title: Leptin mutation and mycobacterial infection lead non-synergistically to a similar metabolic syndrome

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

summary:
The leptin signaling pathway plays an important role as a key regulator of glucose homeostasis, metabolism control and systemic inflammatory responses. However, the metabolic effects of leptin on infectious diseases, for example tuberculosis, is still little known.
For transcriptome studies of zebrafish larvae, deep RNA sequencing was used. Mycobacteria induced a very distinct transcriptome signature in the lepbibl54 mutant zebrafish compared to wild type sibling control larvae.

overall_design: Zebrafish lepb+ and lepbibl54 embryos were collected from 6-month-old wild type and lepbibl54 mutant parents, respectively. The embryos were injected into yolk with M. marinum strain M labelled with mWasabi plasmid pTEC15 vector22 or mock injected with 2% polyvinylpyrrolidone 40 (pvp) at 4 to 6 hour hours post fertilization (hpf). M. marinum preparation were followed by the protocol of a previous study (Benard et al., 2012). Microinjection of zebrafish embryos was performed using an automatic microinjection system (Life Science Methods) described previously (Spaink et al., 2013). Zebrafish larvae at 5 days post fertilization (dpf) were collected and stored at -80℃ for RNA isolation.

first: Yi

last: Ding


title: Functional genomics in primary T cells and monocytes identifies mechanisms by which genetic susceptibility loci influence systemic sclerosis risk

status: Public on Aug 29 2022

city: Manchester

first: chenfu

last: shi

address: AV Hill Building, Upper Brook Street, room 1.023

country: United Kingdom

institute: the university of manchester

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Systemic sclerosis (SSc) is a complex autoimmune disease with a strong genetic component. However, most of the causal genes associated to the disease are still unknown because associated variants affect mostly non-coding intergenic elements of the genome. The challenge in the post-GWAS era is to use functional genomics to translate the genetic findings into a better understanding of the disease, particularly by using disease-relevant cell types. We linked SSc-associated loci to 39 new potential target genes and confirm 7 previously known genes. We highlight novel causal genes, such as CXCR5 as the most probable candidate gene for the DDX6 locus. Some previously known SSc associated genes such as IRF8, STAT4, or CD247 interestingly showed cell type specific interactions. We also identified 15 potential drug targets already in use in other similar immune-mediated diseases that could be repurposed for SSc treatment. Furthermore, we observed that interactions are directly correlated with the expression of important genes implicated in cell type specific pathways and find evidence that chromatin conformation is linked to genotype.Our study reveals potential causal genes for SSc-associated loci, some of them acting in a cell type specific manner, suggesting novel biological mechanisms that might mediate SSc pathogenesis.

overall_design:
Promoter capture Hi-C (pCHi-C) and RNA sequencing experiments were performed in a total of 30 CD4+ T cells and CD14+ monocytes samples from 10 SSc patients and 5 healthy controls to link SSc-associated variants with their target genes, followed by differential expression and differential interaction analyses between cell types. We also aimed to identify potential drugs that could be repurposed for its use in SSc.
NOTE FROM SUBMITTER: Data generated from patient samples. Only processed data files have been uploaded as raw data can be used to re-identify patients.

first: David

last: González-Serna

first: Chenfu

last: Shi

first: Martin

last: Kerick

first: Jenny

last: Hankinson

first: James

first: Amanda

last: McGovern

first: Mauro

last: Tutino

first: Gonzalo

last: Villanueava Martin

first: Noberto

last: Ortego-Centeno

first: José

last: Luis Callejas

first: Javier

last: Martin

first: Gisela

last: Orozco


title: A complete absence of indirect genetic effects on brain gene expression in a highly social context

city: Lausanne

first: Tomas

last: Kay

state: Vaud

address: Biophore building

country: Switzerland

institute: University of Lausanne

summary: Genes not only control traits of their carrier organism (known as Direct Genetic Effects or DGEs) but also shape their carrier's physical environment and the phenotypes of their carrier's social partners (known as Indirect Genetic Effects or IGEs). Theoretical research has shown that the effects that genes exert on social partners can have profound consequences, potentially altering heritability and the direction of trait evolution. Complementary empirical research has shown that in various contexts (particularly in animal agriculture) IGEs can explain a large proportion of variation in specific traits. However, little is known about the general prevalence of IGEs. We conducted a reciprocal cross-fostering experiment with two genetic lineages of the clonal raider ant Ooceraea biroi to quantify the relative contribution of DGEs and IGEs to variation in brain gene expression (which underlies behavioral variation). We find that thousands of genes are differentially expressed by DGEs but not a single gene is differentially expressed by IGEs. This is surprising given the highly social context of ant colonies and given that individual behavior varies according to the genotypic composition of the social environment in O. biroi. Overall, these findings indicate that we have a lot to learn about how the magnitude of IGEs varies across species and contexts.

overall_design: Cross-fostering newly-hatched larvae of lineages B and M into social environments of lineages B or M


title: Transcriptome analysis of 15 different breast cancer cell lines

city: Bethesda

first: Yoshimi

middle: E

last: Greer

state: MD

address: Bldg.10, Room 4B50, 9000 Rockville Pike, Line 2 (Optional)

country: USA

institute: National Cancer Institute

summary: Goal of this study was to investigate gene expression profiling across different molecular subtypes of breast cancers, such as Estrogen Receptor (ER) positive, HER2 amplified, Triple negative Basal A, Triple negative Basal B.

overall_design: RNA-seq in 15 breast cancer cell lines

first: Sudhir

last: Manickavel

first: Markus

last: Hafner

first: Stan

last: Lipkowitz


title: Effects of scd deletion on gene expression during zebrafish liver lipid homeostasis

city: Wuhan

first: Shan

last: Zhong

address: Donghu Road 185

country: China

institute: Wuhan University

summary:
To investigate the role of the zebrafish scd gene in the regulation of lipid homeostasis, we constructed mutant zebrafish with a deletion of the scd gene.
We then performed gene expression profiling using data obtained by RNA-seq of 2 types of zebrafish livers.

overall_design: Comparative gene expression profiling of RNA-seq data from WT and Mutant zebrafish livers.

first: Shan-Shan

last: Xu

first: Wenbo

last: Chen


title: CEACAM 1, 3, 5 and 6 -positive classical monocytes correlate with interstitial lung disease in early systemic sclerosis

city: Fukuoka

first: Kana

last: Yokoyama

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-Ku

department: Department of Medicine and Biosystemic Sciences

country: Japan

institute: Kyushu University Hospital

summary: To clarify the characteristics of CEACAM-positive monocytes in systemic sclerosis (SSc), we performed gene expression microarrays between CEACAM-positive and CEACAM-negative classical monocytes from diffused cutaneous systemic sclerosis(dcSSc) patients. We further analyzed expression levels of each subtype of CEACAM on monocytes from dcSSc by flow cytometry and performed gene expression microarrays between CEACAM1+CEACAM6- and CEACAM1-CEACAM6+ monocytes.

overall_design: Gene expression analysis was performed between CEACAM+ and CEACAM- monocytes from one dcSSc patient. Gene expression analysis was performed between CEACAM1+CEACAM6- and CEACAM1-CEACAM6+ monocytes from another dcSSc patient.

first: Hiroki

last: Mitoma

first: Shotaro

last: Kawano

first: Yusuke

last: Yamauchi

first: Qiaolei

last: Wang

first: Masahiro

last: Ayano

first: Yasutaka

last: Kimoto

first: Ono

last: Nobuyuki

first: Yojiro

last: Arinobu

first: Koichi

last: Akashi

first: Takahiko

last: Horiuchi

first: Hiroaki

last: Niiro


title: Innate type 2 immunity controls hair follicle commensalism by Demodex mites [2019]

city: San Francisco

first: Roberto

last: Ricardo-Gonzalez

state: CA

address: 513 Parnassus Ave, HSE-1001

institute: University of California San Francisco

summary: Demodex mites are obligate commensal parasites of hair follicles (HF) in mammals.  Normally asymptomatic, inflammatory outgrowth of mites can accompany malnutrition, immune dysfunction and aging, but mechanisms restricting Demodex outgrowth and pathogenesis are not defined. Here, we show that control over mite HF colonization of mice requires ILC2s, IL-13, and its receptor IL-4Ra, but not IL-4 or the adaptive immune system.  Epithelial HF-associated ILC2s elaborate IL-13 that attenuates HF and epithelial cell proliferation at anagen onset; in their absence, Demodex colonization leads to increased epithelial proliferation and replacement of gene programs for repair by aberrant inflammatory programs leading to loss of barrier function and premature HF exhaustion over time.  Humans with rhinophymatous acne rosacea, a nasal inflammatory condition associated with a high burden of Demodex, had increased HF inflammatory cells with decreased type 2 cytokines, consistent with the inverse relationship seen in mice. Our studies uncover a critical role for skin ILC2s and IL-13, which comprise an immune checkpoint necessary to sustain cutaneous integrity and restrict pathologic infestation by colonizing HF mites.

overall_design: 2-month-old female WT (uninfected), IL-4Ra-/- (Dedmodex +) or IL-4/IL-13-/- (Demodex +) mice were used to sort CD45+ and CD45- cells from full thickness back skin.

middle: R

first: Andrew

middle: W

last: Schroeder

first: Richard

middle: M

last: Locksley


title: Innate type 2 immunity controls hair follicle commensalism by Demodex mites [2021]

overall_design: 2-month-old female WT (uninfected, control) and WT (Demodex infected for 1 month) mice were used to sort CD45+ and CD45- cells from full thickness back skin.


title: Ataxin-2, Twenty-four and Dicer-2 are components of a non-canonical cytoplasmic polyadenylation complex

city: Barcelona

first: Estefania

last: Mancini

state: Barcelona

address: C/ Dr. Aiguader, 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Centre for Genomic Regulation

summary: Cytoplasmic polyadenylation is a mechanism to promote mRNA translation in a wide variety of biological contexts. A canonical complex centered around the conserved RNA-binding protein family CPEB has been shown to be responsible for this process. We have previously reported evidence for an alternative non-canonical, CPEB-independent complex in Drosophila, of which the RNA-interference factor Dicer-2 is a component. Here, we investigate Dicer-2 mRNA targets and protein co-factors in cytoplasmic polyadenylation. Using RIP-Seq analysis we identify hundreds of novel Dicer-2 target transcripts, ~50% of which were previously found as targets of the cytoplasmic poly(A) polymerase Wispy, suggesting widespread roles of Dicer-2 in cytoplasmic polyadenylation. Large-scale immunoprecipitation revealed Ataxin-2 and Twenty-four among the high-confidence interactors of Dicer-2. Functional analysis indicate that both factors form an RNA-independent complex with Dicer-2, and are required for cytoplasmic polyadenylation of Dicer-2 targets. Our results reveal the composition of a novel cytoplasmic polyadenylation complex that operates during Drosophila early embryogenesis.

overall_design: RNA immunoprecipitation-sequencing (RIP-Seq) was performed to indentify Dicer-2 RNA targets in Drosophila melanogaster early embryo extracts. Three types of samples, in sextuplicates, were produced: (1) RNA eluate from specific immunoprecipitation against Dicer-2, either compared to (2) RNA from non-specific IgG immunoprecipitation (control) or (3) RNA from Input samples.

first: Hima

middle: P

last: Nadimpalli

first: Tanit

last: Guitart

first: Fátima

last: Gebauer


status: Public on Aug 28 2022

first: Kana

last: Yokoyama

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

overall_design: Refer to individual Series


title: Innate type 2 immunity controls hair follicle commensalism by Demodex mites


title: Differentiation-related epigenomic changes define clinically distinct keratinocyte cancer subclasses

city: Heidelberg

first: Llorenç

last: Solé Boldo

address: Im Neuenheimer Feld, 580

country: Germany

institute: DKFZ

type: Methylation profiling by high throughput sequencing


title: Transcriptome profile of melanoma cell lines A375 and A375-BIR (BIR-BRAF INHIBITOR RESISTANT) during dabrafenib treatment

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To analyse gene expression differences between A375 and A375-BIR during the treatment with dabrafenib (DAB)

overall_design: Total RNA was extracted from n=3  A375 and A375-BIR treated with DAB 200nM for 48h and vehicle control (DMSO, 0.1%)

first: R

first: P

last: Carotenuto


title: The pulmonary vasculature in lethal COVID-19 and idiopathic pulmonary fibrosis at single cell resolution

city: Vienna

first: Laura

middle: de

last: Rooij

address: Lazarettgasse 14

country: Austria

institute: CeMM

summary: Aims: SARS-CoV-2 infection causes COVID-19, which in severe cases evokes life-threatening acute respiratory distress syndrome (ARDS). Transcriptome signatures and the functional relevance of non-vascular cell types (e.g. immune and epithelial cells) in COVID-19 are becoming increasingly evident. However, despite its known contribution to vascular inflammation, recruitment/invasion of immune cells, vascular leakage and perturbed hemostasis in the lungs of severe COVID-19 patients, an in-depth interrogation of the endothelial cell (EC) compartment in lethal COVID-19 is lacking. Moreover, progressive fibrotic lung disease represents one of the complications of COVID-19 pneumonia and ARDS. Analogous features between idiopathic pulmonary fibrosis (IPF) and COVID-19 suggest partial similarities in their pathophysiology, yet, a head-to-head comparison of pulmonary cell transcriptomes between both conditions has not been implemented to date.

overall_design: We performed single nucleus RNA-seq (snRNA-seq) on frozen lungs from 7 deceased COVID-19 patients, 6 IPF explant lungs and 12 controls. The vascular fraction, comprising 38,794 nuclei, could be subclustered into 14 distinct EC subtypes. Non-vascular cell types, comprising 137,746 nuclei, were subclustered and used for EC-interactome analyses. Pulmonary ECs of deceased COVID-19 patients showed an enrichment of genes involved in cellular stress, as well as signatures suggestive of dampened immunomodulation and impaired vessel wall integrity. In addition, increased abundance of a population of systemic capillary and venous ECs was identified in COVID-19 and IPF. COVID-19 systemic ECs closely resembled their IPF counterparts, and a set of 30 genes was found congruently enriched in systemic ECs across studies. Receptor-ligand interaction analysis of ECs with non-vascular cell types in the pulmonary micro-environment revealed numerous previously unknown interactions specifically enriched/depleted in COVID-19 and/or IPF.

last: de Rooij

first: Lisa

last: Becker

first: Laure-Anne

last: Teuwen

first: Bram

last: Boeckx

first: Sander

last: Jansen

first: Simon

last: Feys

first: Stijn

last: Verleden

first: Laurens

last: Liesenborghs

first: Anna

middle: K

last: Stalder

first: Sasha

last: Libbrecht

first: Tina

last: Van Buyten

first: Gino

last: Philips

first: Abhishek

last: Subramanian

first: Sébastien

middle: J

last: Dumas

first: Elda

last: Meta

first: Mila

last: Borri

first: Liliana

last: Sokol

first: Amélie

last: Dendooven

first: Anh-Co

last: Truong

first: Jan

last: Gunst

first: Pierre

last: Van Mol

first: Jasmin

middle: D

last: Haslbauer

first: Katerina

last: Rohlenova

first: Thomas

last: Menter

first: Robbert

last: Boudewijns

first: Vincent

last: Geldhof

first: Stefan

last: Vinckier

first: Jacob

last: Amersfoort

first: Wim

last: Wuyts

first: Dirk

last: Van Raemdonck

first: Werner

last: Jacobs

last: Ceulemans

first: Birgit

last: Weynand

first: Bernard

last: Thienpont

first: Martin

last: Lammens

first: Mark

last: Kuehnel

first: Guy

last: Eelen

first: Mieke

last: Dewerchin

first: Luc

last: Schoonjans

first: Danny

last: Jonigk

first: Jo

last: Van Dorpe

first: Alexandar

last: Tzankov

first: Els


title: Bulk RNA-seq of Quiescent and Nutlin3a-Induced Senescent mouse pulmonary fibroblasts

status: Public on Aug 27 2022

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

summary:
Purpose: Use RNA-seq strategy to characterize the differentially expressed genes and significant transposable elements in quiescent and nutlin3a-induced senescent pulmonary fibroblasts to identify the factors and possible neoantigens in activating the cytotoxic T cell immunity.
Methods: FACSorted primary pulmonary fibroblasts were utilized for the preparation of bulk RNA-seq libraries. Quiescence was induced by starvation and senescence was induced by nutlin 3a treatment.

overall_design: Examination of differentially expressed genes and significant transposable elements within quiescent and nutlin3a-induced senescent pulmonary fibroblasts

first: Yoshikazu

last: Johmura

first: Makoto

last: Nakanishi


title: Bulk RNA-seq of Normal and Doxorubicin-Induced Senescent HCA2 cells

summary: Purpose: Use RNA-seq strategy to characterize the PD-L1 correlated genes in sorted PD-L1 negative and positive doxorubicin-induced senescent and normal human foreskin fibroblasts HCA2 cells to identify the upstream transcriptional network for regulating heterogeneous PD-L1 expression in senescent cells.  Methods: Early passaged normal HCA2 cells and senescent HCA2 cells induced by 24 hours of 100 nM doxorubicin treatment were utilized for the preparation of bulk RNA-seq libraries. Among the senescent cells, PD-L1 positive and negative cells were separated by FACSorting.

overall_design: Examination of differentially expressed genes and PD-L1 correlated genes within sorted PD-L1 positive and negative d-Sen HCA2 cells.


title: Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency [scRNA-seq]

city: Haining

first: Xinyu

last: Xiang

address: East Haizhou Road

department: Zhejiang University-University of Edinburgh Institute

institute: Zhejiang University

summary: Single cell transcriptome profiling of human naïve embryonic stem cells.

overall_design: Analyzing transcriptional profiles of naïve hESCs using scRNA-seq. Naïve hESCs were grown in the FINE medium in hypoxia conditions (5% O2, 5% CO2).We generated chromium single cell 3' v3.1 libraries from naive hESCs and sequenced them using Illumina Novaseq platform.

first: Wanlu

last: Liu

first: Hongqing

last: Liang


title: RNA-seq analysis of bta-miR-200b overexpression in bovine endometrial epithelial cells

city: Zhengzhou

first: Shijie

last: Lyu

address: Huayuan Road 116

institute: Henan Academy of Agricultural Sciences

summary: To investigate the gene bta-miR-200b induced cell apoptosis, we used the BEND that transinfected with bta-miR-200b and mimic NC

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BEND with bta-miR-200b mimic and mimic NC

first: Eryao

first: Yaying

last: Zhai


title: Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency [CUT&Tag]

summary: Genomic profiling of NANOG binding in KLF4 KLF5 double knockouts naïve human embryonic stem cells

overall_design: The wild type naïve hESCs and KLF4 KLF5 double knockouts naïve hESCs were collected for NANOG CUT&Tag


title: Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency [RNA-seq]

summary:
Transcriptome profiling for KLF4 and/or KLF5 knockout lines in human naïve embryonic stem cells
Transcriptome profiling for CRISPRa-LTR7Y or KLF5 overexpression in primed human embryonic stem cells

overall_design:
KLF4 and/or KLF5 was knocked out by CRISPR-CAS9 in human primed embryonic stem cells; cells were adapted to naïve culture condition, and profiled for their transcriptome in comparison with wild type naïve and primed state embryonic stem cells
The control primed hESCs and primed hESCs overexpressing CRISPRa-LTR7Y or pLVTH-KLF5 were collected for RNA-seq


title: Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency [ChIP-seq]

summary: We report the genomic binding profile of KLF5, NANOG and H3K27ac in human naïve ESCs

overall_design: DNA binding profiling the KLF5, NANOG, and H3K27ac peaks were detected by antibody pull down of chromatin in human naïve ESCs


title: Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency [ATAC-seq]

summary: ATAC-seq profiling and comparison for chromatin accessibility in human primed embryonic stem cells (ESCs), primed ESCs overexpressing KLF5, and naïve ESCs.

overall_design: The control human primed ESCs or primed hESCs overexpressing KLF5, and naïve ESCs were collected for ATAC-seq


title: Differential plasticity and fate of brain-resident and recruited macrophages during the onset and resolution of neuroinflammation

status: Public on Aug 26 2022

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Microglia and border-associated macrophages (BAMs) are brain-resident self-renewing cells with important homeostatic functions. However, their fate during and after severe episodes of brain inflammation and their relation to recruited monocyte-derived cells remain poorly understood. Here, we show that Trypanosoma brucei parasites invade the brain via its border regions, triggering a disruption of brain barriers and the recruitment of large numbers of monocytes. Fate-mapping combined with single-cell sequencing revealed the remarkable dynamics of resident macrophages, including microglia accumulation around the ventricular ependyma and an expansion of epiplexus cells. Resident macrophages were important for attracting peripheral immune cells and driving a pro-inflammatory response. However, recruited monocyte-derived macrophages reached higher cell densities and exhibited more transcriptional plasticity, adopting anti-microbial gene expression profiles not observed resident macrophages. Remarkably, recruited macrophages were short-lived and rapidly removed upon disease resolution, while activated resident macrophages progressively reverted towards a homeostatic state. Long-term transcriptional alterations were limited for microglia but more pronounced in BAMs. Together our results reveal the diverging responses and dynamics of resident and recruited macrophages upon Trypanosome invasion of the brain.

overall_design: Myeloid cells were isolated from whole brain samples and brain border tissues of naive mice, T. b. brucei infected mice, and mice cured from infection. Cells were sorted by FACS (Fluorescence-activated cell sorting) through detection of CD45 and/or CD11b and CX3CR1 expression, and subsequently analyzed using scRNA-seq. Whole brain samples of naive and infected mice used n=4 mice/group. Whole brain samples of mice cured from late-stage infection (n=2-3 mice/group) was compared to that of late-stage infected mice (or cured day 0; 3 mice/group). Choroid plexus border tissue of infected mice (n=8 mice) was compared to previously published data in naive mice (Van Hove et al. 2019). And border tissues of cured mice (n=8 mice) were compared to non-infected age-matched littermate controls (n=6 mice).

first: Karen

last: De Vlaminck

first: Hannah

last: Van Hove

first: Isabelle

last: Scheyltjens

first: Ana

last: Antunes

first: Jonathan

last: Bastos

first: Monica

last: Vara-Perez

first: Leen

last: Ali

first: Myrthe

last: Mampay

first: Lauren

last: Deneyer

first: Juliana

middle: F

last: Miranda

first: Ruiyao

last: Cai

last: Bouwens

first: Dimitri

last: De Bundel

last: Caljon

first: Benoît

last: Stijlemans

first: Ann

last: Massie

middle: A

last: Van Ginderachter

first: Roosmarijn

last: Vandenbroucke

first: Kiavash

last: Movahedi


title: Genome-wide transcriptional profiling reveals PHACTR1 as a new molecular target of Resveratrol in endothelial homeostasis

city: Hefei

first: Wenqi

last: Zhao

address: No. 96 Jinzhai Road

institute: University of Science and Technology of China

summary: Resveratrol (RES), a polyphenol found in plants and fruits, prevents cardiovascular disease through a variety of signaling pathways. RES plays a pleiotropic and atheroprotective role in the vascular system, and its mechanism is not fully understood. Transcriptome sequencing and bioinformatics analysis of RES-treated human umbilical vein endothelial cells (HUVECs) suggest that differentially expressed mrnas may be new targets for the treatment of cardiovascular diseases.

overall_design: Human umbilical vein endothelial cells (HUVECs) were seeded in 0.2% gelatin-coated petri dishes the day before the experiment. The next day, cells were treated with DMSO or resveratrol (20μM) for 24 hours. After treatment, total RNA was isolated using the RNeasy kit. RNA libraries were prepared for sequencing using the rRNA removal library construction protocol.

first: Meiming

last: Su

first: Suowen

last: Xu

first: Jianping

last: Weng


title: Gene expression-based, COVID autopsies patient

city: MADRID

first: José

last: Palacios

state: MADRID

address: CTRA COLMENAR VIEJO KM. 9.100

department: Pathology

institute: Hospital Universitario Ramón y Cajal

summary: Analyze the expression of 770 human mRNAs associated with fibrotic diseases included in the Fibrosis Panel

overall_design: Analyze 12 covid patients, 7 controls and 4 idiopatic fibrosis

first: Tamara

middle: C

last: Casas

last: Calvo


title: Single cell RNA-seq analysis on human myometrium and leiomyomas

first: Jyoti

last: Goad

state: California

address: 513 Parnassus

institute: University of California, San Francisco

summary: To understand the cellular and molecular heterogeneity in the normal myometrium, we performed single-cell RNA sequencing on normal myometrium samples. We discovered 17 different cell lineages in the normal myometrium. Our work provides a single cell atlas for the normal myometrium.

overall_design: Single cell data is provided from 5 normal myometrium samples, and 5 MED12 positive leiomyomas.

first: Aleksandar

last: Rajkovic


title: The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (bulk RNA-Seq)

city: Aachen

first: Mohamed Hamdy Elsafi

last: Mabrouk

state: NRW

address: pauwelsstraße 20

department: Helmholtz Institute of Biomedical Engineering

institute: RWTH-Aachen

summary: Colonies of induced pluripotent stem cells (iPSCs) reveal aspects of self-organization even under culture conditions that maintain pluripotent state. To investigate the dynamics of this process under spatial confinement we used either PDMS pillars or micro-contact printing of vitronectin. OCT4, E-cadherin, and NANOG were progressively upregulated within about 70 µm from the outer rim of iPSC colonies. Single-cell RNA-sequencing demonstrated that OCT4high subsets have pronounced up-regulation of the TGF-β pathway, particularly of NODAL and its inhibitor LEFTY, at the rim of the colonies. Furthermore, calcium-dependent cell-cell interaction seemed to be relevant for the self-organization. After 5 to 7 days, the iPSC colonies detached spontaneously from micro-contact printed substrates to form 3D aggregates. This new method allowed generation of embryoid bodies (EBs) of controlled size, without any enzymatic or mechanical treatment. Within the early 3D aggregates, the radial organization and differential gene expression continued in analogy to the changes observed during self-organization of flat iPSC colonies. Our results provide further insight into the gradual self-organization within iPSC colonies and at their transition into EBs.

overall_design: In this study, we analyzed the heterogeneity of gene expression within self-organized iPSC colonies and early iPSC aggregates. We used micro-contact printing of vitronectin to confine cell growth to circles of 600 µm in diameter on tissue culture plastic. We seeded iPSCs (two replicas with different cell lines) on the substrates.  We carried out single-cell RNA-sequencing (sc-RNA-seq) using the Chromium platform (10x Geneomics) at day 5 after cell seeding. At this stage the cells reached confluent state and self-organized with up-regulation of pluripotency markers at the rim of the colony. Furthermore, we analyzed early aggregates of iPSCs that formed by self-detachment from the substrates at about day 6. The non-adherent aggregates were then analyzed by sc-RNA-seq at day 8 after the initial seeding on the substrates.

first: Mohamed

middle: H

last: Elsafi Mabrouk

first: Roman

last: Goetzke

first: Giulio

last: Abagnale

first: Burcu

last: Yesilyurt

first: Lucia

last: Salz

first: Kira

last: Zeevaert

first: Zhiyao

last: Ma

first: Marcelo

last: Toledo

first: Ronghui

last: Li

first: Ivan

middle: G

last: Costa

first: Vivek

last: Pachauri

first: Uwe

last: Schnakenberg

first: Martin

last: Zenke

first: Wolfgang

last: Wagner


title: Transcriptomic responses of coralline algae

city: Nathan

first: Tessa

last: Page

state: QLD

address: 170 Kessels Road

department: Science and Environment

country: Australia

institute: Griffith University

summary: Crustose coralline algae (CCA) are calcifying red macroalgae that play important ecological roles including stabilisation of reef frameworks and provision of settlement cues for a range of marine invertebrates. Previous research into the responses of CCA to ocean warming (OW) and ocean acidification (OA) have found magnitude of effect to be species-specific. Response to OW and OA could be linked to divergent underlying molecular processes across species. Here we show Sporolithon durum, a species that exhibits low sensitivity to climate stressors, had little change in metabolic performance and did not significantly alter the expression of any genes when exposed to temperature and pH perturbations. In contrast, Porolithon onkodes, a major coral reef builder, reduced photosynthetic rates and had a labile transcriptomic response with over 400 significantly differentially expressed genes, with differential regulation of genes relating to physiological processes such as carbon acquisition and metabolism. The differential gene expression detected in P. onkodes implicates possible key metabolic pathways, including the pentose phosphate pathway, in the stress response of this species. We suggest S. durum is more resistant to OW and OA than P. onkodes, which demonstrated a high sensitivity to climate stressors and may have limited ability for acclimatisation. Understanding changes in gene expression in relation to physiological processes of CCA could help us understand and predict how different species will respond to, and persist in, future ocean conditions predicted for 2100.

sample_organism:
Sporolithon durum
Porolithon cf. onkodes

overall_design: Pigmented tissue of two coralline algae species, Porolithon onkodes and Sporolithon durum. Four treatments with 5 biological replicates per species per treatment.

first: Carmel

last: McDougall

first: Ido

last: Bar

first: Guillermo

last: Diaz-Pulido


title: Gene expression profiling of mucinous ovarian tumors and comparison with upper and lower gastrointestinal tumors

city: Sydney

first: Susan

last: Ramus

state: NSW

address: L2, Lowy Cancer Research Centre

institute: UNSW Sydney

summary: Advanced stage MOC have poor chemotherapy response and prognosis and biomarkers to help with Stage I adjuvant treatment are lacking. In addition, differentiating primary mucinous ovarian carcinoma (MOC) from gastrointestinal (GI) metastases to the ovary is challenging due to phenotypic similarities. Clinicopathological and gene expression data were analysed to identify prognostic and diagnostic features.

overall_design:
mRNA expression of 19 endogenous genes was measured using NanoString plexset, normalized to housekeeping genes . Samples from formalin-fixed paraffin-embedded (FFPE) tumor tissue were analysed for 604 patients. Associations between gene expression and overall survival were measured as well as associations between pattern of invasion and overall survival in mucinous ovarian carcinoma (MOC). Random Forest and unsupervised heirarchical clustering analyses were used to assess the ability of the selected genes to differentiate diagnoses.
(contributor) Ovarian Tumor Tissue Analysis Consortium
(contributor) Australian Pancreatic Genome Initiative

first: Nicola

middle: S

last: Meagher


title: The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates

first: Mohamed Hamdy Elsafi

last: Mabrouk

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

overall_design: Refer to individual Series


title: The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (scRNA-Seq)

overall_design: In this study, we analyzed the heterogeneity of gene expression within self-organized iPSC colonies and early iPSC aggregates. We used micro-contact printing of vitronectin to confine cell growth to circles of 600 µm in diameter on tissue culture plastic. We seeded iPSCs (two replicas with different cell lines) on the substrates.  We carried out single-cell RNA-sequencing (sc-RNA-seq) using the Chromium platform (10x Geneomics) at day 5 after cell seeding. At this stage the cells reached confluent state and self-organized with up-regulation of pluripotency markers at the rim of the colony. Furthermore, we analyzed early aggregates of iPSCs that formed by self-detachment from the substrates at about day 6. The non-adherent aggregates were then analyzed by sc-RNA-seq at day 8 after the initial seeding on the substrates. To measure the effect spatial self-organization of the self-detached aggregates, they were compared to Spin-EBs during multi-lineage  differentiation assay using bulk RNA-Seq

first: Mohamed

last: Elsafi Mabrouk

first: Roman

last: Goetzke

first: Giulio

last: Abagnale

first: Burcu

last: Yesilyurt

first: Lucia

last: Salz

first: Olivia

last: Cypris

first: Philipp

last: Glück

first: Angelika

last: Lampert


title: A Single-Cell Transcriptome Atlas of Glia Diversity in the Human Hippocampus across the Lifespan and in Alzheimer’s Disease

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

summary: Hippocampus is a critical region involved in learning, memory and various brain disorders. The molecular diversity of various glial cells in the human hippocampus and their temporal changes over the postnatal life remain largely unknown. Here we performed single-nucleus RNA-sequencing to create a transcriptome atlas of the human hippocampus across the postnatal lifespan and in Alzheimer’s disease (AD). Detailed analyses of astrocytes, oligodendrocyte lineages, and microglia identified subpopulations with distinct transcriptomic signatures, transcription factor expression patterns, association with specific biological processes, and changes in their abundance with age. Enrichment analysis of brain disorder risk gene expression further implicates specific glial cells and subpopulations in various brain disorders. Furthermore, we identified dysregulated gene expression in specific glial subpopulations in the hippocampus of AD patients. Together, these data provide a rich resource and significantly extend our understanding of human glial cell diversity and their temporal distribution across the postnatal lifespan.

overall_design: single nucleus RNA-seq on human hippocampus

first: Yi

last: Zhou

first: Hongjun

last: Song

first: Guo-li

last: Ming


title: Molecular and cellular changes underlying evolutionary specializations of primate dorsolateral prefrontal cortex

status: Public on Aug 25 2022

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

institute: Yale University

summary: The granular dorsolateral prefrontal cortex (dlPFC) is an evolutionary specialization of primates that is centrally involved in cognition. Here, we assessed over 600,000 single-nucleus transcriptomes from human, chimpanzee, macaque, and marmoset dlPFC. While major subclasses of transcriptomically-defined cell subtypes are conserved, we detected several subtypes only in some species and substantial species-specific molecular differences across homologous neuronal, glial and non-neural subtypes. The latter are exemplified by human-specific switching between translation of the neuropeptide somatostatin (SST) and tyrosine hydroxylase (TH), the rate-limiting enzyme in dopamine production, in certain interneurons, and also by expression of the neuropsychiatric risk gene FOXP2, which is human-specific in microglia and primate-specific in layer-4 granular neurons. We generated a comprehensive transcriptomic and cellular survey of dlPFC evolution in anthropoid primates.

overall_design: Gene expression profiling of mouse neocortices after being electroporated with GFP or human/mouse FOXP2

first: Shaojie

last: Ma

first: Mario

last: Skarica

first: Andrew

middle: T

last: Tebbenkamp

first: Qian

last: Li

first: Chuan

last: Xu

first: Stephen

last: Strittmatter

first: Andre

last: Sousa


title: ABE8e adenine base editor precisely and efficiently corrects a COL7A1 nonsense mutation

city: Wroclaw

first: Lukasz

last: Laczmanski

address: Weigla 12

country: Poland

institute: Hirszfeld Institute of Immunology and Experimental Therapy

summary: Base editing introduces precise single-nucleotide edits in genomic DNA and has the potential to treat genetic diseases such as the blistering skin disease recessive dystrophic epidermolysis bullosa (RDEB), which is characterized by mutations in the COL7A1 gene and type VII collagen (C7) deficiency. Adenine base editors (ABEs) convert A-T base pairs to G-C base pairs without requiring double-stranded DNA breaks or donor DNA templates. Here, we use ABE8e, a recently evolved ABE, to correct primary RDEB fibroblasts harboring the recurrent RDEB nonsense mutation c.5047 C>T (p.Arg1683Ter) in exon 54 of COL7A1 and use a next generation sequencing workflow to interrogate post-treatment outcomes. Electroporation of ABE8e mRNA into a bulk population of RDEB patient fibroblasts resulted in remarkably efficient (94.6%) correction of the pathogenic allele, restoring COL7A1 mRNA and expression of C7 protein in western blots and in 3D skin constructs. Unbiased off-target DNA and RNA editing analysis did not detect off-target editing in treated patient-derived fibroblasts. Taken together, we have established a highly efficient pipeline for gene correction in primary fibroblasts with a favorable safety profile. This work lays a foundation for developing therapies for RDEB patients using ex vivo or in vivo base editing strategies.

overall_design: The transcriptome-wide RNA sequencing (RNA-seq) on ABE8e-treated and untreated patient fibroblasts

first: Adam

last: Sheriff

first: Ina

last: Guri

first: Paulina

last: Zebrowska

first: Virginia

middle: L

last: Hernandez

first: Imogen

last: Brooks

first: Stavroula

last: Tekkela

first: Kavita

last: Subramaniam

first: Ruta

last: Gebrezgabher

first: Gaetano

last: Naso

first: Anastasia

last: Petrova

first: Katarzyna

last: Balon

first: Alexandros

last: Onoufriadis

first: Dorota

last: Kujawa

first: Martyna

last: Kotulska

first: Greg

last: Newby

first: Łukasz

last: Łaczmański

first: David

last: Liu

first: John

last: McGrath

first: Joanna

last: Jacków


title: Subcapsular sinus macrophages promote melanoma metastasis in the sentinel lymph nodes by releasing IL-1α, which upregulates STAT3 signalling in the tumour

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

summary: We analyzed the expression of multiple genes involved in immunosuppressive and exhaustion pathways in sentinel lymph nodes (sLN) isolated from mice previously depleted of macrophages (CLL treated) and we compared them with non-depleted animals.

overall_design: We profiled the  expression of genes related to immunosuppression and immune exhaustion in metastatic LN from mice depleted for macrophages (4 samples) in comparison to untreated mice (4 samples) and mice without tumor (4 samples).

first: Tommaso

last: Virgilio

first: Santiago

last: Gonzalez


title: A genome-wide CRISPRi screen reveals a StkP-mediated connection between cell-wall integrity and competence in Streptococcus salivarius

city: Lausanne

first: Johann

last: Mignolet

address: Biophore Quartier UNIL-SORGE

department: DMF

institute: UNIL

summary: Synchronizing production of antibacterial compounds and integration of DNA released by dead cells, competence is one of the most efficient bacterial evolutionary and adaptative strategies. In most streptococci, this tactic is orchestrated by the ComRS system, a pheromone communication device providing competence bimodal initiation and sharp time window of activation. Understanding how this developmental process integrates multiple inputs to fine-tune the adequate response is a long-standing question. Actually, essential genes involved in the regulation of ComRS have been challenging to study. In this work, we built a conditional mutant library using the CRISPR-interference technology and developed three complementary screens to investigate competence genetic regulation in the human commensal Streptococus salivarius. We highlighted that competence increases upon cell-wall impairment, suggesting a connection between cell envelope stress and competence activation. Notably, we report the key role played by StkP, a serine-threonine kinase known to regulate cell-wall assembly. We showed that StkP controls competence by a mechanism responding to peptidoglycan fragments. Together, those data suggest a key cell-wall sensing mechanism coupling competence to cell envelope integrity.

overall_design: Comparative guide-RNA (gRNA) abundance by CRIPR-interference (CRISPRi) in Streptococcus salivarius HSISS4 between non-induced (mock condition) and gRNA library induction (Ci condition) or gRNA library induction + competence induction (Ci+C condition)  (4 replicates per condition)

first: Adrien

last: Knoops

first: Alexandra

last: Waegemans

first: Morgane

last: Lamontagne

first: Baptiste

last: Decat

first: Jan-Willem

last: Veening

first: Pascal

last: Hols


title: Downstream targeted genes of Satb2 regulate synaptic formation and axonogenesis in developing cerebral cortex [RNA-seq]

city: Shanghai

first: Yaqiong

last: Wang

address: 399 Wanyuan Rd

institute: Children's hospital of Fudan University

summary: Special AT-rich sequencebinding protein 2 (SATB2) is essential for the development of cerebral cortex and key molecular node for the establishment of proper neural circuitry and function. Mutations in SATB2 gene lead to SATB2-associated syndrome (SAS), which is characterized by abnormal development of skeleton and central nervus system. We generated Satb2 knockout mouse model through CRISPR-Cas9 technology and performed RNA-seq and ChIP-seq of embryonic cerebral cortex. We conducted RT-qPCR, western blot, immunofluorescence staining, luciferase reporter assay and behavioral analysis for experimental verification.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E17.5 wildtype and Satb2 knock-out mouse cerebral cortex

first: Qiufang

last: Guo

first: Yanyan

last: Qian

first: Qing

first: Xinran

last: Dong

first: Huiyao

last: Chen

first: Xiang

first: Xiuyun

first: Sha

last: Yu

first: Jitao

last: Zhu

first: Shifang

last: Shan

first: Bingbing

last: Wu

first: Wenhao

last: Zhou

first: Huijun


title: Global microRNA and protein expression in human term placenta.

city: Örebro

first: Robert

last: Kruse

address: Södra Grev Rosengatan 32

department: Kliniskt forskningslaboratorium

country: Sweden

institute: Örebro University

type: Non-coding RNA profiling by high throughput sequencing

summary: Description of the global expression of microRNAs (miRNAs) and proteins in healthy human term placentas may increase our knowledge of molecular biological pathways that are important for normal fetal growth and development in term pregnancy. The aim of this study was to explore the global expression of miRNAs and proteins, and to point out functions of importance in healthy term placentas. Placental samples (n = 19) were identified in a local biobank. All samples were from uncomplicated term pregnancies with vaginal births and healthy, normal weight newborns. Next-generation sequencing and nano-scale liquid chromatographic tandem mass spectrometry were used to analyse miRNA and protein expression, respectively. A total of 895 mature miRNAs and 6,523 proteins were detected in the placentas, of which 123 miRNAs and 346 proteins were highly abundant. The miRNAs were in high degree mapped to chromosomes 19, 14 and X. Analysis of the highly abundant miRNAs and proteins showed several significantly predicted functions in common, including immune and inflammatory response, lipid metabolism and development of the nervous system. The predicted function inflammatory response may reflect normal vaginal delivery, while lipid metabolism and neurodevelopment may be important processes for the term fetus. The data presented in this study, including supplementary information with complete miR

overall_design: Placental tissue sampled from healthy women. The inclusion criteria were healthy women without chronic disease or malabsorption disorder, a normal body mass index (BMI) 18.5–24.9 in early pregnancy, gestational weight gain within the recommended interval of 11.5–16.0 kg (23) and age 18–35 years at the time of delivery. Further, the woman had to give birth vaginally to a healthy, singleton infant with a normal birth weight defined as +/- 1 SD from the population mean (24) at gestational age 37+0 to 41+6. Maternal exclusion criteria were smoking during pregnancy, any long-term treatment with medicines (excepting folic acid and iron supplements), any pregnancy complications (e.g. gestational hypertension, preeclampsia, gestational diabetes or erythrocyte immunization), preterm premature rupture of membranes, chorionamnionitis, mechanical induction or induction of labour with prostaglandins, or an active second stage of labour > 60 minutes. Fetal exclusion criteria were asphyxia (defined as Apgar score < 7 at 5 minutes), and chromosomal or severe anatomical malformation of the newborn infant.  Next-generation sequencing was used to analyse placental expression of miRNA.

first: Hanna

last: Östling

first: Maria

last: Lodefalk

first: Helena

last: Backman


title: Mapping the glucocorticoid gene regulatory network and alterations that contribute to steroid resistance in childhood acute lymphoblastic leukemia [WGBS]

city: Memphis

first: Daniel

last: Savic

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Glucocorticoids (GCs) are a mainstay of contemporary, multi-drug chemotherapy in the treatment of acute lymphoblastic leukemia (ALL). Although overall survival rates of childhood ALL have improved, resistance to antileukemic agents remains a major clinical concern. In particular, resistance to GCs is predictive of ALL relapse and poor clinical outcome, and it therefore represents a major hurdle limiting further improvements in survival rates. While advances have been made in identifying genes and transcriptional signatures implicated in ALL GC resistance, there remains an insufficient understanding of the impact of glucocorticoid response element (GRE) alterations in GC resistance. To therefore better understand the role of gene regulatory alterations in GC resistance, we comprehensively mapped the GC gene regulatory network in two ALL cell lines using orthogonal functional genomic assays and identified tens of thousands of GREs in the ALL genome. A closer examination revealed binding profiles that were consistent with the long-range flexible billboard model of gene regulation. GCs also induced the formation of over 250 super-enhancers, and these GC-responsive super-enhancers control the expression of genes mediating GC resistance. By further integrating our results with genetic and epigenetic data in primary ALL cells from patient cohorts at St. Jude, we identified 45 DNA sequence variants associated with ex vivo GC resistance that map to GREs and validated an associated variant within the TLE1 gene locus. We also uncovered that 1929 accessible chromatin sites associated with ex vivo GC resistance were significantly enriched at GREs. A CRISPR interference screen of these elements validated their effects on GC resistance. Overall, these data suggest that GCs initiate pervasive, genome-wide effects on the leukemia epigenome and transcriptome, while genetic and epigenetic alterations to GREs are mechanisms contributing to GC resistance in childhood ALL.

overall_design: Whole-genome bisulfite sequencing (WGBS) was performed in two ALL cell lines. Cells grown in standard culture conditions and genomic DNA was isolated for downstream methylation analysis.


title: Single cell RNA-seq of brain from young and old mice

city: Rochester

first: Xu

last: Zhang

state: MN

address: 200 First St SW

department: Physical Medicine and Rehabilitation

institute: Mayo Clinic

summary: We report the scRNA-seq of cells isolated from brain of young and old mice.

overall_design: We isolated single cells from brain of young (6 months, n=2) and old (24 months, n=4) mice and performed the scRNA-seq using 10X Genomics system.

first: Marissa

last: Schafer

first: Nathan

last: LeBrasseur


title: Mapping the glucocorticoid gene regulatory network and alterations that contribute to steroid resistance in childhood acute lymphoblastic leukemia [Hi-ChIP]

overall_design: Hi-ChIP was performed in Nalm6 and 697 cells with or without prednisolone treatment. Cells grown in standard culture conditions were treated with prednisolone (10uM for 697 cells and 5uM for Nalm6 cells) for 6 and 24 hours. 30 million cells were collected for each time point.


title: A glycan-based approach to cell characterization and isolation (scRNA-Seq)

status: Public on Aug 24 2022

city: Bronx

first: Emily

last: Schwenger

state: NY

address: 1300 Morris Park Ave.

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: We leverage the extraordinary molecular diversity of modified heparan sulfate (HS) glycans 8 to establish cellular glycotypes, defined by binding patterns of a panel of flow-cytometry compatible single-chain variable fragment antibodies (scFvs) specific for differentially modified HS. We find distinct glycotypes between closely related hematopoietic progenitors and lineages. The glycotypes of murine and human hematopoietic stem and progenitor cells (HSPCs) reveal dynamic yet similar HS modification patterns in vivo and in vitro, including along megakaryocyte and erythrocyte differentiation. Prospective HS scFv-based sorting identifies new cellular subtypes from both immunophenotypic megakaryocyte-erythrocyte progenitors and heterogeneous pools of HSPCs, thus offering additional discriminative power beyond conventional CD markers. Mechanistically, single-cell RNAseq revealed that a heptad of HS-related genes participate in megakaryocyte-erythrocyte fate determination and are reflective of the HS epitope recognized by specific HS scFvs. In summary, HS glycotyping establishes a role for HS modification patterns in hematopoietic lineage differentiation in mouse and human, and provides an orthogonal approach to define and isolate viable cell types across different cell lineages and species at unprecedented resolution.

overall_design: Single-cell RNA sequencing study of heparan sulfate-fractionated Lin-Kit+ (LK) cells in mouse bone marrow. Control (MPB49), high heparan sulfate binding (HS3A8_high), and low heparan sulfate binding (HS3A8_low) murine hematopoietic stem and progenitor cells (HSPCs).

first: Richard

last: Piszczatowski

first: Ulrich

last: Steidl


title: Effect of early postnatal stress on adult mouse Sertoli cells

city: Zurich

first: Kristina

middle: Maria

last: Thumfart

address: Winterthurerstrasse 190

institute: ETH

summary: To investigate whether early postnatal stress has a long-lasting impact on Sertoli cells up to adulthood, we compared the gene expression of adult Sertoli cells obtained from stressed versus control mice.

overall_design: We collected Sertoli cells from postnatally stressed and control mice and performed RNA-Sequencing.

first: Isabelle

last: Mansuy


title: Mapping the glucocorticoid gene regulatory network and alterations that contribute to steroid resistance in childhood acute lymphoblastic leukemia [ATAC-STARR-seq]

overall_design: DNA fragment libraries obtained from ATAC-seq performed in Nalm6 or 697 cells were electroporated into the cell line of origin. Cells grown in standard culture conditions were treated with prednisolone (10uM for 697 cells and 5uM for Nalm6 cells) for 6 and 24 hours. Approximately 65-75 million cells were collected for each replicate and time point. Four independent experiments were conducted for each time point.


title: The Effects of Bacillus licheniformis-fermented Products on Chronic Feline Diarrhea and Intestinal Microbiota

city: Taipei

first: Yen-Chen

last: Chang

address: No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan (R.O.C.)

country: Taiwan

institute: Graduate institute of molecular and comparative pathobiology, School of veterinary medicine, National Taiwan University

summary: Bacillus licheniformis-fermented products (BLFP) are probiotics with antibacterial, antiviral, and anti-inflammatory properties that can improve growth performance. This study aimed to, firstly, compare the fecal microbiota of cats with chronic diarrhea (n = 8) with that of healthy cats (n = 4) from the same household using next-generation sequencing and, secondly, evaluate the effectiveness of oral administration of BLFP in relieving clinical signs and altering the intestinal microbiota in diarrheal cats. Six out of eight cats with diarrhea showed clinical improvement after BLFP administration for 7 days, and in two cats the stool condition was normal. A higher Firmicutes/Bacteroidetes ratio was noted in the feces of diarrheal cats without clinical improvement as compared with those in the healthy control group and in the diarrheal cats with clinical improvement after receiving BLFP. The phylum Bacteroidetes and class Bacteroidia decreased significantly in diarrheal cats regardless of BLFP administration. Blautia spp., Ruminococcus torques, and Ruminococcus gnavus, which belong to the Clostridium cluster XIVa and have been reported as beneficial to intestinal health, increased significantly in feces after BLFP treatment. Furthermore, a significant decrease in Clostridium perfringens was noted in diarrheal cats after BLFP administration. Overall, BLFP could be a potential probiotic to relieve gastrointestinal symptoms and improve fecal microbiota in cats with chronic diarrhea.

overall_design: Twelve cats from the same household were included in this study. All the cats were fed a similar diet and had the same exercise level. The health status of these cats was observed and evaluated by owners and veterinarians. To evaluate the effects of BLFP on relieving the clinical signs and alteration of the microbiomes in cats with diarrhea, and to ensure that each cat received an equal amount of BLFP intake, 1.1 mg/kg BLFP was prepared as previously described and supplied in a capsule that was manually fed to the cats by the owner once a day for 7 consecutive days. Clinical scoring and fecal samples of these cats were collected before and after 7 days of BLFP treatment.

first: Ting-Wei

last: Lee

first: Tzu-Yi

last: Chao

first: Hui-Wen

first: Yeong-Hsiang

last: Cheng

first: Ching-Ho


title: A glycan-based approach to cell characterization and isolation


title: A glycan-based approach to cell characterization and isolation (bulk RNA-Seq)

summary: We leverage the extraordinary molecular diversity of modified heparan sulfate (HS) glycans to establish cellular glycotypes, defined by binding patterns of a panel of flow-cytometry compatible single-chain variable fragment antibodies (scFvs) specific for differentially modified HS. We find distinct glycotypes between closely related hematopoietic progenitors and lineages. The glycotypes of murine and human hematopoietic stem and progenitor cells (HSPCs) reveal dynamic yet similar HS modification patterns in vivo and in vitro, including along megakaryocyte and erythrocyte differentiation. Prospective HS scFv-based sorting identifies new cellular subtypes from both immunophenotypic megakaryocyte-erythrocyte progenitors and heterogeneous pools of HSPCs, thus offering additional discriminative power beyond conventional CD markers. Mechanistically, single-cell RNAseq revealed that a heptad of HS-related genes participate in megakaryocyte-erythrocyte fate determination and are reflective of the HS epitope recognized by specific HS scFvs. In summary, HS glycotyping establishes a role for HS modification patterns in hematopoietic lineage differentiation in mouse and human, and provides an orthogonal approach to define and isolate viable cell types across different cell lineages and species at unprecedented resolution.

overall_design: Bulk RNA sequencing study of heparan sulfate-fractionated megakaryocyte-erythroid progenitor (MEP, Lin-ckit+CD34-FcγRII/IIIlo) cells sorted from mouse bone marrow. Control (MPB49), high heparan sulfate binding (HS3A8_high), and low heparan sulfate binding (HS3A8_low) murine MEPs.


title: Mapping the glucocorticoid gene regulatory network and alterations that contribute to steroid resistance in childhood acute lymphoblastic leukemia [ATAC-seq]

overall_design: ATAC-seq performed in Nalm6 and 697 cells with or without prednisolone treatment. Cells grown in standard culture conditions were treated with prednisolone (10uM for 697 cells and 5uM for Nalm6 cells) for 2, 6, 12, and 24 hours. Ten thousand cells were transposed for each replicate and time point. Three independent experiments were conducted for each time point.


title: Phosphate promotes osteogenic differentiation through non-canonical Wnt signaling pathway in human mesenchymal stem cells

city: Suita

first: Takuo

last: Kubota

state: Osaka

address: 2-2, Yamadaoka

department: Pediatrics

institute: Osaka University Graduate School of Medicine

summary:
To investigate the phosphate concentration affect on osteogenic differentiation,  we induced hBM-MSCs osteogenic differentiation in vitro, and different concentration of phosphate culture medium were used treat the cells.
We then performed RNA-seq to check three groups genes expression and did bioinformatics analysis on days 7 of osteogenic differentiation induction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hBM-MSCs in different phosphate concentration culture medium on days 7 of osteogenic differentiation induction.

first: Shumin

last: Rui

first: Yasuhisa

last: Ohata

first: Kenichi

last: Yamamoto

first: Makoto

last: Fujiwara

first: Shinji

last: Takeyari

first: Keiichi

last: Ozono


title: Steroid-resistant nephrotic syndrome associated MYO1E mutations have differential effects on myosin 1e localization, dynamics, and activity

city: SYRACUSE

first: Mira

last: Krendel

state: New York

address: 505 Irving Ave

institute: Upstate Medical University

summary: Patients deficient in myosin 1e and mice in which Myo1e is knocked out  develop Focal Segmental Glomerlosclerosis. To study the impact of myo1e deficiency on cultured podocytes, we derived conditionally immortalized glomerular epithelial cells from crosses between the Myo1e-KO mice and a H-2Kb-tsA58 mice (Immortomouse) to obtain Myo1e- heterozygous and Myo1e-KO podocyte-derived cells. The purpose of this study was to analyze the transcriptome differences between wild-type Murine Podocyte Cells (MPC) originally described in PMID 9344605 and mantained in our lab for several passages, Myo1e Heterozygous cells, and Myo1e KO cells. RNAseq and differential gene expression analysis was performed.

overall_design: Three biological replicates from each genotype (MPC, Myosin 1e Heterozygous, and Myosin 1e Knockout) were analyzed.

first: Pei-Ju

last: Liu

first: Michael

last: Garone

first: Chunling

last: Zhang


title: Mapping the glucocorticoid gene regulatory network and alterations that contribute to steroid resistance in childhood acute lymphoblastic leukemia [RNA-seq]

first: Daniel

last: Savic

overall_design: RNA-seq performed in two ALL cell lines. Cells grown in standard culture conditions were treated with prednisolone (10uM for 697 cells and 5uM for Nalm6 cells) for 6 or 24 hours and RNA was extracted. RNA from untreated control samples was also extracted. Three independent experiments were conducted for each time point in both cell lines.


title: Urinary single-cell sequencing captures intrarenal injury and repair processes in human acute kidney injury

city: Berlin

first: Nikolaus

last: Rajewsky

address: Hannoversche Str. 28

department: BIMSB

institute: Max Delbrück Center for Molecular Medicine

summary: Acute kidney injury (AKI) is a major health issue, the outcome of which depends primarily on damage and reparative processes of tubular epithelial cells (TEC). Mechanisms underlying AKI remain incompletely understood, specific therapies are lacking and monitoring the course of AKI in clinical routine is confined to measuring urine output and plasma levels of filtration markers.   Here we demonstrate feasibility and potential of a novel approach to assess the cellular and molecular dynamics of AKI by establishing a robust urine-to-single cell RNA sequencing (scRNAseq) pipeline for excreted kidney cells via flow cytometry sorting. We analyzed 42,608 single cell transcriptomes of 40 urine samples from 32 AKI patients and compared our data with reference material from human AKI post-mortem biopsies and published mouse data. We demonstrate that TEC transcriptomes mirror intrarenal pathology and reflect distinct injury and repair processes, including oxidative stress, inflammation, and tissue rearrangement.   In conclusion, single cell transcriptomics of kidney cells excreted in urine provides non-invasive, unprecedented insight into cellular processes underlying AKI, thereby opening novel opportunities for target identification, AKI sub-categorization and monitoring of natural disease course and interventions.

overall_design: Single-cell RNAseq of flow cytometry sorted viable cells from 40 human urine specimen of 32 patients with acute kidney injury

first: Seungjoon

last: Kim

first: Jan

last: Klocke

first: Anastasiya

last: Boltengagen

first: Christopher

last: Skopnik

first: Christine

last: Kocks

first: Kai-Uwe

last: Eckardt

first: Philipp

last: Enghard


title: Hypoxia induces an early primitive streak signature, enhancing spontaneous elongation and lineage representation in gastruloids

first: Natalia

last: Lopez-Anguita

state: Berlin

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

summary: The cellular microenvironment together with intrinsic regulators shapes stem cell identity and differentiation capacity. Mammalian early embryos are exposed to hypoxia in vivo and appear to benefit from hypoxic culture in vitro. Yet, how hypoxia influences stem cell transcriptional networks and lineage choices remain poorly understood. Here we investigated the molecular effects of acute and prolonged hypoxia on embryonic and extraembryonic stem cells as well as the functional impact on differentiation potential. We find a temporal and cell type-specific transcriptional response including an early primitive streak signature in hypoxic embryonic stem cells (ESCs) mediated by HIF1. Using a 3D gastruloid differentiation model, we show that hypoxia-induced T expression enables symmetry breaking and axial elongation in the absence of exogenous WNT activation. When combined with exogenous WNT activation, hypoxia enhances lineage representation in gastruloids, as demonstrated by highly enriched signatures of gut endoderm, notochord, neuromesodermal progenitors and somites. Our findings directly link the microenvironment to stem cell function and provide a rationale supportive of applying physiological conditions in models of embryo development.

overall_design: Examination of germ layer representation in coventional gastruloids (+Chi) cultured in normoxia and  hypoxia and unconventional gastruloids (-Chi) cultured in hypoxia.

first: Seher

middle: I

last: Gassaloglu

first: Maximilian

last: Stötzel

first: Adriano

last: Bolondi

first: Deniz

last: Conkar

first: Marina

last: Typou

first: René

last: Buschow

first: Jesse

last: Veenvliet

first: Aydan

last: Bulut-Karslioglu


overall_design: Examination of Hif1a binding sites in acute (2 days) and in prolonged (6 days) hypoxia in ES cells.


title: RNA seq on NEO2734, CFI-400945 or SASP treated cells

city: Amsterdam

first: Liqin

last: Wang

address: Plesmanlaan 121

country: Netherlands

institute: NKI-AVL

summary: Senolytics, drugs that kill senescent cells, have been proposed to improve the response to pro-senescence cancer therapies. However, lack of broadly acting senolytic drugs remains a challenge. Using inducible CRISPR/Cas9-based genetic screens in different senescent cancer cell models, we identify here loss of the death receptor inhibitor cFLIP as a universal vulnerability of senescent cancer cells. Senescent cancer cells are primed for apoptotic death by NF-kB-mediated upregulation of death receptor DR5 and its ligand TRAIL but are protected from death by increased cFLIP. Activation of DR5 signaling by agonistic antibody, which can be enhanced further by suppression of cFLIP by BRD2 inhibition, leads to efficient killing of all senescent cancer cells tested. We validate this ?one-two punch? cancer therapy by combining pro-senescence therapy with DR5 activation in different animal models.

overall_design:
The cancer cells (PC9, SK-Hep1 or A549) were treated with the indicated drugs or conditional medium for 1 week, and then RNA were isolated for analysis
Transcriptomic analysis of treatment on different cell models, see the changes on gene expression upon the treatments


title: Characterization of molecular changes associated with Mef2c hypofunction in the mouse auditory nerve

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Overall goal of the study is to investigate the role of Mef2c in cochlear cell function and hearing

overall_design: Four biological replicates of the auditory nerve from postnatal day 21 (P21) wildtype and Mef2c heterozygotes (+/-) mice were compared by RNAseq analysis

first: Hainan

last: Lang


overall_design: Refer to individual Series


title: Hypoxia induces a transcriptional early primitive streak signature in pluripotent cells enhancing spontaneous elongation and lineage representation in gastruloids [RNA-seq]

overall_design: Examination of the transcriptome in embryonic (ES cells) and extraembryonic (TS and XEN cells) cells in normoxia and in acute (for 2 days) and prolonged (for 7 days) hypoxia.


title: RNAseq analysis of USP7 knockdown in  MM16 and MM27 metastatic melanoma PDX  cells

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

institute: European Institute of Oncology

summary:
Purpose:  Study of transcriptomic changes upon depletion of USP7
Methods: Melanoma PDX cells were transduced with lentiviral vectors expressing  Scrambled(shSCR) or USP7 targeting (shUSP7) shRNA

overall_design: Analysis of differential gene expression in control and USP7 knockdown MM16 and MM27 metastatic  melanoma PDX cells

first: Letizia

last: Granieri

first: Alessandro

last: Cuomo

first: Stefano

last: Confalonieri

first: Giuseppina

last: Giardina

first: Tiziana

last: Bonaldi

first: Neda

last: Mohammadi

first: Elena

last: Cavallaro

first: Daniela

last: Bossi

first: Luisa

last: Lanfrancone


title: Developmental transcriptomics reveals novel mechanisms of teleost spermiogenesis

city: Bellaterra (Barcelona)

first: Joan

last: Cerdà

state: Spain

address: Parc de Recerca UAB, Mòdul B

institute: IRTA

summary: The transcriptome of haploid germ cells and ejaculated spermatozoa from wild-type seabream (Sparus aurata) was compared by RNAseq. The data establish the molecular signature during spermatozoa differentiation and reveal the involvement of novel endocrine mechanisms during sperm maturation in the efferent duct.

overall_design: Haploid germ cells were isolated from the testis by fluorescence-activated cell sorting, and ejaculated spermatozoa was collected from after a soft pressure to the abdominal area of the fish. Illumina libraries were constructed for 4 replicates for each of the two samples, and each replicate was a pool of 3 different fish.

first: Julia

last: Castro-Arnau

first: Jessica

last: Gómez-Garrido

first: Anna

last: Esteve-Codina

first: Tyler

last: Alioto


title: Next Generation Sequencing  of Wild Type (Col-0) , fio1-1 and fio1-2 Transcriptomes in Arabidopsis thaliana

city: Frederiksberg C

first: Bin

last: Sun

address: Thorvaldsensvej 40

department: Department of Plant and Environmental Sciences

country: Denmark

institute: Copenhagen Plant Science Centre – University of Copenhagen

summary: Plants were grown on 1/2 MS for 14 days under LD conditions and RNA was extracted and sequenced

overall_design: Examination of three genotypes (wild type/fio1-1/fio1-2) and one condition with two replicates each

first: Stephan

last: Wenkel


title: Next Generation Sequencing  of Wild Type (Col-0), fio1-1 and fio1-2 methylated RNA immunoprecipitation sequencing in Arabidopsis thaliana

overall_design: Examination of three genotypes (wild type/fio1-1/fio1-2) and one condition with one sample each


title: Profiling of Naïve (CD45RA+CD28+), EM (CD45RA-CD28-) and TEMRA (CD45RA+CD28-) CD8+ T cells from kidney transplanted patients

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

summary: RNAseq of 3 CD8 subsets (NAIVE, TEMRA and EM)  from kidney transplanted patients

overall_design: Naïve (CD45RA+CD28+), EM (CD45RA-CD28-) and TEMRA (CD45RA+CD28-) CD3+CD8+ T cells were FACS sorted (FACSAria, BD Biosciences; purity greater than 95%) from freshly isolated human PBMCs obtained from 6 KT

first: Jacquemont

last: Lola

first: Tilly

last: Gaëlle

first: Danger

last: Richard

first: Degauque

last: Nicolas


title: Expression data from purified one-week mouse fracture callus Skeletal Stem Cells (SSCs) and Bone-Cartilage-Stromal Progenitor cells (BCSPs)

status: Public on Aug 23 2022

city: Sacramento

first: Thomas

last: Ambrosi

address: 2700 Stockton Blvd

institute: UC Davis

summary:
Gene expression profiling of purified stem and progenitor cell types from stabilized bicortical femoral fracture calluses one week after injury induction.
We used microarrays to detail the global program of gene expression of stem and progenitor cells responsible for skeletal repair.

overall_design: Mouse skeletal stem and progenitor cells were purified from one-week femoral fracture calluses via flow cytometry for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of SSCs and BCSPs in order to compare the cell type specific expression profiles. To that end, we used 10-12 week-old mice and isolated CD45-Ter119-Tie2-CD51+CD200+6C3-Thy1-CD105- SSCs and CD45-Ter119-Tie2-CD51+6C3-Thy1-CD105+ BCSPs.

first: Charles

last: Chan


title: A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome [RNA-Seq]

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

summary: Many cancers are organized as cellular hierarchies sustained by cancer stem cells (CSC), whose eradication is crucial for achieving long-term remission. Difficulties to isolate and undertake in vitro and in vivo experimental studies of rare CSC under conditions that preserve their original properties currently constitute a bottleneck for identifying molecular mechanisms involving coding and non-coding genomic regions that govern stemness. We focussed on acute myeloid leukemia (AML) as a paradigm of the CSC model and developed a patient-derived system termed OCI-AML22 that recapitulates the cellular hierarchy driven by leukemia stem cells (LSC). Through classical flow sorting and functional analyses, we established that a single phenotypic population is highly enriched for LSC. The LSC fraction can be easily isolated and serially expanded in culture or in xenografts while faithfully recapitulating functional, transcriptional and epigenetic features of primary LSCs. A novel non-coding regulatory element was identified with a new computational approach using functionally validated primary AML LSC fractions and its role in LSC stemness validated through efficient CRISPR editing using methods optimized for OCI-AML22 LSC. Collectively, OCI-AML22 constitutes a valuable resource to uncover mechanisms governing CSC driven malignancies.

overall_design:
OCI-AML22 donor that generated the OCI-AML22 model, or OCI-AML22 cultured for the indicated number of days were then sorted according to CD34 and CD38 cell surface expression as indicated, to sequence RNA.

>>> Submitter states that raw data will be submitted to EGA as it requires controlled access. <<<

first: Helena

last: Boutzen

first: Alex

first: Michelle

last: Chan-Seng-Yue


title: Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis [bulkRNA-seq]

city: San Francisco

first: Bridget

last: Keenan

state: CA

address: 505 PARNASSUS AVE

institute: University of California San Francisco

summary: Suppressive myeloid cells can contribute to immunotherapy resistance, but their role in response to checkpoint inhibition (CPI) in anti-PD-1 refractory cancers, such as biliary tract cancer (BTC), is largely unknown. We use multiplexed single-cell transcriptomic and epitope sequencing to profile greater than 200,000 peripheral blood mononuclear cells from advanced BTC patients (n=9) and matched healthy donors (n=8). Following anti-PD-1 treatment, CD14+ monocytes expressing high levels of immunosuppressive cytokines and chemotactic molecules (CD14CTX) increase in the circulation of patients with BTC tumors that are CPI-resistant. CD14CTX can directly suppress CD4+ T cells and induce SOCS3 expression in CD4+ T cells rendering them functionally unresponsive. The CD14CTX gene signature associates with worse survival in patients with BTC as well as in other anti-PD-1 refractory cancers. These results demonstrate that monocytes arising after anti-PD-1 treatment can induce T cell paralysis as a distinct mode of tumor-mediated immunosuppression leading to CPI resistance.

overall_design: We performed bulkRNAseq on peripheral blood samples for use in demultiplexing single cell RNAseq data used in our publication. RNA was extracted from minimum 2.5 x 105 cells per PBMC sample and each sample was sequenced at a depth of at least 2 x 107 reads per cell on the Illumina Novaseq S4.

first: Elizabeth

middle: E

last: McCarthy

first: Arielle

last: Ilano

first: Hai

last: Yang

first: Li

last: Zhang

first: Kathryn

last: Allaire

first: Zenghua

last: Fan

first: Tony

last: Li

first: David

last: Lee

first: Yang

last: Cheung

first: Diamond

last: Luong

first: Hewitt

last: Chang

first: Brandon

last: Chen

first: Jaqueline

last: Marquez

first: Brenna

last: Sheldon

first: Robin

last: Kelley

first: Chun

last: Ye

first: Lawrence

last: Fong


title: Expression data from purified human long bone fracture callus Skeletal Stem Cells (SSCs) and Osteogenic Progenitor (hOPs) and Chondrogenic Progenitor (hCPs) cells

first: Thomas

last: Ambrosi

state: California

summary:
Gene expression profiling of purified stem and progenitor cell types from femoral fracture calluses of patients hemiarthroplasty or open reduction internal fixation procedures.
We used microarrays to detail the global program of gene expression of stem and progenitor cells responsible for skeletal repair.

overall_design: Human skeletal stem and progenitor cells were purified from femoral fracture tissues via flow cytometry for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of hSSCs, hOPs and hCPs in order to compare the cell type specific expression profiles. To that end, we isolated CD45-CD235a-CD31-TIE2-PDPN+CD146-CD164+CD73+ hSSCs, CD45-CD235a-CD31-TIE2-PDPN-CD146+ hOPs and CD45-CD235a-CD31-TIE2-PDPN+CD146-CD164-/+CD73-/+ hCPs.

first: Charles

last: Chan


title: Expression data from purified long bone fracture callus

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome [WGS]

first: Alexander

last: Murison

type: Genome variation profiling by high throughput sequencing

overall_design:
Comparative WGS profiling analysis of WGS data for the donor that generated OCI-AML22 and grafts generated by OCI-AML22.

>>> Submitter states that raw data will be submitted to EGA as it requires controlled access. <<<

first: Helena

last: Boutzen

first: Alex

first: Michelle

last: Chan-Seng-Yue


title: A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome [ATAC-Seq]

overall_design:
CD34+, CD34- and bulk OCIAML22 were sequenced for ATAC-Seq

>>> Submitter states that raw data will be submitted to EGA as it requires controlled access. <<<


title: Paternally inherited H3K27me3 impacts zygotic genome activation in round spermatid injection [ATAC-seq]

city: Kofu

first: Mizuki

last: Sakamoto

institute: University of Yamanashi

summary: Round spermatid injection (ROSI) gives rise to a lower birth rate than intracytoplasmic sperm injection (ICSI), which uses mature spermatozoa and has limited clinical application. Inefficient development of ROSI-embryos has been attributed to epigenetic abnormalities. However, the chromatin-based mechanism that underpins the low birth rate of ROSI remains to be determined. Here we show that a repressive histone mark H3K27me3 persists from doner round spermatids into zygotes in ROSI and that paternally derived H3K27me3 is associated with less accessible chromatin and impaired zygotic genome activation (ZGA) in ROSI-derived zygotes. These H3K27me3 marked loci in the paternal germline undergo histone turnover in spermiogenesis, resulting in the reduced paternal H3K27me3 in normal spermatozoa. Thus, the lack of histone turnover during spermiogenesis led to the dysregulation of chromatin accessibility and ZGA in ROSI-embryos. Our results unveil a molecular logic by which chromatin states in round spermatids impinge on chromatin states and ZGA in ROSI-embryos, highlighting the importance of chromatin remodeling in spermiogenesis in successful reproduction.

overall_design: Omni ATAC-seq and RNA-seq were perfomed with mouse ROSI- and ICSI-embryos at the 1-cell or 2-cell stages.

first: Masatoshi

last: Ooga


title: Single-cell RNA-Seq of mice treated with lysolecithin at baseline, 5 days post lesioning, 14 days post lesioning and 28 days post-lesioning, 3-4 months old

city: South San Francisco

first: Mitchell

last: Rezzonico

address: 1 DNA Way

institute: Genentech

summary: Here we studied the transcriptional changes in the oligodendrocyte lineage cells of corpus callosum in and around the region lesioned by injection of lysolecithin by using unbiased single cell RNA-seq. We identified three distinct activation states of oligodendrocytes, termed disease associated oligodendrocytes and associated gene expression signatures. We observed increases in proportion of disease associated oligodendrocytes along different timepoints post lysolecithin treatment. This study will provide resources to study the molecular mechanisms driving de/remyelination induced by lysolecithin.

overall_design: RNA isolated from lesioned region of the corpus callosum at baseline(n=3), 5days post lesioning(n=4), 14 days post lesioning(n=2) and 28 days post lesioning(n=3). Mice were treated with 1% lysolecithin. All mice were 3-4 months at the time of perfusion.

first: Shristi

last: Pandey

first: Kimberle

last: Shen

first: Yun-An

first: Tracy

last: Yuen

first: Brad

last: Friedman


title: The role of KDM6B in cognitive functions

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Analysis of mRNA expression in WT and KDM6B KO neurons.

overall_design: WT and KDM6B KO neurons were subjected to mRNA-seq.

first: Yanan

last: Wang

first: Yingfei


title: Paternally inherited H3K27me3 impacts zygotic genome activation in round spermatid injection [RNA-seq]


title: Downstream targeted genes of Satb2 regulate synaptic formation and axonogenesis in developing cerebral cortex [ChIP-seq]

city: Shanghai

first: Yaqiong

address: 399 Wanyuan Rd

institute: Children's hospital of Fudan University

summary: Special AT-rich sequencebinding protein 2 (SATB2) is essential for the development of cerebral cortex and key molecular node for the establishment of proper neural circuitry and function. Mutations in SATB2 gene lead to SATB2-associated syndrome (SAS), which is characterized by abnormal development of skeleton and central nervus system. We generated Satb2 knockout mouse model through CRISPR-Cas9 technology and performed RNA-seq and ChIP-seq of embryonic cerebral cortex. We conducted RT-qPCR, western blot, immunofluorescence staining, luciferase reporter assay and behavioral analysis for experimental verification.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for E17.5 wild-type  mouse cerebral cortex

first: Qiufang

last: Guo

first: Yanyan

last: Qian

first: Qing

first: Xinran

last: Dong

first: Huiyao

last: Chen

first: Xiang

first: Xiuyun

last: Liu

first: Sha

last: Yu

first: Jitao

last: Zhu

first: Shifang

last: Shan

first: Bingbing

last: Wu

first: Wenhao

last: Zhou

first: Huijun


title: Differential timing for glucose assimilation in Prochlorococcus and coexistent microbial populations at the North Pacific Subtropical Gyre

city: Córdoba

first: Muñoz Marin

last: Maria del Carmen

state: Córdoba

address: Campus Rabanales

department: Bioquímica y Biología Molecular

institute: Universidad de Córdoba

summary: Investigation of whole genome gene expression level changes in Prochlorococcus from environmental samples.  The diel gene expression analyzed in this study is further described in Muñoz-Marin, M., Duhamel, S., Björkman, K., Magasin, J., Díez, J., Karl, D.M., Garcia-Fernandez, J.M., 2021. ISME J. (to be submitted).

overall_design:
Six probes of 60 nucleotides in length were designed for each gene, and a total of 7,501 probes (1,326 genes) were designed for Prochlorococcus. These probes were replicated 4 times in the 8 × 60K array slides, which allowed internal evaluation of signals. The sequences of all oligonucleotide probes were tested in silico for possible cross-hybridization as described below. The probe sequences were used as queries in the BLASTN against the following available nt databases in June 2017: Marine microbes, Microbial Eukaryote Transcription, and Non-redundant Nucleotides NCBI SRA website and all rRNA databases from Silva as of February 2, 2016.
Agilent technology allows 5% nt mismatch in the whole probe region; thus, sequences with a range of 95% to 100% nt identity to the target probe are detected. Therefore, all probes with BLASTN hits with ≥95% over 100% of the nt length were deleted. Next, the probe sequences that passed the cross-hybridization filter were clustered using CD-HIT-EST at 95% nt similarity to select unique probes for Prochlorococcus.
In addition, standard control probes (IS-62976-8-V2_60Kby8_GX_EQC_201000210 with ERCC control probes added) were included randomly as part of the Agilent Technology array to feature locations on the microarray slide. The final design of the microarray was synthesized on a platforms of ca. 62,976 experimental probes and 1,319 control probes on each 8 × 60K array slide.

first: Maria

last: del Carmen Muñoz-Marin


title: Epigenetic profiling of 16 look-alike human couples

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: The Illumina Infinium MethylationEPIC Beadchip was used to obtain genomewide methylation profiles of 16 human couples (32 individuals), selected by their facial resemblance.

overall_design: Bisulphite converted DNA from 32 human saliva samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

first: David

last: Piñeyro


title: Whole genome SNP array of 16 look-alike human couples

summary: The Illumina Infinium HumanOmni5-Quad BeadChip was used to obtain genomewide SNP profiling of 16 human couples (32 individuals), selected by their facial resemblance.

overall_design: Genomic DNA from 32 human saliva samples were hybridised to the Illumina Infinium HumanOmni5-Quad BeadChip.


title: Whole genome SNP array and epigenetic profiling of 16 look-alike human couples

type:
Methylation profiling by array
SNP genotyping by SNP array

overall_design: Refer to individual Series


title: A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome

first: Alexander

last: Murison


title: Next Generation Sequencing of Wild Type (Col-0), fio1-1 and fio1-2 methylated RNA immunoprecipitation and transcriptome in Arabidopsis thaliana

first: Bin

last: Sun


title: Identifying common and region-specific disease signatures in Spinocerebellar Ataxia type 1 cortex and cerebellum

status: Public on Aug 22 2022

city: New Haven

first: Janghoo

last: Lim

state: Connecticut

address: 295 Congress Ave, BCMM Ste 139

institute: Yale University

summary: The neurodegenerative disease spinocerebellar ataxia type 1 (SCA1) is known to lead to progressive degeneration of specific neuronal populations, including cerebellar Purkinje cells (PCs), brainstem cranial nerve nuclei and inferior olive nuclei, and spinocerebellar tracts. The disease-causing protein ataxin-1 is fairly ubiquitously expressed throughout the brain and spinal cord, but most studies have primarily focused on the role of ataxin-1 in the cerebellum and brainstem. Therefore, the functions of ataxin-1 and the effects of SCA1 mutations in other brain regions including the cortex are not well known. Here, we characterized pathology in the motor cortex of a SCA1 mouse model and performed RNA sequencing in this brain region to investigate the impact of mutant ataxin-1 towards transcriptomic alterations. We identified progressive cortical pathology and significant transcriptomic changes in the motor cortex of a SCA1 mouse model. We also identified progressive, region-specific, colocalization of p62 with mutant ataxin-1 aggregates in broad brain regions, but not the cerebellum or brainstem. A cross-regional comparison of the SCA1 cortical and cerebellar transcriptomic changes identified both common and unique gene expression changes between the two regions, including shared synaptic dysfunction and region-specific kinase regulation. These findings suggest that the cortex is progressively impacted via both shared and region-specific mechanisms in SCA1.

overall_design: mRNA profiling was conducted on an Illumina HiSeq 2500. Three biological replicates were sequenced for each genotype (SCA1 KI Atxn1 154Q/2Q mice and wild-type littermate controls) in two brain regions (cortex and cerebellum) at 12 weeks of age, yielding 12 biological samples.

first: Kimberly

last: Luttik

first: Victor

last: Olmos

first: Ashley

last: Owens

first: Aryaan

last: Khan

first: Joy

last: Yun

first: Terri

last: Driessen


title: Transcriptome analysis of Hek293Phoenix cells overexpressing POU3F4 WT or mutated

city: Salzburg

first: Emanuele

last: Bernardinelli

state: Salzburg

address: Strubergasse, 22

department: Institute for Pharmacology and Toxicology

institute: PMU - Salzburg

summary: The project was aimed to the identification of novel transcriptional targets of POU3F4

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hek293Phenix cells transiently transfected with pIRES2-EGFP POU3F4 WT, pIRES2-EGFP POU3F4 C327X or an empty vector


title: RNA data of NCI-H446 tumours treated with ERY974 and/or cisplatin in huNOG mice

city: Kajiwara

first: YUJI

last: SANO

state: Kamakura

institute: Chugai Pharmaceutical Co., Ltd

summary:
We found that ERY974 shows only moderate antitumor efficacy in NCI-H446 non-inflamed tumor in huNOG mice. We also observed that ERY974 + cisplatin increases antitumour efficacy in non-inflamed NCI-H446 tumours.
To identify a mechanism of combination effect, we compared RNA expression of NCI-H446 tumors treated with ERY974, cisplatin, or combination.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumors treated with ERY974, cisplatin, or combination in huNOG model.

first: Yuji

last: Sano

first: Yukari

last: Nishito

first: Yumiko

last: Azuma

first: Yasuko

last: Kinoshita

first: Toshiaki

last: Tsunenari

first: Takahiro

last: Ishiguro


title: Whole genome SNP array of 32 look-alike human couples

first: Manel

last: Esteller

summary: The Illumina Infinium HumanOmni5-Quad BeadChip was used to obtain genomewide SNP profiling of 32 human couples (64 individuals), selected by their facial resemblance.

overall_design: Genomic DNA from 64 human saliva samples were hybridised to the Illumina Infinium HumanOmni5-Quad BeadChip.

first: David

last: Piñeyro


title: RNA data of baseline and ERY974-treated tumour samples for various xenograft tumors (PC10, NCI-H446, MKN45, and MKN74).

summary:
GPC3 expression is one of the important predictive marker of ERY974. However, we found that efficacy of ERY974 is sometimes different in tumors with the similar GPC3 expression.
To identify a predictive biomrker of ERY974, we compared baseline RNA expression of tumors in which ERY974 shows moderate efficacy, and/or achives the regression with similar GPC3 expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumors of PC10 (ERY974 shows regression/GPC3 high), NCI-H446 (ERY974 shows moderate efficacy/GPC3 high), MKN74 (ERY974 shows regression/GPC3 low), and MKN45(ERY974 shows moderate efficacy/GPC3 low).


title: A compartmentalized axon-guidance chip to study neuro-effector interactions in the respiratory tract

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

institute: University of Groningen

summary: Airway cholinergic nerves play a key role in airway physiology and disease. In asthma and other diseases of the respiratory tract, airway cholinergic neurons undergo plasticity and contribute to airway hyperresponsiveness and mucus secretion.  We currently lack mechanistic understanding of airway cholinergic neuroplasticity due to the absence of human in vitro models. Here, we developed a  human in vitro model for peripheral cholinergic neurons using human pluripotent stem cell (hPSC) technology. hPSCs were differentiated towards vagal neural crest precursors and subsequently directed towards functional airway cholinergic neurons using the neurotrophin brain-derived neurotrophic factor (BDNF). Cholinergic neurons were characterized by ChAT and VAChT expression, and responded to chemical stimulation with changes in Ca2+ mobilization. To culture these cells, allowing axonal separation from the neuronal cell bodies, a two-compartment PDMS microfluidic chip was subsequently fabricated . The two compartments were connected via microchannels to enable axonal outgrowth. On-chip cell culture did not compromise phenotypical characteristics of the cells compared to standard culture plates. When the hPSC-derived peripheral cholinergic neurons were cultured in the chip, axonal outgrowth was visible, while the somal bodies of the neurons were confined to their compartment. The microfluidic chip developed in this study represents a human in vitro platform to model neuro-effector interactions in the airways that may be used for mechanistic studies into neuroplasticity in asthma and other lung diseases.

overall_design: Two samples

first: Pien

last: Goldsteen

first: Angelica

last: Guaqueta

first: Patty

last: Mulder

first: Sophie

last: Bos

first: Marloes

last: Eggens

first: Luke

last: van der Koog

first: Joana

last: Soeiro

first: Klaus

last: Mathwig

first: Loes

last: Kistemaker

first: Elisabeth

last: Verpoorte

first: Amalia

last: Dolga


title: Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [scATAC-seq]

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

institute: National Cancer Center

summary: Regulatory T (Treg) cells suppress effective antitumor immunity in tumor-bearing hosts, thereby becoming promising targets in cancer immunotherapy. Here, we show that Treg cells in the tumor microenvironment (TME) of human lung cancers harbor a completely different open chromatin profile compared to effector T cells and peripheral Treg cells. The integrative sequencing analyses revealed that BATF, IRF4, NF-κb, and NR4A were important transcription factors for Treg cell differentiation in the TME. Particularly, BATF was identified as a key regulator, which leveraged Treg cell differentiation through epigenetically controlling activation-associated gene expression, resulting in the robustness of Treg cells in the TME. BATF deficiency in Treg cells remarkably inhibited tumor growth and high BATF expression was associated with poor prognosis in lung cancer, kidney cancer, and melanoma. Our results propose the specific chromatin remodeling and differentiation program of Treg cells in the TME, which can be applied in the development of Treg cell-targeted therapies.

overall_design: scATAC-seq about Treg cells

first: Kota

last: Itahashi

first: Takuma

last: Irie