title: The long-non coding RNA HOTAIR shapes the inflammatory response in joints of the lower extremity

city: Schlieren

first: Caroline

last: Ospelt

address: Wagistrasse 14

department: Department of Rheumatology

country: Switzerland

institute: University Hospital Zurich

summary: Various forms of chronic arthritis like osteoarthritis (OA) or rheumatoid arthritis (RA) are major causes of disability and represent a global burden on health care systems. Inter- and intraindividual differences in the phenotype of arthritis often prevent early diagnosis and effective treatment. Previously, we suggested that site-specific differences in the joint stroma influence the development and the outcome of arthritis and showed that the long non-coding RNA HOTAIR is  expressed exclusively in synovial fibroblasts (SF) of lower joints. Here, we further analysed the function of HOTAIR in SF and in arthritis development. We show that joint-specific HOTAIR expression in SF is stronlgy imprinted in the chromatin landscape of SF by epigenetic mechanisms. Nevertheless, HOTAIR expression in knee SF was downregulated by inflammatory cytokines. Accordingly, HOTAIR was more expressed in OA tissues than in RA tissues. Downregulation of HOTAIR regulated relevant arthritis pathways by epigenetic and transcriptional mechanisms and modified the migratory function of SF, decreased SF mediated osteoclastogenesis, and increased the attraction of B cells by SF. We propose that HOTAIR downregulation in inflammation epigenetically regulates important pathways and functions in SF, and thus modulates the phenotype of arthritis in lower extremity joints.

overall_design: Total RNA was extracted from three human knee synovial fibroblasts silenced for HOTAIR and control synovial fibroblasts 48h after transfection. Synovial fibroblasts were transfected with 50 nM antisense LNA HOTAIR GapmeR (Exiqon, Sequence: 5′-AGGCTTCTAAATCCGT-3′) using Lipofectamine 2000 (Invitrogen). Antisense LNA GapmeR Negative Control A (Cat No 300610) was used as transfection control. Chromatin immunoprecipitation sequencing (ChIPseq) H3K27me3 histone analysis in synovial fibroblasts invalidated for HOTAIR compared to control synovial fibroblasts. Single cell RNAseq data from cultured synovial fibroblasts transfected with either control or HOTAIR targeting GapmeR.

first: Muriel

last: Elhai

first: Raphaël

last: Micheroli

first: Malgorzata

last: Maciukiewicz


title: Next generation sequencing comparing the gene expression between ICSI and SCNT blastocysts of monkey [RNA-seq]

status: Public on Dec 27 2022

city: Shanghai

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

country: China

institute: Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: Somatic cell nuclear transfer (SCNT) has been used to clone cynomolgus monkeys (Macaca fascicularis), but the cloning of other non-human primate species remains to be achieved. On the other hand, our histological examination indicated severe calcification of the placenta of SCNT fetuses. Additionally, we found that some of the maternal-biased imprinting genes were aberrantly lost in the cloned embryos by multi-omics analysis. We thus developed a trophoblast replacement (TR) method, providing an ICSI-derived placenta for the SCNT fetus, to support the full-term development of the cloned embryos after implantation. By combining this TR method with treatment with epigenetic modification factors, we obtained a healthy somatic cell cloned rhesus monkey. Thus, TR represents a useful approach for rhesus monkey cloning.

overall_design: Whole genome bisulfite sequencing and mRNA sequencing of monkey ICSI and SCNT blastocysts, transcriptome sequencing of monkey ICSI and SCNT placentas

first: Zhaodi

last: Liao

first: Jixiang

last: Zhang


title: Effect of depletion of NRF1 on gene expression in mouse PMs  infected with VSV for 8 h

status: Public on Dec 31 2022

city: tianjin

first: tian

last: zhao

address: tainjin nankai

institute: nankai university

summary: To investigate NRF1 in the regulation of the innate immunity, we isolated Mouse peritoneal macrophages in  in wild-type and NRF1-KO mouse

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells after VSV treatment  8 hours
Comparative gene expression profiling analysis of RNA-seq data for Wild-type and NRF1-KO mouse PMs.

first: Tian

last: Zhao


title: Synergistic effect and mechanism study of Phycocyanin photosensitizer combined with Selenium against lung tumor in mouse

status: Public on Jan 01 2023

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

institute: Anhui University

summary: We used selenium as a photodynamic anti-tumor synergist of phycocyanin to explore its inhibitory effect on lung cancer and its molecular mechanism in vitro. First of all, we used LLC-luc mouse lung cancer cells to establish a tumor-bearing model. Selenium-enriched phycocyanin was injected next to the tumor. When it was absorbed by the tumor tissue, the tumor site was irradiated by a 620nm wavelength laser. The changes in tumor size were monitored in real-time and the physiological indexes of mice were measured. It was found that selenium phycocyanin photodynamic therapy could enhance the inhibitory effect of tumors and improve the level of antioxidation in tumor-bearing mice. In addition, the pathological section observation and electron microscope microstructure analysis of the tumor tissue showed that the effect of the selenium-enriched phycocyanin photodynamic treatment group was more significant. At the same time, the tumor tissue transcriptional group sequencing analysis and qRT-PCR verification analysis showed that selenium-enriched phycocyanin photodynamic treatment group could reduce the expression of Mmp13, Serpine1, Vegfa, and Ppbp genes inhibit tumor cell metastasis and proliferation, up-regulate the expression of Ccl2, Ccl3, Cxcl2 and down-regulate the expression of Ccl24 chemokine, and promote tumor local immunity. Our results show that selenium phycocyanin photodynamic therapy plays an anti-tumor effect by promoting tumor cell apoptosis, reducing inflammation, and promoting tumor immunity.

overall_design: The tumor tissues of lung cancer mice treated with SePC and PC and irradiated with 620nm Laser were the treatment group, and those irradiated with 620nm Laser were the control group. Experiments were performed in duplicate.

first: B

last: Huang

first: K

first: H

last: Xia

first: X

last: Zhou


title: Single cell analysis of colorectal cancer tissues

status: Public on Dec 22 2022

city: Nanjing

first: linlin

last: ji

state: Jiangsu

address: 305 Zhongshan East Road, Xuanwu District

institute: Nanjing University

summary: Single cell technologies have paved the way for the characterization of colorectal cancer.We performed scRNA-seq on  human colorectal tumors and their matched adjacent-normal tissues and liver metastasis tissue. The heterogneity of  the tumor immune microenvironment were analyzed.

overall_design: sc-RNA-seq of the single cells from the colorectal cancer tissues including 2 human colorectal tumors and their matched adjacent-normal tissues in addition to 1 matched liver metastasis tissue.

first: Linlin

last: Ji

first: Gongbo

last: Fu

first: Xiaoyuan

last: Chu

first: Zengjie

last: Lei


title: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory (RNA-seq)

status: Public on Jan 11 2023

city: Napoli

first: Maria

middle: Rosaria

last: Matarazzo

address: Via Pietro Castellino 111

country: Italy

institute: Institute of Genetics and Biophysics "ABT"

summary:
Bi-allelic hypomorphic mutations in DNMT3B disrupt DNA methyltransferase activity and lead to Immunodeficiency, Centromeric instability, Facial anomalies syndrome, type 1 (ICF1). While several ICF1 phenotypes have been linked to abnormally hypomethylated repetitive regions, the unique genomic regions responsible for the remaining disease phenotypes remain largely uncharacterized. Here we explored two ICF1 patient-induced pluripotent stem cells (iPSCs) and their CRISPR-Cas9 corrected clones to determine whether DNMT3B correction can globally overcome DNA methylation defects and related changes in the epigenome.
Hypomethylated regions throughout the genome were found highly comparable between ICF1 iPSCs carrying different DNMT3B variants, and significantly overlap with those in ICF1-peripheral blood and lymphoblastoid cell lines. These regions include large CpG island domains, as well as promoters and enhancers of several lineage-specific genes, in particular immune-related, suggesting that they are pre-marked during early development. CRISPR-corrected ICF1 iPSCs reveal that the majority of phenotype-related hypomethylated regions re-acquire normal DNA methylation levels following editing. However, at the most severely hypomethylated regions in ICF1 iPSCs, which also display the highest increased H3K4me3 levels and/or abnormal CTCF binding, the epigenetic memory persisted, and hypomethylation was uncorrected.
Overall, we demonstrate that restoring the catalytic activity of DNMT3B can reverse the majority of the ICF1 aberrant epigenome. However, a small fraction of the genome is resilient to this rescue, highlighting the challenge of reverting disease states that are due to genome-wide epigenetic perturbations. Uncovering the basis for the persistent epigenetic memory will promote the development of strategies to overcome this obstacle.

overall_design: In this study we examined the genome-wide DNA methylation level, gene expression, histone H3K4me3 and H3K36me3 marks enrichment, CTCF and DNMT3B binding in iPSCs derived from fibroblasts of healthy individuals, individuals affected by ICF syndrome type1 (ICF1 iPSCs) and ICF1 iPSCs corrected in the DNMT3B mutations following CRISPR/Cas9 editing.

first: Varsha

last: Poondi-Krishnan

first: Barbara

last: Morone

first: Claudia

last: Angelini

first: Sara

last: Selig

middle: R


title: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory (ChIP-seq)

type: Genome binding/occupancy profiling by high throughput sequencing


title: Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a therapeutic vulnerability in mesenchymal colorectal cancer

status: Public on Dec 16 2022

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

country: USA

institute: WEILL CORNELL MEDICINE

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

overall_design: Refer to individual Series


title: Determination of Shavenbaby effect on histone marks in S2 cells [chipseq_histone]

status: Public on Dec 14 2022

city: Toulouse

first: Cedric

last: Polesello

address: 118 Route de Narbonne

country: France

institute: Centre de Biologie Intégrative de Toulouse

summary:
Shavenbaby (Svb) transcription factor is involved in the differenciation  of epidermal cells, the homeostasis of intestinal stem cell. Svb is first synthetized as a long repressor protein called SvbRepressor (SvbREP). In presence of Pri peptides Svb Repressor is clived by the proteasoome into a shorter activator protein called Svb Activator (SvbACT).
We want in this study determine the binding behaviour of the two Svb forms on S2 cells. We performed ChIPseq histones experiment in S2 cell lines which present Svb REP  or SvbACT or S2 cell without Svb.

overall_design:
The experiment was performed in cells that either did not show Svb (Ctrl) or showed either the SvbACT or SvbREP form. 2 independent replicates were done for each condition.
Cells are cross-linked with 0.8% of formaldehyde for 10 min at room temperature. Cross-linking was stopped by adding glycine (2M) and cells were washed twice in cold with 1X PBS 1 mM NaBu . Cells were resuspended in 500 μL of ChIP permeation buffer (1X PBS, 0.2% Triton, 10mM NaBu), and incubated for 20 min at room temperature.
Lysis Buffer no SDS (140 mM NaCl, 15 mM HEPES pH 7.6, 1 mM EDTA, 1% Triton, 0.1% NaDOC, 0.5 mM DTT, 10mM NaBU, 25X protease inhibitor) during 5min with gentle rotation at 4°C , then cells are lysed on Lysis Buffer 1% SDS (Lysis Buffer no SDS + 1% SDS, 0.5% N-lauroylsarcosine) during 30min at 4°C with gentle rotation. Chromatin was sonicated in Bioruptor (Diagenode) using high-power settings, intervals of 30s burst/pause for six cycles to obtain fragments of ≈ 250 pb.
The sonicated chromatin was diluted 10 times with Lysis Buffer (no SDS) on protein low bind tubes (Eppendorf). The chromatin fraction was cleared by centrifugation (16000 g, 10 °C, 5 min), then pre-clarified (incubed with empty beads) O/N at 4° C. Beads were washed and blocked with 0.1 mg/mL BSA in Lysis Buffer 0.1% SDS, 0.5% N- lauroylsarcosyl during 2hours at 4°C with gentle rotation.
Beads are then bound to the antibody O/N at 4°C with gentle rotation. For one immunoprecipitation 20μL of blocked beads, 5μL of antibody and 400μL of Lysis Buffer 0.1% SDS (Lysis Buffer no SDS + 0.1% SDS, 0.5% N- lauroylsarcosine). Immunoprecipitation was performed for 4 hours at 4°C with gentle rotation with 5μl antibody, by adding 100μL pre-washed beads to 500μL cleared chromatin in protein low bind tubes. 2% of each sample was kept as input. Chromatin-bead complexes were eluted twice in the same tube by incubating the beads for 20 minutes at 70 °C first in 10 mM EDTA, 1% SDS, 50 mM Tris-Cl ph8, and then with TE, 0.67% SDS.
Samples were incubated overnight at 65°C to reverse the cross-link. Decrosslinked samples were treated with 1μL RNAse A during 45min at 37°C then with proteinase K solution (35mg/sample glycogen,100μg/sample proteinase K) during 2h at 55°C. DNA fragments were purified by phenol- chloroform protocol and resuspended in TE.)
ChIPseq of Control, SvbREP and SvbACT S2 cells (single-end 50 nt) were performed with HiSeq 2000 (Illumina) at BGI.

first: Alexandra

last: Mancheno-Ferris


title: Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a therapeutic vulnerability in mesenchymal colorectal cancer I

summary: Mesenchymal colorectal cancer (mCRC) is microsatellite stable (MSS), highly desmoplastic, with CD8+ T cells excluded to the stromal periphery, resistant to immunotherapy, and is driven by low levels of the atypical PKCs (aPKCs). We show here that a salient feature of these tumors is the accumulation of hyaluronan (HA), which along with reduced aPKC levels, predict poor survival. HA promotes epithelial heterogeneity, and the emergence of a fetal metaplastic cell population (TFSC) endowed with invasive cancer features through a network of interactions with activated fibroblasts and components of the immune system. TFSCs are sensitive to HA deposition in vivo and organoids, and their gene expression signature has prognostic value. We demonstrate that in vivo HA degradation with a clinical dose of hyaluronidase impairs mCRC tumorigenesis and enables immune checkpoint blockade therapy by promoting the recruitment of B and CD8+ T cells, including a proportion with resident memory features.

overall_design: sgC and sgPrkci/Prkcz MTOs tumors  were profiled in four biological replicates under normal conditions.

first: Anxo

last: Martinez-Ordoñez

first: Angeles

last: Duran

first: Marc

last: Ruiz-Martinez

first: Tania

last: Cid-Diaz

first: Xiao

last: Zhang

first: Qixiu

last: Han

first: Hiroto

last: Kinoshita

first: Yu

last: Muta

first: Juan

middle: F

last: Linares

first: Hiroaki

last: Kasashima

first: Mohamed

last: Omar

first: Masakazu

last: Yashiro

last: Pannellini

first: Alessio

last: Pigazzi

first: Giorgio

last: Inghirami

first: Luigi

last: Marchionni

first: Darren

last: Sigal

middle: T

last: Diaz-Meco


title: Effect of Shavenbaby on gene expression in S2 cells [RNAseq_S2]

first: Cedric

last: Polesello

summary:
Shavenbaby (Svb) transcription factor is involved in the differenciation  of epidermal cells, the homeostasis of intestinal stem cell. Svb is first synthetized as a long repressor protein called SvbRepressor (SvbREP). In presence of Pri peptides Svb Repressor is clived by the proteasoome into a shorter activator protein called Svb Activator (SvbACT).
We want in this study determine the effect of the two Svb forms on gene expression and determine the Svb target genes. We performed RNAseq experiment in S2 cell lines which present Svb REP  or SvbACT or S2 cell without Svb.

overall_design:
The experiment was performed in cells that either did not show Svb (Ctrl) or showed either the SvbACT or SvbREP form. 2 independent replicates were done for each condition.
Cells were harvested and RNA extraction was made with Rneasy Kit (Qiagen). Banks of reads and sequencing were done by HiSeq 200 (Illumina) at BGI at single-end 50nt per replicate.

first: Alexandra

last: Mancheno-Ferris


title: Determination of Shavenbaby target genes in Intestinal Stem Cells (ISCs) [RNAseq_ISC]

summary:
Shavenbaby (Svb) transcription factor is involved in the differenciation  of epidermal cells and the homeostasis of intestinal stem cells (ISCs). Svb is produced as a long repressor protein called SvbRepressor (SvbREP). In presence of Pri peptides SvbREP is processed into a shorter activator form (SvbACT) through partial proteasomal degradation of the REP domain.
In ISCs, Pri triggers SvbREP to ACT maturation, while SvbREP form accumulates in differentiated enterocytes. The absence of Svb promote the apoptosis of the intestinal stem cells. In ISC, the ectopic expression of SvbREP form  promote the differenciation and the SvbACT form overexpression promotes hyperplasia. (Al Hayel, et al 2020)
Based on these functional analyses, Svb appears to control ISC survival and behavior, balancing proliferation and differentiation through a molecular switch between its 2 antagonistic isoforms.
In this study, we determine the Svb target genes in ISCs. To this aim, we analyze the transcriptomes of ISCs upon modulation of Svb function.

overall_design: The samples correspond to control (ISC Ctrl), Svb-knock down ISCs (RNAiSvb), SvbACT constitutive form overexpression (SvbAct) and SvbREP constitutive isoform overexpression (SvbRep). Three biological replicates were performed for each genotype, on different calendar days.

first: Clement

last: Immarigeon


title: Double-deletion of 1p32 defines ultra-high-risk myeloma, but monoallelic del(1p32) remains a strong prognostic factor

first: Laura

last: Do Souto Ferreira

address: 1 Av. Irène Joliot-Curie

institute: IUCT

summary: Cytogenetics abnormalities (CA) are known to be the preponderant prognostic factor in multiple myeloma (MM). Our team has recently developeda prognostic score based on 6 CA, where del(1p32) appears to be the second worst abnormality after del(17p). The aim of this study was to confirm the adverse impact of 1p32 deletion on newly-diagnosed multiple myeloma (NDMM) patients. Among 2551 NDMM patients, 11% were harboring del(1p32). Their overall survival (OS) was half as long as the OS of patients without del(1p32) (49 months vs. 124 months). Likewise, progression-free survival was significantly shorter. More importantly, double-deletion of the 1p32 locus conferred a dramatically poorer prognosis than a monoallelic del(1p32) (OS: 25 months vs. 60 months). As expected, the OS of del(1p32) patients significantly decreased when this abnormality was associated with other high-risk CA  (del(17p), t(4;14) or gain(1q)). In the multivariate analysis, del(1p32) appeared as a negative prognostic factor; after adjustment for age and treatment, the risk of progression was 1.3 times higher among patients harboring del(1p32), and the risk of death was 1.9 times higher. At the dawn of risk-adapted treatment strategies, we have confirmed the adverse impact of del(1p32) in MM and the relevance of its assessment at diagnosis.

overall_design: Clinical data were obtained from 2551 NDMM patients recruited within hospitals involved in the Intergroupe Francophone du Myélome, followed up for ≥ 36 months or having died or progressed within 36 months post-treatment. The diagnosis was established between 2010 and 2021, and 1258 patients were treated with intensive therapy.  PCs were analyzed either by FISH (848 patients), SNP array (1395 patients) or by NGS (308 patients), depending on the date of receipt. We compared survival and characteristics of patients according to del(1p32) status (282 patients harboring del(1p32) versus 2,269 control patients.

first: Anaïs

last: Schavgoulidze

first: Alexis

last: Talbot

first: Aurore

last: Perrot

first: Titouan

last: Cazaubiel

first: Xavier

last: Leleu

first: Salomon

last: Manier

first: Laure

last: Buisson

first: Sabrina

last: Maheo

first: Luka

last: Pavageau

first: Cyrille

last: Hulin

first: Jean-Pierre

last: Marolleau

first: Laurent

last: Voillat

first: Karim

last: Belhadj

first: Marion

last: Divoux

first: Borhane

last: Slama

first: Sabine

last: Brechignac

first: Margaret

last: Macro

first: Anne-Marie

last: Stoppa

first: Laurence

last: Sanhes

first: Frédérique

last: Orsini-Piocelle

first: Jean

last: Fontan

first: Marie-Lorraine

last: Chretien

first: Hélène

last: Demarquette

first: Mohamad

last: Mohty

first: Hervé

last: Avet-Loiseau

first: Jill

last: Corre


title: Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children

status: Public on Dec 19 2022

city: Bethesda

first: Qin

last: Xu

state: Maryland

address: 4 Memorial Drive

department: Laboratory of Immune System Biology

institute: National Institute of Allergy and Infectious Diseases

summary: SARS-CoV-2 infection triggers adaptive immune responses from both T and B cells. However, most studies focus on peripheral blood, which may not fully reflect immune responses in lymphoid tissues at the site of infection. To evaluate both local and systemic adaptive immune responses to SARS-CoV-2, we collected peripheral blood, tonsils, and adenoids from 110 children undergoing tonsillectomy/adenoidectomy during the COVID-19 pandemic. In order to investigate the adaptive immune response locally, we measured the neutralizing antibodies against to multiple SARS-CoV-2 virus variants and performed high dimensional flow cytometry and CITEseq including TCR and BCR analysis for deeper characterization of the immune response to SARS-CoV-2. In our CITE-seq analyses, we sorted SARS-CoV-2 S1 (spike 1) binding (Spike1+) and non-binding (Spike1-) CD19+ B cells from tonsils, adenoids, and PBMCs from two subjects with a history of COVID-19 and one uninfected control. To assess T cells at the single cell level, we sorted CD95+ CD4+ and CD95+ CD8+ T cells, identified expanded T cell clonotypes, and then compared the CDR3 sequences to those previously reported to recognize SARS-CoV-2 antigens. Our results provide evidence for persistent tissue-specific immunity to SARS-CoV-2 in the upper respiratory tract of children weeks to months after acute infection.

overall_design:
Adenoid cells, tonsil cells, and PBMC from 2 COVID-19 convalescent children and 1 uninfected pediatric control were profiled using multi-modal single cell RNAseq including surface protein staining (customized BioLegend TotalSeq-C lyophilized panel), mRNA expression, T cell receptor V(D)J genes, and B cell receptor V(D)J genes using the 10x Genomics Chromium system. The assignment of individual cells to a donor and tissue was done antibody hashtags.
CNMC 89 - COVID-19 convalescent child
CNMC 71 - COVID-19 convalescent child
CNMC 99  - uninfected pediatric control

first: Pedro

last: Milanez-Almeida

first: Andrew

middle: J

last: Martins

first: Andrea

last: Radtke

first: Kenneth

middle: B

last: Hoehn

first: Cihan

last: Oguz

first: Jinguo

last: Chen

first: Can

last: Liu

first: Juanjie

last: Tang

first: Gabrielle

last: Grubbs

first: Sydney

last: Stein

first: Sabrina

last: Ramelli

first: Juraj

last: Kabat

first: Hengameh

last: Behzadpour

first: Maria

last: Karkanitsa

first: Jacquelyn

last: Spathies

first: Heather

last: Kalish

first: Lela

last: Kardava

first: Martha

last: Kirby

first: Foo

last: Cheung

first: Silvia

last: Preite

first: Patrick

middle: C

last: Duncker

first: Moses

middle: M

last: Kitakule

first: Nahir

last: Romero

first: Diego

last: Preciado

first: Lyuba

last: Gitman

first: Galina

last: Koroleva

first: Grace

last: Smith

first: Arthur

last: Shaffer

first: Ian

last: McBain

first: Peter

last: McGuire

first: Stefania

last: Pittaluga

first: Ronald

middle: N

last: Germain

first: Richard

last: Apps

first: Daniella

last: Schwartz

first: Kaitlyn

last: Sadtler

first: Susan

last: Moir

first: Daniel

middle: S

last: Chertow

first: Steven

middle: H

last: Kleinstein

first: Surender

last: Khurana

first: John


title: Determination of Shavenbaby effect in S2 cells

first: Cedric

last: Polesello


title: Effect of palmitic acid on gene expression of two types of endothelial cells

status: Public on Dec 01 2022

city: Beijing

first: Xiao-Hui

last: Tan

address: 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

summary: To investigate the effect of palmitic acid on gene expression of rat corpus cavernosum endothelial cells (RCCECs) and human umbilical vein endothelial cells (HUVECs), we used palmitic acid to treat these two primary cells, which were then subjected to RNA-seq.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Gene expression profiling analysis of RNA-seq data for endothelial cells treated with palmitic acid or not.

first: Rui-Li

last: Guan


title: Whole genome bisulfite sequencing of hybrid monkey fibroblast

first: Liao

last: Zhaodi

type: Methylation profiling by high throughput sequencing

first: Zhaodi

last: Liao

first: Jixiang

last: Zhang


title: RNA-Seq analysis for the antibiotics resistance between two Streptococcus anginosus strains

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

summary: We performed transcriptome sequencing to profile gene expressions upon the treatment of vancomycin in two Streptococcus anginosus strains.

overall_design: Compare gene expression profiles between S. anginosus KHUD_S1 strain and KHUD_S3 strain using RNA-Seq (Illumina platform: Hi-Seq 3000).

first: Ji-Hoi

last: Moon


title: Leukocyte gene expression predicts human temporal lobe epilepsy seizure frequency

status: Public on Nov 15 2022

city: Tucson

first: Ryan

last: Sprissler

state: Arizona

address: 1657 E Helen St

department: Center for Applied Genetics and Genomic Medicine

institute: University of Arizona

summary:
This study was performed to test the hypothesis that systemic leukocyte gene expression has prognostic value differentiating low from high seizure frequency refractory temporal lobe epilepsy (TLE).
A consecutive series of sixteen patients with refractory temporal lobe epilepsy was studied. Based on a median baseline seizure frequency of 2.0 seizures per month, low versus high seizure frequency was defined as < 2 seizures/month and > 2 seizures/month, respectively.

overall_design: Comparative gene expression profiling analysis of RNASeq data for TLE patients with high seizure frequency and low seizure frequency

first: Branden

last: Lau


title: SOURCE OF LIQUID BIOPSY BIOMARKER: EXOSOME VS WHOLE PLASMA, FASTING VS NON-FASTING

status: Public on Oct 28 2022

city: Honolulu

first: Masaki

last: Nasu

state: HI

address: 651 Ilalo st. University of Hawaii, JABSOM BSB 222 Masaki Nasu

institute: University of Hawaii

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: We compare small noncoding RNA (ncRNA) profiles between exosomes and whole plasma to test a better source of small ncRNA biomarkers. We hypothesize that exosome is a better source of small ncRNA biomarkers compared to whole plasma.
Methods: Small ncRNA sequencings were done using Illumina NextSeq500. Single-end 76 bp reads were explored using FASTQC. GeneGlobe Data Analysis Center, an online platform from Qiagen was used for the small ncRNA-seq data analysis. The mapped read counts for miRNA, piRNA and tRNA were used for differential expression analysis using DESeq2 Bioconductor in R. The small RNA species with logFC > |1| and adj.P-value <0.05 were called differentially expressed.
Conclusion: Small ncRNAs extracted from exosomes were found to have the most consistent profiles among healthy individuals. Whole plasma RNA profiles contain high concentrations of blood-derived miRNAs. These miRNA levels can create batch effects among samples due to different levels of hemolysis. Our finding suggests the importance of using purified exosomes as a better source of small ncRNA biomarkers to avoid the batch effect.

overall_design: RNA samples extracted from Human plasma.

first: Vedbar

last: Khadka

first: Mayumi

last: Jijiwa


title: Gene expression profile at single-cell level of human Simpson-Golabi-Behdel syndrome (SGBS) cells undergoing adipogenesis following knock-down of target genes using CRISPRi

city: Stanford

first: Joshua

last: Knowles

state: California

address: 300 Pasteur Dr.

institute: Stanford University

summary: CROP-Seq combines gene silencing using CRISPR interference (CRISPRi) with single-cell RNA sequencing (scRNA-Seq) in a functional reverse genetic screen. Here, we applied the CROP-Seq approach to study the function of novel genes acting in human adipogenesis or adipocyte biology that were derived from genome-wide association studies (GWAS).

overall_design: Human preadipocyte SGBS cell line expressing KRAB-dCas9 was transduced with a sgRNA library. Following selection, individual cells were captured using microfluidics at different timepoints (day 0, day 4, day 8) during adipogenic differentiation and analyzed using scRNA-Seq.

first: Disha

last: Sharma


title: Prostate cancer androgen receptor activity dictates efficacy of bipolar androgen therapy through MYC

status: Public on Nov 01 2022

city: Baltimore

first: Immunometabolism

last: Department

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University


title: Impact of copper oxide particle dissolution on lung epithelial cell toxicity: response characterization using global transcriptional analysis

status: Public on Nov 03 2022

city: Ottawa

first: Sabina

last: Halappanavar

state: ON

address: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

summary:
The in vitro and in vivo toxicity of copper oxide nanoparticles (CuO NPs) is attributed to both particle and dissolved copper ion species. However, a clear understanding of 1) the specific cellular responses that are modulated by the two species and 2) the temporal dynamics in toxicity, as the proportional amount of particulate and ionic forms change over time, is lacking.
In the current study, in vitro responses to microparticulate CuO (CuO MPs), CuO NPs, and dissolved Cu2+ were characterized in order to elucidate particle and ion induced kinetic effects. Particle dissolution experiments were carried out in relevant cell culture medium, using CuO NPs and MPs. Mouse lung epithelial cells were exposed for 2 - 48 h with 1 - 25 µg/mL CuO MPs, CuO NPs, or 7 & 54 µg/mL CuCl2. Cellular viability and genome-wide transcriptional responses were assessed.
Dose and time dependent cytotoxicity was observed in CuO NP exposed cells, which was delayed and subtle in CuCl2 and not observed in CuO MPs treated cells. Analyses of differentially expressed genes and associated pathway perturbations showed that dissolved ions released by CuO NPs in extracellular medium are insufficient to account for the observed potency and cytotoxicity. Further organization of gene expression results in an Adverse Outcome Pathway (AOP) framework revealed a series of key events potentially involved in CuO NPs toxicity. The AOP is applicable to soluble metal oxide nanoparticle induced toxicity in general, and thus, can facilitate the development of in vitro alternative strategies to screen their toxicity.

overall_design: Purified and extracted RNA from pelleted immortalized mouse lung epithelial cells (FE1) exposed to 0, 1, 5, 10, or 25 ug/mL copper oxide nanoparticles (CuO NPs) or microparticles (CuO MPs), or 0, 7 ug/mL CuCl2, or 5 ug/mL NaCl for 2, 24, or 48 hours

first: Andrey

last: Boyadzhiev

first: Andrew

last: Williams


title: Differential gene expression in human pluriptent stem cell-derived sympathetic neurons

status: Public on Oct 26 2022

city: Athens GA

first: Nadja

last: Zeltner

state: GA

address: 325 Riverbend road

institute: University of Georgia

summary: To investigate and compare the gene expression profile of sympathetic neurons differentiated from healthy hESCs and iPSCs from patient with Familial dysautonomia

overall_design: 8 total smaples, 4 day 35 sympathetic neurons from healthy hESC-H9 and 4 day 35 neurons derived from iPSCs from a patient with Familial Dysautonomia

first: Hsueh-Fu

last: Wu

first: Kenyi

last: Saito-Diaz


title: Expression data with olfactory neuronal cells from healthy controls and schizophrenia patients

status: Public on Oct 20 2022

first: Akira

last: Sawa

state: MD

address: 600 North Wolfe St.

department: Psychiatry and Behavioral Sciences

institute: Johns Hopkins University School of Medicine

summary:
The use of biospecimens sampled from patients with active symptomatic manifestation has been regarded as indispensable for studying pathophysiological mechanisms in many medical conditions, such as several types of cancers, liver disorders encompassing hepatitis, and lung disorders including idiopathic pulmonary fibrosis. However, due to the difficulty in accessing the brain in living patients, this strategy has not been utilized in psychiatry. To overcome this limitation, multiple investigators have recently highlighted the utility of olfactory epithelium-derived neuronal cells (henceforth, ‘olfactory neuronal cells’), easily accessible through a nasal biopsy, as a promising surrogate that captures neuron-relevant molecular signatures in the course of functional impairment in living patients with major psychiatric disorders.
We analyzed gene expression profiles of olfactory neuronal cells from patients with schizophrenia compared to those from healthy controls. A microarray analysis identified significantly dysregulated genes in SZ

overall_design: Olfactory neuronal cells derived from healthy controls (n=6) and schizophrenia patients (n=5) were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Ho

last: Namkung

first: Hiroshi

last: Yukitake


title: Microarray analysis of hippocampal brain tissue of Trpc4 deletion mice

first: Jeeyoung

last: Seo

address: 222, Wangsimni-ro

institute: Hanyang university

summary:
Gene expression of hippocampal brain in Trpc4 deletion mice was investigated
We used microarrays to detail the global programme of gene expression underlying brain hippocampus of Trpc4 mice at postnatal day 56.

overall_design: The brain hippocampus was extracted from WT and Trpc4 k/O male mice of P56 for RNA extraction and hybridization on the Affymetrix microarray.

first: Hyeon

last: Son

first: Jee

middle: Y


title: Immune Infiltration in Aggressive Papillary Craniopharyngioma: High infiltration But Low Action

first: Yanfei

last: Jia

state: Beijing

address: South Fourth Ring West Road

department: Department of Neurosurgery

institute: Beijing Tiantan Hospital

summary: Papillary craniopharyngiomas (PCPs) are biologically benign but clinically aggressive lesions hence affect the quality of life. The expression of inflammatory mediators and regulation of the immune microenvironment in PCPs have not been investigated much. In this study, for the first time, we assessed the immune cell infiltration and immune cell signatures in PCPs by analyzing the bulk-RNA sequencing data. Our results indicated that PCPs are in a state of high immune infiltration but low action with abundant inflammatory cells.

overall_design: We obtained Papillary craniopharyngioma tumor samples and normal brain tissues from  the Beijing Tiantan Hospital between May 2019 and June 2020. The tumor samples  were obtained after the surgical treatment and diagnosed via postoperative pathology  results. Furthermore, normal brain tissues from patients with craniocerebral trauma  were used for comparative purposes, and all the tissue samples were conserved in  RNAlater® (Thermo Fisher Scientific, Waltham, MA) at -80 ℃ for subsequent RNA  sequencing.  Corresponding clinical information, including age, gender, clinical symptoms,  hypothalamic invasion, tumor size, location, and prognosis status, were also collected.  Finally, these tumor samples were divided into three groups based on the hypothalamic  invasion level using the Puget grading system: (1) grade 0 was a low aggressive group,  n = 3; (2) grade 1 was a medium aggressive group, n = 4; (3) grade 2 was a high  aggressive group, n = 4.

first: Songbai

last: Gui

first: Kefan

last: Cai

first: Bochao

last: Zhang


title: Niche-inspired tubuloid differentiation enables modeling of the distal nephron in health and disease

status: Public on Oct 18 2022

city: Utrecht

first: Carla

last: Pou Casellas

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Tubuloid culture allows long-term expansion of primary human renal epithelium. However, the progenitor state in expanding tubuloids comes at expense of differentiation, which limits application. To improve differentiation, we developed niche-inspired culture conditions. A single cell atlas revealed that differentiation predominantly generated ascending limb of Henle and principal cells. Using differentiated tubuloids, we subsequently modeled lithium nephropathy in vitro, and performed single-cell RNA sequencing to look at the transcriptional effects caused by lithium. We found that lithium suppresses electrolyte and solute transporters in multiple cell types and induces a progenitor state in kidney tubuloids.

overall_design: Kidney tubuloids were grown for 3 days post-dissociation in expansion medium (EM) and then treated for 7 days with EM or differentiation medium (FAF). Samples were thereafter harvested for sequencing. For sequencing of lithium samples, tubuloids were grown to a confluent 2D monolayers in EM and then treated for 7 days with FAF + 10 mM sodium (Na) or lithium (Li).

first: Fjodor

middle: A

last: Yousef-Yengej

first: Carola

last: Ammerlaan

first: Joep

last: Beumer

first: Charlotte

last: Olde-Hanhof

first: Emre

last: Dilmen

first: Elise

last: Meeder

first: Harry

last: Begthel

first: Joost

middle: G

last: Hoenderop

first: Maarten

last: Rookmaaker

first: Marianne

last: Verhaar

first: Hans

last: Clevers


title: Alveolar epithelial progenitor cells drive lung regeneration via dynamic changes in chromatin topology modulated by lineage-specific Nkx2-1 activity

status: Public on Oct 19 2022

city: CINCINNATI

first: William

last: Zacharias

state: OH

address: 3333 BURNET AVE

institute: Cincinnati Children's Hospital Medical Center

summary: Lung epithelial regeneration after acute injury requires coordination of complex cellular and molecular processes required for progenitor proliferation and differentiation of specialized alveolar cells to pattern the morphologically complex alveolar gas exchange surface. During regeneration, specialized Wnt-responsive alveolar epithelial progenitor (AEP) subset of alveolar type 2 (AT2) cells transition to alveolar type 1 (AT1) cells through specialized progenitor states, though the precise molecular and epigenetic determinants of these processes remain unclear. Here, we report a refined primary murine alveolar organoid assay which recapitulates critical aspects of in vivo regeneration, providing a tractable model to dissect these key regenerative processes. Clonal expansion of single AEPs generated complex alveolar organoids with extensive structural maturation and organization. These organoids contain properly patterned AT1 and AT2 cells surrounding numerous alveolar-like cavities with minimal structural contribution from mesenchymal cells, implying extensive cell autonomous regenerative function encoded in adult AEPs. Leveraging a time series of paired scRNAseq and scATACseq analysis, we identified the AEP state at single cell resolution and defined two distinct AEP to AT1 intermediate states: a widely reported transitional state defined by cell stress markers and a second state defined by differential activation of signaling pathways mediating AT1 cell differentiation. Transcriptional regulatory network (TRN) analysis demonstrates that these AT1 transition states are driven by distinct regulatory networks controlled in part by differential activity of the lung master regulatory factor Nkx2-1. Genetic ablation of Nkx2-1 in AEP-derived organoids is sufficient to cause irreversible transition to a proliferative stressed transitional state characterized by disorganized, uncontrolled growth. Finally, AEP-specific deletion of Nkx2-1 in adult mice leads to rapid loss of AEP state, clonal expansion, and disorganization of alveolar structure, implying a continuous requirement for Nkx2-1 in maintenance and function of adult lung progenitors.  Together, these data provide new insight into lineage hierarchies in lung regeneration and implicate dynamic epigenetic maintenance via lineage transcription factors as central to control of facultative progenitor activity in AEPs.

overall_design: Lung alveolar epithelial progenitor derived organoids were digested into a single cell suspension and analyzed by scRNAseq. Nuclei were prepared from this single cell suspension for separate analysis by scATACseq

first: Andrea

last: Toth


title: Effect of depletion of ZNF692 on gene expression in  DLD1 colorectal human cells

status: Public on Oct 17 2022

city: Birmingham

first: Yanfeng

state: AL

address: Kaul Human Genetics Building 720 20th St S

department: Department of Genetics

institute: University of Alabama at Birmingham

summary:
To investigate the function of ZNF692 in colorectal cancer, we established DLD1 cell lines in which  target gene has been knocked out by CRISPR-cas.
We then performed gene expression profiling analysis using data obtained from DLD1 colorectal human cells wt (sgC for guide control) or crispr knockout for ZNF692 (sgZ1 for guide 1, and sgZ3 for guide 3). We have each condition in triplicates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DLD1 cells and its Ko derivatives (ZNF692).

first: Maria

last: Navarro

first: Maralice

last: Sorrell


title: Acquired resistance to entrectinib or crizotinib drives differential gene expression in ROS1+ NSCLC

status: Public on Oct 06 2022

city: Denver

first: LOGAN

last: TYLER

state: CO

address: 1240 Ulster St

institute: UC Anschutz Medical Campus

summary: Utilizing primary, patient tumor-derived ROS1+ NSCLC cell lines, we derived TKI-resistant cell lines by chronic exposure to TKI in the media. One of our parental, ROS1 TKI-sensitive cell lines harbors a TPM3-ROS1 fusion (CUTO28) and the other harbors a CD74-ROS1 fusion (CUTO37). Entrectinib-resistant (-ER) and crizotinib-resistant (-CR) lines are so named when they are stably proliferating at 500nM concentration of the respective TKI. We sought to investigate transcriptome changes with acquired resistance to entrectinib or crizotinib.

overall_design: Triplicate samples were submitted and analyzed per cell line for bulk RNA sequencing, with the exception of CUTO28-ER where one sample was found to be an outlier and thus duplicates were analyzed. One sample per cell line was submitted for whole exome sequencing.

first: Logan

last: Tyler


title: Amino acid intake strategies define pluripotent cell states

status: Public on Nov 23 2022

first: Lydia

last: Finley

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq of mouse embryonic stem cells undergoing exit from pluripotency

overall_design: Comparative genomic profiling of mouse embryonic stem cells cultured in either 2i/LIF or serum/LIF + 2i media and induced to exit from naïve pluripotency for 12, 24, or 40 hours. 0 hour samples serve as controls.

first: Benjamin

last: Jackson

first: Katrina

middle: I

last: Paras

middle: W


title: FOSL1 modulates Schwann cell responses in the wound microenvironment and regulates peripheral nerve regeneration

status: Public on Oct 02 2022

city: Nantong

first: Qianqian

last: Chen

state: Please Select

address: 19 Qixiu Road, Chongchuan District

institute: Nantong University

summary: Peripheral glial Schwann cells switch to a repair state after nerve injury, proliferate to supply lost cell population, migrate to form regeneration tracks, and generates a permissive microenvironment for nerve regeneration. Exploring essential regulators of the repair responses of Schwann cells may benefit the clinical treatment for peripheral nerve injury. In the present study, FOSL1 regulates Schwann cell phenotype modulation and provided a novel therapeutic approach to orchestrate the regeneration and functional recovery of injured peripheral nerves.

overall_design: ChIP-seq was used to identify FOSL1-FLAG-target protein binding target genes in primary Schwann cells of rat newborn sciatic nerve

first: Qian

last: Zhao

first: Sheng

last: Yi


title: Proteasome inhibition silences oncogenic transcripts in multiple myeloma through HDAC3-mediated DNA condensation and gene relocation [RNA-seq]

status: Public on Nov 21 2022

city: Houston

first: Laure

last: Maneix

state: TX

address: One Baylor Plaza, MS230, Alkek building, Room N830

department: Huffington Center on Aging

institute: Baylor College of Medicine

summary:
Purpose: We report the NGS-derived transcriptome profiling (paired-end RNA-seq) following proteasome inhibition in the multiple myeloma cell line MM.1S.
Methods: MM.1S cells were treated for six hours with the synthetic proteasome inhibitor lactacystin and RNA expression changes were quantified and compared to DMSO control-treated cells by RNA-sequencing.

overall_design: MM.1S myeloma cells were profiled for gene expression after 6h of growth in the presence or the absence of lactacystin (6µM), using Illumina HiSeq 2500 high-throughput sequencing system.

first: Andre

last: Catic


title: Global characterization of prostate cancer cell expression upon treatment with media conditioned from human stromal cells epitopically expressing epiregulin (EREG)

status: Public on Sep 30 2022

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Technical advances in next generation sequencing (NGS) has revolutionized system-based analysis of genome-wide expression, cellular pathways and responses. We performed this study to establish the transcriptomic profiles of human prostate cancer cell lines exposed to conditioned media from human primary stromal cells engineered to express epiregulin (EREG), a typical factor of the senescence-associated secretory phenotype (SASP), the latter a hallmark of senescent cells.

overall_design: Transcript profiles of prostate cancer cell lines mainly PC3 and DU145 were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Changxu

last: Wang


title: Integrative functional genomic analyses identify novel genetic variants influencing skin pigmentation in indigenous Africans [RNA-seq]

status: Public on Sep 15 2022

city: Philadelphia

first: Yuanqing

last: Feng

state: Pennsylvania

address: 430 Clinical Research Building, 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

summary:
Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. We identified 1,157 candidate variants influencing skin pigmentation in indigenous Africans by genome-wide association studies and scans of natural selection based on differentiation in allele frequencies between lightly pigmented southern African Khoesan populations and other darkly pigmented African populations. We applied massively parallel reporter and chromosome conformation capture assays to identify novel regulatory variants and their target genes related to skin pigmentation in melanocytic cells. We identified 165 SNPs showing strong differential regulatory activities between alleles. Combining CRISPR-mediated genome editing, transcriptome profiling and melanin assays, we identified causal regulatory variants impacting pigmentation near MFSD12/HMG20B, MITF, OCA2, and DDB1/CYB561A3/TMEM138. We identified CYB561A3 as a novel gene regulating pigmentation by impacting genes involved in oxidative phosphorylation and melanogenesis. Our results broaden our understanding of the genetic basis of human skin color diversity and human adaptation.
To test the role of candidate enhancers and variants in skin pigmentation, we performed CRISPR inhibition or knockout of enhancers containing the functional variants identified by MPRA in melanocytic cells. Then, we performed gene expression profiling analysis using data obtained from RNA-seq of these CRISPR-edited cells. We also performed RNA-seq using CYB561A3-koncout MNT1 cells or  CYB561A3-overexpressing MNT1 cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MNT-1 cells and enhancer knockdown or knockout  derivatives (CRISPR KO of enhancer E1 of MITF, CRISPR inhibition of enhancer E2 of OCA2, CRISPR KO or inhibition of enhancer E1 of CYB561A3, CYB561A3 KO, CYB561A3 overexpression).

first: Sarah

last: Tishkoff


title: Melatonin inhibited tumorigenesis of bladder cancer via suppressing PPARγ/ENO1 mediated glycolysis

status: Public on Sep 06 2022

city: Wuhan

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary: Bladder cancer (BLCA) is one of the most malignant human cancers in the world. The increasingly prominent phenomenon of chemoresistance has become an essential obstacle to clinical treatment for BLCA, and there is an urgent need to explore novel drugs to improve the current clinical status. Melatonin is a well-known natural hormone that showed a potential anti-cancer effect in multiple human cancers. In our study, we comprehensively explored the inhibitory effect of melatonin on BLCA and found that it could suppress the glycolysis process in BLCA cells. Moreover, we discovered that the ninth step enzyme ENO1 of glycolysis was the downstream effector of melatonin and could be a predictive biomarker of BLCA patients.

overall_design: To investigate the mechanism of how melatonin inhibits bladder cancer, we performed RNA sequencing on DMSO and melatonin-treated bladder cancer cells.

first: Dexin

last: Shen

first: Xinghuan


title: High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci.

status: Public on Sep 09 2022

city: Bethesda

first: Zachary

last: Batz

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

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

overall_design: Refer to individual Series


title: Klf5 regulates trophoblast stem cell pluripotency as a transcription activator via H3K27ac dependent chromatin accessibility

status: Public on Sep 27 2022

first: Wu

last: Linhui

state: Hubei

address: No.1 Shizishan Street

department: College of Animal Science and Veterinary Medicine

institute: Huazhong Agricultural University

summary: The effective proliferation and differentiation of Trophoblast Stem Cells (TSCs) is necessary to ensure the normal development of the placenta, which is the key to maintain fetal growth and development during pregnancy. Previous studies have found that knocking out Klf5 affects abnormally trophoderm development, but its regulatory mechanism is unclear. Here we performed klf5 knockdown in TSCs cultured under stem state condition. Klf5-KD triggred obvious differentiation phenotype.

overall_design: To further evaluate the functional roles of Klf5 in TSCs, we conducted RNA-seq and ATAC-seq in both TSCs and Klf5-KD TSCs. We next performed ChIP-seq to obtain a comprehensive overview of direct targeting for Klf5 in TSCs. Moreover, diverse histone markers were performed in TSCs and Klf5-KD TSCs.

first: Chengli

last: Dou

first: Linhui

last: Wu

first: Yiliang

last: Miao


title: High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci [Hi-C]

summary: Chromatin organization and enhancer-promoter contacts are critical for establishing unique spatiotemporal gene expression patterns in distinct cell types. Non-coding genetic variants can influence cellular phenotypes by modifying higher-order transcriptional hubs and consequently gene expression. To elucidate transcriptional regulation by non-coding genome in human retina, we mapped chromatin contacts at high resolution and integrated this data with histone marks and super-enhancers (SEs). Retinal SEs exhibited abundant local interactions and reside in topologically associated domains (TADs) with weak boundary insulation. Notably, intra-TAD positioning of SEs correlated with the biological function of their target genes in the retina. We also identified regulatory landscapes of retinopathy genes and uncovered candidate genes for risk variants associated with age-related macular degeneration and glaucoma. Our studies of high-resolution genomic architecture of the human retina provide new insights into genetic control of tissue-specific functions, suggest paradigms for missing heritability, and enable the dissection of multifactorial disease phenotypes.

overall_design: High resolution Hi-C, ATAC-seq, and Cut&Run (H3K4me3, H3K9me3) performed on adult human retina samples.

first: Marchal

last: Claire

first: Singh

last: Nivedita

first: Batz

last: Zachary

first: Advani

last: Jayshree

first: Jaeger

last: Catherine

first: Corso-Diaz

last: Ximena

first: Swaroop

last: Anand


title: Efficacy of GV1001 with gemcitabine/capecitabine in previously untreated patients with advanced pancreatic ductal adenocarcinoma having high serum eotaxin levels (KG4/2015): an open-label, randomized, phase 3 trial.

status: Public on Sep 03 2022

city: Seoul

first: Jung Hyun

last: Jo

state: --- Select ---

address: 50-1 Yonsei-ro

institute: Yonsei University Health System

summary: The TeloVac study indicated that GV1001 did not to improve the survival of advanced pancreatic ductal adenocarcinoma (PDAC) patients. However, the cytokine examinations of the study suggested that high serum eotaxin levels may predict responses to GV1001. This phase III trial aimed to assess the efficacy of GV1001 with gemcitabine/capecitabine for eotaxin-high patients with untreated locally advanced and metastatic PDAC. In addition, we proposed potential blood markers to predict response to GV1001 treatment based on correlative studies.

overall_design: To determine potential markers to predict chemoresponse to GV1001, patients’ samples at the time of pretreatment were analyzed using antibody microarray analysis. According to survival, good responders and poor responders were selected from the GV1001 and control groups to compare the difference of marker expression by patients’ treatment response. A total of 73 patients’ samples were analyzed; 49 samples from the GV1001 group (22 good responders and 27 poor responders) and 24 samples from the control group (13 good responders and 11 poor responders). [Sample title header- GV1001 group: GG, control group: CG, good responder: GR, poor responder: PR]

first: Jung

first: Dawoon

middle: E

last: Jung

first: Si

last: Song


title: Immune challenged SC-islets first response profiled by single cell transcription analysis after co-culture with human allogeneic PBMCs [scRNA-seq_invitro]

status: Public on Sep 01 2022

city: Boston

first: VICTOR

last: BARRERA BURGOS

state: Massachusetts

address: Landmark 401 Park Drive 3 East

department: Biostatistics

institute: Harvard School of Public Health

summary: We performed an in vitro co-culture of allogeneic PBMCs and SC-islet clusters. SC-islet clusters were enriched for β cells (using CD49A magnetic sorting; SC-α still remain at lower numbers) (Veres et al., 2019), dissociated and reaggregated to obtain a more uniform cell count between wells. SC-islets were co-cultured with human allogeneic PBMCs for 24 or 48 hours. As controls [time(t)=0], SC-islets remained in culture without PBMC addition. These samples, in addition to PBMCs alone (t=0), were used for scRNA-seq (Figure 2A).

overall_design: Comparing expression datasets from PBMC co-cultured with SC-islets, to SC-islets alone

first: Elad

last: Sintov

first: Victor

last: BARRERA

first: Igor

last: Nikolskiy


title: Whole genome CRISPR screening identifies genetic manipulations to reduce immune rejection of stem cell-derived islets


title: Single cell transcriptional profile of SC-islet grafts in an in vivo humanized model [scRNA-seq_invivo]

summary: To study immune responses in the context of human allogeneic graft rejection, we chose the Hu-PBL-NSG-MHCnull humanized mouse (Brehm et al., 2019). NOD-scid IL-2 receptor subunit γ (IL2rg)null (NSG) immunocompromised mice that lack murine MHC class I and II, were transplanted (under the kidney capsule, n=12) with 5M SC-islets (HLA-A2 positive), followed by human PBMC injection (termed ‘hPi-mice’; 50M/mouse, n=6) from healthy unmatched donors (HLA-A2 negative).  The lack of murine MHC allowed us to monitor the graft function for prolonged durations without the risk of xenogeneic graft vs host disease (GVHD). Half of the SC-islet transplanted cohort (n=6 mice) was used as the control, without PBMC injection (Figure 1A).  Since graft elimination by PBMCs is incomplete and residual endocrine cells remain in the hPi-mice grafts, we retrieved the SC-islet grafts for single cell RNA sequencing (scRNA-seq) analysis. These samples, along with pre-injected PBMCs as controls, were used for 10x Genomics mRNA expression library preparation and Illumina sequencing.

overall_design: Comparing expression datasets from hPi grafts to controls

last: Barrera


title: Single-cell RNA sequencing in Kawasaki disease

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: We performed single-cell RNA sequencing (using Cell Ranger Single Cell Pipeline v.4.0.0 to process data de-multiplexing, barcode processing, and single cell 3' gene counting generated by the 10X Chromium platform) in KD patients (within 24 hours before IVIG treatment) and age-matched fever controls.

overall_design: Peripheral blood samples were collected from five KD patients (include three KD patients with following development of coronary artery lesions) within 24 hours before IVIG treatment, two febrile controls and two healthy subjects in EDTA collection tubes (vender) and centrifuged at 400 × g for 5 min at 4 °C. The cell viability of purified white blood cells (WBC) exceeded 90%.

first: Kuo

last: Ho-Chang

first: Chen

last: Kuang-Den

first: Huang

last: Ying-Hsien

last: Kuang-Jer


title: Identification of Wnt target genes associated with malignant phenotypes in CTNNB1-mutated NSCLC

city: Maebashi

first: Noriaki

last: Sunaga

state: Gunma

address: 3-39-15 Showa-machi

department: Department of Respiratory Medicine

country: Japan

institute: Gunma University Graduate School of Medicine

summary: Microarray analysis comparing the expression profiles of siRNA-mediated CTNNB1-silenced and CTNNB1-retained  HCC15 cells harboring a homozygous CTNNB1 S45F mutation revealed that besides several known Wnt genes, LGR6 was significantly downregulated by CTNNB1 knockdown in HCC15 cells.

overall_design: Gene expression was examined in siRNA-mediated CTNNB1-silenced HCC15 cells and CTNNB1-retained (control siRNA-treated) HCC15 cells. HCC15 cells were transfected with an siRNA targeting CTNNB1 and were collected at 48 h post-transfection, followed by tRNA extraction from the cells.

first: Luc

last: Girard


title: Transcriptional profiling of mouse ST2+ and ST2- Tregs across tissues

status: Public on Jul 24 2022

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Foxp3+ regulatory T cells (Tregs) are critical mediators of peripheral tolerance and immune homeostasis. Tregs that express the IL-33 receptor ST2 are enriched in peripheral nonlymphoid tissues and can exert a variety of tissue-specific functions from metabolic regulation within adipose tissue to skeletal muscle repair. However, the relationship between ST2+ and ST2- Tregs within and across different tissues remains unclear. To compare murine ST2- and ST2+ Tregs within and across tissues, we performed RNA sequencing (RNAseq) of ST2-CD44hi and ST2+CD44hi Tregs from blood, spleen, lungs, visceral adipose tissue (VAT), colon, and skin. RNAseq was also performed on ST2- CD44lo CD62L+ Tregs from the spleen and lungs. We found that the tissue microenvironment was the major factor shaping the transcriptome of Tregs across tissues. Across the tissues studied, Treg transcriptomes displayed an ordered hierarchy that may represent graded levels of activation or differentiation across tissues. We also identified a core signature that distinguished ST2+ Tregs from ST2- Tregs across tissues and a large number of differentially expressed genes between ST2- and ST2+ Tregs within individual tissues that could support the tissue-specific adaptation and function of ST2+ Tregs. In summary, our work highlights the unique, tissue-specific phenotype of ST2+ Tregs and reveals a core ST2+ Treg transcriptional signature shared across tissues.

overall_design: Single cell suspensions were prepared from the blood, spleen, lungs, abdominal visceral adipose tissue (VAT), colonic lamina propria, and back skin of five Foxp3YFP-cre mice. ST2+CD44hi Tregs and ST2-CD44hi Tregs were flow sorted from all tissues; ST2-CD44loCD62L+ Tregs were sorted from spleen and lungs. RNAseq was performed on libraries prepared from amplified cDNA prepared from the sorted populations. Mouse IDs are provided so that samples from a single mouse can be identified.

first: Sabine

last: Spath

first: Florence

last: Roan

first: Scott

last: Presnell

first: Barbara

last: Hoellbacher

first: Steven

last: Ziegler


title: Unique microglial transcriptomic signature within the hippocampal neurogenic niche

status: Public on Aug 30 2022

city: New York

first: Sana

last: Chintamen

state: New York

institute: Columbia University Irving Medical Center

summary: We utilize single cell RNA-sequencing to uncover different myeloid lineage populations in the adult murine hippocampus. By evaluating transcriptome profiles of over 20,000 cells, we have uncovered heterogeneity in innate immune cells of the hippocampus. In particular, we find a transcriptionally distinct population of cells corresponding to microglia in the subgranular zone of the hippocampus, the site of adult neurogenesis. Our results provide a reference for differentially expressed genes that can be used to characterize subpopulations within the hippocampal myeloid population.

overall_design: 3 single cell RNA-sequencing samples of hippocampal myeloid cells originating from 12 biological replicates. Six male and six female samples.

first: Pallavi

last: Gaur

first: Elizabeth

last: Bradshaw

first: Vilas

last: Menon

last: Kernie


title: Transcriptomes analysis of COVID-19 Inactivated Vaccine and Protein Subunit Vaccine as Third Booster Dose in Human

city: Jinan

first: yuwei

last: Zhang

state: Shandong

address: No.16992 Jingshi Road

department: Pathogenobiology

institute: SDCDC

summary: To compare the effects of different types of SARS-CoV-2 vaccines in booster immunization, this study established a population cohort vaccinated with inactivated vaccine and protein subunit vaccine as the third booster vaccine, respectively. We collected serum and PBMC samples from participants in chronological order, and performed a systematic review of distinct antibody signatures and microtranscriptomics to provide data support for booster immunization.

overall_design: Comparative gene expression profiling of RNA-seq data from PBMC samples from a population cohort vaccinated with inactivated vaccine and protein subunit vaccine as a third booster vaccine.

first: Xiaolin

last: Jiang

first: Yuwei

first: Xingyu

last: Guo

first: Mingxiao

last: Yao

first: Shanshan

last: Han

first: Zengqiang

last: Kou


title: Expression of SARS-CoV-2 proteins in Drosophila heart and blood

status: Public on Aug 24 2022

city: Baltimore

first: Hangnoh

middle: Joseph

last: Lee

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

summary: We investigated the transcriptomic impact of SARS-CoV-2 proteins in Drosophila malanogaster with a focus on heart development and hemolymph coagulation.

overall_design: RNA-Seq analysis of fly hearts and blood cells (hemocytes) that express either SARS-CoV-2 Nsp6 (heart) or SARS-CoV-2 Orf7a (hemocytes). Hearts or hemocytes that express GFP (heart) or tubulin-Gal4 (hemocytes) were used as controls. The experiments were biologically duplicated/triplicated.

first: Huang

last: Xiaohu

first: Zhu

last: Junyi

first: Han

last: Zhe


title: Spontaneous metastasis xenograft models link CD44 isoform 4 to angiogenesis, hypoxia, EMT and mitochondria-related pathways in colorectal cancer

status: Public on Jul 18 2022

city: Moscow

first: Stepan

last: Nersisyan

address: Vavilova str 7

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

summary: Objective: To determine the functional relevance of CD44 isoforms for distant metastasis formation in human colorectal cancer (CRC).  Design: We used a pan-CD44 knockdown (kd) approach in a clinically relevant cell line/ xenograft model (HT-29) that spontaneously metastasizes to multiple sites in vivo. Transcriptomics, proteomics and kinomics were used in addition to corresponding validation steps to explain the observed effects. Findings were further corroborated by 3D in vitro culture, tissue microarray and bioinformatics analyses.   Results: HT-29 cells mainly express the clinically relevant CD44 isoforms 3 and 4. CD44 kd impairs primary tumor formation and abrogates distant metastasis in vivo. Both CD44 isoforms are induced in the paranecrotic, hypoxic regions of the xenograft primary tumors but are largely absent in the corresponding lung metastases. Tumor angiogenesis is improved in the paranecrosis upon CD44 kd, accompanied by reduced HIF-1α, EMT, and CEACAM5 expression. Vice versa, mitochondrial genes and proteins are induced upon CD44 kd as is oxidative phosphorylation. Hypoxia increases VEGF release from 3D HT-29 spheres, which is strikingly enhanced in CD44 kd spheres. The metastasis-promoting role of CD44 is reflected by an unfavorable prognostic effect of CD44 isoform 4 in patients (as opposed to isoform 3). Accordingly, the genes regulated by the CD44 kd in vivo concordantly overlap specifically with the genes regulated by CD44 isoform 4 in patients.   Conclusion: In CRC, CD44 kd (most probably isoform 4) evidently impairs metastasis formation by improving VEGF release and thus angiogenesis in hypoxic conditions, thereby decreasing hypoxia, EMT, stemness, and promoting mitochondrial metabolism.

overall_design: Two types of cells were injected into SCID mice: HT-29 cell lines with shRNA-mediated knockdown of CD44 (shCD44) and control HT-29 cell lines transduced with shRNA against firefly luciferase (shLUC). mRNA was isolated from xenograft tumor tissues (seven samples per group) and analyzed using RNA-seq.

first: Arun

last: Everest-Dass

first: Diana

last: Maltseva

first: Hanna

last: Maar

first: Victor

last: Novosad

first: Jennifer

last: Schröder-Schwarz

first: Vera

last: Freytag

first: Mia

last: Beine

first: Alina

last: Schiecke

first: Malte

last: Kriegs

first: Omar

last: Elakad

first: Hanibal

last: Bohnenberger

first: Maria

last: Raygorodskaya

first: Linda

last: Krause

first: Mark

last: von Itzstein

first: Alexander

last: Tonevitsky

first: Udo

last: Schumacher

first: Daniel

last: Wicklein

first: Tobias

last: Lange


title: Transcriptional profiling identifies white matter changes in eNOS+/- mice II

status: Public on Jul 12 2022

city: Charlestown

first: Mahesh Chandra

last: Kodali

state: MA

department: Neurology

institute: Massachusetts General Hospital / Harvard Medical School

summary: To elucidate the effects of Sodium nitrate feeding eNOS deficiency at the transcriptional level, RNA-seq was performed on white matter region dissected from the brains of eNOS+/+ and eNOS-/- and eNOS -/- + Sodium Nitrate treatment

overall_design: RNA-Seq on eNOS+/+ and eNOS-/- and eNOS-/- with Sodium Nitrate treatment

first: Francesca-fang

last: Liao

first: Zhengjun

last: Wang


title: Dynamic changes in cellular atlases and communication patterns within yak ovaries across diverse reproductive states unveiled by single-cell analysis [scRNAseq_Yak_Ovary_Estrus_2]

status: Public on Jul 28 2022

city: Lanzhou

first: Jie

last: Pei

state: Gansu

address: No. 335 Jiangouyan ST, Qilihe District

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

summary: The scRNA-seq technology was performed to delineate an atlas of molecular signature of various cell types in yak ovary. The cell types were identified according to their specifically expressed genes and the functional enrichment of the genes.

overall_design: One sample from yak ovary in estrus

first: Xian

last: Guo


title: Cholesterol and matrisome pathways dysregulated in APOE ε4 human microglia and astrocytes [populationAPOE]

status: Public on Jun 23 2022

first: Julia

last: TCW

address: 700 Albany St.

institute: Boston University

summary: The impact of Apolipoprotein E4 (APOE4), the strongest genetic risk factor for Alzheimer's disease (AD), on human brain cellular function remains unclear. Here we investigated the effects of APOE4 on brain cell types derived from population and isogenic human induced pluripotent stem cell models, post-mortem brain and APOE targeted replacement mice. Population and isogenic models uncover that APOE4 local haplotype rather than a single risk allele alone contributes to the risk. Global transcriptomic analyses reveal human specific, APOE4-driven lipid metabolic dysregulation in astrocytes and microglia. APOE4 leads to elevated de novo cholesterol synthesis despite the intracellular cholesterol accumulation due to lysosomal sequestration of cholesterol in astrocytes. Transcriptome analyses uncovered Matrisome dysregulation associated with upregulated chemotaxis, glial activation and lipid biosynthesis in astrocytes, co-cultured with neurons that recapitulates altered astrocyte matrisome signaling in human brain. Thus, APOE4 initiates glia-specific cell and non-cell autonomous dysregulation that may contribute to increased AD risk.

overall_design: We performed bulk RNA-sequencing on population iPSC-derived, CRISPR-edited isogenic iPSC-derived astrocytes, microglia, mixed cortical cultures, BMECs from APOE 33 vs APOE 44 and mouse astrocytes and microglia from APOE 33, APOE 44, Apoe WT and Apoe KO. This particular dataset is population APOE 33 and APOE 44 cell types.

first: Alison

last: Goate

first: Wayne

last: Poon


title: Plasmodium falciparum and TNF-a Differentially Regulate Inflammatory and Barrier Integrity Pathways in Human Brain Endothelial Cells

status: Public on Aug 20 2022

city: New York City

first: Ze

last: Chen

address: 430 East 29th Street

institute: NYU Grossman School of Medicine

summary: Cerebral malaria is a severe complication of Plasmodium falciparum infection characterized by the loss of blood-brain barrier (BBB) integrity, which is associated with brain swelling and mortality in patients. P. falciparum-infected red blood cells and in!ammatory cytokines, like tumor necrosis factor alpha (TNF-a), have been implicated in the development of cerebral malaria, but it is still unclear how they contribute to the loss of BBB integrity. Here, a combination of transcriptomic analysis and cellular assays detecting changes in barrier integrity and endothelial activation were used to distinguish between the effects of P. falciparum and TNF-a on a human brain microvascular endothelial cell (HBMEC) line and in primary human brain microvascular endothelial cells. We observed that while TNF-a induced high levels of endothelial activation, it only caused a small increase in HBMEC permeability. Conversely, P. falciparum-infected red blood cells (iRBCLs) led to a strong increase in HBMEC permeability that was not mediated by cell death. Distinct transcriptomic pro"les of TNF-a and P. falciparum in HBMECs con"rm the differential effects of these stimuli, with the parasite preferentially inducing an endoplasmic reticulum stress response. Our results establish that there are fundamental differences in the responses induced by TNF-a and P. falciparum on brain endothelial cells and suggest that parasite-induced signaling is a major component driving the disruption of the BBB during cerebral malaria, proposing a potential target for much needed therapeutics.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for a human brain microvascular endothelial cell line incubated with media control, TNF-alpha, a lysate of control uninfected RBC or a lysate of Plasnodium falciparum-infected RBC.

first: Marisol

last: Zuniga

first: Claudia

last: Gomes

first: Criseyda

last: Martinez

first: Joseph

last: Devlin

first: P'ng

last: Loke

first: Ana

last: Rodriguez


title: RNA polymerase II and PARP1 shape enhancer-promoter contacts [ChRO-seq]

status: Public on Jun 18 2022

city: Ithaca

first: Charles

middle: Grahe

last: Danko

state: NY

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

institute: Cornell University

summary: What controls enhancer-promoter communication to allow for cis-transcriptional regulation remains a mystery. Here we studied how transcriptional dynamics shapes enhancer-promoter contacts. We demonstrate that enhancer function is reflected in enhancer-promoter contacts frequency which highly depend on active transcription. Pol II pausing, which is widespread across metazoan enhancers and promoters, has a direct effect on focal enhancer-promoter contacts. We confirmed this effect by depleting NELFB, a subunit of the negative elongation factor complex and a pivotal factor in Pol II pausing. Moreover, the catalytic activity of PARP1, a regulator of transcription and chromatin condensation, stabilizes enhancer-promoter contacts globally, but can destabilize contacts by promoting Pol II escape from pausing. Based on these findings, we propose an updated model that couples transcription and enhancer-promoter contacts.

overall_design: ChRO-seq libraries were prepared for K562 treated for 90 minutes with Olaparib to inhibit PARP1 function and the DMSO control, with two replicates for each condition.

first: Gilad

last: Barshad


title: Gene expression of SP and MP of myeloma cell lines cultured under normoxic or hypoxic conditions

status: Public on Jul 07 2022

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

summary: Gene expression of side population (SP) and major population (MP) of myeloma cell lines (RPMI-8226 and KMS-11) cultured under normoxic or hypoxic conditions for 48 h.

overall_design: We performed comprehensive gene expression analysis on the side population (SP) and major population (MP) of myeloma cell lines (RPMI-8226 and KMS-11) cultured under normoxic or hypoxic conditions for 48 h.


title: Transcriptomic profiling of compensated and decompensated human right ventricles

status: Public on Jul 04 2022

city: Quebec City

first: Olivier

last: Boucherat

state: Quebec

address: 2325 Rue de l'Université

institute: Laval University

summary: In order to better understand the molecular mechanisms underlying right ventricular failure in human PAH, a RNA sequencing analysis was performed in RV tissues obtained from subjects clinically categorized as compensated RV (n=11), decompensated RV (n=7) and donor controls (n=14). The study unveils a plethora of factors dysregulated in the RV of PAH patients, which opens new perspectives for translational research.

overall_design: mRNA profiles for control, compensated and decompensated human right ventricle

first: Francois

last: Potus

first: Sebastian

last: Bonnet


title: Cholesterol and matrisome pathways dysregulated in APOE ε4 human microglia and astrocytes [isogenicAPOE]

overall_design: We performed bulk RNA-sequencing on population iPSC-derived, CRISPR-edited isogenic iPSC-derived astrocytes, microglia, mixed cortical cultures, BMECs from APOE 33 vs APOE 44 and mouse astrocytes and microglia from APOE 33, APOE 44, Apoe WT and Apoe.


title: Expression profiling of Cellvibrio japonicus using starch

status: Public on Jun 28 2022

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Recent interest in rare α-diglucosides such as kojibiose (α-1,2), nigerose (α-1,3), and  isomaltose (α-1,6) reflects developments in pharmaceutical, biotechnological, and  culinary industries that value these sugars as prebiotics, carrier molecules, and low  glycemic index sweeteners. There have been only a few enzymes capable of degrading these substrates characterized, largely due in part to difficulties in identifying potential targets based solely on bioinformatic predictions. Previous genome sequencing of three Cellvibrio japonicus strains adapted to utilize rare α-diglucosides identified multiple, but thus far uncharacterized, mutations in each strain. In this report we analyzed the 36, 44, and 60 mutations that were in the kojibiose, nigerose, and isomaltose-adapted strains, respectively. The majority of mutations were unique to a specific adapted strain, which included indels that resulted a truncated protein, and single nucleotide variations within complete proteins. A single nucleotide variation in the C-terminus cyclomaltodextrin  domain of the amy13E gene product (P606S) was observed in several adapted strains. RNAseq data identified amy13E as highly expressed in starch media, which suggested a key role for this gene in the metabolism of sugars with α-glycosidic bonds. Mutational analysis of amy13E found that this gene was essential for rare α-diglucoside metabolism and critical for the maintenance of adaptation phenotypes. Bioinformatic analysis coupled with biochemical assays using cell-free extracts indicated that the amy13E gene product is located in the periplasm and directly cleaves α-diglucosides into glucose. Our revised model of α-diglucoside degradation by C. japonicus is likely to be useful for making functional enzyme predictions in related bacteria.

overall_design: One carbon condition (starch); Two sample points (exponential phase, stationary phase); Data collected in biological triplicate; Total of 6 samples; Data from GSE90955 (glucose) was used in data analysis


title: RNA polymerase II and PARP1 shape enhancer-promoter contacts

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA polymerase II and PARP1 shape enhancer-promoter contacts [CUT&Tag]

overall_design: CUT&Tag libraries were prepared using antibody against the N-terminal of PARP1 (Active Motif, AB_2793257) or anti-IgG antibody (Cell signaling, Normal Rabbit IgG #2729), with two replicates for each antibody.


title: Whole genome CRISPR screens in SC-islet grafts under allogeneic rejection (Hu. Mice) [CRISPR]

first: VICTOR

last: BARRERA BURGOS

summary: A whole genome screen using a CRISPR lentivirus library (Doench et al., 2016) was performed.  The Brunello CRISPR library consists of a pool of 76,441 human targeting guide RNAs (gRNA) and 1000 control gRNAs [non-targeting (NT) or intergenic], in a lentiviral vector that expresses Cas9. The pooled library targets 19,114 human genes, most of them by four gRNA per gene. To avoid multiple different gRNA in cells and a nonspecific effect on the screen results (Doench, 2018), a low infection lentivirus titer (multiplicity of infection that is <1) was used. Library transduced cells (LT SC-islets) were allowed at least 10 days for CRISPR editing, before transplantation to the NSG-MHCnull mouse model, where PBMCs were injected to half of the cohort (hPi mice: n=6, control mice: n=6) (Figures 3A). hPi mice retained levels of circulating T cells throughout the experiment (Figures S3A and S3B). Graft function and subsequent failure due to human PBMC injection was assessed (Figures 3B and S3C). When hPi graft failure was confirmed, 10 weeks after PBMC injection (Figure 3B), both control and hPi grafts were recovered from kidney sites, genomic DNA (gDNA) was extracted, and gRNA regions were amplified by PCR for Illumina sequencing.

overall_design: Comparing gRNA enrichment in hPi grafts vs controls

first: Elad

last: Sintov

first: Igor

last: Nikolskiy


title: RNA polymerase II and PARP1 shape enhancer-promoter contacts [Micro-C]

overall_design: Micro-C libraries were prepared for K562 and Jurkat human cell lines, with at least one replicate per cell line. Two biological replicates with two technical replicates each were prepared for each condition of K562 cells treated for 90 minutes with either Olaparib to inhibit PARP1 function and the DMSO control. Two biological replicates with two technical replicates each were also prepared for each time point of dTAG-13 incubation for mECSs harboring a homozygous endogenous NELFB-FKBP12F36V fusion protein (0, 30 and 60 minutes) as well as for 8 hours and 24 hours after dTAG-13 washout.


title: Immune cell gene expression in healthy, basal cell carcinoma and melanoma skin

status: Public on Jun 08 2022

city: Manchester

first: Ian

middle: Edward

last: Prise

state: Select state

address: Oxford Road

country: United Kingdom

institute: University of Manchester

summary: Comparison of gene expression profiles of  Mast cells and other CD45+ cells from healthy, basal cell carcinoma and melanoma skin

overall_design: Bulk RNA-seq, 2 cells types (Mast Cells and other CD45+ cells), 3 skin conditions (Healthy, Basal Cell Carcinoma, Melanoma)

first: Silvia

last: Bulfone-Paus


title: Targeting the Sphingolipid Balance via Acid Ceramidase Inhibition toDecrease Growth of TMZ-Resistant Glioblastoma and Block Migration

status: Public on Jun 01 2022

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: We performed 3'RNAseq on U251T or U251P cells treated with vehicle or carmofur.

overall_design: Determine changes in gene expression correalted with cell migration with the addition of carmofur compared to vehicle

first: S

middle: J

first: A

last: Hjelmeland


title: Genome-wide maps of H3K27ac in HDAC3 knockout bone marrow pDCs compared with control pDCs

status: Public on May 27 2022

city: Beijing

first: Zhimin

last: He

address: No. 1 Qinghuayuan Street

department: School of Medicine

institute: Tsinghua University

summary: Hdac3 is highly expressed in pDCs, and its deficiency led to substantially impaired development of pDCs, but not cDCs in bone marrow (BM) and spleen. Meanwhile,further investigation demonstrated that HDAC3 was required for the differentiation of pDC from progenitors at different differentiation stages in vitro. Cut & Tag analysis of H3K27ac level in HDAC3 deficient bone marrow pDCs compared with control pDCs, showed that H3K27ac level significantly increased on cDC related genes with PU.1 binding sites in HDAC3 knockout pDCs.

overall_design: Cut& Tag assay analyzed the H3K27ac level in HDAC3 knockout bone marrow pDCs compared with control pDCs.

first: Li

last: Wu

first: Yijun

last: Zhang


title: Gene expression profile at single cell level for induction of human primordial germ cell-like cells (hPGCLCs) in a biomimetic culture

status: Public on Jun 10 2022

city: Syracuse

first: Yi

last: Zheng

address: 900 S Crouse Ave

department: Biomedical and Chemical Engineering

institute: Syracuse University

summary: Transcriptome at the single-cell level of a biomimetic culture of primed human pluripotent stem cells (hPSCs) was profiled at Day 3 and Day 8.  The biomimetic culture, which mimics the peri-implantation human epiblast development, provides an easily implementable culture protocol for deriving human primordial germ cell-like cells (hPGCLCs) from primed hPSCs .

overall_design: We applied single-cell mRNA sequencing technique to examine the transcriptome of the biomimetic culture of primed human pluripotent stem cells (hPSCs) at Day 3 and Day 8.

first: Sajedeh

last: Esfahani

first: Jianping

last: Fu


title: Next Generation Sequencing of transcriptomes to reveal the role of HDAC3 in regulating the development of LMPP and CD115- CDP and bone marrow pDCs

summary: Hdac3 is highly expressed in pDCs, and its deficiency led to substantially impaired development of pDCs, but not cDCs in bone marrow (BM) and spleen. Meanwhile, the hematopoietic progenitors with DC differentiation potential, including CMP, CLP and CD115+ CDP were significantly decreased. Although the number of HSC and CD115− CDP were increased, their differentiation potential toward pDCs were abolished. Further investigation demonstrated that HDAC3 was required for the differentiation of pDC from progenitors at different differentiation stages.

overall_design: RNA profiles of sorted control or HDAC3 knockout mouse LMPPs and CD115- CDPs and bone marrow pDCs cells


title: RNA-sequencing identifies novel transcriptomic signatures in parenteral nutrition-associated liver disease

city: Shanghai

first: Lu

last: Jiang

address: 1665 Kongjiang Rd

institute: Xinhua hospital affiliated to Shanghai Jiao Tong Unvertsity schoool of medicine

summary: RNA-sequencing in liver from control and parenteral nutrition-associated liver disease (PNALD) rats

overall_design: Total liver RNA was extracted from 3 control rats and 3 PNALD rats and sequenced


title: Transcriptome-wide m6A Methylation Profiling of dHL-60 human neutrophils by m6A-seq

status: Public on May 24 2022

first: Yang

last: Liu

address: Dongdan Santiao 5

department: Immunology

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

summary: By performing m6A-seq analysis on dHL-60 human neutrophils infected with Escherichia coli, we want to identify the m6A methylation pattern in neutrophils after bacteria challenge. m6A-seq analysis revealed that the consensus m6A motifs were most significantly enriched within the m6A peaks with typical m6A peak distribution features, and m6A methylation sites were located primarily in the protein coding sequence region and 3′ untranslated region of mRNA transcripts, in neutrophils with bacterial infection.

overall_design: Identifying the m6A methylation pattern in dHL-60 human neutrophils infected with Escherichia coli. Two biological replicates.


title: The RNA Binding Protein Dead End1 Is Differentially Expressed in Male Germ Cells During Late Gestation and Targets Chromatin Modifiers and Translational Machinery

status: Public on Oct 18 2022

city: Aurora

first: Victor

last: Ruthig

state: CO

department: Pediatrics, Section of Developmental Biology

institute: University of Colorado Anschutz Medical Campus

summary: DND1 is essential to maintain germ cell identity. Loss of Dnd1 function results in trans-differentiation of germ cells to somatic fates in zebrafish or the formation of teratomas in mice. To explore the mechanistic role of DND1, we recently developed a transgenic mouse line in which a functional fusion protein between DND1 and GFP is expressed from the endogenous locus (Dnd1GFP). Surprisingly, we found that this reporter distinguishes two male germ cell populations (MGCs) during late gestation cell cycle arrest (G0). Most MGCs express low levels of DND1-GFP, but 5-12% of the population express high levels of DND1-GFP. An RNA-seq time course during late gestation revealed that Dnd1 transcript levels as well as transcript levels for multiple epigenetic regulators are 5-10-fold higher in DND1-GFP-hi cells. Furthermore, using antibodies against DND1-GFP for RNA immunoprecipitation (RIP) time course sequencing during late gestation, we identified multiple epigenetic and translational regulators that are binding targets of DND1 during G0. Among these targets are DNA methyltransferases (Dnmts), the enzyme Setdb1 that imposes the nuclear lamina associated repressive histone mark (H3K9me3), five Tudor domain proteins (Tdrds), four actin dependent regulators (Smarcs), and a group of ribosomal and Golgi proteins. These data suggest that DND1 binds to transcripts of a group of epigenetic enzymes and gates their translation during MGC G0 arrest in late gestation.

overall_design:
Transcriptome time course (E16.5, E18.5) comparing mouse male germ cells with high and low levels of DND1 done in conjunction with a RNA immunoprecipitation sequencing (RIP-seq) time course (E14.5, E16.5, E18.5), to identify transcript targets of DND1 at each timepoint. Findings were initially corroborated against re-analysis of E16.5 scRNA-seq male germ cell data from Law et al. 2019 Nat Comm (GSE124904).

Demultiplexed fastq files of E16.5 male germ cell scRNA-seq data originally published in Law et al. 2019 (GSE124904; GSM3559066-GSM3559068) was downloaded from the Sequence Read Archive (SRA) using the SRA toolkit (n=3: SRR8427519, SRR8427520, SRR8427521) and re-analyzed as following:

The Cell Ranger (v3.1.0) Count pipeline (read alignment, UMI counting) was performed on each biological replicate referenced to the mm10 mouse genome (GRCm38, v3.0.0).
The Cell Ranger Aggregation pipeline was performed on the molecule_h5 files for each biological replicate to generate a single integrated E16.5 dataset for downstream analysis.
Quality control and clustering was performed on the aggregated data using Seurat (v4.0.5)
resulting in the following data files:

Proc_scRNAseq_OatleyE16.5_aggr.cloupe
scRNAseq_Inter_barcodes.tsv.gz
scRNAseq_Inter_features.tsv.gz
scRNAseq_Inter_matrix.mtx.gz
scRNAseq_Supp_scRNA-seq_OatleyE16.5_aggr.RData

first: Blanche

last: Capel


title: Synonymous codon usage regulates translation initiation

status: Public on May 16 2022

first: Olivia

last: Rissland

address: 12801 East 17th Ave

department: BMG

institute: University Of CO Anschutz Medical Campus

summary: Ribo-seq with firefly luciferase optimality reporters to determine whether incomplete translation and/or inhibited translation initiation is responsible for the reduced ribosome occupancy on nonoptimal transcripts.

overall_design: Performed Ribo-seq, with paired RNA-seq, on HEK293T cells transfected with either optimal or nonoptimal reporters. Experiments were performed in triplicate.

first: Chloe

middle: L

last: Barrington

first: Amanda

last: Koch

first: Gabriel

last: Galindo

first: Emma

last: Larkin-Gero

first: Evan

last: Morrison

first: Samantha

last: Tisa

first: Timothy

last: Stasevich


title: Gene expression data of multiple lesions of a melanoma patient

status: Public on May 31 2022

city: Milano

first: Chiara

last: Gargiuli

address: via Amadeo

department: Dept. of Applied Research and Technological Development

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

summary:
Treatment with antibodies targeting immune checkpoints and kinase inhibitors results in long lasting disease remission in a small fraction of melanoma patients. This outstanding patient showed a complete and durable response after Ipilimumab rechallenge. We studied microenvironment composition and the tumor evolution.
Through gene expression profiling, we detailed the unique microenvironment characterizing this melanoma patient who experienced a complete response to a rechallange with Ipilimumab

overall_design: Formalin-fixed paraffin-embedded (FFPE) tumor specimens sections of 4 multiple lesions (2 pre- and 2 post-therapy) were microdissected and the RNA was extracted to perform gene expression profiling

first: Matteo

last: Dugo

first: Marialuisa

last: Sensi

first: Monica

last: Rodolfo


title: Distinct roles of CKM-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction

status: Public on May 23 2022

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

institute: University of Oxford

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus


title: Neuropilin-2 axis in regulating secretory phenotype of neuroendocrine-like prostate cancer cells: implication in therapy resistance

status: Public on May 09 2022

city: Omaha

first: Samikshan

last: Dutta

state: NE

address: 42 and Emile

department: BMB

institute: univ of nebraska medical center

summary: Gene expression was first compared between prostate adenocarcinoma cell line LNCaP C4-2 and our developed neuroendocrine like derived cell line DKD (LNCaP C4-2 stably depleted with TP53 and RB1). In the next set, we compared the gene  expression of neuroendocrine like DKD under presence and absence of Neurolipilin-2.

overall_design: The gene expression was analyzed in triplicate between adeno and neuroendocrine cell lines. Next following Neuropilin-2 depletion by siRNA for 48hrs, gene expression was compared in neuroendocrine cells with control condition.

first: R

last: Islam

first: K

last: Datta

first: S


title: MYBL2 promotes proliferation and metastasis of bladder cancer through transactivation of CDCA3

status: Public on May 04 2022

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary: The transcription factor MYB proto-oncogene like 2 (MYBL2) plays a critical role in the regulation of gene expression and tumorigenesis. However, the biological function of MYBL2 in bladder cancer (BLCA) remains to be elucidated. Here, we first revealed that MYBL2 was elevated in BLCA tissues and was significantly correlated with clinicopathological parameters and cancer-specific survival of BLCA patients. Phenotypic assays showed that MYBL2 deficiency suppressed the proliferation and migration of BLCA cells in vitro and in vivo, whereas overexpression of MYBL2 contributed to the opposite phenotype. Mechanistically, MYBL2 could bind to the promoter of its downstream target gene cell division cycle-associated protein 3 (CDCA3) and transactivate it, which in turn promoted the malignant phenotype of BLCA cells. Further investigations revealed that MYBL2 interacted with forkhead box M1 (FOXM1) to co-regulate the transcription of CDCA3. In addition, MYBL2 and CDCA3 may activate the Wnt/β-catenin signaling by inhibiting the suppressor dickkopf-1 (DKK1), thereby regulating the malignant phenotype of BLCA cells. In conclusion, the current study has identified MYBL2 as an oncogene in BLCA. MYBL2 can accelerate the proliferation and metastasis of BLCA through the transactivation of CDCA3.

overall_design: To investigate the downstream target genes regulated by CDCA3 in BLCA, RNA-seq was performed in 5637 cells treated by siNC/siCDCA3

first: Wei

last: Liu

first: Xinghuan

last: Wang


title: Orthotopic CRC organoid transplantation in mice: A novel model for the study and treatment of peritoneal carcinomatosis [Bulk RNA-Seq]

status: Public on Jun 27 2022

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

summary: Peritoneal carcinomatosis (PC) originating from colorectal cancer (CRC) is associated with a poor prognosis and rapid disease progression. Metastasis is the major cause of death in patients with CRC whereas primary locoregionally circumscribed tumors are mostly curable. Due to the lack of appropriate and realistic mouse models for metastasis of CRC until recently, the research about metastasis of these tumors and possible therapeutic options is still in its infancy. With the establishment of murine CRC tumor organoids, mouse models were established which realistically mimic the process of tumor cell metastasis to the liver and the lung. However, to date no appropriate model for PC is described. Here, we establish a realistic model for peritoneal metastasis of colorectal cancer upon surgical transplantation of tumor organoids into the cecum wall. This mouse model for PC recapitulates human PC which makes it an ideal model for research of the biology of metastasis of colorectal cancer to the peritoneal cavity and for its usage for preclinical drug screening as well as for the evaluation of new therapeutic approaches which are highly needed in clinical reality.

overall_design: RNA-Seq from organoid-derived primary tumor (PT), peritoneal carcinomatisis (PC) and liver metastasis CRC murine models

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