title: Hijacking a neurodevelopmental epigenomic program in metastatic dissemination of medulloblastoma [Cut & Run]

summary: How dysregulation of neurodevelopment relates to medulloblastoma (MB), the most common pediatric brain tumor, remains elusive. Here, we uncovered a neurodevelopmental epigenomic program being hijacked to induce MB metastatic dissemination. Unsupervised analyses by integrating publicly available datasets with our newly generated data revealed that SMARCD3/BAF60C regulates DAB1-mediated Reelin signaling in Purkinje cell migration and MB metastasis by orchestrating cis-regulatory elements (CREs) at the DAB1 locus. We further identified that a core set of transcription factors, enhancer of zeste homolog 2 (EZH2) and nuclear factor I X (NFIX), coordinates with the CREs at the SMARCD3 locus to form a chromatin hub for controlling SMARCD3 expression in the developing cerebellum and metastatic MB. Elevated SMARCD3 activates Reelin/DAB1-mediated Src kinase signaling, resulting in MB response to Src inhibition. These data deepen our understanding of how neurodevelopmental programming influences disease progression and provide a potential therapeutic option for MB patients.

overall_design: Chromatin accessibility profiles for SMARCD3 WT and KO cells.

first: Han

last: Zou

first: Emily

last: Brown


title: Expression data of GFP-GnRH neurons during rat embryonic development

status: Public on Feb 28 2023

city: Milan

first: Anna

last: Cariboni

address: Via Balzaretti 9

department: Disfeb

country: Italy

institute: Università degli Studi di Milano

summary: During development, gonadotropin releasing hormone (GnRH) neurons are born in the nasal placode and migrate to the hypothalamus, where they position to regulate sexual reproduction. Defective GnRH neuron development may lead to GnRH deficiency (GD) which is characterized by absent or delayed puberty. Several GD causative genes have been identified so far, but half of the cases are still idiopathic. The identification of candidate genes is also hampered by the difficulty in isolating and studying GnRH neurons, which are small in number, develop in a short developmental window and lack specific markers. Gene expression profiles of GnRH neurons are lacking, as obtaining primary GnRH neurons is challenging and no reports on gene expression profiles during the whole developmental process of GnRH neurons are available. In this work, we obtained the transcriptomic profile of sorted GFP-positive and unsorted GFP-negative cells from Gnrh1-GFP rat embryos at three developmental stages, representing the initiation (embryonic day (E)14), the peak (E17) and the completion of GnRH neuronal migration (E20).

overall_design: Sorted GFP-GnRH neurons and unsorted cells from 8-10 pooled rat embryos at three different time points were analyzed

first: Roberto

last: Oleari


title: Hijacking a neurodevelopmental epigenomic program in metastatic dissemination of medulloblastoma [ATAC-Seq]

city: Pittsburgh

first: Baoli

last: Hu

state: PA

address: 4401 Penn Ave

department: Neurological Surgery

country: USA

institute: University of Pittsburgh School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

middle: E


title: Expression data of immortlized GnRH neuron cell lines

summary: During development, gonadotropin releasing hormone (GnRH) neurons are born in the nasal placode and migrate to the hypothalamus, where they position to regulate sexual reproduction. Defective GnRH neuron development may lead to GnRH deficiency (GD) which is characterized by absent or delayed puberty. Several GD causative genes have been identified so far, but half of the cases are still idiopathic. The identification of candidate genes is also hampered by the difficulty in isolating and studying GnRH neurons, which are small in number, develop in a short developmental window and lack specific markers. Immortalized murine cell lines have been developed in past years. Of interest, GT1-7 represent hypothalamic post-migratory neurons, whereas GN11 cells represent GnRH neurons blocked at an early stage of their migration. Here, we obtained the transcriptomic profile of Gn11 abnd GT1-7 cells, representing GnRH neurons at an immature and mature developmental stage, respectively.

overall_design: Mouse immortalized immature (GN11) and mature (GT1-7) GnRH neurons (n=3).


title: Hijacking a neurodevelopmental epigenomic program in metastatic dissemination of medulloblastoma [RNA-Seq]

type: Expression profiling by high throughput sequencing

overall_design: mRNA profiles for SMARCD3 WT and KO cells.


title: Gene expression time series during natural senescence of Arabidopsis thaliana leaves under short-day growth conditions

city: York

first: Katherine

last: Denby

address: Department of Biology

country: United Kingdom

institute: University of York

summary: This experiment profiled a time series of gene expression in leaf 7 of Arabidopsis thaliana plants  grown in a controlled environment under 8 h light: 16 h dark (i.e. short days) to compare to the profiles analysed in Breeze et al. (2011) Plant Cell 23(3):873-94 under long day conditions.

overall_design: Leaf 7 was harvested from an individual Arabidopsis Col-0 plant every 2 days from 25 to 61 days after sowing. At each time point, 4 leves were harvested to generate four biological replicates. Plants were grown in controlled environments under short day conditions (i.e. 8 h light, 16 h dark).

first: Vicky

last: Buchanan-Wollaston


city: Shanghai

first: Yilun

last: Wang

address: No.12 Wulumuqi Zhong Road

country: China

institute: Fudan University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: The aim of our study was to explore lncRNA expression profile in keratinocytes of patients with psoriasis vulgaris to provide new insights into psoriasis.

overall_design: Two-condition experiment, nc (as controls) vs. patient (as patients with psoriasis vulgaris group) cells. Biological replicates: 5 control replicates, 5 patient replicates.

first: Juan

last: Du

first: Xiaonian

last: Lu


title: Clinically Important Alterations in Pharmacogene Expression in Histologically Severe Nonalcoholic Fatty Liver Disease

status: Public on Feb 27 2023

city: Indianapolis

first: Nick

last: Powell

state: United States

address: 950 W. Walnut St.

institute: IUSM

summary: This study aims to determine if patients with NAFLD are at risk for altered drug response by characterizing changes in hepatic mRNA expression of genes mediating drug disposition (pharmacogenes) across the histological NAFLD severity spectrum.

overall_design:
We utilize RNA-seq for 93 liver biopsies with histologically staged NAFLD Activity Score (NAS), fibrosis stage, and steatohepatitis (NASH).
NOTE FROM SUBMITTER: We cannot upload raw data files due to research participant privacy concerns.

first: Naga

last: Chalasani


title: Expression data of liver resident cells from C57BL/6 mouse

city: Boston

first: Xiaolong

last: Zhang

state: Massachusetts

address: 200 Longwood Ave, 142 Warren Alpert Building

institute: Boston Children's Hospital

summary:
The liver is composed of various resident cells, including hepatocytes, Kupffer cells, liver sinusoidal endothelial cells (LSEC), and hepatic stellate cells (HSC). Hepatocytes are the primary type of liver cells, constituting 80% of the liver's mass, and are responsible for tasks such as protein and lipid synthesis, detoxification, and bile secretion. Kupffer cells, on the other hand, are liver-resident macrophages that play a crucial role in detecting foreign antigens and danger signals within the liver, as well as clearing apoptotic cells. LSEC is in charge of blood vessel formation in the liver and is responsible for eliminating cell debris. In the quiescent state, HSC stores vitamin A and is essential in liver fibrosis when activated. Freshly isolated HSCs undergo automatic activation upon culture.
In this study, we present microarray data for freshly isolated mouse hepatocytes, Kupffer cells and LSEC, along with HSCs that have been cultured for 1, 7 or 14 days.

overall_design: Freshly sorted hepatocytes, Kupffer cells, LSECs and culture-activated HSCs were used to obtain microarray data. To culture-activate HSC, the cells were maintained in DMEM supplemented with 10% FBS in a 37°C, 5% CO2 humid incubator for 1, 7, or 14 days. All cells were isolated from naïve C57BL/6 mice. For hepatocytes, Kupffer cells, and LSEC, three biological replicates were included, while one-day cultured HSC had two replicates.

first: Florian

last: Winau


title: Genome Editing with Tyrosinase gRNA

city: Bunkyo-ku

first: Hiroshi

last: Asahara

state: Tokyo

address: 1-5-45 Yushima

department: Department of Systems BioMedicine

country: Japan

institute: Institute of Science Tokyo

summary: We confirmed Tyrosinase genome insertions or deletions of the three Tg mice by deep sequencing using MiSeq. These mice generated gene editing mice by using Tol2 transposon to introduce tyrosinase guide RNA (gRNA) into fertilized eggs obtained by crossing LSL (loxP-stop-loxP)-Cas9 mice with CAG-CreER mice.

overall_design: We have identified insertions or deletions on the tyrosinase genome of tyrosinase gRNA cassette Tg mice by Amplicon-seq

first: Maiko

last: Inotsume

first: Tomoki

last: Chiba


title: Ssu72 phosphatase is essential for thermogenic adaptation by regulating cytosolic translation

city: Suwon

first: Eun-Ji

last: Park

address: 2066 Seobu-ro

country: South Korea

institute: Sungkyunkwan University

summary: Brown adipose tissue (BAT) plays a pivotal role in maintaining body temperature and energy homeostasis. To identify the fuction of Ssu72 phosphatase in BAT thermogenesis, we analyzed gene expression of BAT from SSU72 WT and SSU72aKO.

overall_design: For the comparative gene expression analysis, RNA seq data were obtained from BAT of SSU72 WT and SSU72KO in triplicate.

first: Hyun-Soo

last: Kim

first: Min-Woo

last: Lee

first: Chang-Woo


title: Automating iPSC generation to enable autologous photoreceptor cell replacement therapy

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: scRNAseq profiling of retinal organoids derived from iPSCs generated on a robot platform.

overall_design: Approximately ten representative organoids were selected from culture. Organoids were allowed to settle by gravity in a 1.5 mL tube and medium was aspirated. Organoids were then dissociated with 20 units/mL of papain (Worthington Biochemical Corporation, Lakewood, NJ) with 60 units/mL DNase I (Worthington Biochemical Corporation) on a shaker at 37˚C for approximately 60 minutes. Following dissociation, cells were pelleted at 400 x g for 5 minutes, resuspended in dPBS -/- (Thermo Fisher Scientific) with 0.04% non-acetylated bovine serum albumin (New England Biolabs, Ipswich, MA), and processed immediately for encapsulation and barcoding using the Chromium Controller (10X Genomics, Pleasanton, CA).

middle: K

first: Budd

middle: A

last: Tucker


title: RNA helicase DHX15 exemplifies a unique dependency in acute leukemia

city: Chapel Hill

first: Donghai

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

summary: RNA-binding proteins (RBPs) have emerged as essential regulators to control gene expression and modulate multiple cancer traits. T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy derived from transformation of T-cell progenitors that normally undergo discrete steps of differentiation in the thymus. Yet implications of essential RBPs during T cell neoplastic transformation remain largely unexplored. Systematic evaluation of RBPs identifies the RNA helicase DHX15, a key subunit in the intron lariat spliceosome (ILS) complex, as a potential T-ALL dependency factor. Using cell-based functional assays and the NOTCH1-induced murine T-ALL model, we demonstrate the essential importance of DHX15 in tumor cell survival and leukemogenesis. Moreover, single-cell transcriptomics reveals that DHX15 depletion in T-cell progenitors impairs normal T-cell development and, more specifically, hinders burst proliferation during CD4-CD8-(DN)-to-CD4+CD8+(DP) transition. Mechanistically, abrogation of DHX15 induces altered RNA splicing and downregulation of SLC7A6 and SLC38A5, thereby suppressing glutamine import and mTORC1 activity. Sustained mTORC1 hyperactivation significantly rescues the DHX15-deficient phenotypes, supporting mTORC1 as a prominent downstream effector mediating the pro-proliferative role of DHX15. Moreover, we propose a DHX15 signature modulator drug ciclopirox and demonstrate the prominent anti-T-ALL efficacy. We therefore highlight DHX15 as a crucial regulator during T-cell leukemogenesis, and provide mechanistic insights that DHX15, although functioning at the end of splicing catalysis, modulates a subset of pathogenic mis-splicing events. These findings exemplify a promising therapeutic approach that splicing perturbation by targeting DHX15 may achieve robust anti-tumor efficacy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We used human T-ALL as a model system, and performed multi-omics analysis including RNA-seq and RIP-seq to study the regulatory mechanism of RNA-helicase DHX15. Meanwhile, to further clarify the heterogeneities of thymocyte subsets and the abnormal gene expression profiles in the absence of Dhx15, we performed single-cell RNA sequencing (scRNA-seq) using 10X Genomics platform on isolated single cells from thymus with or without Dhx15 expression

first: Hudan

last: Liu

first: Pieter

last: Van Vlierberghe

first: Zhaoqi


title: Acidosis activates the Nrf2-pathway in renal proximal tubule-derived cells through a crosstalk with renal fibroblasts

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

summary: Crosstalk of renal epithelial cells with interstitial fibroblasts plays an important role in kidney pathophysiology. A former study showed that crosstalk between renal epithelial cells and renal fibroblasts protects against acidosis-induced damage. In order to gain further mechanistic insight into this crosstalk we investigated the effect of acidosis on the transcriptome of renal epithelial cells (NRK-52E) and renal fibroblasts (NRK-49F) in co-culture  by RNASeq, bioinformatics analysis and experimental validation.

overall_design: NRK-52E (proximal tubule-derived epithelial cells) and NRK-49F (kidney fibroblasts) were subjected to acidic conditions, while being co-cultivated.

first: Marie-Christin

last: Schulz

first: Alexander

last: Nolze

first: Michael

last: Kopf

first: Gerald

last: Schwerdt

last: Gekle


title: sRNA profiling in Botryosphaeria dothidea reveals a differentially expressed miRNA named Bdo-milR-204 response to heat stress

status: Public on Mar 01 2023

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

institute: Northwest A&F University

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA sequencing was applied to detected miRNA profiles of Botryosphaeria dothidea

overall_design: For each sample type, sequencing was performed on an Illumina Hiseq 2500 platform

first: Bo

last: Wang

first: Guangyu

last: Sun


title: GEMC1 and MCIDAS interactions with SWI/SNF complexes regulate the multiciliated cell-specific transcriptional program

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: Multiciliated cells (MCCs) project dozens to hundreds of motile cilia from their apical surface to promote the movement of fluids or gametes in the mammalian brain, airway or reproductive organs. Differentiation of MCCs requires the sequential action of the Geminin family transcriptional activators, GEMC1 and MCIDAS, that both interact with E2F4/5-DP1. How these factors activate transcription and the extent to which they play redundant functions remains poorly understood. Here, we carried out a transcriptomic analysis to compare the relative influence of GEMC1 and MCIDAS on gene expression.

overall_design: HEK293T cells were transiently transfected with control FLAG vector, or FLAG-tagged GEMC1 or MCIDAS. Cells were harvested in Trizol 48 hours post-transfection for RNA purification and microarray analysis.

first: Travis

last: Stracker

last: Lewis

first: Berta

last: Terre

last: Reina


title: Granulosa cell mevalonate pathway abnormalities contribute to oocyte meiotic defects and aneuploidy [HiC GGOH-treatment]

status: Public on Feb 26 2023

first: Qian

last: Bian

state: Shanghai

address: Pudong New District, Jinzun Rd, No.115

department: Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: The mechanisms of aging-related oocyte aneuploidy remain elusive. Hi-C and SMART-seq  revealed aging-related decreases in chromosome condensation, particularly for genomic regions proximal to the centromeres, accompanied with disrupted meiosis-associated gene expression in metaphase I (MI) aged oocytes. Further transcriptomic analysis showed that oocyte meiotic maturation was correlated with robust increases in mevalonate (MVA) pathway gene expression in young oocyte-surrounding granulosa cells (GCs), which was largely downregulated in aged GCs. Inhibtion of MVA metabolism in GCs by statins resulted in marked meiotic defects and aneuploidy in young cumulus-oocyte complexes (COCs). Conversely, supplementation with the MVA isoprenoid geranylgeraniol ameliorated meiotic defects and aneuploidy in aged COCs. Meanwhile, geranylgeraniol also activated LHR/EGF signaling in aged GCs and then enhanced the meiosis-associated gene expression in oocytes. Generally, the MVA pathway in GCs is a critical regulator of meiotic maturation and euploidy in oocytes.

overall_design: In this study, the dynamics of chromatin structure of oocytes and the overall transcriptomic landscape of oocytes and GCs throughout oocyte meiosis (growing phase, full-grown phase, metaphase I phase, metaphase II phase) in vivo from control or GGOH-treated aged mice were depicted.

first: Lijun

last: Ding

first: Chuanming

first: Wu

last: Zuo


title: Granulosa cell mevalonate pathway abnormalities contribute to oocyte meiotic defects and aneuploidy [RNA-seq Human oocytes]

summary: The mechanisms of oocyte meiotic defects and low competence during ovarian aging remains elusive for decades. Using Hi-C (genome-wide chromatin conformation capture) and Smart RNA-seq of oocytes from 6- weeks or 10- months aged ovaries, the abnormal loose chromatin structures and disturbing expression of meiosis associated genes at metaphase I phase were disclosed. Furthermore, the transcriptomic landscape of granulosa cells (GCs) surrounding oocytes from young and aged ovaries reveled that oocyte meiotic maturation was accompanied with a robust increased expression of genes involved with the mevalonate (MVA) pathway in GCs from young ovaries but these genes expression was not upregulated to counterpart level in GCs from aged ovaries.The inhibitor of MVA pathway of GCs, Statins significantly decreased polar body extrusion rate and increased the rate of irregularly assembled spindles and misaligned chromosomes remarkably in oocytes of culumus-oocyte complex (COCs) from young ovaries . Correspondingly, the activitor of MVA pathway of GCs, Geranylgeraniol ameliorated ovarian reserve and reduced meiotic defects in oocytes of COCs from aged ovaries. Mechanistically, MVA pathway activation in GCs culminated oocyte meiotic maturation by upregulating EGF signaling via LH receptor on GCs surrounding oocytes. Together, MVA pathway is a promising therapeutic target for prompting quality of oocytes from aged ovaries.

overall_design: RNA-seq of Human oocytes

last: Liu


title: Doxorubicin response in a triple negative breast cancer cell model: long-term resistance versus short-term stress

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

summary: We have used a cell model for triple negative breast cancer, CAL51 cells, to study the transcriptional profiling of chemotherapy drug response. A doxorubicin resistant derivative has been generated, named CALDOX, which is able to proliferate in the continuos presence of 0.4 micro molar doxorubicin in the culture medium. In addition, both naive CAL51 and drug resistant CALDOX cells, the short-term response to doxorubicin treatment has been studied.

overall_design: CAL51 cells were treated with 0.4 micro M doxorubicin until they were able to survive and proliferate in the presence of drug (these drug resistant cells are termed CALDOX). Short-term effects of doxorubicin were studied in CAL51 cells (with treatments for 24 and 48 h with 0.4 micro M doxorubicin) and CALDOX cells (with treatment for 24 h with 4 micro M doxorubicin). For the array experiment, RNA isolated from three independent cultures were used for each condition.

first: Ernesto

last: Yague

first: Uttom

last: Kumar


title: Neural connectivity molecules best identify the heterogeneous clock and dopaminergic cell types in the Drosophila adult brain

status: Public on Feb 25 2023

city: Waltham

last: Rosbash

address: 415 South street

institute: HHMI/Brandeis University

summary: Our recent single-cell sequencing of most adult Drosophila circadian neurons indicated notable and unexpected heterogeneity. To address whether other populations are similar, we sequenced a large subset of adult brain dopaminergic neurons. Their gene expression heterogeneity is similar to that of clock neurons, i.e., both populations have two to three cells per neuron group. There was also unexpected cell-specific expression of neuron communication molecule messenger RNAs: G protein–coupled receptor or cell surface molecule (CSM) transcripts alone can define adult brain dopaminergic and circadian neuron cell type. Moreover, the adult expression of the CSM DIP-beta in a small group of clock neurons is important for sleep. We suggest that the common features of circadian and dopaminergic neurons are general, essential for neuronal identity and connectivity of the adult brain, and that these features underlie the complex behavioral repertoire of Drosophila.

overall_design: Single cell RNA sequencing of Drosophila dopaminergic neurons by modified CEL-se2 method, we also labeled clock neurons and dopaminergic neurons in the same fly and assayed these two populations together with 10X Chromium.

first: Dingbang

last: Ma


title: Targeting Transcriptional Addiction in MYCN-amplified Neuroblastoma via Super Elongation Complex Disruption

first: Donghai

summary: MYCN amplification in neuroblastoma predicts particular poor prognosis and directly targeting of MYCN remains a major challenge. We conducted a targeted screen of transcription elongation factors and identified the super elongation complex (SEC) as a unique vulnerability in MYCN-amplified neuroblastoma. Mechanistically, MYCN directly interacts with the SEC subunit EAF1 and recruits the complex to the target gene loci for ensuing processive transcription elongation, rendering MYCN-mediated transcriptional activation highly dependent on SEC. Pharmacological inhibition of SEC by KL-1 or KL-2 elicits selective cell death in MYCN-overexpressing neuroblastoma cells. Furthermore, drug combination screening identifies the BCL-2 inhibitor ABT-199 synergistic with KL-2. Pre-clinical studies manifest that KL-2 and ABT-199 co-treatment significantly suppresses tumorigenesis and shows therapeutic value in multiple neuroblastoma allograft and xenograft models. These findings highlight SEC as a targetable vulnerability, and simultaneous inhibition of SEC and BCL-2 holds great promise for the treatment of MYCN-driven neuroblastoma.

overall_design: We used human neuroblastoma as a model system, and performed multi-omics analysis including RNA-seq, TT-seq and ChIP-seq to study the regulatory mechanism and functional interplay between MYCN and SEC.

first: Guoliang

last: Qing

first: Kaiwei

last: Liang

first: Hudan


title: GRHL2 and AP2a coordinate early surface ectoderm lineage commitment and craniofacial development [H9_d7_HiChIP_AP2KO]

status: Public on Feb 24 2023

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

summary: Cohesin HiChIP of AP2a KO hESCs treated with RA/BMP4 for 7 days

overall_design: Create a 3D chromatin conformation map of AP2a KO cells.

first: Jillian

last: pattison

first: Sadhana

last: Gaddam


title: Downregulation of KEAP1 in melanoma promotes resistance to immune checkpoint blockade [scBisulfite-seq]

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

type: Methylation profiling by high throughput sequencing

summary: Immune checkpoint blockade (ICB) has demonstrated efficacy in patients with melanoma, but many exhibit poor responses. Using single cell RNA sequencing of melanoma patient-derived circulating tumor cells (CTCs) and functional characterization using mouse melanoma models, we show that the KEAP1/NRF2 pathway modulates sensitivity to ICB, independently of tumorigenesis. The NRF2 negative regulator, KEAP1, shows intrinsic variation in expression, leading to tumor heterogeneity and subclonal resistance.

overall_design: Single cells from a culture of melanoma circulating tumor cells (MEL167, PMID: 33203734) were isolated by cell sorting. A total of 35 cells were used for matched bisulfite- and RNA-sequencing using a previously established protocol (PMID: 30498128 and PMID: 26902283).

first: Douglas

middle: B

last: Fox

first: Richard

middle: Y

last: Ebright

first: Xin

last: Hong

middle: S

first: Shyamala

last: Maheswaran

first: Daniel

last: Haber


title: GRHL2 and AP2a coordinate early surface ectoderm lineage commitment and craniofacial development (Multiome)

summary: scRNA and scATAC in WT and GRHL2 KO hESCs after 7 days of RA/BMP4 (10x multiome)

overall_design: Evalute single cell RNA and ATAC changes in GRHL2 KO cells compared to WT.

first: Annie

last: Collier


title: GRHL2 and AP2a coordinate early surface ectoderm lineage commitment and craniofacial development (ChIP-Seq)

summary: ChIP-seq for GRHL2 or AP2a in hESCs treated with RA/BMP4 for 7 days

overall_design: Compare binding sites for GRHL2 or AP2a in WT and GRHL2 or AP2a KO cells.


title: GRHL2 and AP2a coordinate early surface ectoderm lineage commitment and craniofacial development (RNA-Seq)

summary: RNA-seq in GRHL2 KO hESCs treated with RA/BMP4 for 7 days, or GRHL2 over-expression for 7 days.

overall_design: Evaluate changes in the transcriptiome for GRHL2 KO or overexpression compared to controls.


title: GRHL2 and AP2a coordinate early surface ectoderm lineage commitment and craniofacial development (ATAC-Seq)

summary: ATAC-seq in GRHL2 or AP2a KO hESCs treated with RA/BMP4 for 7 days

overall_design: Compare KO chromatin accesibility to WT

first: Ann


title: Downregulation of KEAP1 in melanoma promotes resistance to immune checkpoint blockade

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

overall_design: Refer to individual Series


title: Downregulation of KEAP1 in melanoma promotes resistance to immune checkpoint blockade [scRNA-seq]


title: Differential expression of human BM-MSCs RNA-Seq and 21-day of chondrogenic differentiation from high-depth transcriptomic profiling of mesenchymal stem cells during chondrogenesis

city: Taichung City

first: Chun-Te

last: Ho

address: 7F, No. 6, Xueshi Rd., North Dist.

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

summary: A comprehensive evaluation of differential gene expression on RNA-seq data of early and late passage hMSCs from three individuals, and undifferentiated and 21-day of chondrogenic differentiation hMSCs from previous publication (GSE109503). Genome-wide RNA-seq and differential expression analysis revealed that signalings such as Pulmonary Fibrosis Idiopathic (IPF) Signaling Pathway and Osteoclasts in Rheumatoid Arthritis (RA) Signaling Pathway were significant differences in early MSC. Differential FOXO1 expression, higher in Early than Late MSCs, was responsible for promoting suspension survival, and cell migration, and induces chondrogenic differentiation.

overall_design:
RNA-Seq of early and late passage bone marrow-derived mesenchymal stem cells with 3 biological replicates (representing 6 samples).
In addition, third-party reanalysis of 6 samples from Series GSE109503.

first: Shih-Chieh

last: Hung


title: Epigenetically programmed ‘stem-like’ tissue resident memory CAR T-cells exhibit robust activity against solid and liquid tumors [scRNA]

status: Public on Feb 23 2023

city: Philadelphia

first: Inyoung

last: Jung

address: SPE, 9-304, 3400 Civic Center Blvd, Bldg. 421

institute: University of Pennsylvania

summary: Chimeric antigen receptor (CAR) T-cells have shown remarkable success in the therapy of hematological malignancies, but they have not yet proven nearly as effective in treating non-hematopoietic cancers. This study proposes augmentation of CAR T-cell function and accumulation in solid tumors by modifying the epigenetic landscape that governs early memory differentiation and adaptation to tissue residency. We identified that a key factor in human tissue-resident memory CAR T-cell (CAR-TRM) formation is activation in the presence of the pleotropic cytokine, TGF-β, which epigenetically enforces a core transcriptional program of both ‘stemness’ and sustained tissue residency. This strategy results in a readily actionable in vitro production method for engineering peripheral blood T-cells into large numbers of ‘stem-like’ CAR-TRM cells resistant to epigenetically-imposed exhaustion that possess enhanced ability to accumulate in situ and rapidly kill cancer cells for more effective immunotherapy.

overall_design: Anti-mesothelin M5 CAR-TCONV and CAR-TRM cells were harvested after nine days of in vitro expansion. Dead cells were eliminated using the Dead Cell Removal Kit (Miltenyi Biotec). Mesothelin-directed M5 CAR-TCONV and -TRM cells were magnetically isolated using anti-mesothelin-coated beads. After isolation, T-cell viability and quantity were evaluated using trypan blue exclusion and cells were resuspended in PBS containing 0.04% BSA.

first: In-Young

first: Estela

last: Noguera-Ortega

first: Robert

last: Bartoszek

first: Sierra

last: McDonald

first: Erik

last: Williams

first: Mega

middle: M

last: Davis

first: Julie

last: Jadlowsky

first: Gabriela

last: Plesa

first: Anne

last: Chew

first: Shelley

middle: L

last: Berger

first: Edmond

last: Moon

first: Steven

last: Albelda

first: Joseph

last: Fraietta


title: Smartseq3 Single-cell RNA-seq analysis of acutely FACS-purified tdTomato+ astrocyte derived cells from aged injured mice in vivo

city: London

first: Simona

last: Parrinello

address: 72 Huntley Street

institute: UCL Cancer Institute

summary: To investigate the mechanisms that underlie astrocyte dedifferentiation, we performed single cell RNA sequencing analysis of tdTomato+ astrocyte derived cells approx 1 year after stab-wound injury. 2-3 month old GFAP-CreERT2;p53flox/flox;LSL-tdTomato (p53Gfap-icKO) mice were subjected to intracortical endoxifen injection to enable deletion of p53 gene and simultaneous expression of tdTomato for fate-mapping specifically in astrocytes (GFAP+) in the context of a stab-wound injury. GFAP-CreERT2;p53wt/wt;LSL-tdTomato (p53Gfapwt/wt) mice were used as control whereby p53 remains fate-mapped tdTomato+ astrocytes remain p53 wildtype after endoxifen injection. Approx 10-12 months after injury, mice were sacrificed and the peri-wound region was dissected. Mice of the same genotypes were pooled (3 p53Gfap-icKO and 2 p53Gfapwt/wt) and digested using the Miltenyi Adult brain dissociation kit. Single cell suspension was FACS sorted for tdTomato+ cells into 384 well plates and then Smartseq3 libraries were generated.

overall_design: FACS-purified tdTomato+ cells from 3 pooled p53Gfap-icKO brains or 2 pooled p53Gfap-wt/wt brains with raw data for 145 KO and 125 WT.

first: Samuel

last: Marguerat


title: Single-cell RNA-seq analysis of p53 knockout primary adult mouse astrocytes in vitro.

summary: To investigate the mechansims that underlie astrocyte dedifferentiation, we performed single cell RNA sequencing analysis of primary astrocytes isolated from adult mouse cortex after p53 loss and exposure to mitogens, EGF and and FGF. Primary astrocytes were isolated from cortices of 2-3month old inducible p53 knockout mice (GFAP-CreERT2;p53flox/flox;LSL-tdTomato) using Miltenyi Adult Brain Dissociation kit and ACSA-2 beads. Treatment with 4-hydroxytamoxifen (4OHT) induces p53 loss and tdTomato labelling in GFAP+ astrocytes. Astrocytes were treated with 4OHT in media supplemented with EGF and FGF to induce recombination and astrocyte dedifferentiation in vitro.

overall_design: Primary astrocytes from 2 pooled mouse brains with raw data for 1562 single cells


title: Chromatin Regulation by TFAP2A

first: Anthony

last: Oro


summary: The objective of this experiment was to determine the DNA binding site for TFAP2A in non-neural ectoderm.

overall_design: Two replicates of non-neural ectoderm were used in this study. An input control was used for normalization.

first: Annie

last: Collier

first: Sadhana

last: Gaddam


title: Dynamics of extracellular vesicle-coupled microRNAs in equine follicular fluid associated with follicle selection

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: The mammalian follicular development is a well-orchestrated and complex molecular process characterized by sequences of follicular waves that yield the ovulatory follicle. It has been reported that bi-directional communication between the growing oocyte and the surrounding somatic cells is a hallmark of mammalian follicular development, partially mediated by extracellular vesicles (EVs) present in the follicular fluid (FF). Bioactive molecules such as the miRNAs encapsulated in the EVs mediate this communication within the follicular environment. Here, we aimed to decipher the dynamics of the miRNAs in the EVs of equine FF aspirated in vivo during different stages of follicular development. Hence, all follicles ≥6 mm were ablated on Days 10–11 of the estrous cycle (ovulation = Day 0) and the new induced wave was ultrasound-monitored daily until the largest growing follicle for at least three consecutive days was randomly allocated to one of the five groups (n = 8 follicles/group) namely: predeviation (preDEV; 18–20 mm), deviation (DEV; 22–25 mm), postdeviation (postDEV; 26–29 mm), preovulatory (preOV; 30–35 mm), and impending ovulation (IMP; ~40 mm). The FF was collected from each target group by ultrasound-guided transvaginal follicle aspiration. After removal of cells, cellular debris, and larger particles, EVs were isolated from FF groups (4 biological replicates/group; 0.5 mL FF/replicate) using high-speed ultracentrifugation (120,000xg for 70 min). Isolated EVs were characterized using western blot for EV marker proteins, NanoSight Tracking Analysis, and electron microscopy. MiRNA enriched total RNA was isolated from EVs using an Exosomal RNA Isolation kit and small-RNA library preparation and RNAseq (NextSeq500; Illumina) was performed by Novogene Co, Ltd. Approximately 180 known miRNAs were detected in each group with 148 mutually found in all groups. Among the expressed miRNAs, miR-148a, miR-21, miR-192, and miR-99a were the top highly abundant miRNAs in all groups. Cluster analysis exhibited 15 different expression patterns during follicular development. Among these patterns, a group of 23 miRNAs (including miR-106b, miR-199a-5p, and miR-125a-5p) exhibited a stable expression at the preDev until the postDev stage, a significant increase at the preOV stage, and then a significant decrease at the IMP stage. This miRNA cluster has been found to target genes involved in TGF-signaling and endocytosis pathways. Another interesting pattern with 22 miRNAs (including miR-146b-5p, miR-140, and miR-143) exhibited a sharp reduction in their expression from the preDEV until the preOV stage and was predicted to target genes associated with fatty acid biosynthesis, cell cycle, and oocyte meiosis pathways. In contrast, a group of 16 miRNAs (including miR-483, miR-128, and miR-192) gradually increased in expression from preDEV to the postDEV and then downregulated at the preOV stage. This miRNA cluster targets several signaling pathways, including ErbB, thyroid, and estrogen signaling. In conclusion, this study provides greater insights into the stage-specific expression dynamics of the FF EV-miRNAs during equine follicular development, which may play a role in folliculogenesis in mares.

overall_design: Quarter horse mares (n = 19; 8 to 14 years old) with normal reproductive tract as determined by ultrasonographic examination were used during the ovulatory season (June and July). Ultrasound-guided ablations of all follicles ≥6 mm were performed on Days 10–11 of the estrous cycle (ovulation = Day 0) to induce a new follicular wave. Thereafter, daily ultrasonographic follicle examinations were performed. Ultrasonographically healthy and growing follicles for at least three consecutive days were assigned to five groups based on the targeted diameters: predeviation (PreDev; 18–20 mm), deviation (Dev; 22–25 mm), postdeviation (PostDev; 26–29 mm), preovulatory (PreOV; 30–35 mm), and impending ovulation (IMP; follicles with signs of imminent ovulation). Samples of FF were collected in vivo by ultrasound-guided transvaginal follicle aspiration

last: Gebremedhn

first: Ghassan

last: Ishak

first: Nico

last: Menjivar

first: Melba

middle: O

last: Gastal

first: Jean

last: Feugang

first: Radek

last: Prochazka

first: Dawit

last: Tesfaye

first: Eduardo


title: Single-cell RNA-seq analysis of p53 knockout primary astrocytes in vitro.

summary: To investigate the mechansims that underly astrocyte dedifferentiation, we performed single cell RNA sequencing analysis of primary astrocytes after p53 loss and exposure to mitogens, EGF and and FGF. Primary astrocytes were isolated from postnatal day 3 inducible p53 knockout mice (GFAP-CreERT2;p53flox/flox;LSL-tdTomato), whereby treatment with 4-hydroxytamoxifen (4OHT) induces p53 loss and tdTomato labelling in GFAP+ astrocytes. Astrocytes were treated with 4OHT in media supplemented with EGF and FGF to induce recombination and astrocyte dedifferentiation in vitro.

overall_design: Primary astrocytes from a total of 4 mouse brains (2 mice pooled per independent replicate) with raw data for 12,040 single cells.


title: KIR+CD8+ and NKG2A+CD8+ T cells are distinct innate-like populations in humans

city: Bundang-gu, Seongnam-si

first: Seong Jin

last: Choi

state: Gyeonggi-do

address: Dolma-ro, 172

department: Internal Medicine

institute: Seoul National University Bundang Hospital

summary: We studied the heterogeneity among human KIR/NKG2A+CD8+ T cells. First, we found that   KIRs and NKG2A are expressed on human CD8+ T cells in a mutually exclusive manner. Therefore, we   compared KIR+CD8+ and NKG2A+CD8+ T cells in regards to TCR overlap and transcriptomic profiles and   demonstrated that KIR+CD8+ and NKG2A+CD8+ T cells are distinct innate-like populations.

overall_design: mRNA profiles and TCR clonotypes of Naive, Memory, NKG2A+ and KIR+ CD8+ T cells in human PBMC

first: June-Young

last: Koh

first: Min-Seok

last: Rha

first: In-ho

last: Seo

first: Hoyoung

last: Lee

first: Seongju

last: Jeong

first: Su-Hyung

last: Park

first: Eui-Cheol

last: Shin


title: Epigenetically programmed ‘stem-like’ tissue resident memory CAR T-cells exhibit robust activity against solid and liquid tumors

first: Inyoung

last: Jung


title: The essential roles of FXR in diet and aging affected metabolic changes and liver disease development: a multi-omics study

status: Public on Feb 22 2023

city: Sacramento

first: Guiyan

last: Yang

address: 4645 2nd Ave

department: Department of Medical Pathology and Laboratory Medicine

institute: University of California at Davis

summary:
Aging and unhealthy diets are risks for metabolic diseases including liver cancer. Bile acid receptor farnesoid X receptor (FXR) knockout (KO) mice develop metabolic liver diseases and progress into liver cancer as they age, and Western diet (WD) intake facilitates liver carcinogenesis in those mice. This study aimed to uncover molecular signatures within the gut-liver axis for diet and age-linked liver diseases in FXR-dependent or independent manners.
Many more transcripts were changed due to WD intake and aging in WT mice than those in FXR KO mice. In other words, WD intake and aging impact the hepatic transcriptomes and metabolomes in an FXR-dependent manner. In WT mice, WD/aging upregulated inflammation-related genes and downregulated genes involved in oxidative phosphorylation (OXPHOS). Urine metabolomes provided clear distinguishing for differential dietary intake. By contrast, the metabolomes of the liver, serum, or urine could reflect age differences. Further, irrespective of differential diets intake or ages, transcriptomes, metabolomes, and cecal microbiota distinguished WT and FXR KO. Western dietary patterns and aging share molecular commonality with FXR deactivation. Notably, WD, aging, and FXR deactivation commonly altered hepatic cell division-related transcripts (Cenpe, Ect2, Top2a, Kif20a, Tpx2, Nuf2, Kif18b, Aspm, E2f8, and Hmmr), which are associated with overall survival rate in HCC patients. In conclusion, FXR is essential for maintaining metabolic homeostasis in response to WD intake and aging. FXR activation helps to alleviate diet and/or aging-induced metabolic health issues.

overall_design: Wild-type and Farnesoid X receptor (FXR) KO mice were fed a control diet (CD) or Western diet (WD) since weaning. Transcriptome profile of livers from these mice at the age of 5, 10, and 15 months (4 mice per group).

first: Yu-Jui

last: Wan


title: p53 ChIP-seq of primary astrocytes in vitro

first: Simona

last: Parrinello

summary: To investigate the transcriptional regulation by p53 in astrocytes, we performed ChIP-sequencing using p53 antibody (Leica CM-5) or rabbit IgG control in wildtype primary mouse cortical astrocytes.

overall_design: Primary astrocytes from a total of 8 P3 mouse brains were cultured in the presence of BMP4. ChIP was performed using the EZ-Magna ChIP kit (Millipore) according to manufacturers instructions.

first: Samuel

last: Marguerat


title: PD-1 expressing CD4 and CD8 lymphocyte populations were compared to PD-1 negative CD4 and CD8 lymphocyte populations from 5 RA patients

city: Adelaide

first: Katie

last: Williams

state: South Australia

address: Sturt Rd, Bedford park

country: Australia

institute: Flinders University

summary:
Programmed cell death protein 1 (PD-1)-expressing T cells are expanded in individuals with established rheumatoid arthritis (RA). However, little is known about their functional role in the pathogenesis of early RA.
We investigated the transcriptomic profiles of circulating CD4+ and CD8+ PD-1+ lymphocytes from patients with early RA (n=5) using fluorescence activated cell sorting in conjunction with total RNA sequencing. Additionally, we assessed for alterations in CD4+PD-1+ gene signatures in synovial tissue (ST) biopsies (n=19) before and after six-month triple disease modifying anti-rheumatic drug (tDMARD) treatment.
Comparisons of gene signatures between CD4+PD-1+ vs. PD-1- cells identified significant upregulation of genes including CXCL13 and MAF, and in pathways including Th1 and Th2, cross talk between dendritic cells and NK cells, B cell development and antigen presentation. Gene signatures from early RA ST before and after six-month tDMARD treatment revealed downregulation of the CD4+PD-1+ signatures following treatment, suggesting the pathogenic nature of CD4+PD-1+ cells and identifying a mechanism through which tDMARDs exert their effect by influencing T cell populations. Furthermore, we identify factors associated with B cell help that are enhanced in the ST compared with PBMCs, highlighting their importance in driving synovial inflammation.

first: K

last: Lowe

first: A

last: Small

first: Q

last: Song

first: L-Y

last: Hao

first: W

last: Murray-Brown

first: S

last: Proudman

first: M

middle: D

last: Smith

last: Nagpal

last: Wechalekar


title: PQBP1 regulates striatum development through balancing striatal progenitor  proliferation and differentiation

status: Public on Feb 21 2023

city: Nan Jing

first: Wen

middle: hua

last: Liu

state: Jiang Su

address: 2 Sipailou Road

institute: Southeast university

summary: The balance between cell proliferation and differentiation is essential for maintaining  the neural progenitor pool and brain development. Although the mechanisms  underlying cell proliferation and differentiation at the transcriptional level have been  studied intensively, post-transcriptional regulation of cell proliferation and differentiation  remains largely unclear. Here, we show that deletion of the alternative splicing  regulator PQBP1 in striatal progenitors resulted in defective striatal development due to  impaired neurogenesis of spiny projection neurons (SPNs). Pqbp1 deficiency striatal  progenitors exhibit declined proliferation and increased differentiation, resulting in a  reduced striatal progenitor pool. We further reveal that PQBP1 associates with  components in splicing machinery. The alternative splicing profiles identify that PQBP1  promotes the exon 9 inclusion of Numb, a variant that mediates progenitor proliferation.  These findings identify PQBP1 as a novel regulator in balancing striatal progenitor  proliferation and differentiation and provide alternative insights into the pathogenic  mechanisms underlying Renpenning syndrome.

overall_design: Total RNA from the Isolating the strong GFP-positive striatal IPs at E15.5  Pqbp1+/Y;Dlx5/6-Cre-IRES-EGFP and Pqbp1fl/Y;Dlx5/6-Cre-IRES-EGFP mice by using fluorescence-activated cell sorting (FACS) extracted for deep sequencing, in triplicate, using Illumina HiSeq X Ten.

first: Wenhua

first: Hao

last: Xie

first: Xian

first: Shoujing

last: Xu

first: Shanshan

last: Cheng

first: Zheng

last: Wang

first: Ting

first: ZiChao

last: Zhang

first: Junhai

last: Han


title: Effect of dietary tryptophan deficiency on intestinal ileum gene expression

city: New York

first: Nicholas

last: Arpaia

state: NY

address: 701 West 168th Street, Hammer Health Sciences Center 906

department: Microbiology and Immunology

institute: Columbia University Irving Medical Center

summary: To investigate the intestinal ileum response to dietary tryptophan deficiency and the contribution of the intestinal microbiome in regulating these responses

overall_design: We performed gene expression profiling analysis of the intestinal ileum of SPF and antibiotics treated C57Bl6 mice fed control and tryptophan deficient diet

first: Lucille

middle: C

last: Rankin


title: Directed Differentiation of Human iPSCs to Functional Ovarian Granulosa-Like Cells via Transcription Factor Overexpression [RNA-seq]

city: Boston

first: Merrick

middle: Pierson

last: Smela

address: 3 Blackfan Circle

institute: Harvard University

summary: An in vitro model of human ovarian follicles would greatly benefit the study of female reproduction. Ovarian development requires the combination of germ cells and their supporting somatic cells, known as granulosa cells. Whereas efficient protocols exist for generating human primordial germ cell-like cells (hPGCLCs) from human iPSCs, a method of generating granulosa cells has been elusive. Here we report that simultaneous overexpression of two transcription factors (TFs) can direct the differentiation of human iPSCs to granulosa-like cells. We elucidate the regulatory effects of several granulosa-related TFs, and establish that overexpression of NR5A1 and either RUNX1 or RUNX2 is necessary and sufficient to generate granulosa-like cells. Our granulosa-like cells have transcriptomes similar to human fetal ovarian cells, and recapitulate key ovarian phenotypes including follicle formation and steroidogenesis. When aggregated with hPGCLCs, our cells form ovary-like organoids (ovaroids) and support hPGCLC development from the premigratory to the gonadal stage as measured by induction of DAZL expression. This model system will provide unique opportunities for studying human ovarian biology, and may enable the development of therapies for female reproductive health.

overall_design: Two experiments are included: 1. Transcript abundance (TPM) measurements for induced pluripotent stem cells (iPSCs), COV434 ovarian cancer cells, and iPSC-derived granulosa-like cells. 2. Differential gene expression analysis to identify effects of transcription factor overexpression during iPSC differentiation.

last: Pierson Smela

first: Christian

last: Kramme

first: Patrick

last: Fortuna

first: Jessica

last: Adams

first: Edward

last: Dong

first: Mutsumi

last: Kobayashi

first: Garyk

last: Brixi

first: Emma

last: Tysinger

first: Richie

last: Kohman

first: Toshi

last: Shioda

first: Pranam

last: Chatterjee

first: George

last: Church


title: FUS modulates the level of ribosomal RNA modifications by regulating a subset of snoRNA expression [Small RNA seq]

city: Poznan

first: Kishor

last: Gawade

address: Uniwersytetu Poznańskiego 10

department: Faculty of Biology

country: Poland

institute: Adam Mickiewicz University

summary: FUS is a nucleocytoplasmic protein involved in many processes such as RNA transport, translation, and metabolism as well as genomic maintenance. FUS mutations are found in several neurodegenerative diseases. We find that FUS knockout (KO) and FUS mutation affects the expression of many C/D box snoRNAs, H/ACA box snoRNAs and scaRNAs. snoRNAs notably serve as adaptors for the 2'-O-methylation (2'-O-me) and pseudouridylation of ribosomal RNA (rRNA).

overall_design: We carried out small RNA sequencing and analyzed the impact on ribosomal RNA 2'-O-methylation and pseudouridylation using RiboMeth-Seq and HydraPsiSeq in FUS knock-out model cell lines (HEK293T FUS KO cells and SH-SY5Y (neuroblastoma) FUS KO cells as well as SH-SY5Y cells with FUS R495X mutation).

first: Sophia

last: Häfner

first: Dorota

last: Raczyńska

first: Yuri

last: Motorin


title: FUS modulates the level of ribosomal RNA modifications by regulating a subset of snoRNA expression [HydraPsiSeq]

summary: FUS is a nucleocytoplasmic protein involved in many processes such as RNA transport, translation, and metabolism as well as genomic maintenance. FUS mutations are found in several neurodegenerative diseases. We find that FUS knockout (KO) affects the expression of many C/D box snoRNAs, H/ACA box snoRNAs and scaRNAs. snoRNAs notably serve as adaptors for the 2'-O-methylation (2'-O-me) and pseudouridylation of ribosomal RNA (rRNA). We show that knockout and FUS mutation alter the levels of 2'-O-Me and pseudouridylation at several rRNA sites.

first: Katarzyna


title: FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer

status: Public on Feb 20 2023

city: İZMİR

first: Serap

last: Erkek Özhan

state: BALÇOVA

address: İzmir Biyotıp ve Genom Merkezi (IBG), Dokuz Eylül Üniversitesi Sağlık Yerleşkesi, Mithatpaşa Caddesi No:58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary: Bladder cancer is mostly present in the form of urothelium carcinoma, causing over 150.000 deaths each year. Its histopathological classification as muscle invasive and non-muscle invasive is the most prominent aspect, affecting the prognosis and progression of this disease. In this study, we defined the active regulatory landscape of MIBC and NMIBC cell lines using H3K27ac-seq and used an integrative data approach to combine our findings with existing data. Our analysis revealed FRA1 and FLI1 as the two critical transcription factors differentially regulating MIBC regulatory landscape. Importantly, we show that FRA1 and FLI1 regulate the genes involved in epithelial cell migration and cell junction organization.  Knock-down of FRA1 and FLI1 in MIBC revealed the downregulation of several EMT-related genes such as MAP4K4 and FLOT1. Further, ChIP-SICAP performed for FRA1 and FLI1 enabled us to infer chromatin binding partners of these two transcription factors and link this information with their target genes, providing a comprehensive regulatory circuit for the genes implicated in invasive ability of the bladder cancer cells. Finally, we show that knock-down of FRA1 and FLI1 results in statistically significant less migration of cells using IC-CHIP assays. Our results collectively highlight the role of these two transcription factors in invasive characteristics of bladder cancer in selection and design of targeted options for treatment of MIBC.

overall_design: Identification of transcriptional regulatory networks in muscle invasive and non-muscle invasive bladder cancer cell lines

first: Perihan

last: Yağmur Güneri Sözeri

first: Gülden

last: Özden Yılmaz


title: Expression data from infiltrating monocytes into lungs

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Rd

department: PMI

institute: University of South Carolina School of Medicine

summary:
Immunometabolism is one of the recent targets to modify the immunological resposes as well as to inhibit the autoimmunity.
We used microarrays to detail the global programme of gene expression underlying immumetabolism and identified distinct classes of up-regulated genes during this process.

overall_design: Ifiltrating cells into lungs were isolated by ficol-layering method, then RNA was extracted and quantified and hybridization on Affymetrix microarrays. We sought to obtain  resolution of expression profiles. To that end, C3H mice were chanllenged with enterotoxin produced by Staphylococcus aureus (SEB). This strain of mice is susceptible to this toxin. The toxin was given intranasally and intraperitoneally with interval of 120 minutes. Before SEB challenge is taken place, the mice were pretreated with resveratrol or vehicle orally twice, 24 hours before SEB challenge and the second dose was given to the mice 90 minutes before intraperitoneal injection of SEB. Forty eight hours post SEB exposure, the mice were euthanized for tissues collection and then downstream analysis.

first: Hasan

last: Alghetaa

first: Amira

last: Mohammed

first: Prakash


title: ROR𝛾t directs upregulation of RAG gene expression in DP thymocytes and serves as a multi-faceted regulator of the Tcra repertoire.

city: Durham

first: Abani

last: Naik

address: 207 Research drive, Jones Bldg, Room 316

department: Immunology

institute: Duke University

summary: Naik et al. show that RAG gene upregulation in DP Thymocytes is controlled by DPASE, a DP-specific open chromatin region in RAG locus. Reduced RAG expression in DPASE KO mice result delayed and incomplete Tcra recombination. Transcription factor RORyt binds to DPASE and Tcra enhancer to regulate Tcra recombination in DP thymocytes.

overall_design: High-throughput sequencing was used to analyze Tcra repertoire from RNA purified from sorted DP thymocytes from groups of 2 mice bearing either wild-type or DPASE KO mice.

first: Danielle

last: Dauphars

first: Michael

last: Krangel


title: Postnatal Oogenesis In the Naked Mole Rat

city: Ithaca

first: Jennifer

last: Grenier

address: 526 Campus Rd

institute: Cornell University

summary: The goal of this analysis is to compare the transcriptome profile (RNA-seq) along different developmental ages in the naked mole rat ovary

overall_design: Methods: Naked mole rat  mRNA profiles of wiltype embryonic day 56, postnatal day 1, 8, 28, and 90 day-old. Ovaries were collected from wildtype subordinate animals. Duplicates and triplicates were collected following the same protocol and same litter.

first: Miguel

last: Brienño-Enriquez

first: Mariela

last: Faykoo-Martinez

first: Meagan

last: Goben

first: Ashley

last: McGrath

first: Alexandra

last: Prado

first: Kate

last: Wagner

first: Paula

last: Cohen

first: Diana

middle: J

last: Laird

first: Melissa

last: Holmes

first: Ned

last: Place


title: FUS modulates the level of ribosomal RNA modifications by regulating a subset of snoRNA expression

first: Kishor

last: Gawade

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

overall_design: Refer to individual Series


title: Extracellular vesicles from human Fallopian tubal fluid benefit embryo development in vitro

status: Public on Feb 16 2023

city: Wuhan

first: Yuehan

last: Li

address: No. 1095, Jiefang Ave.

institute: Huazhong University of Scicence and Technology

summary:
STUDY QUESTION:  Do extracellular vesicles (EVs) from human Fallopian tubes exert an influence on early embryo development in vitro?  SUMMARY ANSWER: Human Fallopian tube EVs carrying miRNAs increase murine embryo viability in vitro.
WHAT IS KNOWN ALREADY: Oviductal EVs (oEVs) are recently identified key players in embryo-oviduct interactions that contribute to successful pregnancy in vivo. Their absence in current in vitro systems may partly explain the suboptimal embryo development observed, therefore further knowledge is needed about their impact on early embryos.
STUDY DESIGN, SIZE, DURATION: The oEVs were isolated from the luminal fluid of human Fallopian tubes using ultracentrifugation. We cocultured oEVs with murine two-cell embryos until the blastocyst stage. The study was conducted between August 2021 and July 2022.
PARTICIPANTS/MATERIALS, SETTING, METHODS: A total of 23 premenopausal women were recruited for Fallopian-tubes collection, and the oEVs were isolated. The micro RNA (miRNA) contents were detected using high-throughput sequencing and their target genes and effects were analyzed. After in vitro culture with or without oEVs, the blastocyst and hatching rates were recorded. Furthermore, for the blastocysts formed, we assessed the total cell number, inner cell mass proportion, reactive oxygen species (ROS) level, number of apoptotic cells and mRNA expression levels of genes involved in development.
MAIN RESULTS AND THE ROLE OF CHANCE: EVs were successfully isolated from the human Fallopian tubal fluid and the concentrations were evaluated. A total of 79 known miRNAs were identified from eight samples that had been sequenced, all involved in various biological processes. The blastocyst rate, hatching rate, as well as total cell number of blastocysts were significantly increased in the oEVs-treated groups (p < 0.05 versus untreated), while the proportion of inner cell mass showed no significant difference between groups. ROS levels and apoptotic cell proportions were decreased in the oEVs-treated groups (p < 0.05 versus untreated). The genes, Actin-Related Protein 3 (Actr3), Eomesodermin (Eomes), and Wnt Family Member 3A (Wnt3a)  were upregulated in blastocysts in the oEVs-treated group.

overall_design: Extracellular vesicles were isolated from eight Fallopian tube samples

first: Lei

last: Jin

first: Cong

last: Sui


title: Expression profiling of pitavastatin in a tumor-immune model in vitro

status: Public on Feb 17 2023

city: Uppsala

first: Tove

middle: Kristina

last: Selvin

address: Akademiska sjukhuset

department: Medical Sciences

country: Sweden

institute: Uppsala University

summary:
We developed a phenotypic screening platform that identified statins as enhancers of immune cell-induced cancer cell death. Statins are currently gaining interest as repurposing candidates for use in oncology as increasing evidence supports that statins exert anti-cancer effects. Considering also our findings, the clinical benefits described for cancer patients receiving statins might be due to a combined effect on both cancer- and immune cells.
Studying gene expression profiles is a well established approach for investigating a compound's mode of action. We performed transcriptome-wide gene expression profiling on the human colorectal cancer cell line HCT116-GFP and peripheral blood mononuclear cells (PBMCs). Monocultured and co-cultured cells were treated with DMSO vehicle or pitavastatin (1µM or 10µM) for 24 hours before gene expression was analyzed using a Human Clariom S array.

overall_design: The colorectal cancer cell line HCT116-GFP and PBMCs were cultured as monocultures or co-cultured. Monocultures and co-cultures were treated with DMSO vehicle or pitavastatin (1µM or 10µM) for 24h. Differentially expressed genes in pitavastatin-treated cells compared to DMSO were then analysed in the different cultures.

first: Claes

middle: R

last: Andersson


title: Transcriptome Analysis of the Mouse Medial Prefrontal Cortex in Chronic Constriction Injury Model

city: Shanghai

first: Qimin

last: Zheng

address: 131 Dongan Road,Xuhui District

department: Institutes of Brain Science

institute: Fudan University

summary:
The medial prefrontal cortex (mPFC) is critical for both the sensory and emotional /cognitive components of pain. However, the underlying mechanism still remains largely unknown. Here, we examined changes in the transciptomic profiles in the mPFC of mice with chronic pain using RNA sequencing (RNA-seq) technology.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different group of mPFC from mice, including ipsilateral part (Left side, the same to our operation part) of mPFC, contralateral part (Right side, opposite to our operation part)  of mPFC after CCI (Chronic Constriction Injury of Sciatic Nerve) operation. Combining with naïve mice, at 28 days after operation.

overall_design: Transcriptomic profiles of the mPFC of male mice at 4 weeks after chronic constriction injury of sciatic nerve Model

first: Zirui

last: Zhou

first: Xinyu

last: Hou

first: Ning

last: Lv

first: Yuqiu

last: Zhang

first: Hong

last: Cao


title: Transthyretin is commonly up-regulated in the hippocampus of two different stress-induced depression mouse models.

city: Uchinada-machi

first: HIDEHITO

last: TAKATSUJI

address: Daigaku 1-1

institute: Kanazawa Medical University

sample_organism:
Mus
Mus musculus


title: Skeletal dysplasia-causing TRPV4 mutations suppress the hypertrophic differentiation of human iPSC-derived chondrocytes

city: St Louis

first: Amanda

last: Dicks

state: MO

address: 1 Brookings Dr

institute: Washington University in St. Louis

summary:
To elucidate how TRPV4 mutations cause skeletal dysplasia, we used CRISPR-Cas9-edited hiPSCs harboring the moderate V620I and lethal T89I mutations to differentiate chondrocytes and hypertrophic chondrocytes.
We then used mRNA sequencing to analyze differential gene expression between 3 cell lines, 2 time points, and 2 treatments.

overall_design: Differential gene expression using mRNA-seq data for TRPV4-V260I and TRPV4-T89I hiPSC-derived chondrocytes compared to WT (n=3-4).

first: Grigory

middle: I

last: Maksaev

first: Zainab

last: Harissa

first: Alireza

last: Savadipour

first: Ruhang

last: Tang

first: Nancy

last: Steward

first: Wolfgang

last: Liedtke

first: Colin

middle: G

last: Nichols

first: Chia-Lung

last: Wu

first: Farshid

last: Guilak


title: Gene expression alteration in the hippocampus of depression mouse model with forced swim stress

summary: We used microarrays to identify the gene with altered expression in the hippocampus of depression mouse model with forced swim stress campared to control mice .

overall_design: Gene expression profiling of hippocampus in mice with or without forced swim stress in vivo.

first: H

last: Saito-Takatusji

last: Yonekura

first: Y

last: Ishigaki


title: RNA-Seq analysis of isolated myeloid cells and melanoma cells, B16F10 and YUMM3.3.

status: Public on Feb 15 2023

city: Houston

first: David

last: Piwnica-Worms

state: TX

address: 1881 East Road, Unit 1907

department: Cancer Systems Imaging

institute: The University of Texas MD Anderson Cancer Center

summary: We evaluated the changes in the transcriptome of spleen and bone marrow isolated myeloid cells in healthy and melanoma bearing animals and melanoma cell lines, B16F10 and YUMM3.3 using RNA-sequencing technologies.

overall_design: mRNA profile changes comparing myeloid cells in healthy compared to melanoma-bearing animals and comparing melanoma cell lines B16F10 and YUMM3.3.

first: Tracy

middle: W

last: Liu

first: Seth

middle: T

last: Gammon


title: Sexually Dimorphic Alterations in the Transcriptome and Behavior with Loss of Histone Demethylase KDM5C

city: Ann Arbor

first: Shigeki

last: Iwase

email: siwase@umich.edu, kbonefas@umich.edu

state: MI

address: 1241 E. Catherine St.

institute: University of Michigan

summary: Chromatin dysregulation has emerged as a major hallmark of neurodevelopmental disorders such as intellectual disability (ID) and autism spectrum disorders (ASD). The prevalence of ID and ASD is higher in males compared to females, with un-known mechanisms. Intellectual developmental disorder, X-linked syndromic, Claes-Jensen type (MRXSCJ), is caused by loss-of-function mutations of lysine de-methylase 5C (KDM5C), a histone H3K4 demethylase gene. KDM5C escapes X-inactivation, thereby presenting at a higher level in females. Initially, MRXSCJ was exclusively reported in males, while it is increasingly evident that females with heterozygous KDM5C mutations can show cognitive deficits. The mouse model of MRXSCJ, male Kdm5c-hemizygous knockout animals, recapitulates key features of human male patients. However, the behavioral and molecular traits of Kdm5c-heterozygous female mice remain incompletely characterized. Here, we re-port that gene expression and behavioral abnormalities are readily detectable in Kdm5c-heterozygous female mice, demonstrating the requirement for a higher KDM5C dose in females. Furthermore, we found both shared and sex-specific con-sequences of a reduced KDM5C dose in social behavior, gene expression, and ge-netic interaction with the counteracting enzyme KMT2A. These observations pro-vide an essential insight into the sex-biased manifestation of neurodevelopmental disorders and sex chromosome evolution.

overall_design: Bulk poly-(A) RNA sequencing of microdissected forebrains (hippocampus and cortex) of postnatal day 6 mice (P6). Sample genotypes are 4 wild type (WT) males, 4 WT females, 4 Kdm5c-KO males, and 4 Kdm5c-Het females

first: Katherine

last: Bonefas

first: Christina

middle: N

last: Vallianatos

first: Brynne

last: Raines

first: Natalie

last: Tronson


title: The molecular phenotype of kisspeptin neurons in the medial amygdala of female mice

status: Public on Feb 13 2023

city: Albany

first: Shannon

last: Stephens

address: 47 New Scotland Ave; MC-136

department: Neuroscience & Experimental Therapeutics

institute: Albany Medical College

summary: Little is known about how Kiss1 cells in the medial amygdala (MeA) are regulated and what other gene transcripts are produced by MeA Kiss1 neurons. Estradiol upregulates Kiss1 expression in the medial amygdala (MeA), but it remains unknown if estradiol regulates other gene transcripts in MeA Kiss1 cells. The goal of this study is to identify novel gene transcripts produced by MeA Kiss1 cells and to determine how estradiol regulates the expression of these transcripts. We selectively isolated mRNA from Kiss1 cells in the MeA of female mice using Ribotag transgenic mice, immunoprecipitation, and RNA-seq. Over 13,000 gene transcripts produced by MeA Kiss1 cells were identified, but only 45 of these transcripts had expression levels altered by estradiol.

overall_design: Kiss1 cells were isolated from brain punches of the medial amygdala of female mice that were ovariectomized or ovariectomized + estradiol treatment.

first: S

middle: B

first: K

last: Hatcher

first: L

last: Costanza

first: A

last: Kauffman


title: Affymetrix SNP array data for induced pluripotent stem cell line

city: Sevilla

first: Yolanda

last: Aguilera

address: Avda Americo Vespucio, 24

institute: Cabimer

summary: Human induced pluripotent stem cells (iPSCs) provide a virtually inexhaustible source of starting material for cell therapies, such as next generation mesenchymal stem/stromal cells (i.e., iPSC-MSCs), offering an increased clinical efficacy in a variety of diseases. In particular, iPSC-derived products are relevant for treating pathologies in pediatric patients, due to the limited amount of biological material that is easily accessible in infants, toddlers, or young children. Despite iPSCs can be generated from many tissue sources, a non-invasive sampling approach would foster and broaden the interest in pediatric research. Here, we report the generation of two iPSC lines using a small amount of urine from pediatric patients with brain tumors (BT-iPSC). Urinary epithelial cells were isolated and reprogrammed using non-integrative Sendai virus vectors encoding the Yamanaka factors KLF4, OCT3/4, SOX2 and CMYC. After reprogramming, BT-iPSC lines were subject to quality assessment and compared to iPSCs obtained from urine samples of non-tumor pediatric patients (nonT-iPSC). We demonstrated that a small volume of urine is a non-invasive and reliable source of somatic cells to generate iPSCs from pediatric patients. In addition, we showed that BT-iPSCs are comparable to nonT-iPSCs and efficiently differentiate into iPSC-MSCs. This is an attractive approach for producing patient-specific cell products, even from those with brain tumors.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's instructions on DNA extracted from iPSC of urine-derived epithelial cells (UDCs).

Grants:

Grant ID: CP19/00046
Title: Miguel Servet
Funding source: funding source:The Institute of Health Carlos III, cofounded by Fondos FEDER

Grant ID: PI20/00341
Title: Terapia Celular Personalizada para Mejorar la Calidad de Vida en el Cáncer Pediátrico
Funding source: The Institute of Health Carlos III, cofounded by Fondos FEDER

Grant ID: +VIDA project
Title: +VIDA project
Funding source: The Asociación Pablo Ugarte

Grant ID: IDEAS20051CAPI
Title: Terapia Celular No-Invasiva para la Prevención de las Secuelas de la Radiación en Cáncer Cerebral Pediátrico
Funding source: The Asociación Española Contra el Cancer

Grant ID: PY20/00481
Title: Evaluación de la seguridad y eficacia de una terapia celular no invasiva en la Esclerosis Lateral Amiotrófica
Funding source: The Consejería de Transformación Económica, Industria, Conocimiento y Universidades of Junta de Andalucia, co-funded by Fondos FEDER

Grant ID: PY20/00480
Title: Evaluación de la modulación de la producción de sulfuro de hidrógeno intracelular en la homeostasis de la glucosa y el envejecimiento saludable
Funding source: The Consejería de Transformación Económica, Industria, Conocimiento y Universidades of Junta de Andalucia, co-funded by Fondos FEDER

Grant ID: PID2021-123965OB-I00
Title: PID2021-123965OB-I00
Funding source: The Spanish Ministry of Science and Innovation

Grant ID: FPU19/04703
Funding source: The Spanish Ministry of Universities

first: Vivian

last: Capilla-Gonzalez

first: Carmen

last: Baliña-Sánchez


title: Gene expression alteration in the hippocampus of depression mouse model with repeated social defeat stress

first: HIDEHITO

last: TAKATSUJI

summary: We used microarrays to identify the gene with altered expression in the hippocampus of depression mouse model with repeated social defeat stress campared to control mice.

overall_design: Gene expression profiling of hippocampus in mice with or without repeated social defeat stress in vivo.

first: H

last: Saito-Takatusji

first: Y

last: Yoshitomi


title: Constitutive expression and distinct properties of IFN-epsilon protect the female reproductive tract from Zika virus infection.

status: Public on Feb 14 2023

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

institute: Hudson Institute of Medical Research

summary: The female reproductive tract (FRT) is vulnerable to sexually transmitted infections and therefore a well-tuned immune surveillance system is crucial for maintaining a healthy FRT. However, our understanding of the factors that impact viral infection of the FRT and the host response are not well understood. In this work, we investigate the role of a hormonally regulated type I interferon, IFN epsilon, in control of Zika virus (ZIKV) infection of the FRT. We demonstrate that IFN epsilon has anti-ZIKV properties using a combination of IFN epsilon KO mice, blockade of endogenous IFN epsilon by neutralising Abs and rescue of IFN epsilon KO mice by recombinant IFN epsilon administered directly to the FRT.

overall_design: We compared cellular responses to stimulation with IFNs alpha, lambda and epsilon in FRT cells (VK2, Ect1) using whole transcriptome profiling by RNA-seq analysis. Cells were either stimulated with the IFN in question or untreated and RNA extracted 6 hrs post stimulation for RNA-seq analysis.

first: Rosa

last: Coldbeck-Shackley

first: Linden

first: Jodee

middle: A

last: Gould

first: Paul

last: Hertzog

first: Michael

last: Beard


title: Endogenous Linear Plasmids lp28-4 and lp25 are Required for Infectivity and Restriction Protection in the Lyme Disease Spirochete Borrelia mayonii

city: Grand Forks

first: Sergei

last: Nechaev

state: North Dakota

address: Columbia Hall Room 1733c, 501 North Columbia Road Stop 9061

institute: University of North Dakota

summary: Single Molecule Real Time (SMRT) sequencing was utilized to map the genome-wide m6A methylation pattern in B. mayonii. Consensus modified motifs were identified in wildtype B. mayonii as well as clonal isolates lacking plasmids that encode predicted methyltransferases. Two conserved m6A modification motifs were identified, and were fully attributable to the presence of specific methyltransferases.

overall_design: In vitro log-phase cultures of Borrelia mayonii isolate MN14-1539 and clones lacking plasmids lp25 and lp28-4 that carry putative restriction modification systems were grown in triplicate. Genomic DNA was isolated from each strain for methylome analysis using PacBio SMRT sequencing.

first: Timothy

last: Casselli

first: Catherine

last: Brissette


title: Type III interferon drives thymic B cell activation and regulatory T cell generation

city: Minneapolis

first: Ryan

last: Martinez

state: MN

address: 2101 6th St SE

department: Laboratory Medicine and Pathology

institute: University of Minnesota

summary: The activation of thymic B cells is critical for their licensing as antigen presenting cells and resulting ability to mediate central tolerance. The processes leading to licensing are still not fully understood. By comparing thymic B cells to activated Peyer’s Patch B cells at steady state, we found that thymic B cell activation starts during the neonatal period and is characterized by TCR/CD40 dependent activation, followed by immunoglobulin class switch recombination (CSR) without forming germinal centers. Transcriptional analysis also demonstrated a strong interferon signature, which was not apparent in the periphery. Thymic B cell activation and CSR were primarily dependent on type III IFN signaling, and loss of type III IFN receptor in thymic B cells resulted in reduced thymocyte regulatory T cell (Treg) development. Finally, from TCR deep sequencing, we estimate that licensed B cells induce development of a substantial fraction of the Treg cell repertoire. Together, these findings reveal the importance of steady state type III IFN in generating licensed thymic B cells that induce T cell tolerance to activated B cells.

overall_design: FACS sorted IgM- IgD- CD19+ B220+ lymphocytes from thymi and peyers patches from 6 week old C57BL/6 mice

first: Elise

last: Breed

first: Kristin

last: Hogquist


title: Single-cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell development

city: Bronx

first: Christopher

last: De Bono

state: New York

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: Disruption of cardiac neural crest cells (CNCCs) results in congenital heart disease, yet we do not understand the cell fate dynamics as these cells differentiate to vascular smooth muscle cells. Here we performed single-cell RNA-sequencing of NCCs from the pharyngeal apparatus with the heart in control mouse embryos and when Tbx1, the gene for 22q11.2 deletion syndrome, is inactivated. We uncover three dynamic transitions of pharyngeal NCCs expressing Tbx2 and Tbx3 through differentiated CNCCs expressing cardiac transcription factors with smooth muscle genes. These transitions are altered non-autonomously by loss of Tbx1. Further, inactivation of Tbx2 and Tbx3 in early CNCCs results in aortic arch branching defects due to failed smooth muscle differentiation. Loss of Tbx1 interrupts mesoderm to CNCC cell-cell communication with upregulation and premature activation of BMP signaling and reduced MAPK signaling, as well as alteration of other signaling, and failed dynamic transitions of CNCCs leading to disruption of aortic arch artery formation and cardiac outflow tract septation.

overall_design: Neural crest cells of the microdissected pharyngeal apparatus and heart of Wnt1-Cre;ROSA-EGFP control embryos at E8.5, E9.5 and E10.5 and Tbx1 null embryos at E9.5 and E10.5 were isolated by fluorescence-activated cell sorting (FACS) to perform single-cell RNA-sequencing.

first: Bernice

middle: E

last: Morrow


title: Hodgkin lymphoma cell lines and tissues express mGluR5: a potential link to Ophelia syndrome and paraneoplastic neurological disease

status: Public on Feb 10 2023

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

summary: Ophelia syndrome is characterized by the coincidence of severe neuropsychiatric symptoms, classical Hodgkin lymphoma, and the presence of antibodies to the metabotropic glutamate 5 receptor (mGluR5). Little is known about the pathogenetic link between these symptoms and the role anti-mGluR5-antibodies play. We investigated lymphoma tissue from patients with Ophelia syndrome and with isolated classical Hodgkin lymphoma by quantitative immunocytochemistry for mGluR5-expression. Further, we studied the L-1236, L-428, L-540, SUP-HD1, KM-H2, and HDLM-2 classical Hodgkin lymphoma cell lines by FACS and Western blot for mGluR5-expression, and by transcriptome analysis. mGluR5 surface expression differed significantly in terms of receptor density, distribution pattern, and percentage of positive cells. Highest levels were found in the L-1236 line. RNA-sequencing revealed more than 800 genes that were higher expressed in L-1236 in comparison to classical Hodgkin lymphoma-controls. High mGluR5-expression was associated with upregulation of PI3K/AKT and MAPK pathways and of downstream targets (e.g. EGR1) known to be involved in classical Hodgkin lymphoma progression. Finally, mGluR5 expression was increased in the classical Hodgkin lymphoma-tissue of our Ophelia syndrome patient in contrast to five classical Hodgkin lymphoma-patients without autoimmune encephalitis. Given the association of encephalitis and classical Hodgkin’s lymphoma in Ophelia syndrome, it is possible that mGluR5-expression on classical Hodgkin lymphoma cells not only drives tumor progression, but may also trigger anti-mGluR5 encephalitis already before classical Hodgkin lymphoma-manifestation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 6 classical Hodgkin Lymphoma cell lines: L-1236, L-428, L-540, SUP-HD1, KM-H2, HDLM-2

first: Marc

last: Nikolaus


title: Fetal Exposure of low dose Methylmercury Enhances CREB Activity to Induce Premature Neuronal Differentiation During Embryonic Cortex Development

city: Ottawa

first: Jing

last: Wang

state: Ontario

address: 501 Smyth Rd

department: Regenerative Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: Methylmercury is a bioaccumulated environmental neurotoxicant, however, it remains largely unknown regarding impacts of non-apoptotic low dose methylmercury on embryonic cerebral cortex development. Here, using single cell RNA-seq analysis we show that prenatal exposure of MeHg favors RGP developmental trajectory towards directly producing cortical neurons, omitting intermediate progenitor stage. Our findings reveal the outcomes of low dose MeHg exposure on the fetal brain development and provide insights into its underlying mechanisms and potential therapeutic strategy.

overall_design: We analyzed isolated the cerebral cortices obtained from two experimental replicates of E15 CD1 mice treated with either 0ppm (control) and 0.2ppm MeHg treated drinking water

first: Laurie

last: Chan

first: David

last: Cook

first: Joseph

last: Leung

first: Allison

last: Loan


title: A Leaky Human Colon Model Reveals Uncoupled Apical/Basal Cytotoxicity in Early Clostridioides difficile Toxin Exposure

city: Durham

first: Jarrett

last: Bliton

address: 6 Davis Drive

institute: Altis Biosystems

summary: Clostridioides difficile (C. difficile) toxins A (TcdA) and B (TcdB) cause antibiotic-associated colitis, increasing morbidity and mortality. Accurate in vitro models are necessary to detect early toxicity kinetics, investigate disease etiology, and develop preclinical models for new therapies. Properties of cancer cell lines and organoids inherently limit these efforts. We developed adult stem cell-derived monolayers of differentiated human colonic epithelium (hCE) with barrier function, investigated the impact of toxin application to apical/basal aspects of monolayers, and evaluated whether a leaky epithelial barrier enhances toxicity. Single-cell RNA-sequencing (scRNAseq) mapped C. difficile-relevant genes to human gut epithelial lineages. Transcriptomics informed timing of stem cell differentiation to achieve in vitro colonocyte maturation like that observed in vivo. Transepithelial electrical resistance (TEER) and fluorescent dextran permeability assays measured cytotoxicity as barrier loss post-toxin exposure. Leaky epithelial barriers were induced with diclofenac. scRNAseq demonstrated broad and variable toxin receptor expression across human gut lineages. Absorptive colonocytes displayed generally enhanced toxin receptor, Rho GTPase, and cell junction expression. 22-day differentiated Caco-2 cells remained immature whereas hCE monolayers were similar to mature colonocytes. hCE monolayers exhibited high barrier function after 1-day differentiation. Basal TcdA/B application to monolayers caused greater toxicity and apoptosis. Diclofenac induced leaky hCE monolayers and enhanced toxicity of apical TcdB exposure. Apical/basal toxicities are uncoupled with more rapid onset and increased magnitude of basal toxicity. Leaky paracellular junctions enhance toxicity of apical TcdB exposure. hCE monolayers represent a physiologically relevant and sensitive culture system to evaluate the impact of microbial toxins on gut epithelium.

overall_design: Bulk RNA sequencing libraries from epithelium isolated from a single human donor Descending Colon and Caco-2 cells as technical triplicates, with or without treatment with 30 pM C. difficile toxins A or B for 20 hours, were compiled.

first: Meryem

last: Ok

first: Jintong

last: Liu

first: R

first: Caroline

middle: M

last: Hinesley

first: Ekaterina

last: San Pedro

first: Keith

last: Breau

first: Ismael

last: Gomez-Martinez

last: Burclaff

first: Scott

last: Magness


title: Discovery and validation of circulating microRNAs as biomarkers for epileptogenesis after experimental traumatic brain injury – the EPITARGET cohort

city: Kuopio

first: Mette

last: Heiskanen

address: Neulaniementie 2, P.O.B. 1627

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

summary: Purpose: Traumatic brain injury (TBI) causes 10%–20% of structural epilepsies and 5% of all epilepsies. The lack of prognostic biomarkers for post-traumatic epilepsy (PTE) is a major obstacle to the development of anti-epileptogenic treatments. In this study, we conducted high throughput small RNA-Seq analysis from tail-vein plasma samples collected from a rat model of PTE to discover miRNA biomarker candidates that could serve as prognostic biomarkers for brain damage severity and the development of PTE. Methods: Epileptogenesis was induced in adult male Sprague-Dawley rats by the lateral fluid-percussion-induced TBI. Epilepsy was defined as the occurrence of at least 1 unprovoked seizure during continuous 1-month video-electroencephalography monitoring in the sixth post-TBI month. Small RNA-seq was performed from tail-vein plasma samples collected from a subset of 20 animals (4 sham-operated controls, 7 TBI rats with epilepsy, 9 TBI rats without epilepsy) at 2 days and 9 days post-TBI. RNA was extracted from 200 μl plasma using an miRNeasy Mini Kit. Small RNA-Seq was conducted by GenomeScan (Leiden, the Netherlands). Small RNA library preparation was performed using the Illumina TruSeq Small RNA Sample Prep Kit. Single-end sequencing was performed on the Illumina HiSeq 4000.

overall_design: Small RNA sequencing of rat plasma samples collected at 2 days and 9 days after lateral fluid-percussion injury (TBI, n=16) or sham-operation (n=4). The TBI group contains 7 rats with epilepsy (TBIE) and 9 rats without epilepsy (TBIN), which was defined by 1-month continuous video-EEG monitoring during the sixth month after TBI.

first: Shalini

last: Das Gupta

first: James

last: Mills

first: Erwin

last: van Vliet

first: Eppu

last: Manninen

first: Robert

last: Ciszek

first: Pedro

last: Andrade

first: Noora

last: Puhakka

first: Eleonora

last: Aronica

first: Asla

last: Pitkänen


title: Identification of novel coloboma candidate genes through conserved gene expression analyses across Four vertebrate species

status: Public on Feb 07 2023

city: Midlothian

first: Joe

last: Rainger

state: Scotland

address: Easter Bush Campus

department: The Division of Functional Genetics and Development

institute: The Roslin Institute

summary: To identify genes that specifically regulate opticFissure closure, we conducted transcriptomic analysis of embronyic eye tissues of chicken at stages during and after optic fisssure closure.

overall_design: Comparative gene expression profiling analysis of RNA-seq data during and after optic fissure closure (corresponding to Hamburger-Hamilton stage 30 and 34 respectively), with stage-matched non-fusing dorsal tissues as controls

first: Ho

last: Chan

last: Prendergast


title: Real-time quantitative PCR analysis of mouse placenta junctional zone and fetal mouse brain

city: Cambridge

first: Jorge

last: Lopez-Tello

state: Please Select

address: Centre for trophoblast research, Dept Physiology, Development and  Neuroscience, DOWNING ST

institute: University of Cambridge

summary:
Placenta junctional zone and brains dissected, kept in -80ºC, RNA extracted with RNAesasy kit kiagen, cDNA performed with normalized RNA levels.
qPCR gene expression profiling

overall_design:
qPCRs done in two batches of samples (2xBrain / 2xJz)
SGA = small for gestational age

first: J

first: Amanda

last: Sferruzzi-Perri


title: Polyvinyl alcohol expanded mouse HSC cultures (scRNA-Seq)

city: Stanford

first: Kyomi

last: Igarashi

state: CA

address: 265 Campus Drive

institute: Stanford University

summary: We previously reported a polyvinyl alcohol-based mouse hematopoietic stem cell (HSC) culture protocol that efficiently expanded transplantable HSCs for at least a month ex vivo (Wilkinson et al., Nature 2019). Here, we investigated the molecular consequences of oxygen concentration on 28-day ex vivo HSC cultures using single cell RNA-seq

overall_design: We examined fresh c-Kit+ bone marrow and day-28 cultured HSCs incubated at 20% oxygen, 5% oxygen, or 1% oxygen

first: Adam

last: Wilkinson

first: Iwo

last: Kucinski


title: Relevance of IL-3 for lung transcriptomic response in murine sepsis followed by HSV infection

status: Public on Feb 08 2023

city: Heidelberg

first: Dominik

last: Schaack

address: Im Neuenheimer Feld 420

institute: Heidelberg University Hospital

summary: To investigate the importance of IL-3 during the pulmonary response to HSV infection after initial polymicrobial sepsis

overall_design: Comparative gene expression profiling analysis of RNA-seq data from whole lung tissue of WT vs. IL-3-deficient septic mice (n=5 each group) 3d after HSV-1 infection

first: Florian

last: Uhle

first: Georg

last: Weber

first: Alan

last: Benard


title: Polyvinyl alcohol expanded mouse HSC cultures

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

overall_design: Refer to individual Series


title: Polyvinyl alcohol expanded mouse HSC cultures (bulk RNA-Seq)

summary: We previously reported a polyvinyl alcohol-based mouse hematopoietic stem cell (HSC) culture protocol that efficiently expanded transplantable HSCs for at least a month ex vivo (Wilkinson et al., Nature 2019). Here, we investigated the molecular consequences of oxygen concentration on 28-day ex vivo HSC cultures using bulk RNA-seq

first: Ian

last: Hsu


title: Gene expression changes in different clones of SAMHD1 knock-out (KO) cells

city: Badalona

first: Lucia

last: Gutierrez-Chamorro

address: Ctra/ del Canyet

institute: IrsiCaixa

summary: To investigate the signalling pathways affected by SAMHD1 depletion, whole transciptome profiling was performed in WT and in different clones of SAMHD1-KO breast cancer cell line (T47D cells)

overall_design: Gene expression changes in SAMHD1 knock-out cell line were analysed. 2 different clones were used: for WT and KO-clone A1, I have three different replicates, for KO-clone A2, two replicates.

first: Lucía

last: Gutiérrez Chamorro

first: Eudald

last: Felip

first: Adrià

last: Bernat-Peguera

first: Ifeanyi

last: Ezeonwumelu

first: Iris

last: Teruel

first: Anna

last: Martínez-Cardú

first: Bonaventura

last: Clotet

first: Eva

last: Riveira-Muñoz

first: Margarita

last: Romeo

first: Mireia

last: Margelí

first: Ester

last: Ballana


title: Single-cell and spatial architecture of human tissue granulomas reveals an aberrant immune-regulatory program underlying sarcoidosis [spatial transcriptomics data]

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary:
Purpose: Granulomas are lumps of immune cells that can form in various organs, causing chronic inflammation and tissue destruction. While most granulomas appear histologically heterogeneous and unstructured, they have a certain resemblance of lymphoid organ formation. We thus pursued the hypothesis that granuloma formation is a highly orchestrated process that mixes and repurposes various regulatory mechanisms of normal development
Methods: We performed single-cell sequencing and spatial transcriptomics on granulomas from patients diagnosed with cutaneous sarcoidosis, and we bioinformatically reconstructed their gene-regulatory networks and cell-cell interactions
Results: We observed regulatory processes underlying granuloma formation that were highly conserved across individuals and followed characteristic spatial patterns. We identified metabolically reprogrammed macrophages, various T cells subsets and structural cells including fibroblasts and endothelial cells as key players in granulomas. Specifically, exhausted interferon-gamma-producing Th17.1 cells with cytotoxic potential and inflammatory fibroblasts were identified as drivers of granuloma formation by attracting various immune cell types.
Summary: we found that granuloma formation in sarcoidosis is a molecular and cellular process that adopts specific aspects of normal lymphoid organ development in aberrant combinations. Our study frames human granuloma formation as a developmental pathology and raises the future perspective of therapeutic targeting of granuloma-specific regulatory programs.

overall_design:
spatial transcriptomics sequencing on granulomas and healthy skin from patients diagnosed with cutaneous sarcoidosis
NOTE FROM SUBMITTER: Raw data will be uploaded to the European Genome-phenome Archive since it contains patient genetic data.

first: Thomas

last: Krausgruber

last: Redl

first: Daniele

last: Barreca

last: Stary


title: THADA deficiency improves glycemic control by promoting pancreatic β-cell function and survival under physiological and diabetic conditions

city: Jinan

first: Shan

last: Han

address: Wenhua West road

institute: Shandong University

summary:
Purpose: The goals of this study are to explore the role of THADA in glucose homeostasis and insulin secretion
Methods: Thada-activated beta-cell line  was  generated  by CRISPR/dCas9-SAM system. Cells infected with dCas9 and non-targeting sgRNA lentiviruses were used as controls.
Results: Transcriptomics analyses revealed that many genes were dys-regulated in beta-cells after THADA activation.

overall_design: mRNA profiles of control min6 cells (CON) and Thada-activated min6 cells (SAM)

first: Yuqing

last: Zhang


title: IFNγ is a central node in cancer immune equilibrium

status: Public on Feb 06 2023

city: Boston

first: Stephanie

last: Dougan

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: The anti-tumor effects of IFNγ are well-known as IFNγ binding to tumor cells increases antigen presentation and can cause cytostatic growth defects. Indeed, the inability of tumors to respond to IFNγ often renders tumors resistant to checkpoint blockade and other immunotherapies reliant on direct T cell cytotoxicity. We demonstrate through RNA-sequencing that IFNgR1-/- and STAT1-/- tumors are defective in their response to IFNγ compared to wild-type tumors.

overall_design: Wild-type, STAT1-/-, and IFNgR1-/- B16-Nectin1+ cells were cultured in vitro for 24 hours with 0 or 100 ng/ml IFNγ. Total RNA was extracted from cells of biological triplicates.

first: Michael

last: Walsh

first: Courtney

last: Stump

first: Rakeeb

last: Kureshi

first: Patrick

last: Lenehan

first: Lestat

last: Ali

first: David

last: Knipe

middle: K


title: Comparative analysis of the cardiomyocyte differentiation potential of induced pluripotent stem cells reprogrammed from human atrial or ventricular fibroblasts

status: Public on Feb 03 2023

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

summary: Background: We had shown that cardiomyocytes (CMs) were more efficiently differentiated from human induced pluripotent stem cells (hiPSCs) when the hiPSCs were reprogrammed from cardiac fibroblasts rather than dermal fibroblasts or blood mononuclear cells. Here, we continued to investigate the relationship between somatic-cell lineage and hiPSC-CM production by comparing the yield and functional properties of CMs differentiated from iPSCs reprogrammed from human atrial or ventricular cardiac fibroblasts (AiPSC or ViPSC, respectively).    Methods: Atrial and ventricular heart tissues were obtained from the same patient, reprogrammed into AiPSCs or ViPSCs, and then differentiated into CMs (AiPSC-CMs or ViPSC-CMs, respectively) via established protocols.    Results: The time-course of expression for pluripotency genes (OCT4, NANOG, and SOX2), the early mesodermal marker Brachyury, the cardiac mesodermal markers MESP1 and Gata4, and the cardiovascular progenitor-cell transcription factor NKX2.5 were broadly similar in AiPSC-CMs and ViPSC-CMs during the differentiation protocol. Flow-cytometry analyses of cardiac troponin T expression also indicated that purity of the two differentiated hiPSC-CM populations (AiPSC-CMs: 88.23±4.69%, ViPSC-CMs: 90.25±4.99%) was equivalent. While the field-potential durations were significantly longer in ViPSC-CMs than in AiPSC-CMs, measurements of action potential duration, beat period, spike amplitude, conduction velocity, and peak calcium-transient amplitude did not differ significantly between the two hiPSC-CM populations. Yet, our cardiac-origin iPSC-CM showed higher ADP and conduction velocity than previously reported iPSC-CM derived from non-cardiac tissues. Transcriptomic data comparing iPSC and iPSC-CMs showed similar gene expression profiles between AiPSC-CMs and ViPSC-CMs with significant differences when compared to iPSC-CM derived from other tissues. This analysis also pointed to several genes involved in electrophysiology processes to be responsible for the physiological differences observed between cardiac and non-cardiac-derived cardiomyocytes.   ¬  Conclusions: AiPSC and ViPSC were differentiated into CMs with equal efficiency. Detected differences in electrophysiological properties, calcium handling activity, and transcription profiles between cardiac and non-cardiac derived cardiomyocytes demonstrated that 1) tissue of origin matters to generate a better-featured iPSC-CMs, 2) the sublocation within the cardiac tissue has marginal effects on the differentiation process.

overall_design: Four cell lines were generated from a 15-day-old patient with dextro-Transposition of the Great Arteries. The patient underwent open chest surgery.  1) AiPSC: human-induced pluripotent stem cell originated from the patient’s atrial cardiac fibroblast.   2) ViPSC: human-induced pluripotent stem cell originated from the patient’s ventricular cardiac fibroblast.  3) AiPSC-CM: human-induced pluripotent stem cell-derived cardiomyocyte; differentiated from AiPSC after 30 days.  4) ViPSC-CM: human-induced pluripotent stem cell-derived cardiomyocyte; differentiated from ViPSC after 30 days.

first: Lu

last: Wang

first: Manuel

last: Rosa-Garrido

first: Yang

last: Zhou

last: Cleveland

first: Jianyi