title: Multiomics analysis of HIF-stabilization in primary renal tubular cells [ChIP-Seq]

summary: The activation of hypoxia-inducible transcription factors (HIF) leading to the expression of hundreds of target genes is a fundamental mechanism in acute and chronic kidney disease, mediating protective but possibly harmful effects. Furthermore, dysregulation of the HIF pathway in chronic kidney disease causes renal anemia through insufficient erythropoietin (EPO) induction in interstitial cells. RNA-seq analysis was performed in human primary renal tubular cells to analyse the effect of HIF stabilization on the expression of genes in tubular cells. ATAC-seq and HIF-CHIP-seq complement the data to analyse transcription factor binding and chromatin configuration changes.

overall_design:
This study consists of HIF-ChIP-seq, ATAC-seq, and RNA-seq samples from the cells of one individual.
Submitter states that raw data are not available due to patient privacy concerns

first: Johannes

last: Schödel

first: Steffen

last: Grampp


title: Multiomics analysis of HIF-stabilization in primary renal tubular cells [ATAC-Seq]

status: Public on May 05 2023

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

country: Germany

institute: RWTH Aachen University Medical School

type: Genome binding/occupancy profiling by high throughput sequencing


title: Soybean Root Transcriptomics: Insights into Sucrose Signaling at the Crossroads of Nutrient Deficiency and Biotic Stress Responses

city: Hayward

first: Claudia

last: Uhde-Stone

state: CA

address: 25800 Carlos Bee Blvd

department: Biological Sciences

country: USA

institute: California State University, East Bay

type: Expression profiling by high throughput sequencing

summary: Soybean (Glycine max) is an important agricultural crop, but nutrient deficiencies frequently limit soybean production. While research has advanced our understanding of plant responses to long-term nutrient deficiencies, less is known about the signaling pathways and immediate responses to certain nutrient deficiencies, such as Pi and Fe deficiencies. Recent studies have shown that sucrose acts as a long-distance signal that is sent in increased concentrations from the shoot to the root in response to various nutrient deficiencies. Here, we mimicked nutrient deficiency-induced sucrose signaling by adding sucrose directly to the roots. To unravel transcriptomic responses to sucrose acting as a signal, we performed Illumina RNA-sequencing of soybean roots treated with sucrose for 20 min and 40 min, compared to non-sucrose-treated controls. We obtained a total of 260 million paired-end reads, mapping to 61,675 soybean genes, some of which are novel (not yet annotated) transcripts. Of these, 358 genes were upregulated after 20 min, and 2416 were upregulated after 40 min of sucrose exposure. GO (gene ontology) analysis revealed a high proportion of sucrose-induced genes involved in signal transduction, particularly hormone, ROS (reactive oxygen species), and calcium signaling, in addition to regulation of transcription. In addition, GO enrichment analysis indicates that sucrose triggers crosstalk between biotic and abiotic stress responses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from soybean roots exposed to 0 (control), 20 min and 40 min of 10 mM sucrose in 3 biological replications

first: Leela

middle: C

last: Manozna Nidumolu

first: Kristina

middle: M

last: Lorilla

first: Indrani

last: Chakravarti


title: Multiomics analysis of HIF-stabilization in primary renal tubular cells [RNA-Seq]


title: The MMP-2 histone H3 N-terminal tail protease is selectively targeted to the transcription start sites of active genes [ChIP-seq]

city: New York

first: Benjamin

middle: H

last: Weekley

state: NY

address: 1470 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Our study examines the role of MMP-2 mediated Histone H3NT proteolysis in U2OS cells. We find binding of MMP-2 at all active protein coding transcription start sites, and examine the role it plays in local chromatin regulation and changes in gene expression.

overall_design: native ChIP-seq of 3XHA tagged Pro-MMP2 as well as a negative control (HA ChIP in WT cells not expressing tagged Pro-MMP2) and positive control (H3K4me3)

first: Judd

last: Rice


title: Histone H3/H4 chaperone CHAF1B prevents the mislocalization of CENP-A for chromosomal stability

city: Chicago

first: Daniel

last: Foltz

state: IL

address: 303 E Superior St

institute: Northwestern University

summary: Mislocalization of CENP-A to non-centromeric regions contributes to chromosomal instability (CIN). Here, we defined a role for the histone H3/H4 chaperone CHAF1B in preventing mislocalization of CENP-A and CIN.

overall_design: CUT&RUN for CENP-A, n=1 of 2 antibodies

first: Roshan

last: Shrestha

first: Vinutha

last: Balachandra

first: Jee

last: Kim

first: Austin

last: Rossi

first: Pranathi

last: Vadlamani

first: Laurent

last: Ozbun

first: Shinjen

last: Lin

first: Ken

last: Cheng

first: Raj

last: Chari

first: Gianluca

last: Pegoraro

middle: R

first: Natasha

middle: J

last: Caplen

first: Munira

middle: A

last: Basrai


title: Mitochondrial citrate metabolism and efflux regulates trophoblast differentiation

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: Cytotrophoblasts fuse to form and renew syncytiotrophoblasts necessary to maintain  placental health throughout gestation. During cytotrophoblast to syncytiotrophoblast differentiation, cells undergo regulated metabolic and transcriptional reprogramming. Mitochondria play a critical role in differentiation events in cellular systems, thus we hypothesized that mitochondrial metabolism played a central role in trophoblast differentiation. In this work, we employed static and stable isotope tracing untargeted metabolomics methods together with gene expression and histone acetylation studies in an established cell culture model of trophoblast differentiation. Trophoblast differentiation was associated with increased abundance of the TCA cycle intermediates citrate and α-ketoglutarate. Citrate was preferentially exported from mitochondria in the undifferentiated state but was retained to a larger extent within mitochondria upon differentiation. Correspondingly, differentiation was associated with decreased expression of the mitochondrial citrate transporter (CIC). CRISPR/Cas9 disruption of the mitochondrial citrate carrier showed that CIC is required for biochemical differentiation  of trophoblast. Loss of CIC resulted in broad alterations in gene expression and histone acetylation. These gene expression changes were partially rescued through acetate supplementation. Taken together, these results highlight a central role for mitochondrial citrate metabolism in the orchestration of histone acetylation and gene expression during trophoblast differentiation.

overall_design: Global expresssion profiling by RNA-seq of wild type and mutant cells under two conditions in triplicate.

first: Sarah

last: Wernimont

middle: D


title: Innate lymphocytes in solid human tumors

city: Boston

first: Cathal

last: Harmon

state: MA

address: 4 Blackfan Circle, Room 625, Harvard Institutes of Medicine,

institute: Brigham and Women's Hospital

summary: Profiling innate lymphocytes, NK cells, MAIT cells and gd T cells, in colorectal and endometrial cancer

overall_design: Tumor infiltrating cells were isolated from human colorectal and endometrial cancer. Innate T cells and NK cells were FACS enriched before sequencing.

first: Lydia

last: Lynch


title: Mdivi-1 treatment regulates mouse ESC epigenome

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

country: China

institute: Huazhong University of Science and Technology

summary: We treated mouse embryonic stem cells (ESCs) with Mdivi-1 and exmained changes of ESC epigenome.

overall_design: We treated mouse ESCs with Mdivi-1 and identified that there were significant changes of ESC epigenome.

first: Shi-meng

last: Guo

first: Yi-ran

last: Zhang

first: Ying

last: Yin

first: Ximiao

last: He


title: Mdivi-1 treatment regulates embryo epigenome

summary: We mouse early embryos with Mdivi-1 and exmained changes of embryo epigenome.

overall_design: We treated mouse early embryos with Mdivi-1 and identified changes of 2-cell embryo epigenome.


title: Meningeal natural killer cells and innate lymphoid cells 1 tune anxiety and memory via interferon-γ and acetylcholine

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

country: Italy

institute: La Sapienza University of Rome

summary: The mechanisms of communication between the brain and the neighboring meningeal immune cells are still unclear. Here we characterized the resident group 1 innate lymphoid cells in the meninges of adult mice, and identified ILC1/NK cell-derived interferon- and acetylcholine as mediators involved in the modulation of brain circuitries underlying anxiety-like behavior and memory. This discloses a new meningeal-to-brain communication mechanism that modulates brain functions under physiological conditions.

overall_design: To expand our understanding of functions of individual meningeal cell populations, we investigated group 1 innate lymphoid cells (ILCs), which comprise conventional NK1.1+ NK cells and type 1 ILCs in adult male mice by single-cell RNA-sequencing.

first: Stefano

last: Garofalo

first: Cristina

last: Limatola

first: Giuseppe

last: Sciumè

first: Silvano

last: Sozzani

first: Eva

middle: P

last: Mortari

first: Rita

last: Carsetti


title: The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [RNA-Seq]

first: Yihao

last: Yang

address: 1230 York Ave

institute: The Rockefeller University

summary: When stem cells activate a member of the SOX family of pioneer factors, they bind their cognate sequences within condensed chromatin, not only evicting the associated nucleosome, but also recruiting H3K4-monomethylases, which modify flanking nucleosomes to open chromatin and activate one lineage program; simultaneously, pioneer factors also silence alternative fates, but in this case act indirectly, through competing for H3K4-monomethylases pre-existing at the original fate genes.

overall_design: FACS-sorted EdpSCs were directly sorted into TRI Reagent, and total RNA was purified using the Direct-zol RNA kit (Zymo Research) according to the kit protocol. RNA quality was determined by Agilent 2100 Bioanalyzer, and RNA libraries were generated using SMARTer RNA kit for low input RNA-seq and sequenced on Illumina HiSeq 4000 or NovaSeq SP 50PE.

first: Nicholas

last: Gomez

first: Elaine

last: Fuchs


title: Whole-genome CRISPR screen to identify regulators of cold-shock protein RBM3

city: Cambridge

first: Emmanouil

last: Metzakopian

address: Addrenbookes Campus

country: United Kingdom

institute: UK Dementia Research Institute

summary: Enhanced expression of the cold-shock protein RNA binding motif 3 (RBM3) is highly neuroprotective both in vitro and in vivo. Whilst upstream signalling pathways leading to RBM3 expression have been described, the precise molecular mechanism of RBM3 induction during cooling remains elusive. To identify temperature-dependent modulators of RBM3, we performed a genome-wide CRISPR-Cas9 knockout screen using RBM3-reporter human iPSC-derived neurons. We found that RBM3 mRNA and protein levels are robustly regulated by several splicing factors, with heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) being the strongest positive regulator.

overall_design: An RBM3 CRISPR knockout pooled screen is performed using two clones of GFP-RBM3 human iPSC-derived neurons (i-neurons). 4-day differentiated iPSCs are transduced with a custom-made whole-genome sgRNA lentiviral library, targeting critical exons of 18466 genes across the human genome, co-expressing a BFP reporter. Day 14-16 i-neurons are incubated at 32°C for 72h before dissociation and fluorescence-activated cell sorting (FACS) on day 17-19. BFP-positive cells with the highest and lowest GFP-RBM3 expression, which falls in the top and bottom quartile of GFP intensity profiles, are separately collected, denoted as high GFP and low GFP populations. Genomic DNA is sequenced to identify sgRNAs enriched in high or low GFP populations.

first: Nikolaos

last: Patikas

first: Julie

middle: Q

last: Lin

first: Sofia

last: Pavlou

first: Sarah

middle: F

last: Field


title: The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates

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

overall_design: Refer to individual Series


title: Deriving Schwann Cells from hPSCs Enable Disease Modeling and Drug Discovery for Diabetic Peripheral Neuropathy

city: San Francisco

first: Faranak

last: Fattahi

state: California

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

summary: We used single cell RNA sequencing (scRNA-seq) for molecular characterization of our hPSC-derived Schwann Cell cultures.

overall_design: For each sample we pooled Schwann Cells from two independent differentiation cultures.

first: Homa

last: Majd

first: Andrius

last: Cesiulis

first: Lorenz

last: Studer


title: RNA m6A methylome from zebrafish zygotes, mouse liver polyA-selected RNAs, mouse embryonic stem cells, spike-in RNA controls, and single mouse oocytes and embryos

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is a prevalent RNA modification that has key roles in distinct biological processes, including meiosis and early embryo development. Despite advances in methodology for m6A mapping, the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing (picoMeRIP-seq) method, also suitable for single-cell (scMeRIP-seq). We validate the down-scaling of the method by profiling m6A from picogram amounts of mouse liver polyA-selected RNA, mouse embryonic stem cells, and zebrafish zygotes. We provide proof-of-principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome-wide manner.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design:
Transcriptome-wide m6A maps were generated from zebrafish and mouse samples as below.
11 zebrafish zygote samples: 3 biological replicates for 10 zygotes, 3 biological replicates for 5 zygotes, and 5 biological replicates for single zygote.
6 mouse liver polyA-selected RNA samples: 10 ng, 1 ng, and 100 pg; 2 biological replicates for each amount.
9 mouse embryonic stem cell (R1 cell line, from ATCC, SCRC-1011) samples: 1000 cells, 100 cells, and 10 cells; 3 biological replicates for each amount.
3 spike-in RNA control (add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without m6A modification into the 12 ng polyA-selected RNAs) related samples: 12 ng polyA-selected RNA from mouse liver; 6 ng polyA-selected RNA from mouse liver and 6 ng polyA-selected RNA from wild-type/WT mouse embryonic stem cells (from Geula, S., et al. Science 2015); and 6 ng polyA-selected RNA from mouse liver and 6 ng polyA-selected RNA from Mettl3 knock-out/KO mouse embryonic stem cells (from Geula, S., et al. Science 2015).
12 single mouse oocyte and embryo samples: oocytes at germinal vesicle (GV) and metaphase II (MII) stages, and embryos at zygote, 2-cell, 8-cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte (GSM5746922), zygote (GSM5746930), 2-cell (GSM5746911) and 8-cell (GSM5746914) stages can be found in GSE192440.

first: Yanjiao

last: Li

first: Yunhao

last: Wang

first: Arne

last: Klungland

first: John

last: Dahl


title: The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [ATAC-Seq]

first: Yihao

last: Yang

overall_design: ATAC-seq was performed as described before in Buenrostro et al., 2013. Briefly, FACS sorted cells were lysed with ATAC lysis buffer on ice for 1 minute. Lysed cells were then tagmented with Tn5 transposase (Illumina) at 37C for 30min. Cleaned up fragments were PCR amplified (NEB) and size selected with 1.8X SPRI beads (Beckman Coulter). All libraries were sequenced on Illumina NextSeq 500 with 40-bp paired-end settings.


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [in_vitro_RNA_seq]

status: Public on May 04 2023

city: Stanford

first: Laura

last: Attardi

address: 269 Campus Drive

institute: Stanford University

summary: Lung cancer is the leading cause of cancer deaths worldwide. TP53 tumor suppressor gene mutations occur in 50% of lung adenocarcinomas (LUADs) and are linked to poor prognosis, but how p53 suppresses LUAD development remains enigmatic. We show here that p53 suppresses LUAD by governing cell state, by promoting alveolar type 1 (AT1) differentiation. Using mice expressing oncogenic Kras and null, wild-type, or hypermorphic p53 alleles in alveolar type 2 (AT2) cells, we observed graded effects of p53 on LUAD initiation and progression. RNA-sequencing and ATAC-sequencing of LUAD cells uncovered a p53-induced AT1 differentiation program during tumor suppression in vivo through direct DNA binding, chromatin remodeling, and AT1 gene induction. Single-cell transcriptomics analyses revealed that during LUAD evolution, p53 promotes AT1 differentiation through action in a transitional cell state analogous to a transient intermediary seen during AT2-to-AT1 differentiation in alveolar injury repair. Notably, p53 inactivation resulted in the inappropriate persistence of these transitional cancer cells accompanied by upregulated growth signaling and divergence from lung lineage identity, characteristics associated with LUAD progression. Analysis of p53wt and p53-null mice showed that p53 also directs alveolar regeneration after injury, by regulating AT2 self-renewal and promoting transitional cell differentiation into AT1 cells. Collectively, these findings illuminate mechanisms of p53-mediated LUAD suppression, in which p53 governs alveolar differentiation, and suggest that tumor suppression reflects a fundamental role of p53 in orchestrating tissue repair after injury.

overall_design: Lung cancer cell lines were harvested and analyzed using RNA-seq

first: Alyssa

last: Kaiser

first: Kathryn

middle: T

last: Bieging-Rolett


title: The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [CUT&RUN]

overall_design: Epidermal stem cells were FACS isolated as mentioned above and CUT&RUN was performed as previously described with minor modifications indicated in methods. CUT&RUN sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. PCR-amplified libraries were purified using 1x ratio of SPRI beads and eluted in 15μL 0.1x TE buffer. All CUT&RUN libraries were sequenced on Illumina NextSeq using 40-bp paired-end reads.

first: Nicholas

last: Gomez

first: Elaine

last: Fuchs


title: The MMP-2 histone H3 N-terminal tail protease is selectively targeted to the transcription start sites of active genes

first: Benjamin

last: Weekley

summary:
This SuperSeries is composed of the SubSeries listed below.
Our study examines the role of MMP-2 mediated Histone H3NT proteolysis in U2OS cells. We find binding of MMP-2 at all active protein coding transcription start sites, and examine the role it plays in local chromatin regulation and changes in gene expression.


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [in_vivo_ATAC_seq2]

overall_design: Mouse lung cancer cells were isolated via FACS and analyzed via ATAC-seq


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [in_vivo_RNA_seq]

overall_design: Mouse lung cancer cells were isolated via FACS and analyzed via RNA-seq


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [in_vivo_ATAC_seq1]


first: Li-quan

last: Zhou

summary: We demonstrat that Mdivi1 treatment impacts transcriptome of mouse embryonic stem cells (ESCs).

overall_design: We treated mouse ESCs with Mdivi-1 to inhibit DRP1 activity and examined transcriptome changes of ESCs.

first: Shi-meng

last: Guo

first: Yi-ran

last: Zhang

first: Ying

last: Yin

first: Ximiao

last: He


title: Effect of gene deletion on gene expression of Penicillium oxalicum

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [10x single cell multiomics RNA-Seq]

overall_design: Mouse lung cancer cells were isolated via FACS and analyzed via 10x single cell multiomics gene expression

last: Hanson


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [scRNA-Seq]

overall_design: Mouse lung cells during injury were isolated via FACS and analyzed via 10x scRNA-seq


title: p53 governs an alveolar type 1 differentiation program in lung cancer suppression [10x_multiome_ATAC]

overall_design: Mouse lung cancer cells were isolated via FACS and analyzed via 10x single cell multiomics ATAC


title: Simultaneous activation of Kras-Akt and Notch pathways induces extrahepatic biliary cancer via mTORC1 pathway

city: Kyoto

first: Mio

last: Namikawa

state: Kyoto

address: 54 Kawaharacho, Shogoin, Sakyoku

department: Gastroenterology and Hepatology

country: Japan

institute: Kyoto University Graduate School of Medicine

summary:
Biliary tract cancer (BTC) has poor prognosis. The Notch receptor is aberrantly expressed in extrahepatic cholangiocarcinoma (eCCA). However, the role of Notch signaling in the initiation and progression of eCCA and gallbladder (GB) cancer remains unknown. We investigated the functional role of Notch signaling during tumorigenesis of the extrahepatic bile duct and GB.
We demonstrated that simultaneous activation of the Kras–Akt and Notch pathways in EHBD and GB resulted in the formation of BilINs and biliary cancer in a mouse model. Mechanistically, the Kras/Notch–Myc axis activates mTORC1 through phosphorylation of TSC2 in biliary tumorigenesis.

overall_design: We used biliary spheroids developed from biliary tract of mice in which KRAS-AKT and Notch pathways were activated (HKN). We also used biliary spheroids developed from biliary tract of wild type mice (C) and mice in which either Kras or Notch pathway is activated (HK, HN) as control samples.

first: Akihisa

last: Fukuda


title: A high ratio of linoleic acid (n-6 PUFA) to alpha-linolenic acid (n-3 PUFA) adversely affects early stage of human neuronal differentiation and electrophysiological activity of glutamatergic neurons in vitro

city: Cardiff

first: Karolina

last: Dec

address: Hadyn Ellis Building, Maindy Road, Cathays

department: Neuroscience and Mental Health Innovation Institute

institute: Cardiff University

summary: There is a growing interest in the possibility of dietary supplementation with polyunsaturated fatty acids (PUFAs) for treatment and prevention of neurodevelopmental and neuropsychiatric disorders. Studies have suggested that of the two important classes of PUFAs, omega-6 (n-6) and omega-3 (n-3) PUFAs support brain development and function, and when used as a dietary supplement may have beneficial effects for maintenance of a healthy brain and via amelioration of psychiatric disorders. However, to date epidemiological studies and clinical trials on children and adults have been inconclusive regarding treatment length, dosage and use of specific n-3 PUFAs. The aim of this study is to generate a simplified in vitro cell-based model system to test how different n-6 to n-3 PUFA ratios affect human brain function and to probe their mechanism of their action.  This study shows that at a n-6:n-3 ratio of 5:1 PUFAs induce stem cell proliferation, generating a large increase in number of cells after 72h treatment; suppress generation of neuronal progenitor cells, as measured by decreased expression of FOXG1 and Nestin in neuronal precursor cells (NPC) after 20 day of development; and disrupt neuronal activity in vitro, increasing spontaneous neuronal firing, reducing synchronized bursting receptor subunits. We observed no significant differences for neuronal precursor cells treated with ratios 1:3 and 3:1, in comparison to 1:1 control ratio, but higher ratios of n-6 to n-3 PUFAs adversely affect early stages of neuronal differentiation. Moreover, a 5:1 ratio in cortical glutamatergic neurons induce expression of GABA receptors which may explain the observed abnormal electrophysiological activity.

overall_design: All experiments were performed by use of human induced pluripotent stem cells (iPSCs). In this study, we examined the effect of different ratios of linoleic acid (n-6) to alpha-linolenic acid in cell growth medium on iPSC proliferation, generation of neuronal precursors, gene expression pattern in NPCs and electrophysiology of cortical glutamatergic neurons by multielectrode array (MEA) analysis.

first: Mouhamed

last: Alsaqati

first: Joanne

last: Morgan

first: Sumukh

last: Deshpande

first: Jamie

last: Wood

first: Jeremy

last: Hall

first: Adrian

last: Harwood


title: The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [MINT ChIP-Seq]

first: Yihao

last: Yang

overall_design: FACS sorted cells were used for MINT-ChIP according to van Galen et al (doi::10.1016/j.molcel.2015.11.003). All MINT-ChIP libraries are sequenced on NextSeq.

first: Nicholas

last: Gomez

first: Elaine

last: Fuchs


title: Gene expression profiling of shCtrl and shCNN2 RKO cells from Clariom S array.

city: Shanghai

first: Jinghu

address: 168 Changhai Road, Yangpu District, Shanghai

institute: Changhai Hospital Affiliated to Navy Medical University

summary:
CNN2 is identified as a tumor promotor in the development of colorectal cancer. Herein, gene expression in RKO cells infected with shCtrl and shCNN2 (for CNN2 knockdown) was detected with a Clariom S array.
Gene expression profiling of shCtrl and shCNN2 RKO cells was acquired and analyzed. Differentially expressed genes were identified based on fold change of mean of expression (fold change ≥ 1.3) and FDR (< 0.05) from P value calculated based on linear model of empirical Bayesian distribution. In total, 523 upregulated genes and 648 downregulated genes were characterized.

overall_design: Gene expression in shCNN2 (CNN2 knockdown) RKO cells and shCtrl (negative control) RKO cells was detected using Human gene expression array. Firstly, total RNA was extracted and RNA quality and integrity was determined by Nanodrop 2000 (Thremo Fisher Scientific) and Agilent 2100 and Agilent RNA 6000 Nano Kit (Agilent). Then, gene chip was performed with Clariom S array According to the instructions.

first: Xiaohong

first: Chuansen

last: Zhang

first: Ang

last: Li

first: Wei

last: Wang

first: Junjie

last: Xing

first: E

last: Jifu

first: Xiaodong

last: Xu

first: Hao

first: Enda

last: Yu

first: Debing

last: Shi

first: Hantao


title: A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

city: Indianapolis

first: Michael

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University


title: Neutralizing IFNγ improves safety without compromising efficacy of CAR-T cell therapy in B-cell malignancies

first: Marika

last: Guercio

state: RM

address: Viale di San Paolo, 15

department: Oncohematology

institute: Ospedale Pediatrico Bambino Gesù

sample_organism:
Homo sapiens
Mus musculus


title: Neutralizing IFNγ improves safety without compromising efficacy of CAR-T cell therapy in B-cell malignancies II

summary:
IFNγ neutralization by the clinically approved monoclonal antibody emapalumab mitigates severe toxicity related to CAR-T therapy
Emapalumab does not impair CAR.CD19 T-cell activation signaling

overall_design: hGM-CSF/hIL3 NOG mice (n=10) were infused with irradiated FF-Luciferase positive Daudi cells at Day-2 and treated with 10x106 CAR.CD19 T-cells/mouse either in the presence of 100mg/Kg/day emapalumab (n=5) or of the vehicle (n=5). Two mice were considered as for negative control, being infused only with DAUDI cells. Mice were sacrified 3 days after CAR T-cell infusion to evaluate the brain damage occurrence in this murine model of acute CAR T-cell toxicity.

first: Simona

last: Manni


title: Brain transcriptomics reveal the activation of neuroinflammation pathways during acute Orientia tsutsugamushi infection in C57BL/6 mice

city: Galveston

first: Lynn

last: Soong

state: TX

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: We performed RNAseq on total RNA extracted from brains of mice infected with Orientia tsutsugamushi to investigate the transcriptomic signature of this tissue throughout infection.

overall_design: Female C57BL/6J mice (6-9 weeks-old, purchased from the Jackson Laboratory #000664) were intravenously inoculated with a lethal dose (6 × 10e4 FFU, 200 µl) of bacteria or PBS (mock). Mice were sacrificed at established timepoints, and spleens were collected in RPMI 1640 medium. Spleen single-cell suspensions were made by passing splenic tissue through a 70-μm cell strainer in RPMI 1640 medium, and these were then treated with Red Blood Cell Lysis Buffer. Untouched B cells were isolated from spleen single-cell suspensions by using the mouse B Cell Isolation Kit (Miltenyi Biotec). B cell samples were then evaluated for purity (~97-98%, based on B220 expression assessed by flow cytometry) and stored in RNALater. Total RNA was extracted by using the RNeasy Mini kit (Qiagen). Total RNA (≥ 1ug) was sent to LC Sciences (Houston, TX) for Poly(A) RNA-Seq Sequencing Service.The Mus musculus genome build mm10 was used as a reference genome. Quality control analysis was done by using FastQC (Andrews, 2010) and RSeQC6 (Wang, Bioinformatics, 2012). Semi-supervised hierarchical clustering analysis and heatmap generation were performed by using the Morpheus tool. Principal component analysis and volcano plot were done in R using PCAtools and EnhancedVolcano packages.         GSEA analysis    Pathway enrichment analysis using gene set enrichment analysis with GSEA version 3.0 was performed with a ranked gene list (33, 34). Specifically, ranked gene list is prepared from the differential gene expression analysis by using the following metrics: sign of the Log2fold change multiplied by the inverse of the p-value. GSEAPreranked was run with 2000 permutations. Primary gene sets investigated were obtained from the MSigDB and published reports. GSEA FDR Q <0.05 cutoff was applied to examine enriched gene sets in our dataset.         Cytoscape analysis    Enrichment results from the GSEA analysis were visualized using Cytoscape. GSEA output files were uploaded in the EnrichmentMap app of Cytoscape and FDR Q value cut off was set to 0.01. Clusters are automatically defined using AutoAnnotate Cytoscape app.         Statistical Analysis    Data were presented as mean ± standard error of mean (SEM). Differences between individual treatment and control groups were determined by using unpaired Student’s t test, utilizing Welch’s correction when appropriate. One-way ANOVA was used for multiple group comparisons, with a Tukey’s Post Hoc for comparisons between groups. All data were analyzed by using GraphPad Prism software 8.0. Statistically significant values are denoted as *, p < 0.05; **; p < 0.01, ***; p < 0.001, and ****; p < 0.0001, respectively.

first: Liang

last: Yuejin

first: Gonzales

last: Casey

first: Soong

last: Lynn


title: Neutralizing IFNγ improves safety without compromising efficacy of CAR-T cell therapy in B-cell malignancies I

overall_design: Un-transduced (NT) and CAR.CD19 T-cells were activated with 0.5 μg/ml recombinant human CD19 Fc Chimera Protein for 16 hours before the analysis of the gene signature in presence or absence of Emapalumab


title: Targeted transcriptomic analysis of pancreatic adenocarcinoma in EUS-FNA samples by NanoString technology

city: BARCELONA

first: Leire

last: Pedrosa

state: Barcelona

address: Carrer del Villarroel 170

country: Spain

institute: IDIBAPS

summary:
Background: Integration of transcriptomic testing into EUS-FNA samples is a
growing need for precision oncology in pancreatic ductal adenocarcinoma
(PDAC). The NanoString platform is suitable for transcriptome profiling in low
yield RNA samples.
Methods: Inclusion of patients that underwent EUS-FNA cytological diagnosis of
pancreatic ductal adenocarcinoma using 19G and/or 22G needles and subsequent
surgical resection. Formalin fixed paraffin embedded (FFPE) cytological and
surgical samples underwent RNA extraction and transcriptomic analysis using a
custom 52-gene NanoString panel of stromal PDAC features. Cell type abundance
was quantified in FFPE specimens and correlated.
Results: 18 PDAC patients were included. Mean EUS-FNA passes was 2 + 0.7. All
FFPE passed the RNA quality control for genomic analysis. Hierarchical clustering
on the global gene expression data showed that genes were differentially
expressed between EUS and surgical samples. A more enriched cancerassociated
fibroblasts and epithelial-mesenchymal transition transcriptomic
profile was observed across surgical specimens whereas immunological
biomarkers were more represented in EUS-FNA samples. Cytological
examination confirmed a scanty representation of CAF and more
immunological cell abundance in cytological samples in comparison to
surgical specimens.
Conclusion: Targeted transcriptomic NanoString profiling of PDAC samples
obtained by EUS-FNA is a feasible approach for pre-surgical molecular analysis
although stromal CAF/EMT mRNA biomarkers are underrepresented.

overall_design: 18 PDAC patients were included. EUS-FNA- and surgical samples were obtained from each patient.

first: Isis

last: Araujo

first: Miriam

last: Cuatrecasas

first: Guillem

last: Soy

first: Sandra

last: Lopez

first: Juan

last: Maurel

first: Cristina

last: Sanchez

first: Carla

last: Montironi

first: Tamara

last: Sauri

first: Oriol

last: Sendino

first: Francisco

last: Manuel

first: Fabio

last: Ausania

first: Gloria

last: Fernandez-Esparrach

first: Francis

last: Esposito

first: Eva

last: Vaquero

first: Àngels

last: Ginès


title: Upregulation of extracellular proteins in a mouse model of Alzheimer’s Disease [Bisulfite-Seq]

city: New Orleans

first: Sangkyu

last: KIM

state: LA

address: 1430 Tulane Ave.

department: Center for Aging, Medicine

institute: Tulane University Health Sciences Center

summary: In Tg2576 mice that express a mutant form of human amyloid precursor protein linked to familial AD, genes involved in extracellular matrix structures and functions are transcriptionally upregulated, and genes involved in extracellular protein secretion and localization are differentially methylated in the transgenic mice. Integrative analysis found enrichment of GO terms related to memory and synaptic functionability. Our results indicate a possibility of transcriptional modulation by DNA methylation underlying AD neuropathology.

overall_design:
We applied transcriptomics and DNA methylomics to brain (dorsal hippocampus and cortex) samples from ~11-month-old Tg2576 transgenic mice
This submission corresponds to DNA methylomics component of study.

last: Kim

first: Andrea

last: Zsombok

first: S

last: Jazwinski


title: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways [LIS1_ESCs_totalRNAseq]

city: Rehovot

first: Orly

last: Reiner

address: 234, Herzl Street,

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: We analyzed gene expression changes in mouse embryonic stem cells.

overall_design: Total RNA expression profiling by high throughput sequencing in TT-AGO2-OE:Lis1 F/- ErT2 in mouse embryonic stem cells.

first: Aditya

last: Kshirsagar

first: Svetlana

last: Maslov


title: Gain and loss of function variants in EZH1 disrupt neurogenesis and cause overlapping neurodevelopmental disorders.

city: Philadelphia

first: Carolina

last: Gracia-Diaz

state: PA

address: 3501 Civic Center Boulevard

department: Raymond G. Perelman Center for Cellular and Molecular Therapeutics

institute: The Children's Hospital of Philadelphia

overall_design: Refer to individual Series


title: Gain and loss of function variants in EZH1 disrupt neurogenesis and cause dominant and recessive neurodevelopmental disorders [RNA-seq]

summary: Genetic disruption of chromatin regulators is frequently found in neurodevelopmental disorders (NDDs). While chromatin regulators are attractive therapeutic targets, studies to determine their implication in the etiology of NDDs are limited, preventing advances in diagnosis and treatment strategies. Here, we uncover pathogenic variants in the chromatin modifier Enhancer of Zeste Homologue 1 (EZH1) as the cause of overlapping dominant and recessive NDDs in 19 individuals. EZH1 encodes one of the two alternative histone H3 lysine 27 (H3K27) methyltransferases of the Polycomb Repressive Complex 2 (PRC2). Unlike the other PRC2 subunits, which are associated with the pathogenesis of human cancers and developmental disorders with overgrowth, the implication of EZH1 in human development and disease is largely unknown. Using cellular models and biochemical studies, we demonstrate that EZH1 variants identified in our study alter EZH1 molecularly. While recessive variants are EZH1 loss of function (LOF) variants that impair EZH1 expression, dominant variants are all missense mutations that affect evolutionarily conserved aminoacids likely impacting EZH1 structure or function. Accordingly, we found increased H3K27 methyltransferase activity for two EZH1 missense variants we tested, thus generating EZH1 gain of function (GOF) variants. Furthermore, we show that EZH1 is necessary and sufficient to differentiate neural stem cells in the developing chick embryo neural tube. Finally, using human pluripotent stem cell (hPSC)-derived neural cultures and forebrain organoids, we demonstrate that EZH1 LOF and GOF variation perturbs cortical projection neuron differentiation. Our work identifies EZH1 LOF and GOF variants as the genetic basis of previously undefined recessives and dominant NDDs and uncovers an essential role of EZH1 in regulating neurogenesis.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for 8-week 2D neuron differentiated from isogenic stem cell lines carrying WT EZH1, synonymous variants of EZH1, EZH1+/A678G, and EZH1-/-.

week8_H9: 8-week differentiated neurons, EZH1+/+ (WT 1)
week8_WTS5: 8-wk differentiated neurons, EZH1+/+ (WT 2, S5: silent mutation)
week8_8del: 8-wk differentiated neurons, EZH1-/- (KO clone 1 - 8 bp deletion)
week8_16del: 8-wk differentiated neurons, EZH1-/- (KO clone 2- 16 bp deletion)
week8_het5: 8-wk differentiated neurons, EZH1+/A678G (Het clone 5)
week8_het6: 8-wk differentiated neurons, EZH1+/A678G (Het clone 6)

first: Yijing

last: Zhou

first: Shuo

last: Zhang

first: Naiara

last: Akizu


title: Mdivi1 treatment impacts mouse embryonic stem cells and early embryos.

first: Li-quan

address: 13 Hangkong road

institute: Huazhong University of Science and Technology


title: Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis

city: St. Louis

first: Christopher

last: Maher

state: Missouri

address: 1 Brookings Dr

institute: Washington University in St. Louis

type: Non-coding RNA profiling by high throughput sequencing

summary: Colorectal cancer (CRC) is the most common gastrointestinal malignancy in the U.S.A. and approximately 50% of CRC patients develop metastatic disease (mCRC) with an average 5-year survival rate of 13%. Despite our understanding of circular RNAs (circRNAs) in primary cancer, their role throughout mCRC remains poorly characterized. Further, despite the availability of bulk RNA-Seq data for monitoring circRNA expression little is known about their cell-type specific expression profiles to fully understand their functions between tumor cells and the microenvironment. To evaluate circRNAs in mCRC progression, total RNA-Seq was performed on 30 matched normal, primary, and distant metastatic samples from 14 mCRC patients. Additionally, the transcriptome of five CRC cell lines were sequenced to construct a circRNA catalog in CRC. Differential expression (DE) analysis identified circRNAs dysregulated between normal, primary, and metastatic tissues. Differential backsplicing (DS) analysis was used to highlight circRNAs with an altered tendency in backsplicing as compared to their linear counterparts. Cell-type deconvolution was performed using published CRC single-cell RNA-Seq datasets as signature matrices. The cell-type specific expression of circRNAs was then estimated through a non-negative least squares statistical model.

overall_design: Comparative gene & circRNA expression profiling analysis of RNA-seq data between matched normal, primary, metastasis tissue in colorectal cancer patients. Cell lines serve as a reference catalog or circRNAs.

first: Sidi

last: Zhao

first: Amy

last: Ly

first: Ryan

last: Fields


title: A Spatial Transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

first: Michael

last: Eadon

summary: Kidney stone disease causes significant morbidity and increases health care utilization. The pathogenesis of stone disease is incompletely understood, due in part to the poor characterization of the cellular and molecular makeup of the human papilla and its alteration with disease. In this work, we characterize the human renal papilla in health and calcium oxalate stone disease using single nuclear RNA sequencing, spatial transcriptomics and high-resolution large scale multiplexed 3D and Co-Detection by indexing (CODEX) imaging. We define and localize subtypes of principal cells enriched in the papilla as well as immune and stromal cell populations. We further uncovered an undifferentiated epithelial cell signature in the papilla, particularly during nephrolithiasis.

overall_design: Frozen 10 µm sections were mounted on to etched frames of the Visium spatial gene expression (VSGE) slides with capture areas according to 10x Genomics protocols (Visium Spatial Protocols—Tissue Preparation Guide, Document Number CD=G000240 Rev A, 10x Genomics). H&E-stained sections were imaged with a Keyence BZ-X810 microscope equipped with a Nikon 10× CFI Plan Fluor objective at 0.7547 um/pixel and camera dimensions of 1920x1440. Stained tissues were permeabilized for 12 minutes. mRNA bound to oligonucleotides on the capture areas of the Visium slides was extracted. cDNA libraries were prepared with second strand synthesis and sequenced utilizing the NovaSeq 6000 Sequencing system (Illumina) in the 28 bp + 120 bp paired-end sequencing mode. Samples were mapped using Space Ranger 1.2.0 with the reference genome GRCh3-2020-A. The data were normalized by SCTransform and merged to build a unified UMAP and dataset.

first: Tarek

last: El-Achkar

first: Ricardo

last: Ferreira

first: Ying-Hua

last: Cheng


title: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways [8_totalRNA_B]

overall_design: Total RNA expression profiling by high throughput sequencing in TT-FHAgo2 and TT-FHAgo2:LIS1-OE in mouse embryonic stem cells.


title: Elevated expression of histone deacetylase HDAC8 suppresses arginine-proline metabolism in necrotizing enterocolitis

first: Ting

last: Guo

state: Shanghai

address: Shanghai Putuo District,Luding road No.355

department: Department of General surgery

institute: Shanghai Children's Hospital

summary:
To further explore the role of HDAC8 in NEC, we analyzed the signaling pathways that were altered in mice with NEC.
We then performed gene expression profiling analysis using data obtained from RNA-seq of intestinal tissues (control group, NEC group).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for intestinal tissues from control or NEC mice.

first: Shaohua

last: Hu

first: Weijue

last: Xu

first: Jin

first: Feng

last: Chen

first: Tingting

last: Gao

first: Wenqian

last: Qu

first: Faling

first: Zhibao

last: Lv

first: Li

last: Lu


title: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways [3_seCLIP_seq]

first: Orly

last: Reiner

summary: LIS1 dosage substantially affects gene expression, and we uncovered RNA binding properties in embryonic stem cells.

overall_design: Two replicate seCLIP experiments were performed with LIS1 IP and two sized match input in mouse embryonic stem cells.

first: Aditya

last: Kshirsagar


title: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways [7_smRNA_B]

summary: We analyzed small RNA expression changes in embryonic stem cells.

overall_design: smallRNA expression profiling by high throughput sequencing in TT-FHAgo2 and TT-FHAgo2:LIS1-OE in mouse embryonic stem cells.


title: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways [1_MARS_seq_A]

summary: We analyzed LIS1 dosage dependent gene expression changes in mouse and human embryonic stem cells.

overall_design: Bulk MARS-seq from LIS1 mutant mESCs and hESCs in different media conditions, LIS1 seCLIP-seq in mESCs, small RNA-seq and total RNA-seq from Lis1 and Argonaute mutant mESCs.


title: Single cell RNA sequencing reveals distinct clusters of Irf8 dependent pulmonary conventional dendritic cells

city: Hannover

first: Svenja

last: Gaedcke

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: We hereby report application of single cell RNA sequencing  in order to understand heterogeneity within macrophages and conventional dendritic  cells found in murine lungs. In this paper we specifically show different populations of cDCs as revealed through single cell RNA sequencing

overall_design: single cell sequencing  of murine lung samples, sorted for DC, AM and IM cells

first: Adan

last: Jirmo

first: Ruth

last: Grychtol

first: Bin

last: Liu

first: Stephanie

last: DeStefano

first: Christine

last: Happle

first: Olga

last: Halle

first: Joao

last: Monteiro

first: Anika

last: Habener

first: Oliver

last: Breitholz

first: David

middle: S

last: DeLuca

first: Gesine

last: Hansen


title: GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells

city: Oxford

first: Sven

last: Turkalj

address: John Radcliffe Hospital/Headley Way, Oxford OX3 9DS

department: Radcliffe Department of Medicine

institute: WIMM

summary: Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link chromatin accessibility with genotype in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factors motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors towards a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.

overall_design: Plate-based single-cell ATAC-seq coupled with single-cell targeted genotyping of genomic loci. Results are from cell lines and primary human samples

first: Niels

last: Jakobsen

first: Angus

last: Groom

first: Marlen

last: Metzner

first: Batchimeg

last: Usukhbayar

first: Miriam

last: Salazar

first: Kevin

last: Clark

first: ERavza

last: Gur

first: Lance

last: Hentges

first: Paul

last: Sopp

first: James

last: Davies

first: Jim

last: Hughes

first: Paresh

last: Vyas

first: Simone

middle: G

last: Riva

first: Gerda

last: Mickute


title: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways [5_smRNA_A]

first: Orly

last: Reiner

overall_design: smallRNA expression profiling by high throughput sequencing in LIS1 Floxed/-, WT and OE mouse embryonic stem cells.

first: Aditya

last: Kshirsagar


title: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways

summary: Lissencephaly-1 (LIS1) is associated with neurodevelopmental diseases and is known to regulate the molecular motor cytoplasmic dynein activity. Here we show that LIS1 is essential for the viability of mouse embryonic stem cells (mESCs), and it governs the physical properties of these cells. LIS1 dosage substantially affects gene expression, and we uncovered an unexpected interaction of LIS1 with RNA and RNA-binding proteins, most prominently the Argonaute complex. We demonstrate that LIS1 overexpression partially rescued the extracellular matrix (ECM) expression and mechanosensitive genes conferring stiffness to Argonaute null mESCs. Collectively, our data transforms the current perspective on the roles of LIS1 in post-transcriptional regulation underlying development and mechanosensitive processes.

platform_organism:
Homo sapiens
Mus musculus

overall_design: This SuperSeries is composed of the SubSeries listed below. Please refer to individual Series.


title: Transcriptional changes in macrophages after engulfing human cord tissue mensenchymal stromal cells

city: Durham

first: Anthony

last: Filiano

state: NC

address: 701 West Main St.

department: Neurosurgery

institute: Duke University

summary:
Purpose: The ability of MSCs to modulate macrophages is well documented but the mechanism is unknown. The goal of this study was to compare the transcriptome of macrophages that engulf MSCs to those that do not.
Methods: Mouse splenocytes were cocultured with Qtracker labelled human cord tissue derived MSC for 3 days. Afterwards, CD11b+Ly6G- macrophages that were either Qtracker positive or negative were FACs sorted for RNA sequencing.
Results: We determined that gene involved in antigen presentation and the activation of T cells were differentially expressed  in macrophages that engulfed MSCs.
Conclusion: Our study suggests that macrophages which engulf components of hCT-MSCs and are subsequently reprogrammed to suppress the activation of T cells, even after hCT-MSCs are no longer present.

overall_design: RNA profiles of macrophages that either engulf MSCs or do not were generated in paired biological triplicates using an Illumina HiSeq 4000.

first: Hyunjung

last: Min

first: Li

last: Xu

first: Roberta

last: Parrott

first: Christopher

last: Overall

first: Melina

last: Lillich

first: Emily

last: Rabjohns

first: Rishi

last: Rampersad

first: Teresa

last: Tarrant

first: Norin

last: Meadows

last: Fernandez-Castaneda

first: Alban

last: Gaultier

first: Joanne

last: Kurtzberg


title: HapX-mediated H2B deub1 and SreA-mediated H2A.Z deposition coordinate in fungal iron resistance

status: Public on May 03 2023

city: Hangzhou

first: SUN

last: Kewei

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Plant pathogens are challenged by host-derived iron starvation or excess during infection, but the mechanism through which pathogens counteract iron stress is unclear. Here, we found that Fusarium graminearum encounters iron excess during the colonization of wheat heads. Deletion of heme activator protein X (FgHapX), siderophore transcription factor A (FgSreA) or both attenuated virulence. Further, we found that FgHapX activates iron storage under iron excess by promoting histone H2B deubiquitination (H2B deub1) at the promoter of the responsible gene. Meanwhile, FgSreA is shown to inhibit genes mediating iron acquisition during iron excess by facilitating the deposition of histone variant H2A.Z and histone 3 lysine 27 trimethylation (H3K27 me3) at the first nucleosome after the transcription start site. In addition, the monothiol glutaredoxin FgGrx4 is responsible for iron sensing and control of the transcriptional activity of FgHapX and FgSreA via modulation of their enrichment at target genes and recruitment of epigenetic regulators, respectively. Taken together, our findings elucidated the molecular mechanisms for adaptation to iron excess mediated by FgHapX and FgSreA during infection in F. graminearum and provide novel insights into regulation of iron homeostasis at the chromatin level in eukaryotes.

overall_design: RNA-seq and ChIP-seq

first: K

last: SUN

first: Y

last: YIN


title: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways [6_ATAC_seq]

first: Orly

last: Reiner

summary: Genome binding/occupancy profiling by high throughput sequencing in mouse embryonic stem cells

overall_design: ATAC-seq from LIS1 Floxed/-, WT and OE mouse embryonic stem cells in 2i+LIF, FGF+Activin and FBS+LIF culture media.

last: Kshirsagar


title: The inhibitory receptor Siglec-G controls the severity of chronic lymphocytic leukemia

city: Erlangen

first: Simon

last: Schaefer

state: Bavaria

address: Glueckstr. 6

department: Genetics

institute: FAU Erlangen

summary:
Chronic Lymphocytic Leukaemia (CLL) is the most common leukemia in adults in the Western world. B cell receptor (BCR) signalling is known to be crucial for the pathogenesis and maintenance of CLL cells develop from mature CD5+ B cells. BCR signalling is regulated by the inhibitory co-receptor Siglec-G and Siglec-G-deficient mice have an enlarged CD5+ B1a cell population.
Here, we determine how Siglec-G expression influences the severity of CLL.

overall_design:
Immunoglobulin specific repertoire analysis of murine B cell receptor heavy chain
Samples were collected by drawing blood at the age of 12, 24, 36 and 48 weeks for TCL1, TCL1 x Siglecg-/- mice and their corresponding controls and at the age of 28, 36 and 48 weeks for TCL1 x Siglecg-R26ki/ki and TCL1 x Siglecg-R26ki/ki x mb1cre mice and controls. Then CD19+ B cells were sorted.

The igblast output data consists of reads of antibodies created from mRNA with UMIs and annotated to the germline reference, which are listed in v_call, d_call, j_call columns and are already normalised with unique UMIs to single mRNA molecules.
The first sequence ID column contains the header from the normalised fasta files:
1|IgA|CTGCAAAAGTAGAGGTTGAG-9
UniqueNumber|Isotype|UMI|-UMIcount
The last number in the header after the dash is UMI abundance/unique read count.
For BCRseq research in this case only unique mRNA molecule are relevant for fidelity (in contrast to bulk RNAseq where read counts of multiple genes are compared to evaluate expression levels).

first: Bettina

last: Röder

first: Hannah

last: Fahnenstiel

last: Schäfer

last: Budeus

first: Maria

last: Dampmann

first: Melanie

last: Eichhorn

first: Sieglinde

last: Angermüller

first: Claudia

last: Brost

first: Thomas

last: Winkler

first: Marc

last: Seifert

first: Lars

last: Nitschke


title: Upregulation of extracellular proteins in a mouse model of Alzheimer’s Disease

first: Sangkyu

last: KIM

overall_design: Transcriptomics and DNA methylomics were applied to brain (dorsal hippocampus and cortex) samples from ~11-month-old wild-type and Tg2576 transgenic mice

last: Kim

first: Andrea

last: Zsombok

first: S

last: Jazwinski


title: Genome-wide profiling of miRNA-gene regulatory networks in mouse postnatal heart development – implications for cardiac regeneration

city: Helsinki

first: Lotta

last: Pohjolainen

address: Viikinkaari 5 E

country: Finland

institute: University of Helsinki

summary: This study investigated differential expression in miRNAs during neonatal mouse heart development; particularly in ventricular tissues. We developed a predictive miRNA-gene regulatory network using computational approach. Based on this approach we demonstrated miRNAs role in neonatal heart development and potential role in heart regeneration.

overall_design: Neonatal mouse heart tissues were collected on P01, P04, P9, P23 days. RNA sequencing was performed in all collected heart tissue samples. Four biological replicates were used for each time point.

first: Umesh

last: Chaudhari

first: Heikki

last: Ruskoaho

first: Virpi

last: Talman


title: Cytoskeletal Keratins Are Overexpressed in a Zebrafish Model 2 of Idiopathic Scoliosis

city: Aurora

first: Nancy

last: Hadley Miller

state: Colorado

department: Orthopedics

institute: University of Colorado Anschutz Medical Campus

summary: Idiopathic scoliosis (IS) is a three-dimensional rotation of the spine >10 degrees with an unknown etiology. Our laboratory established a late-onset IS model in zebrafish (Danio rerio) containing a deletion in kif7. 25% of kif7co63/co63 zebrafish develop spinal curvatures and are otherwise developmentally normal, although the molecular mechanisms underlying the scoliosis are unknown. To define transcripts associated with scoliosis in this model, we performed bulk mRNA sequencing on 6 weeks past fertilization (wpf) kif7co63/co63 zebrafish with and without scoliosis. Additionally, we sequenced kif7co63/co63, kif7co63/+, and AB zebrafish (n= 3 per genotype).  Sequencing reads were aligned to the GRCz11 genome and FPKM values were calculated. Differences between groups were calculated for each transcript by t-test. Principal component analysis showed that transcriptomes clustered by sample age and genotype. kif7 mRNA was mildly reduced in both homozygous and heterozygous zebrafish compared to AB. Sonic hedgehog target genes were upregulated in kif7co63/co63 zebrafish over AB, but no difference was detected between scoliotic and non-scoliotic mutants. The top upregulated genes in scoliotic zebrafish were cytoskeletal keratins.. Pankeratin staining of 6 wpf scoliotic and non-scoliotic kif7co63/co63 zebrafish showed increased keratin levels within the zebrafish musculature and intervertebral disc (IVD). Keratins are major components of the embryonic notochord, and aberrant keratin expression has been associated with intervertebral disc degeneration (IVDD) in both zebrafish and humans. The role of increased keratin accumulation as a molecular mechanism associated with the onset of scoliosis warrants further study.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in 6 week post fertilization (wpf) and 4 days post fertilization (dpf) zebrafish. Samples include 6wpf wild-type (n=3), 6wpf kif7co63/+ (n=3), 6wpf non-scoliotic kif7co63/co63 (n=3), 6wpf scoliotic kif7co63/co63, 4dpf wild type (n=2), 4dpf kif7co63/+ (n=2), and 4dpf kif7co63/co63 (n=2).

first: Melissa

last: Cuevas

first: Elizabeth

last: Terhune

first: Cambria

last: Wethey

first: MkpoutoAbasi

last: James

first: Rahwa

last: Netsanet

first: Denisa

last: Grofova

first: Anna

last: Monley


title: Obesity and dyslipidemia are associated with partially reversible modifications to DNA hydroxymethylation in swine adipose-derived mesenchymal stem/stromal cells [Sus scrofa]

city: Rochester

first: Lilach

middle: O

last: O Lerman

state: Minnesota

address: 200 First St. SW

department: Division of Nephrology & Hypertension

institute: Mayo Clinic

summary:
Female domestic pigs were fed a 16-week Lean or Obese diet. Mesenchymal stem/stromal cells (MSCs) were harvested from subcutaneous adipose tissue and expanded for 3-4 passages, and 5hmC profiles were examined through hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq)
We hypothesized that obesity and cardiovascular risk factors induce functionally-relevant, locus-specific changes in overall exonic coverage of 5hmC in swine adipose-derived MSCs, and evaluated their reversibility using an epigenetic modulator, vitamin-C.

overall_design: Lean-MSCs and Obese-MSCs were harvested from swine fed a Lean or Obese diet, respectively (n=3, each), and Obese-MSCs were additionally co-incubated with vitamin-C in-vitro

last: Lerman

first: Alfonso

last: Eirin

first: Logan

last: Glasstetter

first: Tomiwa

last: Oderinde

first: Kamalnath

last: Rajagopalan

first: Roman

last: Thaler


title: Effect of obesity and dyslipidemia on DNA hydroxymethylation in human adipose-derived mesenchymal stem/stromal cells [Homo sapiens]

summary:
Mesenchymal stem/stromal cells (MSCs) were harvested from subcutaneous adipose tissue of patients with obesity or healthy controls and expanded for 3-4 passages, and 5hmC profiles were examined through hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq).
We hypothesized that obesity and cardiovascular risk factors induce functionally-relevant, locus-specific changes in overall exonic coverage of 5hmC in human adipose-derived MSCs.

overall_design: In human subjects, subcutaneous abdominal fat (0.5-2g) was collected during bariatric (Obese, n=5) or kidney donation (Lean, n=5) surgeries. Inclusion criteria for the Obese patients were age of 18-80 years and body mass index (BMI)>30kg/m2. For age- and sex-matched Lean controls, inclusion criteria were age>18 years, BMI<30kg/m2, and healthy overall state. For both groups, exclusion criteria were recent stroke or myocardial infarction, solid organ transplant recipients, chronic inflammatory disease, immunosuppressive treatment, pregnancy, active malignancy, or blood thinners/chronic anticoagulant therapy.


title: PAO1 Hfq-V  RIL-seq and RNA-seq

city: Iowa City

first: Michael

last: Gebhardt

state: IA

address: 431 Newton Road, 200A EMRB

department: Department of Microbiology and Microbiology

institute: University of Iowa

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

sample_organism:
Pseudomonas aeruginosa
Pseudomonas aeruginosa PAO1

overall_design: Refer to individual Series


title: Gain and loss of function variants in EZH1 disrupt neurogenesis and cause dominant and recessive neurodevelopmental disorders [ChIP-seq]

first: Carolina

last: Gracia-Diaz

summary: Genetic disruption of chromatin regulators is frequently found in neurodevelopmental disorders (NDDs). While chromatin regulators are attractive therapeutic targets, studies to determine their implication in the etiology of NDDs are limited, preventing advances in diagnosis and treatment strategies. Here, we uncover pathogenic variants in the chromatin modifier Enhancer of Zeste Homologue 1 (EZH1) as the cause of overlapping dominant and recessive NDDs in 19 individuals. EZH1 encodes one of the two alternative histone H3 lysine 27 (H3K27) methyltransferases of the Polycomb Repressive Complex 2 (PRC2). Unlike the other PRC2 subunits, which are associated with the pathogenesis of human cancers and developmental disorders with overgrowth, the implication of EZH1 in human development and disease is largely unknown. Using cellular models and biochemical studies, we demonstrate that EZH1 variants identified in our study alter EZH1 molecularly. While recessive variants are EZH1 loss of function (LOF) variants that impair EZH1 expression, dominant variants are all missense mutations that affect evolutionarily conserved aminoacids likely impacting EZH1 structure or function. Accordingly, we found increased H3K27 methyltransferase activity for two EZH1 missense variants we tested, thus generating EZH1 gain of function (GOF) variants. Furthermore, we show that EZH1 is necessary and sufficient to differentiate neural stem cells in the developing chick embryo neural tube. Finally, using human pluripotent stem cell (hPSC)-derived neural cultures and forebrain organoids, we demonstrate that EZH1 LOF and GOF variation perturbs cortical projection neuron differentiation. Our work identifies EZH1 LOF and GOF variants as the genetic basis of previously undefined recessives and dominant NDDs and uncovers an essential role of EZH1 in regulating neurogenesis.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K27me3 in ReNcells VM overexpressing EZH1 or EZH1 GOF variant (p.A678G).

first: Yijing

last: Zhou

first: Shuo

last: Zhang

first: Naiara

last: Akizu


title: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways [4_totalRNA_A]

first: Orly

last: Reiner

summary: We analyzed gene expression changes in mouse embryonic stem cells.

overall_design: total RNA expression profiling by high throughput sequencing in LIS1 Floxed/-, WT and OE mouse embryonic stem cells.

first: Aditya

last: Kshirsagar


title: Establish a rapid and efficient chemical reprogramming platform [scRNA-Seq]

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

summary: Chemically reprogramming somatic cells to iPSCs is time-consuming and low-efficiency. Here, we discribe a rapid chemical reprogramming condition enabling generating iPSCs from MEFs in 12 days. To further investigate the mechemisms and draw an epigenetic maps during the rapid chemical reprogramming, we performed time-course RNA-seq, ATAC-seq, RRBS, CUT&Tag (H3K4me3, H3K18la, H3K9me3, H3K27me3 and H3K27ac) and scRNA-seq.

overall_design: Cells were collected every 4 days of reprogramming along with riPSCs were used for scRNA-seq.

first: Xi

last: Chen

first: Saiyong

last: Zhu


title: PAO1 Hfq-V RIL-seq

summary:
A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. We subjected cells of P. aeruginosa strain PAO1 and a derivative of PAO1 harboring a C-terminal VSV-G epitope on Hfq to UV-irradiation, immune-precipitated the Hfq-RNA complexes, ligated neighboring RNA molecules together with RNA Ligase, and then purififed the resulting RNAs. These RNAs were converted into cDNA libraries and sequenced using the Illumina NextSeq platform and then subjected to RIL-seq analysis pipeline (version 0.78) to identify chimeric RNA molecules.
We also performed RNA-seq for PAO1 ∆phrS cells harboring an empty vector (pEV) or a vector expressing PhrS (pPhrS).

overall_design:
Applying RIL-seq to strains carrying chromosomally-encoded Hfq-VSVG for two different growth conditions.
Applying RNA-seq to strains lacking phrS and harboring an empty vector or a vector containing a copy of phrS.

first: Sahar

last: Melamed

first: Simon

middle: L

last: Dove


title: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways [2_MARS_seq_B]

summary: We analyzed LIS1 dosage dependent gene expression changes in human embryonic stem cells.

overall_design: Bulk MARS-seq from LIS1 control and mutant hESCs.


title: Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Anthracyclines are a class of widely prescribed anti-cancer drugs that disrupt chromatin by intercalating into DNA and enhancing nucleosome turnover. To understand the molecular consequences of anthracycline-mediated chromatin disruption, we utilized CUT&Tag to profile RNA polymerase II during anthracycline treatment in Drosophila cells. We observed that treatment with the anthracycline aclarubicin leads to elevated levels of elongating RNA polymerase II and changes in chromatin accessibility. We found that promoter proximity and orientation impacts chromatin changes during aclarubicin treatment, as closely spaced divergent promoter pairs show greater chromatin changes when compared to codirectionally-oriented tandem promoters. We also found that aclarubicin treatment changes the distribution of non-canonical DNA G-quadruplex structures both at promoters and at G-rich pericentromeric repeats. Our work suggests that aclarubicin's anti-cancer activity is driven by the effects of nucleosome disruption on RNA polymerase II, chromatin accessibility and DNA structures.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.

first: Matthew

last: Wooten

first: Brittany

last: Takushi

first: Kami

last: Ahmad

first: Steven


title: PhrS pulse expression RNA-seq

first: Michael


title: Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of cellular nucleic acid binding protein (CNBP)

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Cellular nucleic acid binding protein (CNBP) is a 19 kDa conserved protein containing seven tandem cysteine-cysteine-histidine-cysteine zinc finger repeats. However, the action modes and underlying mechanisms of CNBP in NB progression remain largely unknown. We identify CNBP as an independent prognostic factor for poor outcome of neuroblastoma. CNBP exerts oncogenic roles in ribosome biogenesis, tumorigenesis, and aggressiveness. To investigate the mechanisms underlying the oncogenic functions of CNBP, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma IMR-32 cells in response to stable over-expression of CNBP. The results showed that stable over-expression of CNBP led to altered expression of 3524 human mRNAs, including 889 up-regulated genes and 2635 down-regulated genes. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to CNBP over-expression in human tumor cells, and these findings will help us understand the pathogenesis of tumor progression.

overall_design: Total RNA of cells stably transfected with empty vector or CNBP was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.

first: Tong

last: Qiangsong

first: Zheng

last: Liduan


title: Global transcriptional characterization of differentiating non-human primate (cynomolgus) iPAX7 iPS cells and comparison with their human counterpart

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

summary: Pluripotent stem (PS) cells enable the scalable production of tissue-specific derivatives with therapeutic potential for various clinical applications, including muscular dystrophies. Given the similarity to human counterparts, the non-human primate (NHP) is an ideal preclinical model to evaluate several questions, including delivery, biodistribution and immune response. While the generation of human induced PS (iPS) cell-derived myogenic progenitors is well established, there has been no data for NHP counterparts, probably due to the lack of an efficient system to differentiate NHP iPS cells towards the skeletal muscle lineage.  Here we report the generation of three independent Macaca fascicularis iPS cell lines and their myogenic differentiation using PAX7 conditional expression. Whole transcriptome analysis confirmed the successful sequential induction of mesoderm, paraxial mesoderm, and myogenic lineages. NHP myogenic progenitors efficiently gave rise to myotubes under appropriate in vitro differentiation conditions and engrafted in vivo into TA muscles of NSG and FKRP-NSG mice. Lastly, we explored the pre-clinical potential of these NHP myogenic progenitors in a single wild-type NHP recipient, demonstrating engraftment and characterizing the interaction with the host immune response. These studies establish an NHP model system in which to study iPS cell-derived myogenic progenitors.

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens

overall_design: Cynomolgous and human PAX7-inducible iPS cells were directed to differentiate into myogenic progenitors. Biological replicates were collected at multiple time points of the differentiation process (iPS cell stage, mesoder, paraxial mesoderm, myogenic progenitor and myotube) and used for gene expression analysis using RNA-seq.

first: Juan

middle: E

last: Abrahante

first: June

last: Baik

first: Carolina

last: Ortiz-Cordero

first: Rita

last: Perlingeiro


title: CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [CUT&Tag]

first: Yunkun

last: Lu

summary:
We show that CD-RXRα axis significantly promotes mouse chemical reprogramming of fibroblasts. To identify the molecular mechanisms of CD-RXRα axis  in chemical reprogramming, we construct Flag-Rxra-OE cells.
We performed Flag-Rxra CUT&Tag with reprogramming intermediate, also we performed CUT&Tag with or without CD treatment for reprogramming intermediates.

overall_design: Flag-Rxra CUT&Tag to find Rxra binding locus. And DMSO and CD-treated H3K27ac CUT&Tag to identify enhancers in reprogramming.

first: Yan

last: Jin

first: Saiyong


title: CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [RNA-seq]

summary:
We show that CD-RXRα axis significantly promotes mouse chemical reprogramming of fibroblasts. To identify the molecular mechanisms of CD-RXRα axis  in chemical reprogramming, we compared reprogramming efficiency for CD-treated, Rxra-OE and shE3 cells.
We then performed RNA-seq  for 3 different treatments of 6 samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD-treated, Rxra-OE and shE3 reprogramming intermediates.

last: Zhu


title: PAO1 Hfq-V RNA-seq

last: Gebhardt

first: Sahar

last: Melamed

first: Simon


title: Establish a rapid and efficient chemical reprogramming platform (RNA-Seq II)

overall_design: Fibroblasts, intermediate cells and iPSCs were collected for RNA-seq at indicated time points.

first: Xi

last: Chen


title: Establish a rapid and efficient chemical reprogramming platform (RRBS)

summary: Chemically reprogramming somatic cells to iPSCs is time-consuming and low-efficiency. Here, we discribe a rapid chemical reprogramming condition enabling generating iPSCs from MEFs in 12 days. To further investigate the mechemisms and draw an epigenetic maps during the rapid chemical reprogramming, we performed time-course RNA-seq, ATAC-seq, RRBS and CUT&Tag (H3K4me3, H3K18la, H3K9me3, H3K27me3 and H3K27ac).

overall_design: Cells were collected every 2 days of reprogramming along with riPSCs were used for RRBS.


title: Establish a rapid and efficient chemical reprogramming platform (RNA-Seq)

overall_design: Cells were collected every 2 days of reprogramming along with riPSCs and mESCs were used for RNA-seq.


title: Establish a rapid and efficient chemical reprogramming platform


title: BMP4 triggers regulatory circuits specifying the cardiac mesoderm lineage

city: Berlin

first: Pavel

last: Tsaytler

address: Ihnestrasse  63-73

institute: MPI Molecular Genetics

summary:
Cardiac lineage specification in the mouse is controlled by TGFβ and
WNT signaling. From fly to fish, BMP has been identified as an
indispensable heart inducer. A detailed analysis of the role of Bmp4
and its effectors Smad1/5, however, was still missing. We show that
Bmp4 induces cardiac mesoderm formation in murine embryonic
stem cells in vitro. Bmp4 first activates Wnt3 and upregulates Nodal.
pSmad1/5 and the WNT effector Tcf3 form a complex, and together
with pSmad2/3 activate mesoderm enhancers and Eomes. They then
cooperate with Eomes to consolidate the expression of many
mesoderm factors, including T. Eomes and T form a positive
feedback loop and open additional enhancers regulating early
mesoderm genes, including the transcription factor Mesp1
establishing the cardiac mesoderm lineage. In parallel, the neural
fate is suppressed. Our data confirm the pivotal role of Bmp4 in
cardiac mesoderm formation in the mouse. We describe in detail the
consecutive and cooperative actions of three signaling pathways,
BMP, WNT and Nodal, and their effector transcription factors, during
cardiac mesoderm specification.

overall_design: Transcriptomes (RNA-Seq) and chromatin accessibility (ATAC-Seq) from cardiac mesoderm differentiated WT, Smad4, Eomes, T, and double Eomes/T knockout mouse ESCs. ChIP-Seq of P-Smad1/5/9, P-Smad2, Eomes, and T from cardiac mesoderm differentiated WT mouse ESCs.

first: Jinhua

last: Liu

first: Gaby

last: Blaess

first: Dennis

last: Schifferl

first: Jesse

middle: V

last: Veenvliet

first: Lars

last: Wittler

first: Bernd

last: Timmermann

first: Bernhard

last: Herrmann

first: Frederic

last: Koch


title: Rewiring Cancer Drivers to Activate Apoptosis

city: Stanford

first: Sai

last: Gourisankar

state: CA

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

summary: Genes that drive the proliferation, survival, invasion and metastasis of malignant cells have been identified for manyhuman cancers. Independent studies have identified cell death pathways that eliminate cells by an altruistic form of suicide. The coexistence of the cell death pathways with the driver mutations suggest that the cancer driver could be reprogrammedto activate cell death. We have invented a new class of molecules: TCIPs (Transcriptional/EpigeneticChemical 20Inducers of Proximity) that recruit the cancer driver, or a downstream transcription factor,to the promoters of cell death genesmthereby activating their expression. To develop this concept, we have focused on diffuse largeB cell lymphoma(DLBCL),in which BCL6 is amplified or mutated. BCL6 binds to the promoters of cell death genes and epigenetically suppresses their expression. We produced the first TCIPs by chemically linking BCL6 inhibitors with small molecule binders to transcriptional activators. Several of these molecules robustly kill DLBCL at single-digit nanomolar concentrations, including chemotherapy-resistant, TP53-mutant lines. The dominant gain-of-function approach provided by TCIPs allows access to therapeutic space unreachable to conventional small molecule inhibitors or degraders, RNAi,or CRISPR(i). TCIPs are relatively non-toxic to normal cells and selective in malignant cells, reflecting their need for coincident expression of both target proteins for effective killing. The later attribute should allow highly personalized treatment. The general TCIP concept has applications in elimination of senescent cells, enhancing expression of therapeutic genes, treatment of diseases produced by haploinsufficiency,and activation of immunogens for immunotherapy.

overall_design:
ChIP-seq experiment to understand chromatin changes upon TCIP1 treatment
RNA-seq experiment to understand gene expression changes upon TCIP1 treatment

first: Andrey

last: Krokhotin

first: Wenzhi

last: Ji

first: Xiaofan

first: Chiung-ying

last: Chang

first: Samuel

last: Kim

first: Zhengnian

last: Li

first: Wendy

last: Wenderski

first: Juste

last: Simanauskaite

first: Tinghu

last: Zhang

first: Haopeng

last: Yang

first: Michael

last: Green

first: Nathanael

last: Gray

first: Gerald

last: Crabtree


title: CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression

first: Yunkun

last: Lu


title: Identification of BRCA1/2 mutation carriers using circulating microRNA profiles

status: Public on May 02 2023

city: Łódź

first: Zuzanna

last: Nowicka

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Łódź

summary:
Identifying germline BRCA1/2 mutation carriers is vital for reducing their risk of breast and ovarian cancer; however, many carriers are not referred for genetic testing. While population-wide testing is not feasible, a cheap functional screen for phenotypic ‘BRCAness’ could guide efforts for focused genetic counseling and improve cancer prevention and early detection. The aim of this study was to derive a serum-based miRNA panel to identify BRCA1/2 mutation carriers among healthy controls.
We performed a diagnostic biomarker study based on serum samples collected between by six international cohorts. Serum samples from 653 healthy women with known mutation status of BRCA1 and BRCA2 were used in the analysis. All individuals had no history of prior cancer or any detected malignancies for at least 12 months after sample collection. Among the study population, 350 (53.6%) subjects had BRCA mutations and 303 (46.4%) were BRCA1/2 – wild-type. In all individuals, we isolated and quantified miRNAs expression using RNA-sequencing. Variable selection based on differential expression analysis on merged, batch adjusted cohorts was performed to identify a set of miRNAs associated with BRCA mutation carrier status.

overall_design: Comparative miRNA expression profiling analysis of miRNA-seq data for healthy women with or without germline BRCA1/2 mutations.

first: Wojciech

last: Fendler

first: Dipanjan

last: Chowdhury


title: Costimulatory domains direct distinct fates of CAR-driven T cell dysfunction [ATAC-seq]

first: Nathan

last: Singh

state: MO

institute: Washington University School of Medicine

summary: Chimeric antigen receptor (CAR) engineered T cells often fail to enact effector functions after infusion into patients. Understanding the biological pathways that lead CAR T cells to failure is of critical importance in the design of more effective therapies. We developed and validated an in vitro model that drives T cell dysfunction by chronic CAR stimulation and interrogated how CAR costimulatory domains contribute to T cell failure. We found that dysfunctional CD28-based CARs targeting CD19 bear hallmarks of classical T cell exhaustion while dysfunctional 41BB-based CARs are phenotypically, transcriptionally and epigenetically distinct. We confirmed activation of this unique transcriptional program in CAR T cells that failed to control clinical disease. Further, we demonstrate that 41BB-dependent activation of the transcription factor FOXO3 is a significant contributor to this dysfunction and disruption of FOXO3 significantly improves 41BB-based CAR T cell function. These findings identify that chronic activation of 41BB leads to novel state of T cell dysfunction that can be alleviated by genetic modification of FOXO3.

overall_design: Comparative profiling analysis of ATAC-seq data for CD19-directed human CAR T cells with CD28 and 41BB during chronic activation by CD19+ ALL cell line Nalm6. T cells were sequenced in technical triplicate.

first: Mehmet

last: Selli

first: Jack

last: Landmann

first: John

last: Lattin

first: Amanda

last: Heard

first: Yu-Sung

last: Hsu

first: Tien-Ching

first: Jufang

last: Warrington

first: Helen

last: Ha

first: Natalie

last: Kingston

first: Graham

last: Hogg

last: Slade

first: Melissa

last: Berrien-Elliot

first: Mark

last: Foster

first: Samantha

last: Kersting-Schadek

first: Agata

last: Gruszczynska

first: Marina

last: Terekhova

first: David

last: DeNardo

first: Todd

last: Fehniger

first: Maxim

last: Artyomov


title: Reduced binding of apoE4 to complement factor H promotes amyloid-β oligomerization and neuroinflammation

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

summary: Alzheimer’s disease (AD) is characterized by neuroinflammation, accumulation of amyloid-β (Aβ) plaques and neuronal degeneration in the brain. The APOE4 variant of apolipoprotein E (apoE) is the most prevalent genetic risk allele associated with late-onset AD. ApoE interacts with complement regulator factor H (FH) but the role of this interaction in AD pathogenesis is unknown.

overall_design: The aim of the experiment was to find differentially expressed genes between apoE and or FH treated microglial cells in the presence of  amyloid-β 1-42 to understand the role of these proteins in microglial mediated inflammatory responses and amyloid-β clearance. The experiment was done as three separate experiments using duplicates.

first: Katarzyna

last: Leskinen

first: Karita

last: Haapasalo

first: Laura

last: Teirilä

first: Giorgio

last: Ratti


title: Myelin insulation as a risk factor for axonal degeneration in autoimmune demyelinating disease

city: Leipzig

first: Ruth

middle: Martha

last: Stassart

address: Liebigstraße 19. Haus C

department: Paul-Flechsig-Institute of Brain Research

institute: University Clinic Leipzig

summary: Axonal degeneration determines the clinical outcome of multiple sclerosis (MS), and is thought to result from exposure of denuded axons to immune-mediated damage. We challenge this view after finding in MS and its mouse models that myelin itself increases the risk of axons to degenerate under inflammatory conditions. We propose a model for demyelinating diseases in which for axons that remain myelinated, and thus shielded from the extracellular milieu, dependence from oligodendroglial support turns fatal in an autoimmune disease environment.

overall_design:
CD45+ cells were isolated from the lumbosacral spinal cord white matter of C57BL/6J (WT) and hMBP mice via MACS and analysed with scRNAseq (10x technology)
hMBP mice described in: https://doi.org/10.1038/s41467-020-19152-7

first: Erik

last: Schäffner

first: Mar

last: Bosch-Queralt

first: Julia

last: Edgar

first: Maria

last: Lehning

first: Judith

last: Strauß

first: Niko

last: Fleischer

first: Ting

last: Sun

first: Theresa

last: Kungl

first: Peter

last: Wieghofer

first: Stefan

last: Berghoff

first: Tilo

last: Reinert

first: Martin

last: Krueger

first: Markus

last: Morawski

first: Wiebke

last: Möbius

first: Alonso

last: Barrantes-Freer

first: Jens

last: Stieler

first: Gesine

last: Saher

last: Schwab

first: Christoph

last: Wrede

first: Maximilian

last: Frosch

first: Marco

last: Prinz

first: Daniel

last: Reich

first: Alexander

last: Flügel

first: Christine

last: Stadelmann

first: Robert

last: Fledrich

first: Klaus-Armin

last: Nave


title: Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability [ncRNA-seq]

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: Studying the role of circular RNAs in cancer initiation by profiling the interaction of circRNAs with DNA in human cells. The first step of oncogenesis is the acquisition of a repertoire of genetic mutations to initiate and sustain the malignancy. An important example of this initiation phase in leukaemia is the formation of a potent oncogene by chromosomal translocations between the histone methyltransferase Mixed Lineage Leukaemia (MLL) gene and one of over 100 translocation partner genes. Here we show that circular RNAs (circRNAs) - which are a family of covalently-closed, alternatively-spliced RNA molecules - bind DNA, forming circRNA:DNA hybrids (circR-loops) at their cognate loci, and promote transcriptional pausing and DNA breaks. The MLL recombinome concentrates these circR-loops and by overexpressing circRNAs from MLL in human cells we could generate de novo chromosomal translocations, mimicking the MLL recombinome. We anticipate our findings will illuminate this critical phase in cancer initiation and provide a framework to investigate the action of endogenous RNA molecules underlying various genetic aberrations through a process of Endogenous RNA-Directed DNA Damage (ER3D).

overall_design: Guthrie cards/neonatal blood spots from 8 control individuals (with no known blood, or other cancer) and 8 individuals who developed infant leukemia under the age of 10 associated with rearrangements in the MLL gene.

first: Shashikanth

last: Marri


title: Spatiotemporally organized immunomodulatory response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia

city: Farmington

first: Carolyn

last: Paisie

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

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

overall_design: Refer to individual Series


title: The Pediatric Leukemia Oncoprotein NUP98-KDM5A Induces Genomic Instability That May Facilitate Malignant Transformation

city: Granada

first: Verónica

last: Ramos-Mejia

state: Granada

address: P. T. Ciencias de la Salud, Avda. de la Ilustración 114

department: Gene Regulation, Stem cells and Development

institute: GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government

summary: Pediatric Acute Myeloid Leukemia (AML) is a rare and heterogeneous disease characterized by a high prevalence of gene fusions as driver mutations. Despite the improvement of survival in the last years, about 50% of patients still experience a relapse. It is not possible to improve prognosis only with further intensification of chemotherapy, as come with a severe cost to the health of patients, often resulting in treatment-related death or long-term sequels. To design more effective and less toxic therapies we need a better understanding of pediatric AML biology. The NUP98-KDM5A chimeric protein is exclusively found in a particular subgroup of young pediatric AML patients with complex karyotypes and poor prognosis. In this study, we investigated the impact of NUP98-KDM5A expression on cellular processes in human Pluripotent Stem Cell models and the CHRF-288-11 cell line. We found that NUP98-KDM5A generates genomic instability through two complementary mechanisms that involve accumulation of DNA damage and direct interference of RAE1 activity during mitosis. Overall, our data support that NUP98-KDM5A promotes genomic instability and likely contributes to malignant transformation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from induced pluripotent stem cells (iPSC) PBMC2-iPS4F8 transduced with an empty vector (control) and a NUP98-KDM5A-expressing vector (NK5A).

first: Joan

last: Domingo-Reinés

first: Iván

last: Ellson

first: Adrián

last: Garcia-Moreno

first: Pedro

last: Carmona-Sáez


title: Establish a rapid and efficient chemical reprogramming platform (ATAC-Seq)

first: Yunkun

last: Lu

institute: Zhejiang University

overall_design: Cells were collected every 2 days of reprogramming along with riPSCs were used for ATAC-seq.

first: Xi

last: Chen

first: Saiyong

last: Zhu


title: The conserved RNA-binding protein Seb1 promotes cotranscriptional ribosomal RNA processing by controlling RNA polymerase I progression

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

summary: Transcription by RNA polymerase I (RNAPI) represents the majority of the transcriptional activity in eukaryotic cells and is associated with the production of mature ribosomal rRNAs (rRNAs). As several rRNA maturation steps are coupled to RNAPI transcription, the rate of RNAPI elongation directly influences processing of nascent rRNA, and changes in RNAPI transcription rate can result in alternative rRNA processing pathways in response to growth conditions and stress. However, factors and mechanisms that control RNAPI progression by influencing transcription elongation rate remain poorly understood. We show here that the conserved fission yeast RNA-binding protein Seb1 associates with the RNAPI transcription machinery and promotes RNAPI pausing states along the rDNA. The overall faster progression of RNAPI at the rDNA in Seb1-deficient cells impaired cotranscriptional rRNA processing and the production of mature rRNAs. Given that Seb1 also influences pre-mRNA processing by modulating RNAPII progression, our findings unveil Seb1 as a pausing-promoting factor for RNA polymerases I and II to control cotranscriptional RNA processing.

overall_design: CRAC  (Cross-linking and Analysis of cDNA) experiment to measure nascent RNAP I transcription in wild-type and cells deficient for the Seb1 protein.

first: Maxime

last: Duval

first: David

last: Tollervey

first: Tomasz

last: Turowski

first: Elisabeth

last: Petfalski

first: François

last: Bachand


title: Intracellular labile iron is a key regulator of hepcidin expression and iron metabolism

city: Beijing

first: Anjian

last: Xu

address: No. 95 Yong'an road, Xicheng District, Beijing

institute: Capital medical university

summary: Liver iron overload can induce hepatic expression of hepcidin and regulates iron metabolism. However, the mechanism of iron regulating iron metabolism remains known. Intracellular labile iron represents the nonferritin-bound, redox-active iron which is transitory and serves as a crossroad of cell iron metabolism. The role of intracellular labile iron played in iron metabolism has largely been elucidated. Here we show that intracellular labile iron of hepatocytes has dual function in iron metabolism. It can induce hepatocytes expressing hepcidin via ER stress induced transcription factors on the one hand, on the other hand stimulate BMP2 and BMP6 expression of liver sinusoidal endothelial cells (LSECs) though TNFα secreted by hepatocytes to further regulate iron metabolism. Blockade of TNFα could dysregulate the iron metabolism during iron overload. Our findings reveal the important role of intracellular labile iron in iron metabolism and represent a novel way to modulate iron metabolism during iron overload.

overall_design: HepG2 mRNA profiles of DMOS, 8HQ, FAC and 8HQ/FAC treated HepG2 cells


title: Mammary ductal epithelium controls cold-induced adipocyte thermogenic program

status: Public on May 01 2023

city: Los Angeles

first: Douglas

last: Arneson

address: 2000 Terasaki Life Sciences Bldg 610 Charles E Young Drive East

department: Integrative Biology and Physiology

institute: UCLA

summary: Sympathetic activation during cold exposure increases adipocyte thermogenesis via the expression of mitochondrial protein uncoupling protein 1 (UCP1)1. The propensity of adipocytes to express UCP1 is under a critical influence of the adipose microenvironment and varies between sexes and among various fat depots2-7. Here, we report that cold-induced adipocyte UCP1 expression in a female mouse subcutaneous white adipose tissue (scWAT) is regulated by mammary gland ductal epithelial cells in the adipose niche. Single-cell RNA-sequencing (scRNA-seq) shows that glandular luminal epithelium subtypes express transcripts that encode secretory factors in controlling adipocyte UCP1 expression under cold conditions. We term luminal epithelium secretory factors as “mammokines”. Using whole-tissue immunofluorescence 3D visualization, we reveal previously undescribed sympathetic nerve-ductal points of contact. We show sympathetic nerve-activated mammary ducts limit adipocyte UCP1 expression via lipocalin 2. Both in vivo and ex vivo ablation of mammary ductal epithelium enhances cold-induced scWAT adipocyte thermogenic gene program. Since the mammary duct network extends throughout most scWATs in female mice, females show markedly less scWAT UCP1 expression, fat oxidation, energy expenditure, and subcutaneous fat mass loss compared to male mice, implicating sex-specific roles of mammokines in adipose thermogenesis. These results show a previously uncharacterized role of sympathetic nerve-activated glandular epithelium in adipocyte UCP1 expression and suggest an evolutionary function of mammary duct luminal cells in defending glandular adiposity during cold exposure. Overall, our findings highlight mammary gland epithelium as a highly active metabolic cell type and implicate a broader role of mammokines in controlling female adipose metabolism, mammary gland physiology, and systemic energy homeostasis.

overall_design: 10X Genomics single cell sequencing was performed on the SVF fourth inguinal white adipose tissue (iWAT) depot mgWAT from 8-week old mice exposed to cold stress (4°C) or room temperature for 24 hr.

first: P

last: Rajbhandari

first: D