title: Transcriptomic (DNA microarray) and Metabolome (LC-TOF-MS) analyses of the liver in high-fat diet mice after intranasal administration of GALP (Galanin-Like Peptide)

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: The aim of this basic research is to test the efficacy of intranasal administration of Galanin-like Peptide (GALP) and its clinical application under the hypothesis that GALP prevents obesity in mice fed a high-fat diet (HFD). Focusing on the mechanism of regulation of lipid metabolism in peripheral tissues via the autonomic nervous system, we confirmed body weight changes after intranasal administration of GALP in diet-induced obesity (DIO) mice.

overall_design: Whole genome DNA microarray was carried out on the liver samples (liver tissue of DIO C57BL/6J mice was ground into a fine powder in liquid nitrogen and stored at -80°C until RNA isolation, and total RNA was extracted from powdered mouse liver tissue using the RNeasy Mini Kit ) to aimed to confirm the anti-obesity effects of intranasal administration of GALP in the diet-induced obesity (DIO) model mice.  To detect significantly differentially expressed genes between control (n=8) and GALP-treated (greater weight loss group, n=4) and control and GALP-treated (less weight loss group, N=4) samples, total RNA extracted from mouse liver tissue for each control (n=8) , GALP-treated (greater weight loss group, n=4) and GALP-treated (less weight loss group, N=4)  was pooled in each group, prior to DNA microarray analysis.

first: Fumiko

last: Takenoya

first: Junko

last: Shibato

first: Michio

last: Yamashita

first: Ai

last: Kimura

first: Satoshi

last: Hirako

first: Yoshihiko

last: Chiba

first: Naoko

last: Nonaka

first: Seiji

last: Shioda

first: Randeep

last: Rakwal


title: A snoRNA–tRNA modification network governs codon-biased cellular states [PARIS2-seq]

status: Public on Sep 21 2023

city: Tianjin

first: Minjie

last: Zhang

address: No22.Qixiangtai Rd.,Heping Dist

department: Department of Bioinformatics

country: China

institute: Tianjin Medical University

summary:
The dynamic balance between tRNA supply and codon usage demand is a fundamental principle in the cellular translation economy. However, the regulation and functional consequences of this balance remain unclear. Here, we use PARIS2 interactome capture, structure modeling, conservation analysis, RNA–protein interaction analysis, and modification mapping to reveal the targets of hundreds of snoRNAs, many of which were previously considered orphans. We identify a snoRNA–tRNA interaction network that is required for global tRNA modifications, including 2′-O-methylation and others. Loss of Fibrillarin, the snoRNA-guided 2′-O-methyltransferase, induces global upregulation of tRNA fragments, a large group of regulatory RNAs. In particular, the snoRNAs D97/D133 guide the 2′-O-methylation of multiple tRNAs, especially for the amino acid methionine (Met), a protein-intrinsic
antioxidant. Loss of D97/D133 snoRNAs in human HEK293 cells reduced target tRNA levels and induced codon adaptation of the transcriptome and translatome. Both D97/D133 single and double knockouts in HEK293 cells suppress Met-enriched proliferation-related gene expression programs, including, translation, splicing, and mitochondrial energy metabolism, and promote Met-depleted programs related to development, differentiation, and morphogenesis. In a mouse embryonic stem cell model of development, knockdown and knockout of D97/D133 promote differentiation to mesoderm and endoderm fates, such as cardiomyocytes, without compromising pluripotency, consistent with the enhanced development-related gene expression programs in human cells. This work solves a decade-old mystery about orphan snoRNAs and reveals a function of snoRNAs in controlling the codon-biased dichotomous cellular states of proliferation and development.

overall_design:
To investigate the novel functions of snoRNAs that guide 2’-O-methylation (Nm) modifications on tRNAs, we enriched the target snoRNAs using antisense oligos (ASOs), and also extracted the chromatin-associated RNAs (caRNAs).
The PARIS2 method was performed to capture the snoRNAs structure and interactions.

first: Kongpan

last: Li

first: Jianhui

last: Bai


title: A snoRNA–tRNA modification network governs codon-biased cellular states [RNAseq & Riboseq]

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To investigate the novel functions of snoRNAs that guide 2’-O-methylation (Nm) modifications on tRNAs, we established SNORD97, SNORD133 single and double knock out HEK293 and mESCs using CRISPR/Cas9 technology, we also generated FBL and DKC1 knock down HEK293 cells by siRNAs.
Total RNA sequencing was performed to analyze comparative gene expression profiles. Small RNA sequencing was performed to analyze the tRNA fragmentation after loss of the snoRNA-guided 2’-O-methylation modifications on tRNA. Ribosome profiling sequencing (ribo-seq) was performed to analyze the cause of reduced translation after CRISPR knockout of the D97/D133 family of snoRNAs,


title: Genome-wide Human Placenta Enhancer Identification and Association with Function, Differentiation, and Disease [PRO-seq]

status: Public on Sep 22 2023

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

summary: Genome-wide sites of active transciption were determined using an in-vitro transcription assay and filtered to identify extragenic enhancer RNAs (eRNAs) as markers of active genomic regulatory regions

overall_design: PRO-Seq was perfomed in human placenta tissue from first, second, and third trimester pregnancies

first: David

middle: M

last: Owen

first: Xuan

last: Huang

first: Anusha

last: Nagari

first: Tulip

last: Nandu

first: W

middle: L


title: A snoRNA–tRNA modification network governs codon-biased cellular states [RMseq]

overall_design:
To investigate the novel functions of snoRNAs that guide 2’-O-methylation (Nm) modifications on tRNAs, we isolated the small RNA (70-300nt) for RiboMethSeq to detect the Nm level.
The optimized RiboMethSeq method was performed to capture the 2’-O-methylation levels.


title: U2932 cells treated with ibrutinib and/or miR-28 in vitro

city: Madrid

first: Carmen

middle: Gómez-Escolar

last: Arias

state: Madrid

address: Calle Melchor Fernández Almagro 3

country: Spain

institute: CNIC

summary: Diffuse large B cell lymphoma (DLBCL) is the most common aggressive B cell lymphoma and accounts for nearly 40% of cases of B cell non-Hodgkin lymphoma. DLBCL is generally treated with R-CHOP chemotherapy, but many patients do not respond or relapse after treatment. Here, we analyzed the therapeutic potential of the tumor suppressor microRNA-28 (miR-28) for DLBCL, alone and in combination with the Bruton’s tyrosine kinase inhibitor ibrutinib. Combination therapy with miR-28 plus ibrutinib potentiated the anti-tumor effects of monotherapy with either agent by inducing a specific transcriptional cell-cycle arrest program that impairs DNA replication. The molecular actions of miR-28 and ibrutinib synergistically impair DNA replication by simultaneous inhibition of origin activation and fork progression. Moreover, we found that downregulation of the miR-28-plus-ibrutinib gene signature correlates with better survival of ABC-DLBCL patients. These results provide evidence for the effectiveness of a new miRNA-based ibrutinib combination therapy for DLBCL and unveil the miR-28-plus-ibrutinib gene signature as a new predictor of outcome in ABC-DLBCL patients.

overall_design: U2932 cells transduced with pTRIPZ-scramble or pTRIPZ-miR-28 were induced with doxycycline (0.5 µg/ml) for 24 hours. Cells were then treated with 25 µM ibrutinib, while maintaining doxycycline in the medium. As a control, cells were treated with vehicle (DMSO). RFP+ cells were isolated in a FACS Aria cell sorter at 20 h after the start of ibrutinib treatment. RNA-Seq analysis was performed on two independent combined-treatment experiments.Libraries for gene expression were generated.

first: Teresa

last: Fuertes

first: Emigdio

last: Álvarez-Corrales

first: Patricia

last: Ubieto-Capella

first: Álvaro

last: Serrano-Navarro

last: Gómez-Escolar

first: Antonio

last: de Molina

first: Juan

last: Méndez

first: Almudena

middle: R

last: Ramiro

first: Virginia

middle: G

last: de Yébenes


title: SUDHL4 cells treated with ibrutinib and/or miR-28 in vitro

overall_design: SUDHL4 cells transduced with pTRIPZ-scramble or pTRIPZ-miR-28 were induced with doxycycline (0.5 µg/ml) for 24 hours. Cells were then treated with 25 µM ibrutinib, while maintaining doxycycline in the medium. As a control, cells were treated with vehicle (DMSO). RFP+ cells were isolated in a FACS Aria cell sorter at 20 h after the start of ibrutinib treatment. RNA-Seq analysis was performed on two independent combined-treatment experiments.Libraries for gene expression were generated.


title: A snoRNA–tRNA modification network governs codon-biased cellular states

first: Minjie

last: Zhang

overall_design: Refer to individual Series


title: MD-901 cells treated with ibrutinib and/or miR-28 in vitro

overall_design: MD-901 cells transduced with pTRIPZ-scramble or pTRIPZ-miR-28 were induced with doxycycline (0.5 µg/ml) for 24 hours. Cells were then treated with 25 µM ibrutinib, while maintaining doxycycline in the medium. As a control, cells were treated with vehicle (DMSO). RFP+ cells were isolated in a FACS Aria cell sorter at 0, 4, and 20 h after the start of ibrutinib treatment. RNA-Seq analysis was performed on two independent combined-treatment experiments.Libraries for gene expression were generated.


title: Control or miR-28-transduced MD-901 tumors grown in NSG mice and treated with ibrutinib

overall_design: pTRIPZ-scramble (control) or miR-28-transduced MD-901 cells were grown subcutenously in NSG mice. Detectable tumors were treated with miR-28, ibrutinib or combined miR-28+ibrutinib treatment. At day 10 after treatment, three independent tumors treated with each condition were used for RNA-Seq.Libraries for gene expression were generated.


title: Gene expression profiles at the single nuclei level of hypothalamic oxytocin neurons from mice fed either standard chow (SC) diet or high-fat/high-sugar (HFHS) diet

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

summary: To explore the transcriptional heteroeneity of oxytocin neurons, we fluorescence-assisted nuclei sorting (FANS) conditionally tagged nuclei from Oxt-ires-Cre;CAG-Sun1sfGFP mice. All mice were littermates and fed either SC diet or HFHS diet for 4 months. Individual nuclei were sorted into 384w plates and subjected to SMART-seq2.

overall_design: Hypothalamic oxytocin neurons from Oxt-ires-Cre;CAG-Sun1sfGFP mice were  isolated by Fluorescence-activated nuclei sorting (FANS) according to the presence or absence of sfGFP signal and analyzed using snRNAseq2.

first: Tim

last: Gruber

first: Franziska

last: Lechner

first: Cahuê

last: De Bernardis Murat

first: Raian

last: Eduardo Contreras

first: Eva

last: Sanchez-Quant

first: Viktorian

last: Miok

first: Ophelia

last: Le Tuc

first: Ismael

last: Gonzales-Garcia

first: Elena

last: Garcia-Clave

first: Ferdinand

last: Althammer

first: Quirin

last: Krabichler

first: Lisa

last: DeCamp

first: Russell

last: Jones

first: Rhiannan

last: Hope Williams

first: Paul

last: Pfluger

first: Timo

middle: D

last: Müller

first: Steve

last: C Woods

first: Celia

last: P Martinez-Jimenez

first: Matthias

middle: H

last: Tschöp

first: Valery

last: Grinevich

first: Cristina

last: García-Cáceres


title: Enhancer retargeting at the PAX5/ZCCHC7 locus

city: New York

first: Uttiya

last: Basu

address: 701 West 168 Street

institute: Columbia University

summary: 2 kinds of SU-DHL-10 cell clones (Pax5-TSS2mut/deletion) were generated to  investigate enhancer relocation, we campared 4C-seq data between the Pax5-TSS2mut/deletion clones and wild type SU-DHL-10.

overall_design: 2 baits were designed within the Zcchc7 promotor region according to Hi-C data in GM12878, 4C-seq data were compared between the Pax5-TSS2mut/deletion clones and wild type SU-DHL-10

first: Lijing

last: Wu

first: Wanwei

last: Zhang

first: Gerson

last: Rothschild

first: Junghyun

last: Lim

first: Rebecca

last: Leeman-Neill


title: Modeling the nascent RNA transcriptome with chrTT-seq to extract chromatin dissociation dynamics on newly transcribed RNA.

city: Heraklion

first: Evgenia

last: Ntini

address: Nik. Plastira 100

country: Greece

institute: IMBB-FORTH

summary:
To capture chromatin dissociation dynamics of nascent RNA transcripts we labeled MCF-7 cells with 4-thio-uridine (4-SU) for 8 minutes, then chased with an excess of uridine for 5, 10, 15 and 20 min. At each pulse-chase time point we performed TT-seq from the chromatin-associated and nucleoplasmic fraction.
The ratios of spike-in normalized chromatin-associated to chromatin-released nascent RNA read coverage over genomic features (transcripts' last exons) were fitted on an exponential decay function to extract an estimated chromatin association half-live time for each transcript.

overall_design: Briefly, chromatin fractionation was performed at 0.5 M urea. RNA was extracted with acidic phenol from the chromatin-associated and chromatin-released fraction, and chemically fragmented (0.1 M NaOH on ice) before 4-SU based purification of newly transcribed RNA. A mix of three 4SU-labeled and three unlabeled ERCC spike-ins were added to RNA prior to fragmentation. Libraries for Illumina sequencing were constructed according to the TrueSeq Stranded mRNA Library Preparation Kit.

first: Annalisa

last: Marsico


title: miR28-based combination therapy impairs aggressive B Cell Lymphoma growth by rewiring DNA replication

first: Carmen

last: Arias

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


title: MiR34 Contributes to Spinal Muscular Atrophy and AAV9-mediated Delivery of MiR34a Ameliorates the Motor Deficits in SMA Mice

city: Taipei

first: Jun-An

last: Chen

address: 128 Academia Road, Section 2

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary:
MiR34 exhibits consistent downregulation during SMA progression in both human and rodent contexts. Mir34 family-knockout mice display axon swelling and reduced neuromuscular junction (NMJ) end-plates, recapitulating SMA pathology. MiR34 family may target synapse formation and several core pathways that are disrupted in SMA at early postnatal stages.
We performed RNA seq on thoracic and lumbar spinal cord and compare gene expression profiles between P14 wild type (WT) and  Mir34/449 triple knockout (TKO) mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and TKO spinal cord samples.

first: Shih-Hsin

last: Chang


title: DFBL-18689-V2 PDX (ABC-DLBCL) tumors treated with miR-28 or control mimics

overall_design: Three independent pairs of DFBL-18689-V2 PDX (PROXE) tumors treated with miR-28 or control obtained at day 5 after the mimic treatment (0.5 nmol) were used for RNA-seq sequencing. Libraries for gene expression were generated.

first: Teresa

last: Fuertes

first: Emigdio

last: Álvarez-Corrales

first: Patricia

last: Ubieto-Capella

first: Álvaro

last: Serrano-Navarro

last: Gómez-Escolar

first: Antonio

last: de Molina

first: Juan

last: Méndez

first: Almudena

last: Ramiro

first: Virginia

last: de Yébenes


title: Alpha-1 adrenergic signaling drives cardiac regeneration through activation of extracellular matrix remodeling transcriptional program in macrophages

city: Berlin

first: Suphansa

last: Sawamiphak

address: Robert Rossle strasse, 10

institute: Max Delbruck Centrum

summary: Autonomic drive plays a pivotal role in cardiac regeneration. Sympathetic or cholinergic denervation impairs myocardial regrowth in neonatal mouse and zebrafish hearts. Here, we uncovered the mechanistic underpinning of adrenergic signaling in regenerative repair of the heart to be critically dependent on immunomodulation. Through pharmacological and genetic manipulations, we identified adrenergic receptor alpha-1 as a key regulator of macrophage phenotypic diversification following myocardial infarction in zebrafish. Single-cell transcriptomics revealed that the receptor signals activation of an ‘extracellular matrix remodeling’ transcriptional program characterized by upregulation of matrix proteins and matrix-modifying enzymes in a macrophage subset. Functionally, adrenergic receptor alpha-1-activated macrophages regulate fibrotic response of the heart by mediating collagenous extracellular matrix turnover and myofibroblast activation, allowing vascularization and cardiomyocyte cell cycle entry at the infarcted lesion. These findings not only unravel the mechanism of adrenergic signaling in macrophage phenotypic and functional determination, but also highlight the potential of neural modulation for regulation of fibrosis and coordination of myocardial regenerative response.

overall_design: Zebrafish hearts subjected to cryoinjury were collected at 7 dpi, dissociated and live cells ,sorted by FACS, analyzed with scRNAseq

first: Onur

last: Apaydin

first: Akerke

last: Altaikyzy

first: Alessandro

last: Filosa


title: The APOE-R136S mutation protects against APOE4-driven Tau pathology, neurodegeneration and neuroinflammation

city: San Francisco

first: Ayushi

last: Agrawal

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

summary: Apolipoprotein E4 (APOE4) is the strongest genetic risk factor for late-onset Alzheimer’s disease (LOAD), leading to earlier age of clinical onset and exacerbating pathologies. There is a critical need to identify protective targets. Recently, a rare APOE variant, APOE3-R136S (Christchurch), was found to protect against early-onset AD in a PSEN1-E280A carrier. We sought to determine if the R136S mutation also protects against APOE4-driven effects in LOAD. We generated tauopathy mouse and human iPSC-derived neuron models carrying human APOE4 with the homozygous or heterozygous R136S mutation. We found that the homozygous R136S mutation rescued APOE4-driven Tau pathology, neurodegeneration, and neuroinflammation. The heterozygous R136S mutation partially protected against APOE4-driven neurodegeneration and neuroinflammation, but not Tau pathology. Single-nucleus RNA-sequencing revealed that the APOE4-R136S mutation increased disease-protective and diminished disease-associated cell populations in a gene dose-dependent manner. Thus, the APOE-R136S mutation protects against APOE4-driven AD pathologies, providing a target for therapeutic development against AD.

overall_design: Single-nucleus RNA sequencing of hippocampus from 10 months old PS19-fE3, PS19-fE4, PS19-fE4-R/S, and PS19-fE4-S/S mice.

first: Maxine

last: Nelson

first: Peng

last: Liu

first: Brian

last: Grone

first: Michela

last: Traglia

first: Reuben

last: Thomas

first: Yadong

last: Huang


title: Effect of Creb1 KD on TVA dependent CD8+ T cell activation

city: Chicago

first: fan

last: hao

state: IL

address: 5801 S Ellis Ave

institute: University of Chicago

summary:
To investigate the role of Creb1 in TVA dependent CD8+ T cell activation, we knocked down Creb1 of mouse CD8+ T cells with siRNAs then treated with DMSO or TVA
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4 groups: CON,TVA,siCREB,siCREBTVA

first: Hao

last: Fan

first: Lei

last: Dong

first: Rui

last: Su

first: Xue

last: Gao

first: Jing

last: Chen


title: Effect of trans-vaccenic acid(TVA) diet on 16S ribosomal RNA (rRNA) expression of mouse gut microbiome

summary:
To investigate the TVA diet's effect on mouse gut microbiome, we fed C57/BL6 mice with TVA diet or CON diet for 18 days
We then collected feces of the mice and performed 16S ribosomal RNA (rRNA) sequencing.

overall_design: Comparative gene expression profiling analysis of 16S rRNAseq data for CON group and TVA group.


title: Effect of trans-vaccenic acid(TVA) treatment on gene expression of mouse CD8+ T cells

summary:
To investigate the TVA's effect on mouse CD8+ T cells in vitro, we treated activated mouse CD8+ T cells with DMSO or 20 µM TVA for 24 hours.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse CD8+ T cells treated with DMSO or 20 µM TVA.


title: scCNVseq Datasets Supporting Integrated Epigenetic and Transcriptional Single-Cell Analysis of t(11;14) Multiple Myeloma and Its BCL2 Dependency

city: Calgary

first: Nizar

last: Bahlis

state: Alberta

address: 3330 Hospital Dr NW HMRB328

department: Divisions of Hematology and Oncology

country: Canada

institute: University of Calgary

summary: The translocation t(11;14) occurs in 20% of multiple myeloma (MM) patients and results in the upregulation of CCND1. Nearly two-thirds of t(11;14) MM cells are BCL2 primed and highly responsive to the oral BCL2 inhibitor venetoclax. While it is evident that this unique sensitivity to venetoclax depends on the BH3-proapoptotic protein priming of BCL2, the biology underlying t(11;14) MM dependency on BCL2 is poorly defined. Importantly, the epigenetic regulation of t(11;14) transcriptomes and its impact on gene regulation and clinical response to venetoclax remains elusive. In this study, by integrating ATACseq and RNAseq at the single-cell level in primary MM samples, we have defined the epigenetic regulome and transcriptome associated with t(11;14) MM. A "B cell-like" epigenetic signature was enriched in t(11;14) MM, confirming its phylogeny link to B cell rather than plasma cell biology. Of note, a loss of a "B cell-like" epigenetic signature with a gain of canonical plasma cell transcription factors was observed at the time of resistance to venetoclax. In addition, MCL1 and BCL2L1 copy number gains and structural rearrangements were linked to venetoclax resistance in t(11;14) MM patients. To date, this is the first study in which both scATAC-seq and scRNA-seq analysis are integrated into primary MM cells to obtain a deeper resolution of the epigenetic regulome and transcriptome associated with t(11;14) MM biology and venetoclax resistance.

overall_design:
Single-cell DNA sequencing (scDNA-seq)
Frozen cells were thawed at 37 °C, resuspended in RPMI 1640 medium  (Gibco) and washed twice with cells being collected by centrifugation at 2000 rpm for 5 min. Viable CD138+ cells were counted and resuspended in a resuspension buffer at 1,000 cells per ul. Single-cell capture was then performed according to the manufacturer’s protocol, using Single Cell Bead Kit (10x Genomics, PN-1000057) and Chromium Chip C (PN-1000022) and D (PN-1000042) with a target capture of 1,000 cells. Quality control and quantification were performed using a KAPA Library Quantification qPCR kit (Roche, Basel, Switzerland) on a BioRad qPCR instrument. DNA libraries were prepared using Single Cell DNA Library & Gel Bead Kit (10x Genomics, PN-1000040) and sequenced on an Illumina NextSeq 500 sequencer with a high-output v2.5 300 cycle sequencing kit as per the standard Illumina protocols. After sequencing, bcl data were converted to fastq data files using the Illumina BCL2FASTQ utility. Samples were processed with CellRanger DNA v1.0.0 and downstream analyses were performed as indicated below.

first: Noémie

last: Leblay

first: Sungwoo

last: Ahn

first: Rémi

last: Tilmont

first: Mansour

last: Poorebrahim

first: Ranjan

last: Maity

first: Holly

last: Lee

first: Elie

last: Barakat

first: Jean-Baptiste

last: Alberge

first: Sarthak

last: Sinha

first: Arzina

last: Jaffer

first: Benjamin

last: Barwick

first: Lawrence

last: Boise

middle: J

first: Paola

last: Neri


title: scRNAseq Datasets Supporting Integrated Epigenetic and Transcriptional Single-Cell Analysis of t(11;14) Multiple Myeloma and Its BCL2 Dependency

overall_design:
Single-cell mRNA sequencing (scRNA-seq):
Frozen cells were thawed at 37 °C, resuspended in RPMI 1640 medium (Gibco, Waltham, MA, USA) and washed twice with cells being collected by centrifugation at 2000 rpm for 5 min. Viable CD138+ cells were counted and resuspended in a resuspension buffer at 1,000 cells per ul. Single-cell capture, reverse transcription, and library preparation were carried out on the Chromium platform (10x Genomics, Pleasanton, CA, USA) using the Single Cell 3ʹ reagent kits v3 (10x Genomics, CG000183) according to the manufacturer’s protocol. Four thousand cells were used as input per channel. Quality control and quantification were performed using a KAPA Library Quantification qPCR kit (Roche, Basel, Switzerland) on a BioRad qPCR instrument before preparing a single pool containing equal-molar amounts of each library. This pool was then subjected to on-board cluster formation and sequencing on an Illumina NextSeq 500 sequencer with a high-output v2.5 150-cycle sequencing kit per the standard Illumina protocols. After sequencing, bcl data were converted to fastq data files using the Illumina BCL2FASTQ utility. Samples were processed with CellRanger suite v3.0.2, and downstream analyses were performed as indicated below.


title: Integrated Epigenetic and Transcriptional Single-Cell Analysis of t(11;14) Multiple Myeloma and Its BCL2 Dependency

type: Genome binding/occupancy profiling by high throughput sequencing

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

The translocation t(11;14) occurs in 20% of multiple myeloma (MM) patients and results in the upregulation of CCND1. Nearly two-thirds of t(11;14) MM cells are BCL2 primed and highly responsive to the oral BCL2 inhibitor venetoclax. While it is evident that this unique sensitivity to venetoclax depends on the BH3-proapoptotic protein priming of BCL2, the biology underlying t(11;14) MM dependency on BCL2 is poorly defined. Importantly, the epigenetic regulation of t(11;14) transcriptomes and its impact on gene regulation and clinical response to venetoclax remains elusive. In this study, by integrating ATACseq and RNAseq at the single-cell level in primary MM samples, we have defined the epigenetic regulome and transcriptome associated with t(11;14) MM. A "B cell-like" epigenetic signature was enriched in t(11;14) MM, confirming its phylogeny link to B cell rather than plasma cell biology. Of note, a loss of a "B cell-like" epigenetic signature with a gain of canonical plasma cell transcription factors was observed at the time of resistance to venetoclax. In addition, MCL1 and BCL2L1 copy number gains and structural rearrangements were linked to venetoclax resistance in t(11;14) MM patients. To date, this is the first study in which both scATAC-seq and scRNA-seq analysis are integrated into primary MM cells to obtain a deeper resolution of the epigenetic regulome and transcriptome associated with t(11;14) MM biology and venetoclax resistance.

overall_design: Experiments were conducted on primary patient samples provided by the Tom Baker Cancer Center, after informed consent, in accordance with the Declaration of Helsinki and following the approval by the Medical Center Institutional Review Board. Unbiased mRNA and DNA profiling were conducted by using scRNA-seq, single cell ATAC-seq and sc-CNV-seq from the GemCode system (10x Genomics) accordingly to the manufacturer’s protocols.


title: ERα/PR crosstalk is altered in the context of the ERα Y537S mutation and contributes to endocrine therapy-resistant tumor proliferation

status: Public on Sep 20 2023

first: Rosemary

last: Huggins

address: 929 E 57th St

department: Ben May Department for Cancer Research

summary: Background: The constitutively active ESR1 Y537S mutation is associated with endocrine therapy resistance and progression of metastatic breast cancer through its effects on estrogen receptor (ERα) gene regulatory functions. However, the complex relationship between ERα and the progesterone receptor (PR), known as ERα/PR crosstalk, has yet to be characterized in the context of the ERα Y537S mutation. This study aimed to elucidate the effects of the ERα Y537S mutation on ERα/PR crosstalk and resultant transcriptional activity and to identify potential therapeutic sensitivities that may offer novel treatment options to patients with endocrine therapy-resistant breast cancer. Methods: Proximity-based interactions of ERα and PR were assessed via proximity ligation assay (PLA). Gene expression in MCF7 and T47D cells was assessed by RNA-seq analysis with comparison to publicly available patient tumor transcriptome data. Chromatin immunoprecipitation (ChIP)-qPCR and immunoblotting were used to assess ERα/PR-associated gene expression and protein expression, respectively. Data were analyzed by ordinary two-way ANOVA (α = 0.05) with Tukey’s multiple comparisons tests. Results: Physical interaction of ERα and PR was increased in the context of the ERα Y537S mutation, including in the nucleus where this interaction may translate to altered gene expression. As such, more than 30 genes were differentially expressed in both patient tumor and cell line data (MCF7 and/or T47D cells) in the context of the ERα Y537S mutation compared to ERα WT. Of these, IRS1 stood out as a gene of interest, and ERα and PR occupancy at chromatin binding sites along IRS1 were uniquely altered in the context of ERα Y537S. Furthermore, siRNA knockdown of IRS1 or treatment with the IRS1 inhibitor NT-157 indicated a significant anti-proliferative effect of IRS1 depletion or inhibition in ERα Y537S cell lines. Conclusions: Previous research has characterized gene regulatory changes associated with the ERα Y537S mutation from the viewpoint of ERα. Here, we identify consequential changes to both ERα and PR transcription factor activity, including at chromatin binding sites for the signaling adaptor protein IRS1. We identified a significant dependence of ERα Y537S-expressing cells on IRS1 for proliferation, implicating IRS1 as a potential therapeutic target for restoring treatment sensitivity to patients with breast cancers harboring ERα Y537S mutations.

overall_design: MCF7 and T47D cell variants (ERα WT, ERα Y537S-heterozygous, or ERα Y537S-homozygous) were hormone-deprived in charcoal-stripped media for 48 hours. Cells were then treated with vehicle or 10 nM R5020 for PR stimulation and collected via trypsinization after 2 hours of treatment. RNA was extracted using the Qiagen RNeasy Plus kit (#74104) according to the manufacturer's protocol. RNA concentrations were quantified by Nanodrop nucleic acid measurement. RNA library preparation for sequencing was completed using the KAPA mRNA HyperPrep Kit (#KR1352) according to the manufacturer's protocol. Sequencing was completed on the Illumina NovaSeq 6000 by the University of Chicago Functional Genomics core (RRID: SCR_019196). DESeq2 was used to determine differentially expressed genes between each cell variant and between each treatment.

first: Geoffrey

last: Greene


title: RNASeq analysis for EBV-immortalized B-cells from individuals with an AIOLOS E82K mutation and healthy controls

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr.

department: Dept. of Lab. Medicine

institute: NIH Clinical center

summary: RNA-seq was performed using RNA extracted from EBV-immortalized B-cells for the following study groups: healthy controls (HC, n=3) and patients with AIOLOSE 82K (n=4 ). Illumina libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian Components (Takara San Jose, CA). Libraries were sequenced on a Illumina NextSeq 2000 instrument using 2 x 75 bp paired-end reads, and alignment and mapping analyses were performed by the Takara Cogent NGS Analysis Pipeline v1.5.0 (also known as CogentAP). Differential gene expression analysis was performed by DESeq2 v1.32.0 [Bioconductor version: Release (3.15)].

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EBV-immortalized B-cells from individuals with an AIOLOS E82K mutation and healthy controls

first: S

last: Rosenzweig

first: H

middle: S

last: Kuehn

first: J

last: Stoddard


title: scATACseq Datasets Supporting Integrated Epigenetic and Transcriptional Single-Cell Analysis of t(11;14) Multiple Myeloma and Its BCL2 Dependency

first: Nizar

last: Bahlis

overall_design:
Single-cell chromatin accessibility (scATAC-seq):
Frozen cells were thawed at 37 °C, resuspended in RPMI 1640 medium (Gibco, Waltham, MA, USA) and washed twice by centrifugation at 2000 rpm for 5 min. The desired number of nuclei [2000-8000] was targeted and processed according to the Nuclei Isolation for Single Cell ATAC sequencing (CG000169, 10x Genomics, Pleasanton, CA, USA). Nuclei isolation was performed as indicated in the nuclei isolation protocol for Single Cell ATAC Sequencing (10x Genomics). Based on the starting number of cells and desired final nuclei concentration, primary MM cells were lysed and resuspended in an appropriate volume of chilled Diluted Nuclei Buffer. The resulting nuclei were then immediately used to generate scATAC-seq libraries using the Chromium Single Cell ATAC reagent kit (CG000168, 10x Genomics) according to the manufacturer’s protocol. Quality control and quantification were then performed using the KAPA Library Quantification qPCR kit (Roche, Basel, Switzerland) on a BioRad qPCR instrument before preparing a single pool containing equal-molar amounts of each library. This pool was subjected to on-board cluster formation and sequencing on an Illumina NextSeq 500 sequencer with a high-output v2.5 150-cycle sequencing kit per standard Illumina protocol (Illumina, San Diego, CA, USA). After sequencing, bcl data were converted to fastq data files using the Illumina BCL2FASTQ utility. Samples were processed with CellRanger suite v3.0.2, and downstream analyses were performed as indicated below.

first: Noémie

last: Leblay

first: Sungwoo

last: Ahn

first: Rémi

last: Tilmont


title: A novel breast cancer therapeutic strategy through Hsp90 inhibition and activation of the immune system

city: Augusta

first: Ahmed

last: Chadli

state: GA

address: 1410 Laney Walker BLVD

department: Cancer Center

institute: Augusta University

summary: Low response rates and immune-related adverse events limit the impact of cancer immunotherapy. In the quest for improved clinical outcomes, preclinical studies have shown that combining immune checkpoint blockade therapies with N-terminal Hsp90 inhibitors resulted in improved efficacy, even though induction of an extensive heat shock response (HSR) with these inhibitors limited their clinical efficacy as monotherapies. We discovered that Enniatin A (EnnA) binds to the interface between the middle domains of the Hsp90 dimer and destabilizes Hsp90 client oncoproteins without inducing an HSR. We found that EnnA induces cancer cell immunogenic cell death in aggressive breast cancer models and exhibits superior anti-tumor activity compared to Hsp90 N-terminal inhibitors. Further, we show that EnnA reprograms the tumor microenvironment in syngeneic mouse models to promote CD8+ T cell-dependent anti-tumor activity mediated through the CX3CR1 signaling pathway. We propose that EnnA is a promising anti-tumor agent with a novel mechanism of action involving immunogenic cancer cell toxicity and the mobilization of CD8+ T cells into the tumor site.

overall_design: Examination of the impact of Enniatin A (EnnA) and 17-AAG treatment on the transcriptome of murine breast cancer cell line E0771.

first: Nada

last: Eisa


title: Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [scRNAseq_ATRT_CAL]

city: Paris

first: Mamy

middle: Jean de Dieu

last: ANDRIANTERANAGNA

state: Ile de France

address: 26 rue d'Ulm

department: Centre de Recherche

country: France

institute: Institut Curie

summary: Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosisand the precise anatomic origin of brain tumors in the Rosa26; Cre-ERT2::Smarcb1flox/flox model. This cross-species analysis points to an extra-cerebral origin for MYC tumors. Additionally, we clearly distinguish SHH ATRT emerging from the cerebellar anterior lobe (CAL) from those emerging from the basal ganglia (BG) and intra-ventricular (IV) regions. Molecular characteristics point to the midbrain-hindbrain boundary as the origin of CAL SHH ATRT, and to the ganglionic eminence as the origin of BG/IV SHH ATRT. Single-cell RNA sequencing on SHH ATRT supports these hypotheses. Trajectory analyses suggest that SMARCB1 loss induces a de-differentiation process mediated by repressors of the neuronal program such as REST, ID and the NOTCH pathway.

overall_design: 4 fresh tumor samples, localized at the Cerebellar Anterior Lobe from 4 different patients were collected and analysed by single cell RNA-seq.

first: Maria-Jesus

last: Lobon-Iglesias

last: Andrianteranagna

first: Zhi-Yan

last: Han

first: Valeria

last: Manriquez

first: Rachida

last: Bouarich-Bourimi

first: Sandrina

last: Turczynski

first: Nicolas

last: Servant

first: Franck

last: Bourdeaut


title: In vitro Modeling of the Human Dopaminergic System using spatially arranged ventral Midbrain-Striatum-Cortex Assembloids [scRNAseq]

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

summary: Dopaminergic neurons located in the ventral Midbrain (vMid) innervate the striatum and cortex and are involved in movement control and reward-related cognition. Degeneration of dopaminergic neurons causes Parkinson’s disease (PD), while their over-activation is implicated in addiction. Thus, modeling the dopaminergic system is of broad relevance for disease research and drug discovery, although limited availability of patient material and inherent differences in animal model systems are restricting the study of distinctive human specific features such as development and neurodegeneration. Here, we show that spatially arranged assembloids can recapitulate dopaminergic innervation of striatum and cortex and offer methods for their use in cell replacement therapy and addiction research. We describe improved protocols for growing vMid, striatal and cortical organoids and use custom embedding molds to fuse them in a linear manner. Linear assembloids form functional long-range dopaminergic connections with striatal and cortical tissues that can release dopamine. We demonstrate that vMid grafts derived from hPSCs for cell replacement therapy of PD can integrate into the tissue and structurally mature. Additionally, we demonstrate that our model can be used to study dopaminergic circuit perturbations in the example of chronic cocaine treatment which causes morphological, functional and transcriptional changes that remained altered even after drug withdrawal. Our method opens new avenues for dopaminergic cell replacement therapy and the analysis of drugs affecting the dopaminergic system, directly in a human system.

overall_design: scRNAseq of organoid tissue

first: Daniel

last: Reumann

first: Jürgen

last: Knoblich


title: In vitro Modeling of the Human Dopaminergic System using spatially arranged ventral Midbrain-Striatum-Cortex Assembloids

overall_design: Refer to individual Series


title: CITE-sequencing profiling establishes immune cell repertoire in peripheral blood and pancreas of new-onset diabetic NOD mice

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: miR-193b-3p and miR-365-3p expression values are increased in pancreas infiltrating neutrophils and basophils of new-onset diabetic NOD mice. We performed CITE-sequencing technology to investigate their phenotype and frequency. Using differentially expressed gene (DEGs) analysis, we further compared the different transcriptome profiles of pancreas infiltrating versus blood circulating neutrophils and basophils in new-onset diabetic NOD mice.

overall_design: CITE-sequencing was performed using a panel of 190 DNA-barcoded antibodies. The experiment was carried out on FACS-sorted CD45+ leukocytes isolated from peripheral blood and pancreas of four new-onset diabetic NOD mice. After filtering and pre-processing, we obtained a dataset of 43,706 cells.

first: Gabriele

last: Sassi

first: Giada

last: Licata

first: Giuliana

last: Ventriglia

first: Ruth

last: Seurinck

first: Alessia

last: Mori

first: Darcy

last: Ellis

first: Silvia

last: Caluwaerts

first: Pieter

last: Rottiers

first: Niels

last: Vandamme

first: Chantal

last: Mathieu

first: Francesco

last: Dotta

first: Conny

last: Gysemans

first: Guido

last: Sebastiani

first: Jana

last: Roels


title: Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [bulkRNAseq_primaryATRT]

first: Mamy

last: ANDRIANTERANAGNA

overall_design: 10 primary ATRT samples from 1 different patient were collected and analysed by RNA sequencing

first: Maria

last: Lobon-Iglesias

last: Andrianteranagna

first: Zhi-Yan

last: Han

first: Nicolas

last: Servant

first: Franck

last: Bourdeaut


title: Metabolic dependencies of metastasis-initiating cells in breast cancer [RNA-Seq 2]

city: Lausanne

first: Candice Megan

last: Young

state: Vaud

address: Rue du Bugnon 25A

department: SV

country: Switzerland

institute: EPFL

summary: We investigated gene expression changes between the cells having the highest and lowest levels of mitochondrial membrane potential.

overall_design: Comparative gene expression between cells with high and low levels of mitochondrial membrane potential

first: Candice

first: Laurent

last: Beziaud

first: Pierre

last: Dessen

first: Angela

last: Madurga-Alonso

first: Joerg

last: Huelsken


title: Metabolic dependencies of metastasis-initiating cells in breast cancer


title: Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [scRNAseq_mouseRT_R26SHH]

overall_design: 3 fresh mouse rhabdoid tumor samples, developped in 3 different Rosa 26-CreERT2::Smarcb1flox/flox engineered mice were collected and analysed by single cell RNA-seq.

first: Maria-Jesus

first: Rachida

last: Bouarich

first: Valeria

last: Manriquez

first: Magali

last: Frah

first: Sandrina

last: Turczynski


title: Spatiotemporal trascriptomics of Bacillus subtilis swarming colony

city: Basel

first: Kazuki

last: Nosho

address: Spitalstrasse 41

department: Biozentrum

institute: University of Basel

summary: Using transcriptomics, we studied the spatiotemporal dynamics of B. subtilis swarming colonies on soft-agar surface and identified functional subpopulations.

overall_design: B. subtilis cells swarming on soft-agar were collected by our custom sampling robot at various locations and time points and analyzed using RNA-Seq with 3 biological replicates.

first: Hannah

last: Jeckel

first: Konstantin

last: Neuhaus

first: Knut

last: Drescher


title: Metabolic dependencies of metastasis-initiating cells in breast cancer [ChIP-Seq]

summary: We investigated the changes in acetylation peaks on H3K27ac in cells in response to inhibitors that alter the activity of acetyl-coa generating enzymes

overall_design: H3K27ac ChIP-Seq on cells that have been treated in vitro for 48 hours with vehicle, acetate, etomoxir, acetate+etomoxir, etomoxir+SB204990, and acetate+etomoxir+SB204990


title: Single-nucleus RNA and ATAC sequencing of IDH1 mutant gliomas

city: Heidelberg

first: Sevin

last: Turcan

address: Im Neuenheimer Feld 460

institute: Heidelberg University Hospital

summary: We perform high-throughput single-nucleus RNA and ATAC sequencing (snRNA- and snATAC-seq) on primary IDH mutant gliomas and snRNA-seq on a cohort of primary and recurrent IDH mutant glioma pairs to comprehensively resolve tumor diversity and TAM states. Our results resemble previously described differentiation hierarchies, but also reveal a novel group of epigenetically and transcriptionally distinct non-cycling stem-like tumor cells in diffuse gliomas. Further, we identify significant transcriptional differences in TAM states between oligodendrogliomas and astrocytomas, with a notable interaction between immunosuppressive TAMs and astrocytic tumor subpopulations in astrocytomas. These results suggest that TAM-tumor interactions may contribute to the clinical course of oligodendrogliomas and astrocytomas.

overall_design: Nuclei were isolated from fresh frozen tumors and single-nucleus RNA sequencing (10x Genomics) was performed.

first: Enrique

last: Blanco-Carmona


title: In vitro Modeling of the Human Dopaminergic System using spatially arranged ventral Midbrain-Striatum-Cortex Assembloids [Smartseq]

first: Maria

last: Novatchkova

overall_design: Smartseq of organoid tissue

first: Daniel

last: Reumann

first: Jürgen

last: Knoblich


title: Metabolic dependencies of metastasis-initiating cells in breast cancer [RNA-Seq 3]

first: Candice Megan

last: Young

summary: We investigated the gene expression changes in endogenous MICs vs. Non-MICs in the MMTV-PyMT mouse model

overall_design: Comparative gene expression analysis between ex vivo cells that have been sorted for the MIC or non-MIC markers (Lin-CD24+CD90+, Lin-CD24+CD90-, respectively)

first: Candice

first: Laurent

last: Beziaud

first: Pierre


title: Cre-dependent massively parallel reporter assay  for cell-type specific assessment of the functional effects of 3'UTR genetic variants in vivo

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: Couch Biomedical Research Bldg 06316

department: Genetics

institute: Washington University of St. Louis

summary: Here, we examined de novo variants identified within annotated 3′UTRs from the whole-genome sequencing of 519 families from the Simons Simplex Collection (Werling et al., 2018), totaling 342 mutations from probands and 299 from unaffected siblings within the same cohort. For each variant we synthesized an allelic pair of 3′UTR ‘elements’ spanning 120 bp of sequence centered on the variant. To be able to compare biological to non-biological sequences, for 322 variants, we randomly shuffled the sequence to generate a set of GC-matched controls. We tagged all 1,624 elements with six unique barcodes to provide internal replicates and control for potential barcode effects. To enable eventual cell-type specific studies, we cloned the final library of 9,744 synthesized oligos into the 3′UTR of a membrane-localized tdTomato reporter embedded in a Double-floxed inverse Orientation (DiO) cassette (Schnütgen et al., 2003), such that the reporter library would only express following Cre-mediated recombination. We completed the analysis of this library in vitro in N2a cells and in vivo in Vglut-Cre mice. Additional code and results corresponding to this GEO submission can be found at  https://bitbucket.org/jdlabteam/asd_3utr_mpra_analysis/src/master/

overall_design: 6 replicates of N2a cells, 11 replicates of Vglut-cre mice,6 replicates of Vgat-cre

first: Tomas

last: Lagunas

first: Stephen

last: Plassmeyer


title: Inflammatory macrophage-derived extracellular vesicles trigger the non-canonical pyroptosis pathway in chondrocytes leading to cartilage catabolism and degeneration in osteoarthritis

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

summary: The severity of osteoarthritis (OA) and cartilage degeneration are highly correlated with the development of synovitis, which is mediated by the activity of inflammatory macrophages. A better understanding of intercellular communication between inflammatory macrophages and chondrocytes should aid in the discovery of novel therapeutic targets. Here, we explored the pathological role of inflammatory macrophage-extracellular vesicles (EVs) in cartilage degeneration. Macrophages were stimulated by treatment with bacterial lipopolysaccharides to mimic the state of inflammatory macrophages and the resulting EVs (M-LPS EVs) were harvested for chondrocyte stimulation and intraarticular injection in a mouse model. This stimulation resulted in increased catabolism of chondrocytes and cartilage degeneration.   Consistently, RNA-seq analyses of stimulated chondrocytes indicated that upregulated genes are mainly categorized into apoptotic process and TNF-signaling pathway which suggests the induction of apoptotic process. These chondrocytes exhibited a significant elevation in the expression of pyroptosis-related molecules that were correlated with the expression of chondrocyte catabolic factors. The disruption of caspase-11 significantly alleviated pyroptotic and catabolic processes in stimulated chondrocytes and the pathological changes in collagenase-induced OA model. Our results provide a new insight into the pathological mechanisms of OA and suggest that non-canonical pyroptosis signaling in chondrocytes represents an attractive therapeutic target for future treatment.

overall_design: RNA-seq for mouse chondrocytes stimulated with extracellular vesicles derived from inflammatory macrophage

first: Taku

last: Ebata

first: Terkawi

last: Alaa

first: Gen

last: Matsumae

first: Norimasa

last: Iwasaki


title: Antiviral State of CD1c+ cDC associates with increased  Natural Killer maturation and activation in Sjögren´s Syndrome

city: Madrid

last: Vazquez de Luis

address: Melchor Fernandez Almagro, 3

institute: CNIC

summary: Primary Sjögren´s syndrome (pSS) is a heterogeneous inflammatory autoimmune disorder characterized by the infiltration of different immune subsets in exocrine glands and potential development of extra-glandular manifestations. pSS pathology and glandular tissue destruction have been linked to increased IFN responses and the induction of autoreactive T and B cells. However, association of innate immune cells such as Natural Killer (NK) cells and conventional dendritic cells (cDC) with the tissular damage and IFN environment in pSS remains understudied. Here, we identified higher expression of NKG2D, CD107a and superior cytotoxic function on circulating NK cells from pSS which was associated with significant enrichment in a subpopulation of CD16+CD56Hi NK cells in the blood of these patients. In addition, Granzyme B+ NK cells and MICab+ CD1c+ cDC could be found in proximity in tissue sections of salivary glands from pSS patients. Importantly, murine populations of CD64Hi CD11b+CD11c+ cDC and transitional NKG2Dhi CD11b+CD27+ NK1.1 cells, infiltrated in vivo into the salivary gland in a stablished pSS mouse model. Interestingly, transcriptional IFN signatures present on CD1c+ cDC from pSS are characterized by the upregulation of RIG-I and DDX60 sensors and the ISGs IFIT1 and IFIT3. These transcriptional patterns on CD1c+ cDC associated with high basal expression of MICa/b and SLAMF7 ligands for NK receptors, the Fc receptor CD64 and increased ability to induce maturation and CD107a expression in NK cells. Finally, expression of SLAMF7 and MICa/b after Poly I:C exposure was regulated by RIG-I and DDX60 on CD1c+ cDC.  Therefore, crosstalk between CD1c+ cDCs and NK cells could contribute to the pathogenesis of pSS, and represent new cellular therapeutic targets for treatment of pSS.

overall_design: We performed RNA sequencing using RNA from Monocytes, Dendritic Cd1c+ and Dendritic Cd141 cells obtained from blood of Sjögren´s Syndrome versus healthy matched controls. Healthy samples are available in GSE157047 (matched controls are listed in the GSM descriptions).

first: Ildefonso

last: Sánchez-Cerrillo

first: Marta

last: Calvet-Mirabent

first: Ana

last: Triguero-Martinez

first: Diego

last: Calzada-Fraile

first: Cristina

last: Delgado-Arévalo

last: Vázquez de Luis

first: Alberto

last: Benguría

first: Roberto

last: Moreno-Vellisca

first: Maria-Magdalena

last: Adrados de Llano

first: Hortensia

last: de la Fuente

first: Ilya

last: Tsukalov

first: Almudena

last: Ramiro

first: Francisco

last: Sánchez-Madrid

last: Dopazo

first: Isidoro

last: Gonzalez-Álvaro

first: Santos

last: Castañeda

last: Martín-Gayo


title: Single cell expression profiling of whole B16F10 melanoma tumors, treated with PBS or DCP-IL-12/FLT3L.

status: Public on Sep 19 2023

first: Nadine

last: Fournier

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Dendritic cells (DCs) are specialized myeloid cells with the ability to uptake, process, and present antigens to T lymphocytes. They also generate cytokine and chemokine gradients that regulate immune cell trafficking, activation, and function. Monocyte-derived DCs (moDCs) pulsed with tumor antigens have been used as a platform for therapeutic vaccination in cancer. However, in spite of significant development and testing, antigen-loaded moDCs have delivered mixed clinical results. Here we present a DC therapy that uses a population of mouse or human DC progenitors (DCPs) engineered to produce two immunostimulatory cytokines, IL-12 and FLT3L. In the absence of antigen loading, cytokine-armored DCPs efficiently differentiated into conventional type I DCs (cDC1) and inhibited tumor growth in melanoma and autochthonous liver cancer models. Tumor response to DCP therapy involved synergy between IL-12 and FLT3L and was associated with early NK cell activation and massive effector T cell infiltration, robust M1-like macrophage programming, and ischemic tumor necrosis. Mechanistically, anti-tumor immunity was dependent on endogenous cDC1 expansion and interferon-γ (IFNγ) production and signaling, but did not require CD8+ T cell cytotoxicity. In one application, cytokine-armored DCPs synergized with antigen-specific CAR-T cells to eradicate intracranial gliomas in mice.

overall_design: Single cell expression profiling of whole B16F10 melanoma tumors, treated with PBS or DCP-IL-12/FLT3L, in triplicates.

first: Rachel

last: Marcone

first: Ali

last: Ghasemi

first: Michele

last: De Palma


title: Forebrain neuronal Smc3 regulates weight and metabolic parameters partly through regulation of hypothalamic Melanocortin 4 receptor

status: Public on Sep 18 2023

city: Safed

first: Evan

last: Elliott

address: Henrietta Szold Street, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

summary: SMC3 is a major component of cohesin complex that regulates higher-order chromatin organization and gene expression. Mutations in SMC3 gene are found in patients with Cornelia de Lange syndrome (CdLs). This syndrome is characterized by intellectual disabilities, behavioral patterns as self-injury, as well as metabolic dysregulation. Nonetheless, little is known about the role of neuronal SMC3 in gene expression and physiology especially in adulthood. This study determined the role of SMC3 in adulthood brain, by knocking out Smc3 specifically in adulthood forebrain excitatory neurons. Neuron-specific SMC3 knockout mice displayed a very strong metabolic phenotype in both male and female mice, including a robust overweight phenotype, loss of muscle mass, increased food consumption, lower respiratory exchange ratio, lower energy expenditure  and hormonal changes. The hypothalamus of these mice displayed dysregulated morphology and RNA-seq in the hypothalamus reveals dysregulation in multiple cellular pathways, including decrease of Melanocortin 4 receptor (Mc4r) expression level  , a main regulator of appetite. Treatment of these mice with Setmelanotide, a MC4r agonist, induced a decrease of weight and food consumption in these mice. Therefore, we have identified specific metabolic pathways that are regulated by Smc3 in forebrain neurons, and specific mechanisms that are involved.

overall_design: To understand the function of SMC3 in the adulthood brain, we established a neuron-specific knockout of Smc3 specifically in adulthood in mice.  Mice with floxed Smc3 and Camk2a-cre/ERT2+ (Cre+) or Camk2a-cre/ERT2- (Cre-). Mice with Cre+ named as cKO due the lack of Smc3 gene after tamoxifen treatment; mice with Cre- served as WT.

first: Natalia

last: Saleev

first: Dmitriy

last: Getselter

first: Roee

last: Gutman

first: Asaf

last: Marco

first: Joanna

last: Bartman


title: CRISPR screens by human betacoronaviruses SARS-CoV-2 and HCoV-OC43 using IGROV-1 cells

city: Singapore

first: Wharton

middle: O Y

last: Chan

state: Singapore

address: 8 College Road

department: Emerging Infectious Disease

country: Singapore

institute: Duke-NUS Medical School

summary: The emergence of novel betacoronaviruses has posed significant financial and human health burdens, necessitating the development of appropriate tools to combat future outbreaks. In this study, we have characterized a human cell line, IGROV-1, as a robust tool to detect, propagate, and titrate betacoronavirus SARS-CoV-2 and HCoV-OC43. IGROV-1 cells can be used for serological assays, antiviral drug testing, and isolating SARS-CoV-2 variants from patient samples. Using time-course transcriptomics, we confirmed that IGROV-1 cells exhibit a robust innate immune response upon SARS-CoV-2 infection, recapitulating the response previously observed in primary human nasal epithelial cells. We performed genome-wide CRISPR knockout genetic screens in IGROV-1 cells and identified Aryl hydrocarbon receptor (AHR) as a critical host dependency factor for both SARS-CoV-2 and HCoV-OC43. Using DiMNF, a small molecule inhibitor of AHR, we observed that the drug selectively inhibits HCoV-OC43 infection but not SARS-CoV-2. Transcriptomic analysis in primary normal human bronchial epithelial cells revealed that DiMNF blocks HCoV-OC43 infection via basal activation of innate immune responses. Our findings highlight the potential of IGROV-1 cells as a valuable diagnostic and research tool to combat betacoronavirus diseases.

overall_design: IGROV-1 cells CRISPR Brunello libraries, selected by SARS-CoV2 or HCoV-OC43 infection

first: Meisam

last: Yousefi

first: Yaw

last: Ooi

middle: O


title: Polycomb Repressive Complex 2 regulates basal cell fate during adult olfactory neurogenesis [EEDKO_H3K27me3_ChIP]

city: Durham

first: Bradley

last: Goldstein

state: NC

address: 203 Research Dr

department: Head and Neck Surgery & Communication Sciences

institute: Duke University

summary: We show that Polycomb repressive complexes (PRCs) regulate lineage choice between neural and non-neural fates in the olfactory epithelium. Conditional loss of Polycomb repressive complex 2 perturbs lesion-induced neurogenesis and misexpression of lineage-specific transcription factors in multipotent olfactory globose basal cells.

overall_design: Chromatin immunoprecipitation DNA sequencing for histone modifications H3K27me3 and H3K27ac on c-KIT immunoselection-purified globose basal cells acutely dissociated from the olfactory epithelium of Krt5-CreERT2;Rosa-Ai9;Eed-fl/fl mice

first: Tiffany

last: Ko


title: Polycomb Repressive Complex 2 regulates basal cell fate during adult olfactory neurogenesism [scRNA-seq]

overall_design: Single cell 3' RNAseq of olfactory epithelium from 3 Eed-KO and 3 pooled Eed-Het mice using the 10X Genomics Chromium platform and sequenced on Illumina Novaseq 6000


title: Ophiostoma piceae CECT 20416 RNA-Seq, Nov 29 '22

first: Jorge

last: Barriuso

address: C. Ramiro de Maeztu, 9

institute: CIB-CSIC

summary: Quorum sensing (QS) is a complex cell-cell communication mechanism that coordinates population-level behaviors in microbes. In eukaryotes, this phenomenon has been extensively described in the dimorphic yeast Candida albicans as its main QS molecule, the sesquiterpene alcohol farnesol, is responsible for various phenotypic (i.e., inhibition of yeast-to-hyphae transition, biofilm formation and, hence, pathogenesis) and metabolic (i.e., induction of oxidative stress and apoptosis) changes. Ophiostoma piceae CECT 20416 is a dimorphic saprotrophic ascomycete with biotechnological interest that also produces farnesol as a QS molecule, but in this case, the alcohol promotes the morphological transition to the mycelial form, biofilm formation, enzyme secretion, and melanin production. Here, we characterized the physiological response of Ophiostoma piceae to farnesol, and the molecular components of the QS system of this fungus have been investigated using a ‘multiomics’ approach that involved genomic, transcriptomic, and proteomic analyses. Some genes identified in this work are proposed as key factors in farnesol transport and signaling. We have also cataloged the genes undergoing major transcriptional changes triggered by the presence of the autoinducer, such as cell-wall remodeling, ROS protection, and melanin biosynthesis, using self-organizing maps (SOMs). This analysis could be useful for applications in the forestry industry, for enzyme production, and for the valorization of residues. Furthermore, it might as well help to investigate the QS mechanisms of clinically relevant fungi phylogenetically related to Ophiostoma.

overall_design: Culture samples of Ophiostoma piceae at three different times (22h, 47h, 68h) with and without addition of FaOH (farnesol), CTL samples are control samples, with two replicates each.


title: Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis [mg633_ATACseq]

city: Cleveland

first: Peter

last: Scacheri

state: OH

address: Biomedical Research, 2109 Adelbert Rd Building, 6th FL, Room 647

department: Genetics and Genome Sciences

institute: Case Western Reserve University School of Medicine

summary: ATAC-seq was performed on MG63.3-GFP cells in vitro or isolated from mouse lung 1 day or 22 days post-innoculation to assess chromatin accessbility dynamics during lung colonization.

overall_design: Comparison of chromatin accessibility between MG63.3-GFP cells grown in vitro or at two timepoints during lung colonization. For the in vivo conditions, mouse lungs were dissociated using the Miltenyi human tumor dissociation kit and mouse cell depletion kit.

first: Scacheri

last: Peter

first: Pontius

last: W Dean


title: Cytokine-armored dendritic cell progenitors for antigen-agnostic cancer immunotherapy

first: Nadine

last: Fournier

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

overall_design: Refer to individual Series


title: TCR profiling of whole MC38 tumors, treated with PBS + IgG , Cis + PBS + aPD-1, Cis + DCP-IL-12/FLT3L + IgG or Cis + DCP-IL-12/FLT3L + ɑPD-1.

overall_design: TCR profiling of whole MC38 tumors, treated with PBS + IgG , Cis + PBS + aPD-1, Cis + DCP-IL-12/FLT3L + IgG or Cis + DCP-IL-12/FLT3L + ɑPD-1 in replicates (n=3-7).

first: Rachel

last: Marcone

first: Ali

last: Ghasemi

first: Michele

last: De Palma


title: Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis [RNA-Seq]

summary: RNA-seq was performed on MG63.3-GFP cells in vitro or isolated from mouse lung 1 day or 22 days post-innoculation to assess gene expression dynamics during lung colonization.

overall_design: Comparison of gene expression between MG63.3-GFP cells grown in vitro or at two timepoints during lung colonization. For the in vivo conditions, mouse lungs were dissociated using the Miltenyi human tumor dissociation kit and mouse cell depletion kit.


title: Inhibition of CDK12 induces cancer cell dependence on activated P-TEFb via the ATM-stimulated p53 and NF-kB transcriptional programs

status: Public on Sep 17 2023

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A, 17165 Solna, Sweden

department: Department of Gene Technology

country: Sweden

institute: Science for Life Laboratory, KTH Royal Institute of Technology

summary: P-TEFb and CDK12 facilitate transcription elongation by RNA polymerase II and play prominent roles in cancer. Understanding their functional interplay could inform novel anti-cancer strategies. While inhibition of CDK12 downregulates unique sets of genes, eliciting genomic instability that is being exploited for novel therapies, little is known about the significance of transcriptional induction in CDK12-targeted cells. We show that inhibition of CDK12 in colon cancer-derived cells activates P-TEFb and induces genes of key cancer signaling pathways, including p53 and NF-kB. Mechanistically, cancer cells become exquisitely dependent on P-TEFb through activation of p53-dependent apoptosis and attenuation of NF-kB-dependent proliferation. Furthermore, we show that the DNA damage-responsive ATM kinase mediates these effects. While ATM is required for the synthetic lethality of CDK12 and P-TEFb co-targeting in p53-proficient cells, co-inhibition of ATM and CDK12 synergizes in decreasing viability of p53-deficient cells. Finally, pairwise targeting of CDK12, P-TEFb and transcription initiation kinase CDK7 stimulates p53-dependent apoptosis of cancer cell spheroids. We propose that the stimulation of Pol II pause release by P-TEFb at the signal-responsive genes underlies the dependence of CDK12-targeted cancer cells on P-TEFb. Together, our work provides a rationale for combinatorial targeting of CDK12 and P-TEFb or the induced oncogenic pathways in cancer.

overall_design: Precision run-on sequencing (PRO-seq) analysis of nascent transcription in human colorectal carcinoma cell line, HCT116, during the inhibition of CDK12 and CDK9.

first: Samu

middle: V

last: Himanen

first: Wang

last: Zhijia


title: Distinct Functions and Transcriptional Signatures in Orally Induced Regulatory T Cell Populations

status: Public on Sep 16 2023

city: Indianapolis

first: Moanaro

last: Biswas

state: IN

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University

summary: We compared scRNA expression analysis of 3 populations of regulatory CD4+ T cells induced in oral tolerance to factor VIII in a mouse model of hemophilia: FoxP3+LAP-, FoxP3+LAP+, FoxP3-LAP+

overall_design: Hemophilia A mice were orally gavaged with transplastomic lettuce expressing recombinant factor VIII. Animals then received intravenous injections of factor VIII. We performed scRNA analysis of FoxP3-LAP+ and FoxP3+ cells from spleen. FoxP3+ cells were further separated into FoxP3+LAP-, and FoxP3+LAP+ populations

first: Roland

middle: W

last: Herzog

first: Hongyu

last: Gao

first: Sha

last: Cao


title: Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer

city: Guangzhou

first: Xiaoxue

last: Ren

state: Guangdong

address: 58 Zhong Shan Road 2, Guangzhou, China

institute: The First Affiliated Hospital of Sun Yat-Sen University

summary: The tumor microenvironment is distinctive in primary and secondary liver cancer. B cells represent an important component of immune infiltrates. Here, we demonstrated that B cells are an important regulator in hepatocellular carcinoma (HCC) and colorectal cancer liver metastasis (CRLM) microenvironments. B cells displayed distinct developmental trajectories in HCC and CRLM. Single-cell analysis revealed that IgG+ plasma cells preferentially accumulated in HCC while IgA+ plasma cells were preferentially enriched in CRLM. Mechanistically, IgG+ plasma cells in HCC were recruited by tumor-associated macrophages via the CXCR3-CXCL10 axis, whereas IgA+ plasma cells in CRLM were recruited by metastatic tumor cells via CCR10-CCL28 signaling. Functionally, IgG+ plasma cells preferentially promoted pro-tumorigenic macrophages formation in HCC, and IgA+ plasma cells preferentially induced granulocytic myeloid-derived suppressor cells activation in CRLM. Clinically, increased infiltration of IgG+ plasma cells and macrophages in HCC was correlated to worse survival, while increased intratumoral IgA+ plasma cells and neutrophils in CRLM indicated poor prognosis. Taken together, this study demonstrated plasma and myeloid cell-mediated immunosuppression in HCC and CRLM, suggesting that selectively modulating primary or secondary tumor-related immunosuppressive regulatory networks might reprogram the microenvironment and provide an immunotherapeutic strategy for treating liver cancer.

overall_design: To investigate the functional state of these immune cells, we performed single sample gene set enrichment analysis (ssGSEA) analysis (29) on RNA-seq data and focused more specifically on immune-related genes.

first: Sui

last: Peng


title: Accessible high-throughput single-cell whole genome sequencing with paired chromatin accessibility

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

summary: We present a technique that leverages nucleosome disruption methodologies with the widely adopted 10x Genomics ATAC-seq library preparation workflow to produce scWGS profiles for copy number analysis in high throughput. We further demonstarte the ability to leverage indexed tagmentation using off-the-shelf reagents to perform scWGS multiplexing, or a co-assay that produces scWGS+ATAC data fromt he same cells, also witht he ability to multipelx samples.

overall_design: We performed standard 10x scATAC v2 as a control along with our nucleosome-disruption to produce scWGS data. Data for multipelxed scWGS were produced on the same control cell line as well as for the dTag experiments that produce both ATAC and WGS data from the same cells.

middle: C

first: Konstantin

last: Quietsch


title: In vitro production of cat-restricted Toxoplasma pre-sexual stages by epigenetic reprogramming

city: La Tronche

first: Christopher

last: Swale

address: Batiment Jean Roger

department: U1209 - Institute of Advanced Biosciences

institute: INSERM


title: identifying all AR binding regions in PC346C cell line

city: Rotterdam

first: Selçuk

last: Yavuz

state: South-Holland

address: wytemaweg 80

department: Department of pathology

country: Netherlands

institute: Erasmus MC

summary: The Androgen Receptor plays in general an important role in Prostate Cancer biology. The Androgen Receptor orchestrates as transcription factor the activity of AR-regulated genes at destinct genomic regions by binding to specific sequences (known as Androgen Responsive Elements - ARE). However, the biophysical nature of the Androgen Receptor at these binding sites on the DNA are not well characterized. In order to investigate the biophysical properties of these molecules at AR binding sites by super resolution microscopy in living cells, we performed a AR-ChIP sequencing for the PC346C target cell line. Based on the sequencing results, we selected certain target regions based on relative AR-enrichment for further studying the local AR dynamics in these target regions.

overall_design: Chromatin immunoprecipitation followed by DNA sequencing for the wild type Androgen Receptor

first: Raymond

middle: A

last: poot

first: Marti

last: Quevedo

first: Martin

last: van Royen

first: Tsion

last: Abraham


title: Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid

city: Bloomington

first: Xindan

last: Wang

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: Histone-like nucleoid structuring (H-NS) and H-NS-like proteins serve as global gene silencers and work with antagonistic transcriptional activators (counter- silencers) to properly coordinate the expression of virulence genes in pathogenic bacteria. In Brucella, MucR has been proposed as a novel H-NS-like gene silencer, but direct experimental evidence is lacking. Here, we show that MucR serves as an H-NS-like silencer of the Brucella abortus genes encoding the polar autotransporter adhesins BtaE and BmaC, the c-di-GMP-specific phosphodiesterase BpdB, and the quorum-sensing regulator BabR. We also demonstrate that the MarR-type transcriptional activator MdrA can displace MucR from the btaE promoter, supporting the existence of MucR counter- silencers in Brucella. Moreover, our chromatin immunoprecipitation (ChIP)-seq analysis identified 546 MucR enrichment peaks along the genome, including in the promoters of the genes encoding the Type IV secretion machinery and effectors and the quorum- sensing regulator VjbR. Importantly, MucR ChIP-seq peaks overlap with the previously described binding sites for the transcriptional activators VjbR, BvrR, and CtrA suggesting that these regulators serve as MucR counter-silencers and work in concert with MucR to coordinate virulence gene expression in Brucella. In addition, using chromosome conformation capture (Hi-C), we show that like H-NS in Escherichia coli, MucR alters the global structure of the Brucella nucleoid. Finally, a copy of the E. coli hns rescues the distinctive growth defect and elevated btaE expression of a B. abortus mucR mutant. Together, these findings solidify the role of MucR as a novel type of H-NS-like protein and suggest that MucR’s gene-silencing properties play a key role in virulence in Brucella.

overall_design: Hi-C and ChIP-seq experiments were performed on wild type and mutant cells of Brucella abortus 2308 growing in brucella broth.

first: X


title: In vitro production of cat-restricted Toxoplasma pre-sexual stages by epigenetic reprogramming [ATAC-seq]

summary: Here we show that AP2XII-1 and AP2XI-2, two transcription factors expressed in tachyzoites, a stage that causes acute toxoplasmosis, silence genes specific to merozoites, a developmental stage critical for sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a drastic change in the transcriptional program, promoting a complete transition from tachyzoites to merozoites. Pre-gametes produced in vitro are characterized by specific protein markers and undergo typical asexual endopolygenic division cycles. AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit the epigenitors MORC and HDAC3, which in turn restrict the accessibility of chromatin to the transcriptional machinery.

overall_design: We report Tn5 transposase accessiblity data (ATAC-Sequencing) on the RHK80  AP2XII-1 mAID_AP2XI-2 mAID strain in an untreated condition (UT) and induced knockdown of both AP2s (IAA 24h)

first: Ana

last: Antunes

first: Martina

last: Shahinas

first: Farhat

last: Dayana

first: Chandra

last: Ramakrishnan

first: Lucid

last: Belmudes

first: Dominique

last: Cannella

first: Charlotte

last: Corrao

first: Yohann

last: Couté

first: Adrian

middle: B

last: Hehl

first: Alexandre

last: Bougdour

first: Isabelle

last: Coppens

first: Mohamed

last: Hakimi


title: Retinoic acid drives intestine-specific adaptation of effector ILC2s originating from distant sites [bulk RNA-Seq]

status: Public on Sep 15 2023

city: Hamburg

first: Nikhat

last: Shaikh

address: Martinistraße 52

institute: University Medical Center Hamburg-Eppendorf

summary: Adaptation of immune cells to tissue-specific microenvironments is a crucial process in homeostasis and inflammation. Here, we show that murine effector type 2 innate lymphoid cells (ILC2s) from various organs are equally effective in repopulating ILC2 niches in other anatomical locations where they adapt tissue-specific phenotypes of target organs. Single-cell transcriptomics of ILC2 populations revealed upregulation of retinoic acid (RA) signaling in ILC2s during adaptation to the small intestinal microenvironment, and RA signaling mediated reprogramming of kidney effector ILC2s towards the small intestinal phenotype in vitro and in vivo. Inhibition of intestinal ILC2 adaptation by blocking RA signaling impaired worm expulsion during Strongyloides ratti infection, indicating functional importance of ILC2 tissue imprinting. In conclusion, this study highlights that effector ILC2s retain the ability to adapt to changing tissue-specific microenvironments, enabling them to exert tissue-specific functions, such as promoting control of intestinal helminth infections.

overall_design: To study how tissue-specific factors shape the ILC2s transcriptome originating from kidney, lung and small-intestine lamina propria, we performed bulk RNA sequencing of ILC2s from these organs of naive C57BL/6 mice

first: Alex

last: Waterhölter

first: Ann-Christin

last: Gnirck

last: Becker

first: Virginia

last: Adamiak

first: Lena

last: Henneken

first: Malte

last: Wunderlich

first: Wiebke

last: Hartmann

first: Lara

last: Linnemann

first: Tobias

last: Huber

first: Christian

middle: F

last: Krebs

first: Ulf

last: Panzer

first: Richard

middle: M

last: Locksley

first: Christoph

last: Wilhelm

first: Minka

last: Breloer

first: Jan-Eric

last: Turner


title: Polycomb Repressive Complex 2 regulates basal cell fate during adult olfactory neurogenesis

first: Bradley

last: Goldstein


title: Polycomb Repressive Complex 2 regulates basal cell fate during adult olfactory neurogenesis [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA sequencing for histone modifications H3K27me3 and H3K27ac on c-KIT immunoselection-purified globose basal cells acutely dissociated from the olfactory epithelium of wild-type mice

first: Tiffany

last: Ko


title: RNA sequence (RNA-seq) profiling of synthesized chromosome SynI in Saccharomyces cerevisiae

city: New York

first: Jitong

last: Cai

state: NY

address: 435 E 30th street

department: NYU Langone Health

institute: NYU Langone Health

summary: We designed and synthesized synI, which is ~21.4% shorter than native chrI, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns surrounding potential instability and karyotype imbalance, and is now attached to synIII, yielding the first synthetic yeast fusion chromosome. We constructed additional fusion chromosomes to investigate effects of fusions on nuclear function. We observed unexpected loops and twisted structures in chrIII-I and chrIX-III-I fusion chromosomes dependent on silencing protein Sir3. ChrI faces special challenges in assuring meiotic crossovers required for efficient homolog disjunction. Centromere deletions engineered into fusion chromosomes revealed opposing effects of core centromeres and pericentromeres in modulating deposition of meiotic recombination protein Red1. These effects extended over >100kb, to disproportionally promote meiotic recombination of small chromosomes like chrI. These findings reveal the power of synthetic genomics to uncover new biology and deconvolute complex biological systems.

overall_design: We chemically synthesized the first fusion yeast chromosome SynIII-I. RNA-seq profiling of SynIII-I strain was compared to SynIII-wildtype I strain to detect potential transcriptome changes.

first: Jingchuan

last: Luo

first: Jef

last: Boeke


title: Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastomas [ATAC-seq]

city: La Jolla

first: Lukas

last: Chavez

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Circular extrachromosomal DNA (ecDNA) in patient tumor genomes is an important driver of oncogenic gene expression, evolution of drug resistance, and poor patient outcomes. Applying computational methods for detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma (MB) tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA+ MB were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. Individual tumors harbor multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging, and CRISPR inhibition experiments in MB models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative "enhancer rewiring" events on ecDNA. This study reveals the frequency and diversity of ecDNA in a subset of highly aggressive MB tumors, and suggests copy number heterogeneity and enhancer rewiring as clinically relevant features of ecDNA in MB.

overall_design: Bulk ATAC-seq of frozen primary medulloblastomas (MB***). ATAC-seq of frozen patient-derived xenograft (PDX) mouse model (RCMB56). ATAC-seq of cell line D458.

first: Owen

last: Chapman

first: Jill

middle: P

last: Mesirov

first: Ernest

last: Fraenkel


title: Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis [143b_ATACseq]

first: Peter

last: Scacheri

summary: ATAC-seq was performed on 143b-GFP cells in vitro or isolated from mouse lung 1 day or 22 days post-innoculation to assess chromatin accessbility dynamics during lung colonization.

overall_design: Comparison of chromatin accessibility between 143b-GFP cells grown in vitro or at two timepoints during lung colonization. For the in vivo conditions, mouse lungs were dissociated using the Miltenyi human tumor dissociation kit and mouse cell depletion kit.

first: Scacheri

last: Peter

first: Pontius

last: W Dean


title: DNA methylation profiling of blood from healthy Australian donors

city: Bayswater

first: Brady

last: Owen

state: Victoria

address: 885 Mountain Hwy

country: Australia

institute: Systematic Medicine

summary: We assessed DNA methylation in whole blood samples from an Australian population across different age groups. Our study focused on evaluating the accuracy of DNA methylation age estimation using the Horvath 2018 and PhenoAge clocks. Additionally, we examined previously reported functional measures of aging in peripheral blood mononuclear cells (PBMCs). Our findings indicated that DNA methylation age effectively predicted donor age, while only a limited number of tested cell functions showed correlations with donor age.

overall_design: As part of a study on biomarkers of aging, whole blood was collected in Tempus RNA tubes from 35 adults from Melbourne, Australia in November 2022. All donors were clinically healthy at the time of donation. DNA was isolated directly from whole blood in Tempus tubes using the QIAamp DNA micro kit with a modified protocol (Owen, BM; 2023)

first: James

last: Phie

first: Jennifer

last: Huynh

first: Scott

last: Needham

first: Cameron

last: Fraser


title: Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis [scATAC-Seq]

summary: Temporal profiling of chromatin accessibility during metastasis revealed dynamic changes in chromatin accessibility during osteosarcoma lung colonization. We sought to determine whether these changes were due to epigenomic reprogramming, or shifts in subclonal frequency. To do this we performed scATAC-seq on MG63.3-GFP cells grown in vitro.

overall_design: MG63.3-GFP cells were profiled in vitro using the 10x chromium system.


title: Low RNA stability signifies strong expression regulatability of tumor suppressors

city: Boston

first: Xinlei

last: Gao

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

type: Methylation profiling by high throughput sequencing

summary: RNA expression of a gene is determined by not only transcriptional regulation, but also post-transcriptional regulation of RNA decay. The precise regulation of RNA stability in the cell plays an important role in normal development. Dysregulation of RNA stability can lead to diseases such as cancer. Here we found tumor suppressor RNAs tended to decay fast in normal cell types when compared with other RNAs. Consistent with a negative effect of m6A modification on RNA stability, we observed preferential deposition of m6A on tumor suppressor RNAs. Moreover, abundant m6A and fast decay of tumor suppressor RNAs both tended to be further enhanced in prostate cancer cells relative to normal prostate epithelial cells. Further, knockdown of m6A methyltransferase METTL3 and reader YTHDF2 in prostate cancer cells both posed stronger effect on tumor suppressor RNAs than on other RNAs. These results indicated a strong post transcriptional expression regulatability mediated by abundant m6A modification on tumor suppressor RNAs.

overall_design: Total T cells, PrEC and C4-2 cells (control, knockdown of METTL3 and YTHDF2) were treated with transcription inhibitor actinomycin D (ActD) for 0, 15 min, 1h and 2h. RNA samples of these cells were than used to generate RNA-Seq libraries. MeRIP-Seq libraries were generated using PrEC cells, C4-2 cells and C4-2 cells with METTL3 knockdown.

first: Yang

last: Yi

first: Jie

last: Lv

first: Qi

last: Cao

first: Kaifu

last: Chen


title: Novel time-resolved reporter mouse reveals spatial and transcriptional heterogeneity during alpha cell differentiation

city: Tokyo

first: MIWA

last: HIMURO

address: Hongo 2-1-1, Bunkyo-ku

department: Department of Metabolism and Endocrinology

institute: Juntendo University Graduate School of Medicine

summary: Glucagon-expressing pancreatic α cells have attracted much attention for their plasticity to transdifferentiate into insulin-producing β cells; however, it remains unclear precisely when and where α cells emerge from and what regulates α-cell fate. We therefore explored the spatial and transcriptional heterogeneity of 　α-cell differentiation by a novel time-resolved reporter system.  We established the mouse model, ‘Gcg-Timer’, in which newly generated α cells can be distinguished from more differentiated cells by their fluorescence. Transcriptome analysis of Gcg-Timer embryos revealed that the mRNAs related to angiogenesis were enriched in newly generated-α cells. Novel time-resolved analysis with Gcg-Timer reporter mouse uncovered spatiotemporal features of α-cell neogenesis, which will enhance our understanding of cellular identity and plasticity within the islets.

overall_design: This study characterizes the transcriptomes of mouse pancreatic α-lineage cells. Pancreas from Gcg-Timer at E17.5 were dissociated and sorted by FACS into 3 groups (N: non-α cell, A: green dominant_newly generated-α cell, and B: green and red_more differentiated-α cell). 4 replicate data were colleced from different mother mice. RNA were extracted and RNA sequencing was performed.

first: Miwa

last: Himuro

first: Yuka

last: Wakabayashi

first: Tomomi

last: Taguchi

first: Takehiro

last: Katahira

first: Luka

last: Suzuki

first: Hitoshi

last: Iida

first: Takeshi

last: Ogihara

first: Yuya

last: Nishida

first: Shugo

last: Sasaki

first: Francis

last: Lynn

first: Yuichi

last: Hiraoka

first: Shigeru

last: Oshima

first: Ryuichi

last: Okamoto

first: Yoshio

last: Fujitani

first: Hirotaka

last: Watada

last: Miyatsuka


title: DUX4-r neomorphic activity depending on GTF2I in acute lymphoblastic leukemia [CUT&Tag]

city: Milan

first: Davide

last: Gabellini

address: Via Olgettina 60

department: Division of Genetics and Cell Biology

country: Italy

institute: SAN RAFFAELE SCIENTIFIC INSTITUTE

summary: Translocations producing rearranged versions of the transcription factor DUX4 (DUX4-r) are one of the most frequent causes of B-cell acute lymphoblastic leukemia (B-ALL). DUX4-r retains the DNA binding domain of wt DUX4, but is truncated on the C-terminal transcription activation domain. The precise mechanism through which DUX4-r causes leukemia is unknown and no targeted therapy is currently available. We found that the rearrangement leads to both a loss and a gain of function in DUX4-r. Loss of CBP/EP300 transcriptional co-activators interaction and inability to bind and activate repressed chromatin. Gain of interaction with the transcription factor GTF2I, which redirects DUX4-r toward leukemogenic targets. Importantly, this neomorphic activity exposes an Achilles' heel whereby DUX4-r positive leukemia cells are exquisitely sensitive to GTF2I targeting, which inhibits DUX4-r leukemogenic activity. Our work elucidates the molecular mechanism through which DUX4-r causes leukemia and suggest a possible therapeutic avenue tailored to this B-ALL subtype.

overall_design:
CUT&Tag of WT DUX4 and DUX4-r variants REH cells. CUT&Tag on H3K27Ac and CUTAC (chromatin accessibility profiling) in REH cells expressing WT DUX4 and DUX4-IGH
CUT&Tag of WT DUX4 and DUX4-IGH in HEK cells transfected with EV or GTF2I. CUT&Tag of GTF2I in HEK cells, DUX4-IGH expressing and EV control expressing REH cells
Please note that the processed data files generated from both rep1 and rep2 samples are linked to the corresponding *rep1 sample records.

first: Daniele

last: Campolungo

first: Anna

last: Tascini


title: Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer

first: Cigall

last: Kadoch

address: 44 Binney St

country: USA

institute: Dana-Farber Cancer Institute

summary: Acquired resistance to tyrosine kinase inhibitors, such as Osimertinib used to treat EGFR-mutant lung adenocarcinomas, limits long-term efficacy and is frequently caused by non-mutational mechanisms. Here, we generate and comprehensively characterize the chromatin accessibility and gene regulatory signatures of pairs of parental and Osimertinib-resistant EGFR-mutant cell lines. Specifically, we profile the genome-wide localization of mSWI/SNF chromatin remodeling complexes in these cell line pairs, identifying both pan-cell and tumor cell-specific gene targets underlying the resistance state. Importantly, genetic and small molecule-based pharmacologic disruption of the SMARCA4/SMARCA2 mSWI/SNF ATPases re-sensitizes a subset of resistant cell lines and in vivo tumor models to Osimertinib. This re-sensitization is linked to mSWI/SNF-mediated regulation of cell proliferative, epithelial to mesenchymal transition, and epithelial cell differentiation-related programs, as well as NRF2 signaling. These data highlight the role for mSWI/SNF complexes in supporting TKI resistance and suggest potential utility of mSWI/SNF inhibitors in TKI-resistant lung cancers.

overall_design: Genomics-based approaches were used to characterize the epigenetic landscape of osimertinib-resistant lung cancer cell lines. Moreover, pharmacological inhibition of SMARCA4/A2 using a small molecule inhibitor was performed and shRNA hairpins were design to target SMARCA4 in EGFR-mutant lung cancer cell lines and PDX-derived tumor cells to investigate how the mSWI/SNF chromatin remodeling complex can re-senstize osimertinib-resistant cell line models to osimertinib treatment.

first: Claudia

last: Gentile

first: Akshay

last: Sankar


title: Expression data from primary astrocyte cell in CRTC3 KO and WT mice

city: Seoul

first: Sukyoung

last: Park

address: 88, Olympic-ro 43-gil

country: South Korea

institute: Ulsan University

summary:
CRTC3 is CREB regulated transcriptional co-activators and prominently expressed in astrocyte cells. CRTC3 plays a specific role in determining the social heirarchical ranking in mice by confirming social rank test in CRTC3 KO mice. Loss of CRTC3 in astrocyte induced neuronal change and caused exchanging protein expression pattern.
We used microarrays to determine the astrocyte-derived factors that were regulated by CRTC3 and related with social dominance behaviours of CRTC3 KO mice. We identifed distinct factor of down-regulated gene during primary astrocyte cell in CRTC3 KO.

overall_design: Primary astrocyte were cultured from CRTC3 KO and WT mouse pups. To confirm the genes associated with cAMP responsive in CRTC3 KO astrocytes, WT and CRTC3 KO astrocyte cell were treated with vehicle and forskolin(FSK) for 0.5 and 2 hours.

first: Ji-Seon

first: Seung-Young

last: Yoon


title: In vitro production of cat-restricted Toxoplasma pre-sexual stages by epigenetic reprogramming [ChIP-seq]

first: Christopher

last: Swale

overall_design: We report genome-wide AP2-XII-1, AP2-XI-2, MORC and HDAC3, profiles in Toxoplasma gondii RHKU80 using ChIP-seq in the context of inducible knock downs of AP2-XII-1, AP2-XI-2 or both simultaneously.

first: Ana

last: Antunes

first: Martina

last: Shahinas

first: Farhat

last: Dayana

first: Chandra

last: Ramakrishnan

first: Lucid

last: Belmudes

first: Dominique

last: Cannella

first: Charlotte

last: Corrao

first: Yohann

last: Couté

first: Adrian

last: Hehl

first: Alexandre

last: Bougdour

first: Isabelle

last: Coppens

first: Mohamed

last: Hakimi


title: Methionine biosynthesis enzyme MoMet2 is required for rice blast fungus pathogenicity by promoting virulence gene expression via reducing 5mC modification

city: Nanjing

first: Huimin

last: Li

state: Jiangsu

address: No. 1, Weigang,Xiaolingwei Street, Xuanwu District

department: Department of Plant Pathology

country: China

institute: College of Plant Protection, Nanjing Agricultural University

summary:
To investigate the function of Momet2 in Magnaporthe oryzae, we generated Momet2 mutant.
To understand the impact of MoMET2-depentent 5mC to gene expression at the transcriptional level, we performed comparative transcriptome analysis using the materials harvested from Guy11 and ΔMomet2 mycelium samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Guy11 and Momet2 mutant mycelium samples

first: Zhengguang

last: Zhang


title: Expression data from pulmonary artery endothelial cell after exposure to hypoxia for 24 hours

status: Public on Sep 24 2023

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
A number of mediators that have been found to be involved in the pathogenesis of hypoxic pulmonary hypertension, these mediators including mRNA, microRNAs and long noncoding RNAs. Endothelial dysfunction plays a major role in the initiation of pulmonary vascular remodeling and is thought to be a major contributor to this process. However, mRNA and no-coding RNAs expression profiles and their biological functions in pulmonary artery endothelial cells (PAECs) exposed to hypoxia need to be investigated further.
Pulmonary artery endothelial cells (PAECs) were exposed to normoxia condition (21% O2, 5% CO2, 74% N2) or hypoxia condition (3% O2, 5% CO2, 92% N2) (n=3 for each group).PAECs were harvested after 24 hours and performed to further analysis.

overall_design: cDNAs of samples from normoxia and hypoxia group were hybridized to Affymetrix Clariom D human GeneChip® arrays (Affymetrix, America) according to the User Manuals. Affymetrix® Expression Console Software (version 1.2.1) was used for microarray analysis. Raw data (CEL files) were normalized at transcript level using robust multiaverage method (RMA workflow). Median summarization of transcript expressions was calculated. Gene-level data was then filtered to include only those probe sets that are in the ‘core’ metaprobe list, which represent RefSeq genes.

first: Jie

last: Liu

first: Lei

last: Wang


title: Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein

city: Dijon

first: Binnaz

last: Yalcin

address: 15 boulevard Maréchal De Lattre de Tassign

summary: Using mouse genetic studies and systematic assessments of brain neuroanatomical phenotypes, we set out to identify which of the 30 genes causes brain defects at the autism-associated 16p11.2 locus. We show that multiple genes mapping to this region interact to regulate brain anatomy, with female mice exhibiting far fewer brain neuroanatomical phenotypes. In male mice, among the 13 genes associated with neuroanatomical defects (Mvp, Ppp4c, Zg16, Taok2, Slx1b, Maz, Fam57b, Bola2, Tbx6, Qprt, Spn, Hirip3 and Doc2a), Mvp is the top driver implicated in phenotypes pertaining to brain, cortex, hippocampus, ventricles and corpus callosum sizes. The major vault protein (MVP), the main component of the vault organelle, is a conserved protein found in eukaryotic cells, yet its function is not understood. Here, we find MVP expression highly specific to the limbic system and show that Mvp regulates neuronal morphology, postnatally and specifically in males. We also recapitulate a previously reported genetic interaction and show that Mvp+/-;Mapk3+/- mice exhibit behavioral deficits, notably decreased anxiety-like traits detected in the elevated plus maze and open field paradigms. Our study highlights multiple gene drivers in neuroanatomical phenotypes, interacting with each other through complex relationships. It also provides the first evidence for the involvement of the major vault protein in the regulation of brain size and neuroanatomy, specifically in male mice.

overall_design: To investigat the differential expression changes of the loss of the Mvp gene in the cingulate gyrus of male mice.


title: Retinoic acid drives intestine-specific adaptation of effector ILC2s originating from distant sites

first: Nikhat

last: Shaikh

country: Germany

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

overall_design: Refer to individual Series


title: Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute