: Yosuke

last: Igarashi

state: Tokyo

address: 3-25-8, Nishi-Shimbashi

country: Japan

institute: The Jikei University School of Medicine

summary: SETDB1 is an epigenetic regulator via H3K9me3. Much is not known about the role of SETDB1 in hepatocellular carcinoma. In this study, we established an shRNA-based Setdb1-knockdown strain in the mouse hepatocellular carcinoma line Hepa1-6 and performed RNA sequencing to identify genes regulated by Setdb1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Hepa1-6 NC cells and the Hepa1-6 Setdb1-KD cells subclones.

first: Shu

last: Shimada


title: N-Cadherin promotes cardiac regeneration by potentiating pro-mitotic β-Catenin signaling in cardiomyocytes

city: Taipei

first: Kai-Chien

last: Yang

address: No.1, Sec. 1, Ren-Ai Rd

department: Department and Graduate Institute of Pharmacology

country: Taiwan

institute: National Taiwan University, College of Medicine

summary: Loss of cardiomyocytes (CMs) following injury can lead to myocardial dysfunction, heart failure (HF) and ultimately death. The limited regenerative ability of the adult human heart after injury, however, poses a significant obstacle to restore cardiac function effectively. While mammalian hearts, including those of mice and humans, do have the potential to regenerate, this capacity is restricted to a narrow window during early stages of life. The molecular mechanisms governing the regenerative capacity of mammalian hearts remain incompletely understood. Exploring a comparative transcriptome analysis in regenerative neonatal vs. non-regenerative adult mouse CMs, we identified N-Cadherin, a member of Ca2+-dependent cell adhesion protein cadherin superfamily, as a potential novel regulator of CM proliferation/renewal. The primary objectives of this study were to elucidate the molecular mechanisms through which N-Cadherin regulates cardiomyocyte proliferation and regeneration, and to determine the therapeutic potential to promote CM renewal and restore cardiac function following injury by targeting N-Cadherin. Cardiac N-Cadherin expression exhibits a strong positive correlation with that of cell cycle- and proliferation-related genes. Its expression levels show an age-dependent reduction, with a 75% decrease of N-Cadherin in adult, compared to P1 neonatal, CMs. N-Cadherin expression is upregulated in the neonatal mouse heart in response to apical resection, especially in the peri-injury region, coinciding with increased CM mitotic activities in the neonatal heart. Knocking down N-Cadherin reduced, whereas overexpression of N-Cadherin increased, the proliferation activity of neonatal mouse CMs and human induced pluripotent stem cell-derived CMs. Mechanistically, increased N-Cadherin potentiates CM renewal through direct binding with and stabilization of a pro-mitotic transcription regulator β-Catenin, leading to increased CMs proliferative activity. Deletion of β-Catenin-binding domain on N-Cadherin abrogated its pro-regenerative activity. Importantly, targeted depletion of N-Cadherin in CMs resulted in incomplete cardiac repair/regeneration and excessive fibrotic scar formation in neonatal mouse hearts following injury. Cardiac-specific overexpression of N-Cadherin in adult mouse heart using adeno-associated viral vectors, by contrast, resulted in increased CM proliferation and protected against myocardial infarction-induced adverse remodeling and contractile dysfunction. Adherent junction protein N-cadherin is demonstrated to play a crucial role in maintaining CM renewal potential by post-translational stabilization of β-Catenin. Enhancing N-cadherin expression levels and downstream signaling activities in the heart, therefore, could be a powerful new approach to promote cardiac regeneration and restore myocardial function in adult human heart following injury.

overall_design: To identify mediators of cardiac muscle regeneration, deep RNA sequencing was conducted utilizing isolated ventricular cardiomyocytes from neonatal (on postnatal day 1 & 3 [P1 & P3], both n=4 ) and adult (8-12 weeks, n=7) mice.

first: Yi-Wei

last: Tsai

first: Yi-Shuan

last: Yseng

first: Yu-Shuo

last: Wu

first: Wei-Lung

last: Song

first: Ming-Yi

last: You

first: Yun-Chia

last: Hsu

first: Wen-Pin

last: Chen

first: Wei-Han

last: Huang

first: JiaCi

last: Chng

first: Chai-Ling

last: Lim

first: Ke-Hsuan

last: Wei

first: Shih-Lei

last: Lai

first: Wen-Chih

last: Lee


title: Transcriptome expression of W38 and transgenic tobacco overexpressing IbTLD treating with/without hydrogen peroxide

status: Public on Dec 07 2024

first: Jeng-Shane

last: Lin

address: No. 1, Sec. 4, Roosevelt Road

department: Plant Biology

institute: National Taiwan University

summary: To understand regulation mechanism of IbTLD, transcriptomes of W38 and trangenic tobacco overexpressing IbTLD with/withouthydrogen peroxide were dissected. 12-day-old seedlings were treated with10 mM H2O2 for 6 hrs. Total RNAs were isolated for library construction and analyzed by RNA-seq via Solexa platform. Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0 and expected to generate 20M (million reads or Gb) per sample.

overall_design: Examination of transcriptome expression inW38 and trangenic tobacco overexpressing IbTLD treating with/without hydrogen peroxide


title: Evaluating the transcriptional regulators of arterial gene expression via a catalogue of characterized arterial enhancers

city: Oxford

first: Susann

last: Bruche

address: Institute of Developmental and Regenerative Medicine

department: Physiology, Anatomy & Genetics

institute: University of Oxford

summary: The establishment and growth of the arterial endothelium requires the coordinated expression of numerous genes. However, regulation of this process is not yet fully understood. Here, we combined in silico analysis with transgenic models to characterize arterial-specific enhancers associated with eight key arterial identity genes (Acvrl1/Alk1, Cxcr4, Cxcl12, Efnb2, Gja4/Cx37, Gja5/Cx40, Nrp1 and Unc5b). Next, to elucidate the regulatory pathways upstream of arterial gene transcription, we investigated the transcription factors binding each arterial enhancer compared to a similar assessment of non-arterial endothelial enhancers. These results found that binding of SOXF and ETS factors was a common occurrence at both arterial and pan-endothelial enhancers, suggesting neither are sufficient to direct arterial specificity. Conversely, FOX motifs independent of ETS motifs were over-represented at arterial enhancers. Further, MEF2 and RBPJ binding was enriched but not ubiquitous at arterial enhancers, potentially marking an arterial sub-set. Lastly, there was no shared or arterial-specific signature for WNT-associated TCF/LEF, TGFβ/BMP-associated SMAD1/5 and SMAD2/3, shear stress-associated KLF4 or venous-enriched NR2F2. This cohort of well characterized and in vivo-verified enhancers can now provide a platform for future studies into the interaction of different transcriptional and signalling pathways with arterial gene expression.

overall_design: CUT&RUN of SOX7, SOX17 and SOX18 in HUVEC at baseline conditions. Two biological reapts were performed for each target.

first: Svanhild

last: Nornes

first: Niharika

last: Adak

first: Ian

last: McCracken

first: Sarah

last: De Val


title: RNA-Sequence of the liver after administration of adenovirus associated with metabolic liver zonation

status: Public on Dec 06 2024

city: Tokyo

first: Kenji

last: Uno

address: 2-11-1 Kaga, Itabashi-ku

institute: Teikyo University

summary: Metabolic zonation in the liver is broadly defined as spatiotemporal variability in the intra-hepatic distribution of nutrients. R-spondin3 (Rspo3) regulates metabolic features around hepatic central veins. Herein, we demonstrate that altered hepatic metabolic zonation due to Rspo3 contributes to maintaining systemic glucose metabolism and body composition via inter-organ communication mechanism. Hepatic Rspo3 induction in obesity improves obesity-associated features by restoring insulin sensitivity, reversing adipose tissue enlargement and reversing overstimulated adaptive thermogenesis. These remote effects partly consist of neuronal communication via the afferent vagus from the liver. In contrast, hepatic Rspo3 suppression exacerbates diabetes due to insulin resistance and develops fatty liver.

overall_design: To examine whether a molecule associated with metabolic liver zonation has an effect on systemic metabolism, we first administer adenoviruses expressing Rspo3 or LacZ (control) into the murine liver. Then, by performing RNA-Sequence analysis, we compare hepatic gene expression of Rspo3-mice with that of LacZ-mice.


title: ALFIN-like proteins link histone H3K4me3 with H2A ubiquitination and coordinate diverse chromatin modifications in Arabidopsis [RNA-seq]

city: Beijing

first: xinjian

last: He

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

institute: National Institute of Biological Sciences

summary: The Arabidopsis H3K4me3-binding ALFIN-like proteins are components of the PRC1 complex and promote H2A ubiquitination, thereby establishing a connection between H3K4me3 and H2A ubiquitination across the genome. Additionally, the ALFIN-like proteins interact with various chromatin-related proteins involved in H2A.Z deposition, H3K27me3 demethylation, histone deacetylation, and chromatin accessibility. The ALFIN-like proteins play a crucial role in coordinating H3K4me3 with diverse other chromatin modifications.

overall_design: Examination of the mRNA expression of 11-day-old wild type and two mutants in Arabidopsis

first: XinJian


title: ALFIN-like proteins link histone H3K4me3 with H2A ubiquitination and coordinate diverse chromatin modifications in Arabidopsis

overall_design: Examination of protein binding levels in transgenic plants; For H2Aub ChIP-seq, examination of H2Aub levels in wild type and four mutants; For H3K27me3 ChIP-seq, examination of H3K27me3 levels in wild type and al2/4/5/6/7 mutant; For H2A.Z ChIP-seq, examination of H2A.Z levels in wild type and al2/4/5/6/7 mutant;  For H3K4me3 ChIP-seq, examination of H3K4me3 levels in wild type and al2/4/5/6/7 mutant

first: Xin-Jian


title: MAIT cell plasticity enables functional adaption that drives anti-bacterial immune protection

city: Melbourne

first: Shihan

last: Li

state: Victoria

address: 792 Elizabeth Street

institute: Peter Doherty Institute, University of Melbourne

summary: Single Cell RNA Sequencing was used to describe temporal transcriptomic changes on MAIT cells upon F.tularensis infection. We find that MAIT17-derived MAIT1 cells were distinct from canonical MAIT1 cells could migrate out of mucosal tissues to contribute to the global MAIT1 pool in subsequent systemic infections

overall_design: MAIT cells were sorted (BD FACS Aria III) from pooled lungs of IL-17a-fm mice intranasally infected with 80 CFU F. tularensis LVS at 6 (4 mice), 9 (2 mice), 13 (2 mice) or 60 days (4 mice) after infection. Cells were then incubated with TotalSeqTM-C mouse hashtags for 20 minutes on ice and washed three times with PBS containing 2% BSA and resuspended in PBS containing 0.04% BSA. Approximately 7,000 cells from each sample were pooled together and loaded onto a Chromium controller (10x Genomics) for generation of gel bead-in-emulsions using 5’ gene expression kits (v2; 10x Genomics). cDNA libraries were generated according to the manufacturer’s instructions (10x Genomics) and then converted using the MGIEasy Universal Library Conversion Kit (BGI) before sequencing on a MGISEQ-2000 instrument (BGI).

first: Huimeng

last: Wang

first: Zhengjun

last: Cheng

first: Alexandra

last: Corbett


title: Effect of Lrp1 knockdown on the gene expression of EO771 cells

first: Wenbin

last: Mei

overall_design: To investigate how LRP1 affects breast cancer cell gene expression, we knockdown Lrp1 in EO771 cells and conducted RNASeq.

first: Schayan

last: Faraj Tabrizi


title: ALFIN-like proteins link histone H3K4me3 with H2A ubiquitination and coordinate diverse chromatin modifications in Arabidopsis [ATAC-seq]

overall_design: Examination of chromatin accessibility in wild type and al2/4/5/6/7 mutant


title: Expression Data from C10 cells and C10 tumours treated with live and UV BHV-1 with and without Mitomycin C

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

summary:
The field of viral immunotherapies is beginning to appreciate that eliciting an anti-tumour immune response, as opposed to viral replication, is what's most critical for efficacy.
Here was treated tumours and cells with our live virus and inactivated virus to measure their gene expression kinectics and examine what genes could be necessary for therapeutic efficacy

overall_design:
For in vitro analysis, C10 cells were infected with either live or UV BHV-1. RNA was harvested 6 and 12 hours post-infection. For in vivo analysis, mice bearing C10 tumours were treated with UV or live BHV-1 with Mitomycin C (mito) and RNA was harvested at 5 days post beginning of treatment

The 1M0-12, 2M0-12, and 3M0-12 have two sample records (i.e. analysis1 and analysis2). Each sample data table contains the data generated from the same raw CEL file but in a different analysis (ie. 2 separate .chp files). The .CEL file is linked to the corresponding analysis1 sample records.

The GSE223637 samples have been re-analyzed in the current study.

first: Enzo

last: Baracuhy

first: Olga

last: Cormier


title: ECM29/Proteasome-Mediated Self-Antigen Generation by CNS-Resident Neuroglia Promotes Regulatory T Cell Activation

first: Pei-Lin

address: No. 128 Acdemia Rd., Section 2, Nankang

institute: Institue of Molecular Biology, Academia Sinica

summary: Proteasomes generate antigenic peptides presented on cell surfaces - a process that in neuroglia is highly responsive to external stimuli. However, the function of the self-antigens presented by CNS parenchymal cells remains unclear. Here, we report that the fidelity of neuroglial self-antigens is crucial to suppress encephalitogenic T cell responses via elevating regulatory T cell (Treg) populations. We demonstrate that loss of the proteasome adaptor protein Ecm29 alters the efficacy and accuracy of antigen generation. Inducible oligodendroglia- or microglia conditional Ecm29 knockout mice exhibit higher susceptibility of experimental autoimmune encephalomyelitis (EAE) than control counterparts, coincident with reduced Tregs populations in spinal cord. Immunopeptidome profiling identifies self-antigens that modulate myelin-reactive T cell responses. Intraspinal AAV/Olig001-mediated expression of the self-antigen NDUFA1p ameliorated EAE and expands NDUFA1p-recognizing CD103+CD8+CD122+ Tregs. Thus, Ecm29/proteasome-controlled, neuroglia-derived self-antigens modulate CNS immune tolerance.

overall_design: To assess the influences of oligodendroglial Ecm29 cKO on proinflammatory response in the CNS parenchyma, we conducted transcriptomic analysis on spinal cord and brain tissues affected by EAE. Comparitive gene expression profilling RNA-seq data for the O4+ oligodendrocytes/Schwann isolated from the oligodendroglial Ecm29 cKO mice.

first: Cheng

last: Pei-Lin

first: Chen

last: Sheng-Wen


title: YTHDC1 affects the ubiquitination level of RAD51 by negatively regulating UBE3A expression and inhibits colorectal cancer cells apoptosis

city: shenzhen

first: jiadong

last: liu

address: 1088 Xueyuan Avenue

institute: Southern university of science and and technology

summary: Understanding the role of YTHDC1 in colorectal cancer development and DNA damage repair is crucial for advancing treatment strategies. In our study, we found that YTHDC1 is expressed at significantly higher levels in high-malignancy tissues compared to low-malignancy tissues. Silencing YTHDC1 effectively inhibits the proliferation of colorectal cancer cell lines and significantly increases cell apoptosis. We identified RAD51 as a key downstream target of YTHDC1. Knockdown of YTHDC1 reduced RAD51 protein levels, while silencing RAD51 also inhibited cancer cell proliferation. Interestingly, RNA sequencing indicated that YTHDC1 deletion did not affect RAD51 transcription but increased its ubiquitination through WB experiment. Our analysis revealed that reducing YTHDC1 raised E3 ligase UBE3A levels, which is involved in RAD51 ubiquitination and ubiquitination experiments confirmed that RAD51 is one of the ubiquitination substrates of UBE3A. Co-immunoprecipitation experiments confirmed interactions among YTHDC1, UBE3A, and RAD51, suggesting they form a complex that regulates homologous repair processes. Our study provides new insights into how YTHDC1 modulates RAD51 ubiquitin levels through post-translational modifications, offering valuable information for developing effective colorectal cancer therapies.

overall_design: In order to investigate the role of YTHDC1 in colorectal cancer, we utilized siRNA to knock down YTHDC1 in two different colorectal cancer cell lines in vitro, HCT116 and SW480.

first: Mingwei

last: Gao


title: Effect of Digoxin on clusters of circulating tumor cells in patients with metastatic breast cancer: a phase 1 trial

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

summary: The presence of circulating tumor cell (CTC) clusters is associated with disease progression, new metastasis formation and reduced survival in a variety of cancer types. In breast cancer, pre-clinical studies showed that inhibitors of the Na+/K+-ATPase can suppress CTC clusters shedding and block metastasis. Here, we conducted a prospective, open-label, phase I study in patients with metastatic breast cancer, where the primary endpoint was to determine whether a short (one week) treatment with the Na+/K+-ATPase inhibitor digoxin could reduce mean CTC cluster size. Mechanistically, transcriptome profiling of CTCs highlighted downregulation of cell-cell adhesion and cell cycle-related genes upon treatment with digoxin, in line with its cluster-dissolution activity. ClinicalTrials.gov identifier: NCT03928210.

overall_design: We isolated CTCs from a breast cancer patient (patient 5) at different time points. Single CTCs, CTC clusters and CTC-white blood cell (WBC)-clusters were pooled into tubes for molecular characterisation using next-generation sequencing. Amplified cDNA was prepared on-bead according to the Smart-seq2 protocol. Libraries were prepared using Nextera XT (Illumina) and sequenced on an Illumina NextSeq2000 instrument in 101-base-pair single-read mode. This yielded a median raw sequencing depth of 7.8 million reads per sample.

first: Marcus

last: Vetter

first: Bich

middle: D

last: Nguyen-Sträuli

first: Ilona

last: Krol

first: Alexander

last: Ring

first: Selina

last: Budinjas

first: Ana

last: Gvozdenovic

first: Maren

last: Vogel

first: Angela

last: Kohler

first: Cvetka

last: Grasic

first: Fabienne

last: Schwab

first: Viola

last: Heinzelmann-Schwarz

first: Walter

last: Weber

first: Christoph

last: Rochlitz

first: Grabiela

last: Pfister Kuster

first: Christian

last: Kurzeder

first: Nicola

last: Aceto


title: Diagnosing recipient- vs. donor-derived posttransplant myelodysplastic neoplasm via targeted single-cell mutational profiling

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Targeted genotyping-based identification of donor- and recipient-derived cells to resolve the origin of myelodysplastic syndrome (MDS) following allogeneic stem cell transplantation in the context of aplastic anemia (AA).

overall_design:
Single-cell whole transcriptome and U2AF1S34Y-specific profiling of bone marrow-derived mononuclear cells after diagnosis of AA, onset and progression (prog) of MDS following allogeneic stem cell transplantation.

Due to institutional data regulation and privacy policies, raw sequencing data files can currently not be released to protect the patient’s identity.

first: Jana

last: Ihlow

first: Samantha

last: Praktiknjo


title: Bulk RNAseq of Day 7 heart and lung iECs

status: Public on Dec 05 2024

city: Chapel Hill

first: Li

last: Qian

state: North Carolina

address: 111 Mason Farm Road, MBRB

department: Department of Pathology

institute: UNC

summary: Sox17-Erg direct reprogramming converts adult murine cardiac and lung fibroblasts into induced endothelial cells. This data evaluates the conversion of organ-specific Sox17-Erg iECs compared native fibroblast and endothelial cells.

overall_design: Day 7 heart iECs, lung iECs, lung fibroblasts, heart fibroblasts, lung native ECs, and heart native ECs.  Gene expression of each condition was then compared to look at the acquisition of organ-specific endothelial identity.

first: Gregory

last: Farber


title: Multiplexed inhibition of immunosuppressive genes with Cas13d for on-demand combinatorial cancer immunotherapy

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

summary: We devise Multiplex Universal Combinatorial Immunotherapy via Gene-silencing (MUCIG), as a versatile approach for combinatorial cancer immunotherapy. We harness CRISPR-Cas13d to efficiently target multiple endogenous immunosuppressive genes on demand, allowing us to silence various combinations of multiple immunosuppressive factors in the TME. Intra-tumoral AAV-mediated administration of MUCIG elicits significant anti-tumor activity with several Cas13d gRNA compositions (AAV-Cas13d-MUCIG). Optimization of TME targets by expression analysis led to a simplified off-the-shelf MUCIG targeting a four gene combination (PGGC: Pdl1/Cd274, Galectin9/Lgals9, Galectin3/Lgals3 and Cd47). AAV-Cas13d-PGGC showed significant in vivo anti-tumor efficacy in syngeneic tumor models. Single cell and flow profiling revealed that AAV-Cas13d-PGGC remodeled the TME by increasing CD8+ T cell infiltration and reducing neutrophils. MUCIG thus serves as a universal method to silence multiple immune genes in vivo, and can be delivered via AAV as a therapeutic approach. We devised an approach MUCIG (Multiplex Universal Combinatorial Immunotherapy via Gene-silencing) and designed MUCIG for targeting immunosuppressive genes at different scales of library pools. The first MUCIG pool included 313 genes selected based on these criteria. Subsequently, with a tiered approach, we designed three additional MUCIG pools (pool2: 152 genes; pool3: 55 genes; pool4: 19 genes). The distribution and coverage of gRNAs across all four pools were verified, confirming the robustness and specificity of this approach in the context of cancer immunosuppressive gene targeting therapy.

sample_organism:
Mus
Mus musculus
synthetic construct

platform_organism:
Mus
Mus musculus
synthetic construct

overall_design:
29 days post tumor injection , CD45+ cells were isolated from the colon26 or E0771 tumor following treatment with PBS, AAV-Cas13d-Vector or AAV-Cas13d-PGGC. The gRNA library readout PCR was performed for the MUCIG pool plasmids. And MUCIG gRNA library pool representation was analyzed.

*** Please note that the records have been updated with scRNAseq raw data on Mar 6,2025 ****

first: Feifei

last: Zhang

first: Ryan

last: Chow

first: Emily

last: He

first: Shan

last: Xin

first: Daniyal

last: Mirza

first: Yanzhi

last: Feng

first: Xiaolong

last: Tian

first: Nipun

last: Verma

first: Medha

last: Majety

first: Yueqi

first: Guangchuan

last: Wang

first: Sidi

last: Chen


title: BRAFV600E induces key features of LCH in iPSCs with cell type–specific phenotypes and drug responses

city: Vienna

first: Sebastian

last: Eder

address: Zimmermannplatz 10

country: Austria

institute: Children's Cancer Research Institute

summary: Langerhans cell histiocytosis (LCH) is a clonal hematopoietic disorder defined by tumorous lesions containing CD1a+/CD207+ cells. Two severe complications of LCH are systemic hyperinflammation and progressive neurodegeneration. The scarcity of primary samples and lack of appropriate models limit our mechanistic understanding of LCH pathogenesis and affect patient care. We generated a human in vitro model for LCH using induced pluripotent stem cells (iPSCs) harboring the BRAFV600E mutation, the most common genetic driver of LCH. We show that BRAFV600E/WT iPSCs display myelo-monocytic skewing during hematopoiesis and spontaneously differentiate into CD1a+/CD207+ cells that are similar to lesional LCH cells and are derived from a CD14+ progenitor. BRAFV600E modulates the expression of key transcription factors regulating monocytic differentiation and leads to an upregulation of pro-inflammatory molecules and LCH marker genes early during myeloid differentiation. BRAFV600E-induced transcriptomic changes are reverted upon treatment with MAPK-pathway inhibitors (MAPKi). Importantly, MAPKi does not affect myeloid progenitors but reduces only the mature CD14+ cell population. Furthermore, iPSC-derived neurons (iNeurons) cocultured with BRAFV600E/WT microglia-like cells (iMGL), differentiated from iPSC-derived CD34+ progenitors, exhibit signs of neurodegeneration with neuronal damage and release of neurofilament light chain. In summary, our model provides a platform to study the effect of BRAFV600E in different hematopoietic cell types and provides a tool to compare and identify novel approaches for the treatment of BRAFV600E-driven diseases.

overall_design:
Patient-derived iPSCs were created and analysed using single-cell RNA-seq. For iMonocyte differentiation 8 samples were processed: 2 are derived from iPSC_LCH_8 cell line (patient derived), one is WT, the other is V600E (the mutated one  has a XYY karyotype). Both samples are harvested at D14 of Monocytic differentiation. 4 are derived from iPSC_LCH_15 cell line (patient derived) 2 are WT, 2 are V600E. All 4 samples are harvested at D14 of Monocytic differentiation. 2 are derived from iPSC_LCH_15 cell line (patient derived) one is WT, the other is V600E.  These are the samples harvested at D11 of Monocytic differentiation; For iMonocyte treatment :3 samples in total, all derived from iPSC_LCH15 (patient derived) and all V600E; For iLCH: 2 samples in total, both derived from iPSC_LCH15 (patient derived) and both V600E.
***Submitters state that, using patient-derived samples of a rare disease in a small country, raw data could not be provided due to patient privacy concerns****

first: Giulio

last: Abagnale

first: Raphaela

last: Schwentner

first: Philipp

last: Soussia-Weiss

first: Wouter

last: van Midden

first: Caterina

last: Sturtzel

first: Ulrike

last: Pötschger

first: Ingrid

last: Simonitsch-Klupp

first: Christoph

last: Hafemeister

first: Florian

last: Halbritter

first: Martin

last: Distel

first: Caroline

last: Hutter


title: ChIPseq iEC reprogramming

first: Li

last: Qian

summary: SOX17 and ERG ChIPseq of SEG aiEC reprogramming of cardiac fibroblasts into endothelial cells

overall_design: SOX17 and Erg ChIP sample preperation of Day 3 samples

first: Gregory

last: Farber


title: A single nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation [Bulk mRNA-seq]

city: La Jolla

first: Wolfgang

last: Busch

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: The periderm, forming during secondary growth in the Arabidopsis root, serves as a protective outer barrier in many seed plant species. This multi-layered tissue is comprised of three distinct cell types: the phellogen, phellem and phelloderm. Periderm development has become a trait of interest to increase plant resilience and plant-mediated CO2 sequestration in soils. However, the genes underlying periderm development remain largely unknown. Employing single-nuclei sequencing, we have generated an expression atlas capturing the transcriptional landscape of the Arabidopsis root periderm. Using transcriptional reporter lines, we show that these data can be used to accurately track the progression of the three distinct periderm cell layers across multiple, transcriptionally unique, developmental stages. Making use of these data, we identify MYB67 as a novel regulator of periderm development and show that this gene serves as a developmental switch for the onset of phellem cell maturation. Our periderm expression atlas represents a rich resource that can be used to fuel novel discoveries and engineering efforts in this fascinating and important tissue.

overall_design: RNA Sequencing of 14 day-old Arabidopsis thaliana myb67 mutant to identify genes and pathways this transcription factor regulates.

first: Charlotte

middle: N

last: Miller

first: Sean

last: Jarell Hurtardo

first: Manisha

last: Haag

first: Sara

last: Ye

first: Mathew

last: Simenc

first: Paloma

last: Alvarez-Maldonado

last: Behnami

first: Ling

last: Zhang

first: Joseph

last: Swift

first: Jingting

last: Yu

middle: R

last: Ecker

first: Julie

last: Law


title: DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs [rna_seq_kc_ddx50_kd]

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: Glucose, traditionally recognized as a primary energy source, has recently emerged as a key regulator of protein interactions, particularly when intracellular glucose levels increase during cellular differentiation. Recent research has unveiled the intriguing phenomenon of glucose binding to a variety of proteins. Here, we focus on DDX50, a pivotal RNA helicase with a crucial role in epidermal differentiation. The interaction between glucose and the ATP-binding domain of DDX50 induces a significant change in the protein's conformation, resulting in the dissociation of DDX50 dimers. In the context of cellular differentiation, the increase in glucose levels promotes the formation of a complex involving DDX50, RNA, and STAU1. This complex, in turn, influences RNA structures and functions as a stabilizing force for the mRNA of key pro-differentiation genes. These genes include TINCR, OVOL1, CEBPB, PRDM1 and JUN. These findings reveal a previously unrecognized mechanism by which glucose exerts its influence, demonstrating its remarkable capacity to modulate the dimerization and function of the RNA helicase DDX50, which plays a critical role in tissue differentiation.

overall_design:
10 samples: shDDX50 knock-downs vs shControl. Four sets of donor tissue and four control shRNA samples. Three different shRNAs against DDX50.

***Raw data have been deposited in dbGaP (phs003766.v1.p1)***

first: Weili

last: Miao

first: Paul

last: Khavari


title: DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs [clip_stau1]

overall_design:
18 samples of CLIP-seq for DDX50 in primary keratinocytes. 6 biological replicates, three conditions (progenitor, differentiated in low glucose, and differentiated in high glucose).

***Raw data have been deposited in dbGaP (phs003766.v1.p1)***


title: Bulk RNAseq of Day 3 and Day 7 aiECs

last: Qian

summary: Sox17-Erg direct reprogramming converts adult murine cardiac fibroblasts into induced endothelial cells. This data evaluates the conversion of the Sox17-Erg iECs compared to single gene constructs.

overall_design: SEG aiECs, Sox17 aiECs, Erg aiECs, or control fibroblasts were harvested at Day 3 and Day 7.  Gene expression of each condition was then compared to look at the acquisition of endothelial identity.

last: Farber


title: DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs [DMS-Seq]

overall_design:
24 samples of in vitro DMS probing data against total RNA from keratinocytes, with no DMS control, BSA control, glucose, or other proteins added.

***Raw data have been deposited in dbGaP (phs003766.v1.p1)***


title: DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs [rna_seq_stability_stau1]

overall_design:
Effect of STAU1 on RNA stability. 14 samples, two biological replicates, each with its own shRNA control. Three shRNAs against STAU1 (#1, #2 #3). RNA levels assayed before or after 4 h of actinomycin D treatment.

***Raw data have been deposited in dbGaP (phs003766.v1.p1)***


title: DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs [rna_seq_stability_ddx50]

overall_design:
Effect of DDX50 on RNA stability. 12 samples, two biological replicates, each with its own shRNA control. Two shRNAs against DDX50 (#1 and #4). RNA levels assayed before or after 4 h of actinomycin D treatment.

***Raw data have been deposited in dbGaP (phs003766.v1.p1)***


title: A single nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation [DAP-seq]

last: Busch

overall_design: DNA Affinity Purification Sequencing using the transcription factor MYB67 to identify its direct targets in Arabidopsis thaliana.

last: Miller


title: DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs [rna_seq_organoid_ddx50]

overall_design:
20 samples. 2 technical replicates and 2-4 biological replicates per condition. 4 conditions: control shRNA and three different shRNAs against DDX50.

***Raw data have been deposited in dbGaP (phs003766.v1.p1)***


title: A single nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation [snRNA-seq]

overall_design: Single-nucleus RNA Sequencing of samples of 6-14 day-old Arabidopsis thaliana whole root without the tip to explore the transcriptional landscape and development of mature roots.

last: Jarell Hurtardo

last: Haag


title: DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs [ClIP-Seq ddx50]


title: Single cell analysis of MCF7-derived multi-organ metastases

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Bone metastases can disseminate to secondary sites and promote breast cancer progression creating additional clinical challenges. The mechanisms contributing to secondary metastasis are barely understood. Here, we evaluate the prediction power of Her2+ circulating tumor cells (CTCs) after analyzing over 13,000 CTCs from a cohort of 137 metastatic breast cancer (MBC) patients with initial HR+/Her2- status and employed preclinical models of bone metastasis (BM) to validate the role of Her2+ CTCs in multi-organ metastases. While Her2+ expression was higher in patients with bone metastasis, experimental analyses revealed that a majority of these Her2+ CTCs derived from bone lesions were more dependent on Her2 activity and more susceptible to anti-Her2 treatment. Targeting the bone-mediated Her2 induction reduces CTC detection and abrogates secondary metastasis from bone. Overall, we elucidate that Her2+ CTCs can serve as a non-invasive biomarker for BM formation with high therapeutic benefit for HR+ MBC patients.

overall_design:
Multi-organ metastasis model of MCF7 cells: Single cell analysis.
5x105 luciferase- and RFP-expressing MCF7 were injected simultaneously to the right hind limb of nude mice via intra-iliac artery inject and in the mammary fat pad of nude mice. This led to multi-organ metastasis formation in various organs including ovaries and lung. Following bioluminescence ex vivo imaging validation, various organs were enzymatically dissociated, and expanded in vitro in regular DMEM (10% FBS, 1x Pen/Strep) media for a few weeks. Cancer cells which were purified through Cell sorting based on RFP expression. Samples were sequenced using a CellPlex multiplexing approach from 10X Genomics

first: Igor

last: Bado

first: Dan

last: Hasson

first: Deniz

last: Demircioglu

first: Gargi

last: Damle


title: RNA-Seq analysis of 9G8-RNAi intestines in Drosophila

status: Public on Dec 04 2024

city: Reading

first: Justin

last: DiAngelo

state: PA

address: 2100 Stoudt Rd

institute: Penn State Berks

summary: Previous studies from our lab have characterized a group of splicing factors called SR proteins that function to identify intron/exon borders in regulating metabolic homeostasis in the Drosophila fat body.  Decreasing the function of one SR protein, 9G8, causes an increase in triglyceride storage; however, the function of 9G8 in other metabolic tissues like the fly intestine is not known.  Decreasing 9G8 in the Drosophila intestine results in the accumulation of triglycerides; however, the 9G8 target genes responsible for this phenotype are unknown.  To address this question, we performed RNA sequencing on Drosophila intestines with 9G8 levels reduced by RNAi.

overall_design: Drosophila intestine mRNA profiles of yolk-Gal4>9G8-RNAi intestines compared to yolk-Gal4>GFPdsRNA control fat bodies (3 samples of each genotype).


title: DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs [RNA-Seq adipocytes]

overall_design: 10 samples, two replicates, 5 conditions (control shRNA, two shRNAs against DDX50 and two against STAU1).


title: Cell-Type-Specific Splicing of Transcription Regulators and Ptbp1 by Rbfox1/2/3 in the Developing Neocortex

city: Chicago

first: Xiaochang

last: Zhang

state: IL

department: Department of Human Genetics

institute: University of Chicago

summary: This study investigates how master splicing regulators interact and the extent to which transcription regulators are spliced differently during brain development. Cell-type-specific RNA-Seq analyses of the developing neocortex uncover variable expression of the Rbfox1/2/3 genes and enriched splicing events in transcription regulators, altering protein isoforms or inducing nonsense-mediated mRNA decay. Transient expression of Rbfox proteins in radial glial progenitors induces neuronal splicing events preferentially in transcription regulators such as Meis2 and Tead1. Surprisingly, Rbfox proteins promote the inclusion of a mammal-specific alternative exon and a previously undescribed poison exon in Ptbp1. Simultaneous ablation of Rbfox1/2/3 in the neocortex downregulates neuronal isoforms and disrupts radial neuronal migration. Furthermore, the progenitor isoform of Meis2 promotes Tgfb3 transcription, while the Meis2 neuron isoform promotes neuronal differentiation. These observations indicate that transcription regulators are differentially spliced between cell types in the developing neocortex.

overall_design: This study includes RNA-seq data from four sets of experiments: [1] RNA-Seq of enriched mouse cortical neural progenitor and neuron populations isolated from embryonic 14.5 day (E14.5) dorsal forebrains, using Tg(Eomes/Tbr2:EGFP) and Tg(Tubb3:EGFP) BAC transgenic lines: Tbr2_EGFP_negative (2 replicates, enriched for radial glial cells or RGCs); Tbr2_EGFP_positive (2 replicates, enriched for intermediate progenitor cells, or IPCs); Tubb3_EGFP_positive( 2 replicates, enriched for neurons). [2] Single-cell Long-Read RNA-sequencing (PacBio): Wild-type E14.5 dorsal cortex. [3] Rbfox3 overexpression and RNA-Seq in the developing brain: In utero electroporation on E13.5 and RNA-Seq of FACS-sorted EGFP-positive cells on E14.5: Control pCAG-IRES-EGFP empty vector (2 replicates); Rbfox3 overexpression, pCAG-Rbfox3-IRES-EGFP (2 replicates). [4] Meis2 isoform overexpression and RNA-Seq in the Neuro2a cell line: Control empty vector (4 replicates); Meis2 neuron-isoform overexpression (4 replicates); Meis2 RGC-isoform overexpression (4 replicates)

first: Xiangbin

last: Ruan

first: Kaining

last: Hu

first: Yalan

last: Yang

first: Runwei

first: Elizabeth

last: Tseng

first: Bowei

last: Kang

first: Aileen

last: Kauffman

first: Rong

last: Zhong


title: Matrix stiffness enhances cancer-macrophage interactions and M2-like macrophage accumulation in the breast tumor microenvironment

city: Houston

first: Cynthia

last: Reinhart-King

state: TX

address: 6100 Main Street

department: Biomedical Engineering

institute: Rice University

summary: We used single-cell RNA sequencing to investigate the differences in the transcriptional landscapes between stiff and compliant MMTV-PyMT mouse mammary tumors. We found similar compositions of cancer and stromal subpopulations in compliant and stiff tumors but differential intercellular communication and a significantly higher concentration of tumor-promoting, M2-like macrophages in the stiffer tumor microenvironments.

overall_design: To investigate the architectural effects of matrix stiffness on the tumor microenvironment, we performed scRNAseq on stiff and compliant MMTV-PyMT mammary tumors. To obtain compliant and stiff tumors, MMTV-PyMT mice were treated with BAPN, a lysyl oxidase inhibitor, or vehicle control, respectively. Tumors were dissociated to form single cell suspensions and encapsulated using a custom inDrop platform. Tumors were excised, encapsulated, and sequenced pairwise in 3 batches on separate days and sequencing runs. All sequencing results were filtered using several quality control methods prior to analysis. Inflection point gating for total counts per cell was applied to each sample individually to remove cells with low library size and an upper threshold was applied to remove droplets that may have contained more than 1 cell. Additionally, cells containing a high proportion of mitochondrial genes were removed.

last: Taufalele

first: Wenjung

last: Wang

first: Alan

last: Simmons

first: Austin

last: Southard-Smith

first: Bob

last: Chen

first: Joshua

last: Greenlee

first: Michael

last: King

first: Ken

last: Lau

first: Duane

last: Hassane

first: Francois

last: Bordeleau


title: Activation of imprinted gene Pw1 promotes cardiac fibrosis after ischemic injury [ChIP-seq]

city: shanghai

first: Shan

last: Kou

address: No.393 Middle Huaxia Road

department: Life Science and Technology

institute: ShanghaiTech University

summary: The activation of fibroblasts and production of extracellular matrix (ECM) after cardiac injury has been the focus of research on cardiac fibrosis. Whether imprinted genes play a role in the fibrogenesis or extracellular matrix production after heart damage has not been studied. Here, we show that the imprinted gene Pw1 directed ECM production by regulating de novo purine synthesis (DNPB) after myocardial infarction (MI). After MI, the DNA methylation of the imprinting control region (ICR) of Pw1 gene in the injured area was reduced and both alleles of Pw1 in fibroblasts are activated. Further, loss of Pw1 in fibroblasts can enhance cardiac function, reduce cardiac fibrosis and extracellular matrix secretion after cardiac injury. To screen the targets of PW1, we contrasted chromatin immunoprecipitation (ChIP)-seq and RNA-seq using the injured left ventricles at 7 days post-MI, we next found PW1 binds directly upstream of the Pfas gene that encodes one of the DNPB enzymes phosphoribosylformylglycinamidine synthase (PFAS) in heart after injury. Similarly, specific knockout of pfas in fibroblasts also improves cardiac function and reduces ECM production. Moreover, de novo purine biosynthesis is necessary for ECM production in activated fibroblasts. These observations implicate understanding the mechanism of Pw1 in the repair of cardiac injury will provide new ideas for the treatment of cardiovascular diseases.

overall_design: To screen the targets of PW1, we performed chromatin immunoprecipitation (ChIP)-seq using the injured left ventricles at 7 days post-MI

first: Zhengkai

last: Lu

first: Defang

last: Deng

first: Min

last: Ye

first: Yu

last: Sui

first: Lieyang

last: Qin

first: Teng

last: Feng

first: Zhen

last: Jiang

first: Jufeng

last: Meng

first: Chao-Po

last: Lin

first: Xiajun

last: Li

first: Chen

last: Liu

first: Juan

last: Tang

first: Hui

last: Zhang


title: Comparative proteomic landscapes elucidate human preimplantation development and failure

city: Shanghai

address: Yueyang Road Street

institute: Center for Excellence in Brain Science and Intelligence Technology, Chineses Academy of Sciences

summary: Understanding mammalian preimplantation development, particularly in humans, at the proteomic level remains limited. Here, we applied our comprehensive solution of ultrasensitive proteomic technology to measure the proteomic profiles of oocytes and early embryos and identified nearly 8,000 proteins in humans and over 6,300 proteins in mice. We observed distinct proteomic dynamics before and around zygotic genome activation (ZGA) between the two species. Integrative analysis with translatomic data revealed extensive divergence between translation activation and protein accumulation. Multi-omic analysis indicated that ZGA transcripts often contribute to protein accumulation in blastocysts. Using mouse embryos, we identified several transcriptional regulators critical for early development, thereby linking ZGA to the first lineage specification. Furthermore, single-embryo proteomics of poor-quality embryos from over 100 patient couples provided insights into preimplantation development failure. Our study may contribute to reshaping the framework of mammalian preimplantation development and opening avenues for addressing human infertility.

overall_design: For gene knock out, mouse zygotes were collected by superovulation of 3- to 4-week-old B6D2F1 females mated with males of the same strain. Cas9 protein (final concentration 100 ng/μL) was mixed with three different sgRNAs (final concentration 50 ng/μL per sgRNA) and injected into the cytoplasm of zygotes in M2 medium with CB using a Piezo-driven micromanipulator (Prime Tech). Then, the injected embryos were cultured in KSOM medium at 37 °C with 5% CO2.

first: Wencheng

last: Zhu

first: Yan

first: Lei

last: Gu

first: Wenjun


title: Transcriptomic and Epigenomic Signatures Distinguish High- and Low-Risk Endotypes for Liver Tumor Development [RNA-Seq liver]

first: Amrit

last: Koirala

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: The epigenome is a target for environmental exposures, and a potential determinant of inter-individual differences in response.  In genetically identical C57Bl/6 mice exposed from gestation to weaning to the endocrine disrupting chemical (EDC) tributyltin (TBT), tumor development later in life varied across multiple cohorts over time and depending on sex and diet.  In one cohort where approximately half of TBT-exposed male mice developed tumors at 10 months (Katz, 2020), transcriptomic (RNA-seq) and epigenomic (ChIP-seq) profiling was performed on blood and liver tissue from mice that developed tumors (i.e. “high-risk”) and equivalently exposed mice did not (i.e “low-risk”).  Blood transcriptomic signatures separated TBT-exposed from vehicle controls but did not discriminate between animals that developed tumors vs those that did not.  However, uninvolved liver tissue of mice with tumors exhibited transcriptomic and epigenomic signatures distinct from liver tissue of mice without tumors and had many features in common with tumors.  These high-risk transcriptomic and epigenomic features were also found in 10/26 TBT-exposed mice at 5 months, indicating that this risk signature preceded tumor development.  Thus, while early life exposure to TBT exhibits variable penetrance for tumor development, indicating TBT-exposure is not sufficient for tumorigenesis, increased risk for tumor development is linked to epigenomic and transcriptomic reprogramming of the liver induced by this EDC.

overall_design: This dataset consists of bulk RNA-seq data generated from the livers of3-week, 5-month, or 10-month-old WT C57Bl/6 mice in response maternal exposure to tributyltin (TBT) through weaning

first: Cheryl

middle: L

last: Walker

first: Cristian

last: Coarfa

first: Rahul

middle: K

last: Jangid

first: Sandra

last: Grimm

first: Tia

last: Talley


title: Sequestration of ribosomal subunits as inactive 80S by targeting eIF6 limits mitotic exit and cancer progression

city: Saint Louis

first: Sofia

last: Origanti

state: MO

address: 3507 laclede avenue

institute: Saint Louis University

summary: Moderating the pool of active ribosomal subunits is critical for maintaining global translation rates. A crucial factor for modulating the 60S ribosomal subunits is eukaryotic translation initiation factor 6. Release of eIF6 from 60S is essential to permit 60S interactions with 40S. Here, using the N106S mutant of eIF6, we show that disrupting eIF6 interaction with 60S leads to an increase in vacant 80S. It further highlights a dichotomy in the anti-association activity of eIF6 that is distinct from its role in 60S biogenesis and shows that the nucleolar localization of eIF6 is not dependent on uL14-BCCIP interactions. Limiting active ribosomal pools markedly deregulates translation especially in mitosis and leads to chromosome segregation defects, mitotic exit delays and mitotic catastrophe. Ribo-Seq analysis of the eIF6-N106S mutant shows a significant downregulation in the translation efficiencies of mitotic factors and specifically transcripts with long 3′UTRs. eIF6-N106S mutation also limits cancer invasion, and this role is correlated with the overexpression of eIF6 only in high-grade invasive cancers suggesting that deregulation of eIF6 is probably not an early event in cancers. Thus, this study highlights the segregation of eIF6 functions and its role in moderating 80S availability for mitotic translation and cancer progression.

overall_design: This study includes Ribo-seq and RNA-seq data for both Wt and eIF6 mutant cells.

first: Poonam

last: Roshan

first: Aparna

last: Biswas

first: Stella

last: Anagnos

first: Riley

last: Luebbers

first: Kavaya

last: Harish

first: Sinthyia

last: Ahmed

first: Megan

first: Nicholas

last: Nguyen

first: Gao

last: Zhou

first: Frank

last: Tedeschi

first: Vivian

last: Hathuc

first: Zhenguo

first: Zachary

last: Hamilton


title: CD103+CD56+ ILCs are associated with an immunosuppressed tumour microenvironment (bulk RNA-Seq)

city: Toronto

first: Pamela

last: Ohashi

address: 610 University Ave

institute: Princess Margaret Cancer Centre

summary: Immunotherapies have had unprecedented success for multiple cancer types, albeit with variable response rates. Unravelling the complex network of immune cells within the tumour microenvironment (TME) may provide additional insights to enhance anti-tumour immunity and improve clinical response. Here, we identified a CD103-expressing CD56+ ILC subset that were associated with a poor proliferative capacity of tumour-infiltrating lymphocytes (TILs) in culture. We demonstrate that CD103+CD56+ ILCs isolated directly from tumors represent a distinct ILC population that expressed unique surface markers, transcription factor networks, and transcriptomic profiles compared to CD103-CD56+ NK cells. Using multiple approaches, we found that these CD103+CD56+ ILCs were associated with CD8+ T cells with a reduced expression of GZMB. This study identifies 59 a population of CD103+CD56+ ILCs with potentially inhibitory functions, that are associated with a TME that includes CD8+ T cells with poor anti-tumour activity. Further studies focusing on these potentially inhibitory cells may provide insights into understanding the biology of an inhibitory TME.

overall_design: 4 paired samples of CD103+CD56+ and CD103-CD56+ ILC cells, sorted from 4 High Grade Serous Ovarian Cancer patient samples, profiled by bulk Illumina RNA-Seq.

first: Chung

last: Douglas

first: Ohashi

last: Pamela


title: Transcriptome analysis of Dyrk1a-knockin (Ile48LysfsX2) and wild-type mice age of P21 and P60

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

summary: Dyrk1A deficiency is linked to various neurodevelopmental disorders, including developmental delays, intellectual disability (ID) and autism spectrum disorders (ASD). Haploinsufficiency of Dyrk1a in mice reportedly leads to ASD-related phenotypes. However, the key pathological mechanisms remain unclear and human DYRK1A mutations remain uncharacterized in mice. Here, we generated and studied Dyrk1a-knockin mice carrying a human ASD patient mutation (Ile48LysfsX2; Dyrk1a-I48K mice). These mice display severe microcephaly, social and cognitive deficits, dendritic shrinkage, excitatory synaptic deficits, and altered phospho-proteomic patterns enriched for multiple signaling pathways and synaptic proteins.

overall_design: Whole brain transcriptome analysis of Dyrk1a-knockin ((Ile48LysfsX2)) and wild-type mice age of P21 and P60

first: Junyeop

last: Roh

first: Mihyun

last: Bae

first: Hyojin

last: Kang


first: Sofia

last: Origanti

first: Poonam

last: Roshan

first: Aparna

last: Biswas

first: Stella

first: Riley

last: Li

last: Lin


title: Transcriptomic and Epigenomic Signatures Distinguish High- and Low-Risk Endotypes for Liver Tumor Development [ChIP-Seq]

first: Amrit

last: Koirala

overall_design: This dataset consists of ChIP-Seq data generated from the livers of5-month or 10-month-old WT C57Bl/6 mice in response to maternal exposure to tributyltin (TBT) through weaning

first: Cheryl

last: Walker

first: Cristian

last: Coarfa

first: Rahul

last: Jangid

first: Sandra

last: Grimm

first: Tia

last: Talley


title: Transcriptomic and Epigenomic Signatures Distinguish High- and Low-Risk Endotypes for Liver Tumor Development [RNA-Seq blood]

overall_design: This dataset consists of bulk RNA-seq data generated from the blood of10-month-old WT C57Bl/6 mice in response maternal exposure to tributyltin (TBT), with 8 TBT samples and 7 vehicle control samples.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Pericarps from Wild-type and Mutant Fruits.

first: Ruohe

last: Yin

address: 800 Dongchuan RD. Minhang District

institute: Shanghai Jiao Tong University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analyze the difference of gene expression between wild-type and mutant during tomato fruit ripening progress.

overall_design: Fruit mRNA profiles of mature green (35) and breaker (38) stages in both wild-type (A) and mutant (cr) were generated by deep sequencing, in triplicate, using Illumina Novoseq 6000.


title: EMT-driven plasticity prospectively increases cell-cell variability to promote therapeutic adaptation in breast cancer

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

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

overall_design: Refer to individual Series


title: Impact of EMT-driven plasticity on phenotypic diversity dynamics under chemotherapy [organoids]

summary: Triple negative breast cancer (TNBC) is the most lethal breast cancer subgroup, as lack of targeted therapies and drug resistance reduce survival rates. Cellular plasticity enables cells to adapt non-genetically and overcome therapeutic pressure, thereby embodying a critical clinical hurdle. The epithelial-mesenchymal transition (EMT) is an example of phenotypic reprogramming linked to plasticity, drug resistance and metastasis. However, its exact impact on population diversity under therapeutic pressure is unknown. Here, we used single cell transcriptomics to investigate phenotypic diversity dynamics upon drug treatment in two human in vitro models of TNBC plasticity.

overall_design:
This series contains data on organoid cultures of human mammary epithelial (HME) cells in which EMT-driven plasticity is induced by ZEB1 expression prior to HRASG12V-mediated oncogenic transformation (48k cells)
Single cell cloning experiments were performed for each of the 2 populations analyzed (EMT- and EMT+). 2 different clones were used as replicates per population, and analyzed under two conditions : untreated (4 weeks) or treated (1 week untreated, followed by three weeks of doxorubicin treatment).

first: Lauriane

last: Muller

first: Frédérique

last: Fauvet


title: Impact of EMT-driven plasticity on phenotypic diversity dynamics under chemotherapy [spontaneous]

overall_design:
We used 2D cultures of ME cells in which part of mammary epithelial (Epi) cells spontaneously converts to a mesenchymal (Mes) subpopulation upon oncogenic transformation by shTP53-HRASG12V-hTERT, of which a fraction displayed further phenotypic drift (InB) (32k cells).
Single cell cloning experiments were performed for each of the 3 populations analyzed (Epi, Mes and InB). 2 different clones were used as replicates per population, and analyzed under two conditions : untreated (4 weeks) or treated (1 week untreated, followed by three weeks of doxorubicin treatment).


title: Cancer epigenome intervention by in-cell chemical catalysis for histone modification (ChIP-seq)

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: Chemical modification of histones dynamically regulates gene transcription and is closely related to disease pathogenesis including cancer. Targeting epigenome is thus a promising strategy for cancer chemotherapy. Here we report a novel histone acetylation catalyst BAHA-LANA-PEG-CPP44 that can intervene into cancer epigenome. The catalyst selectively entered leukemia cells, bound to chromatin, and acetylated endogenous histones, especially at H2BK120, in a HAT-independent manner. The catalytic histone acetylation attenuated chromatin binding of negative elongation factor E (NELFE), an RNA polymerase II pausing factor, and reprogramed transcription profile in leukemia cells. The in-cell chemical catalysis retarded proliferation of leukemia cells and reduced their tumorigenic potential in mice. Our catalyst is orthogonal to cancer epigenetic drugs targeting histone-modifying enzymes and may lead to a novel anti-cancer strategy.

overall_design: ChIP-seq in THP-1 cells treated by histone acetylation chemical catalyst system.

first: Yuki

last: Yamanashi

first: Shinpei

last: Takamaru

first: Atsushi

last: Okabe

last: Kaneda

first: Shigehiro

last: Kawashima

first: Motomu

last: Kanai


title: Cancer epigenome intervention by in-cell chemical catalysis for histone modification (RNA-seq)

overall_design: RNA-sequencing (RNA-seq) in THP-1 cells treated by histone acetylation chemical catalyst system.


title: Histopathology of the tongue in a mouse model of oculopharyngeal muscular dystrophy reveals progressive PABPN1 deposition associated with muscle wasting.

city: Leiden

first: Vered

last: Raz

address: Einthovenweg

department: Human genetics

country: Netherlands

institute: LUMC

summary: The tongue facilitates vital activities such as swallowing. Swallowing difficulties (dysphagia) are common in the elderly and in many adult-onset neuromuscular diseases. In oculopharyngeal muscular dystrophy (OPMD), dysphagia is often the first symptom. OPMD is an autosomal dominant myopathy caused by a trinucleotide expansion mutation in the gene encoding PABPN1. The expanded PABPN1 forms insoluble nuclear aggregates that reduce the levels of the soluble form. Clinical tongue involvement in OPMD has been documented but is poorly understood. Tongue histopathology was investigated in OPMD mouse models using light and electron microscopy. Muscle histopathology was predominantly affected by age. PABPN1 nuclear aggregates were found at moderate levels, whereas deposition of insoluble PABPN1 in blood vessels was already prominent in 4-month-old mice. RNA signatures of the OPMD tongue were enriched for mitochondrial and cytoskeletal genes, suggesting an energy and contractile deficit.

overall_design: Tongues from wild type in PABPN1A17/+ 12-month-old mice. N=4 per genotype.

first: V

first: M

last: Shademan


title: Cytokine stimulated keratinocytes

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: In order to study the molecular changes of keratinocytes under different inflammatory responses, we stimulated keratinocytes with different cytokines and conducted RNA-seq to profile the gene expression.

overall_design: Keratinocytes from 50 individuals were stimulated with 7 different cytokines.

first: Johann

last: Gudjonsson

first: Lam

last: Tsoi


title: A developmental atlas of mouse vestibular-like inner ear organoids

first: Alan

last: Cheng

address: 240 Pasteur Drive

institute: Stanford University

summary: In 2014, a method was introduced to differentiate mouse embryonic stem cells into inner ear vestibular-like sensory epithelia in vitro. The resulting inner ear organoids represent a potentially inexhaustible source of tissues for investigating mechanosensory hair cell development, function, and responses to ototoxic and regenerative treatments. However, there has been limited exploration into how closely the molecular characteristics of organoid-derived hair cells match those that develop in vivo. To address this gap, we have employed single-cell RNA sequencing (scRNA-seq) to generate a comprehensive atlas of inner ear organoid development at six stages, spanning the formation of definitive ectoderm to the emergence of sensory hair cells. Here, we specifically utilize our inner ear organoid atlas to define the dynamic changes in gene expression that occur during otic vesicle cell maturation into sensory epithelial supporting cells and hair cells.

overall_design: Inner ear organoids were generated using Fbxo2-Venus-Hygromycin-Cre mESCs following established protocols with minor modifications. Organoids were dissociated in biological duplicate at six developmental time points: days in vitro (DIV) 3, DIV4, DIV8, DIV11, DIV16, and DIV21. Cells were processed for scRNA-seq using 10X Genomics Chromium Single Cell 3' Reagents v3.1. After sequencing, we used Cell Ranger for read mapping and quantification, followed by further analysis using Seurat.

first: Maggie

middle: S

last: Matern

first: Stefan

last: Heller


title: Cancer epigenome intervention by in-cell chemical catalysis for histone modification


title: DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs [RNA-Seq cervical]

first: Douglas

last: Porter

institute: Stanford

summary: Glucose, traditionally recognized as a primary energy source, has recently emerged as a key regulator of protein interactions, particularly when intracellular glucose levels increase during cellular differentiation. Recent research has unveiled the intriguing phenomenon of glucose binding to a variety of proteins. Here, we focus on DDX50, a pivotal RNA helicase with a crucial role in epidermal differentiation. The interaction between glucose and the ATP-binding domain of DDX50 induces a significant change in the protein's conformation, resulting in the dissociation of DDX50 dimers. In the context of cellular differentiation, the increase in glucose levels promotes the formation of a complex involving DDX50, RNA, and STAU1. This complex, in turn, influences RNA structures and functions as a stabilizing force for the mRNA of key pro-differentiation genes. These genes include TINCR, OVOL1, CEBPB, PRDM1 and JUN. These findings reveal a previously unrecognized mechanism by which glucose exerts its influence, demonstrating its remarkable capacity to modulate the dimerization and function of the RNA helicase DDX50, which plays a critical role in tissue differentiation.

overall_design: 6 samples, control shRNA vs shRNAs against DDX50.

first: Weili

last: Miao

middle: F

first: Paul

last: Khavari