title: Comparative transcriptomic analysis of Pseudomonas aeruginosa isolates from ICU patients with acute and chronic pneumonia

city: Blacksburg

first: RODERICK

middle: V.

last: JENSEN

state: VA

address: Life Sciences 1, Room 119

institute: Department of Biological Sciences at Virginia Tech

summary: In this study, a comparative analysis was performed on two clinical Pa strains from pneumonia patients, 1) an acute strain (CMC-115) and 2) a chronic multidrug- and carbapenem-resistant strain (CMC-097), with distinct phenotypic and genetic characteristics. A transcriptome analysis using both the Pseudomonas DNA GeneChip microarray and Illumina RNA-Seq technologies was carried out for both strains at early-stationary growth phase in laboratory culture. The comparative transcriptomic analysis identified 134 genes differentially expressed ≥4.0-fold by both technologies between the two strains, which included virulence genes such as flagellar, pyoverdine, and phenazine genes, that were higher in the acute strain, CMC-115, and type 3 secretory system (T3SS) and pyochelin biosynthesis genes, that were higher in the chronic strain, CMC-097. In particular, the DNA microarrays suggested and the RNA-Seq analysis confirms the type 3 secretory system genes were completely missing from the acute strain, CMC-115. The combined analysis using the RNA-Seq and DNA microarray methods also identified important genes that were either missing or highly divergent from the Reference PAO1 genome used for the DNA microarray design. For example, the RNA-Seq data identified an operon containing several multidrug resistance genes: aacA27, beta-lactamase (blaOXA-2), qacΔE, sul1, and GNAT-N, in the chronic strain, CMC-097.

overall_design: This GEO DataSet contains the Illumina RNA-Seq analysis  carried out for 3 biological  replicates of both strains at early-stationary growth phase in laboratory culture.

first: Jayasimha

last: Rao

first: Adenike

last: Adenikinju

first: James

last: Gray

first: Lily

last: Colpitts

first: Alyson

last: Prorock

first: Yongde

last: Bao

first: Thomas

last: Kerkering

first: Dorothy

last: Garner

first: Roderick

last: Jensen


title: Profiling intestinal T cell subsets and their dynamics in Crohn's disease after treatment with the anti-integrin therapeutic etrolizumab

status: Public on Jul 23 2021

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

country: USA

institute: Genentech, Inc.

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression dynamics of HAND1/2 in in vitro human cardiomyocyte differentiation

status: Public on Jul 22 2021

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

summary: Hand1 and Hand2 are transcriptional factors, and knockout mice of these genes show left and right ventricular hypoplasia, respectively. However, their function and expression in human cardiogenesis are not well studied. To delineate their expressions and assess their functions in human cardiomyocytes (CMs) in vitro, we established two triple reporter human induced pluripotent stem cell lines, HAND1mCherry, HAND2EGFP, with MYH6-driven iRFP670 or constitutive tagBFP expression and investigated their expression dynamics during cardiac differentiation. On day 5 of the differentiation, HAND1 expression marked cardiac progenitor cells. We profiled the CM subpopulations on day 20 with RNA-sequencing and found that mCherry+ CMs showed higher proliferative ability than mCherry- CMs and identified CD105 as a surface marker of highly proliferative CMs. Finally, we revealed that LEF1 is a key regulator of proliferation and is repressively regulated by HAND1 and HAND2.

overall_design: HAND1-mCherry, HAND2-EGFP and MYH6-iRFP670 triple reporter human induced pluripotent stem cells (hiPSCs) were differentiated into cardiomyocytes. RNA-seq were performed with samples of day 0, 1 , 3 , 5 (purified mCherry+/-), 9 (purified iRFP670+/-), 20 (purified mCherry+EGFP-, mCherry-EGFP+, mCherry+EGFP- and mCherry+EGFP+ in ventricular protocol, and mCherry-EGFP+ in atrial protocol). All day 20 samples were isolated from iRFP670+ cardiomyocytes. For knockdown experiments, cardiomyocytes were isolated on day 15 and transfected with siRNAs of negative control (siNC), HAND1 (siHAND1), HAND2 (siHAND2), LEF1 (siLEF1) using MYH6-EGFP hiPSCs. RNAs were sampled on day 20. The transcriptomes of three/four independent samples were analyzed.

first: Chikako

last: Okubo

first: Megumi

last: Narita


title: Functional HPV-specific PD-1+ stem-like CD8 T cells in head and neck cancer

status: Public on Jul 20 2021

city: Atlanta

first: Haydn

last: Kissick

address: 1462 Clifton Rd.

institute: Emory University

summary: The goals of this study were to gain a better understanding of the heterogeneity and transcriptional profile of tumor specific and bulk PD1+ CD8 T cells in HPV primary tumors and metatstatic LNs

overall_design: Activated (live CD3+ CD19- CD14- CD16- CD4- CD8+) and double tetramer positive cells from primary tumors and metastatic lymph nodes of HPV+ HNSCC patients and as comparison, bulk PD1+ CD8 T cells from primary tumors and metastatic LNs from 6 patients were FACS-purified. Single-cell suspensions of FACS-purified cells were loaded onto the 10X Genomics Chromium Controller. Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit followed by sequencing on a HiSeq3000.

first: Christiane

last: Eberhardt

first: Rafi

last: Ahmed


title: TCF7L2 lncRNA: A Link between Bipolar Disorder and Body Mass Index through Glucocorticoid Signaling [ChIP-Seq]

status: Public on Jul 21 2021

city: Rochester

first: Thanh Thanh

middle: Le

last: Nguyen

state: Minnesota

address: 200 1st St. SW

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Bipolar disorder (BD) and obesity are highly comorbid. We previously performed a genome-wide association study (GWAS) for BD risk accounting for the  effect of body mass index (BMI) which identified a genome-wide significant single-nucleotide polymorphism (SNP) in the gene encoding the transcription factor 7 like 2 (TCF7L2). However, the molecular function of TCF7L2 in the central nervous system (CNS) and its possible role in BD and BMI interaction remained unclear. In the present study, we demonstrated by studying human induced pluripotent stem cell (hiPSC)-derived astrocytes, cells which highly express TCF7L2 in the CNS, that the BD-BMI GWAS risk SNP is associated with glucocorticoid-dependent repression of the expression of a previously uncharacterized TCF7L2 transcript variant. That transcript is a long non-coding RNA (lncRNA-TCF7L2) that is highly expressed in the CNS but not in peripheral tissues such as the liver and pancreas which are involved in metabolism.  In astrocytes, knock-down of the lncRNA-TCF7L2 resulted in decreased expression of the parent gene, TCF7L2, as well as alterations in the expression of a series of genes involved in insulin signaling and diabetes.  We also studied the function of TCF7L2 in hiPSC-derived astrocytes by integrating RNA sequencing data after TCF7L2 knock-down with TCF7L2 chromatin-immunoprecipitation sequencing (ChIP-seq) data. Those studies showed that TCF7L2 directly regulated a series of BD-risk genes. In summary, these results support the existence of a CNS-based mechanism underlying BD-BMI genetic risk, a mechanism based on a glucocorticoid-dependent expression quantitative trait locus that regulates the expression of a novel TCF7L2 non-coding transcript.

overall_design: ChIP-seq using antibody targeting TCF7L2 was conducted in human iPSC-derived Astrocytes.

first: Duan

last: Liu

middle: L

first: Huanyao

last: Gao

first: Huaizhi

last: Huang

first: Daniel

last: Kim

first: Brenna

last: Sharp

first: Zhenqing

last: Ye

first: Jeong-Heon

last: Lee

first: Brandon

last: Coombes

first: Tamas

last: Ordog

first: Liewei

last: Wang

first: Joanna

last: Biernacka

first: Mark

last: Frye

first: Richard

middle: M

last: Weinshilboum


title: Identification of heterogeneity of immune cells in healthy colonic biopsies

first: Jason

last: Hackney

summary: To better understand the heterogeneity of different immune cell subsets at and near mucosal surfaces, we performed single cell RNA-sequencing on CD45+ cells from colonic biopsies. A total of 6 healthy donors were profiled using the 10x Genomics platform. We clustered cells into broad groups of T cells, B cells and myeloid cells, and then further refined the clustering of T cells. We identified 5 types of T cells present in our data, including intra-epithelial T cells, cytotoxic lamina propria CD8+ T cells, memory T cells, regulatory T cells and finally type 3 innate lymphoid cells (ILC3s).

overall_design:
Six biological replicates of sorted CD45+ cells from colonic biopsies were profiled using the 10x genomics single cell RNA-seq platform
Raw data not provided due to patient privacy concerns

first: Mary

middle: E

last: Keir

first: Ryan

last: Ichikawa


title: Individual sorted T cell profiling from healthy donor

summary: Etrolizumab, a humanized monoclonal antibody that selectively binds the b7 subunit of the heterodimeric integrins a4b7 and aEb7, is currently in development for patients with moderate-to-severely active UC. Integrin aE forms a heterodimer with b7; and aEb7 interacts with E-cadherin to mediate retention of aEb7+ cells in the intestinal epithelium. Baseline integrin aE levels have been identified as a potential predictive biomarker for etrolizumab response. Materials and methods: Mucosal lymphocytes were isolated using a collagenase digestion from resected tissue from a patient without inflammatory bowel disease. Individual CD45+TCRab+TCRgd- cells were sorted into 96 well plates. Cell numbers were normalized across CD4+aE+, CD4+aE-, CD8+aE+ and CD8+aE- groups.

overall_design:
RNA was isolated from individual CD45+TCRab+TCRgd- T cells sorted into CD4+aE+, CD4+aE-, CD8+aE+ and CD8+aE- subsets.

Raw data not provided due to patient privacy concerns

first: Luz

last: Orozco


title: Anti-CD4 treatment-induced IL18Rαhi CD8+ T cells show highly effector profile

city: Goyang-si

first: Chungyong

last: Han

state: Gyeonggi-do

address: 323 Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National Cancer Center

summary: Anti-CD4 monoclonal antibody, a prominent immunomodulatory agent, enriches IL18Rαhi CD8+ T cells that elicit robust anti-tumor immunity in B16F10 melanoma. To investigate gene-expression profile of IL18Rαhi subset, we conducted transcriptome analysis.

overall_design: The model of mouse melanoma (B16F10) was used to study IL18Rαhi CD8+ T cells. We designed a regimen that utilizes cyclophosphamide treatment, adoptive transfer of tumor-specific T cells, and anti-CD4 treatment, a combination that synergistically increases the efficacy of adoptive T cell therapy. Three days after the B16F10 challenge, C57BL/6 mice sequentially received cyclophosphamide, ex vivo-primed Pmel-1 cells (melanoma-specific TCR-transgenic CD8+ T cells), and IL-2. A transient treatment (on day 10, 17, and 24) of anti-CD4 started seven days after cyclophosphamide treatment. Twenty-five days after the tumor challenge, cells from lymphoid tissues of the mice were magnetically isolated based on the IL18Rα expression and subjected to transcriptome analysis.

first: Seon-Hee


title: Chromoanagenesis event underlies a de novo pericentric and multiple paracentric inversions in a single chromosome causing Coffin-Siris Syndrome

city: Houston

first: Christopher

last: Grochowski

state: Texas

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Chromoanagenesis is a descriptive term that encompasses classes of catastrophic mutagenic processes that generate localized and complex chromosome rearrangements in both somatic and germline genomes. Herein we describe a 5-year-old female presenting with a constellation of clinical features consistent with a clinical diagnosis of Coffin-Siris syndrome 1 (CSS1). Initial G-banded karyotyping detected a 90 Mb pericentric and 47 Mb paracentric inversion on a single chromosome. Subsequent analysis using short-read whole genome sequencing, and genomic optical mapping revealed additional inversions, all clustered on chromosome 6, one of them disrupting ARID1B for which haploinsufficiency leading to CSS1. In all, the resolved derivative chromosome architecture presents four de novo inversions, one pericentric and three paracentric, involving six breakpoint junctions in what appears to be a shuffling of genomic material on this chromosome. Each junction was resolved to nucleotide-level resolution with mutational signatures suggestive of non-homologous end joining. The disruption of the gene ARID1B is shown to occur between the 4th and 5th exon of the canonical transcript with subsequent qPCR studies confirming a decrease in ARID1B expression in the patient versus healthy controls. Deciphering the underlying genomic architecture of chromosomal rearrangements and complex structural variants may require multiple technologies and can be critical to elucidating the molecular etiology of a patient’s clinical phenotype or resolving unsolved Mendelian disease cases.

overall_design: The goal of this experiment was to determine the genomic architecture of a proband with multiple de novo inversions on chromsome 6.

first: Claudia

last: Carvalho


title: Project_Summary_Rat_primary_cortical_neurons_asyn_3K_RNA_Seq

status: Public on Jul 19 2021

city: Cambridge

first: Justin

last: Nicholatos

state: Massachusetts

address: 225 Binney St

department: Neurodegeneration

institute: Biogen

summary: Identify early and late stage expression/pathway changes induced during aSyn 3K mediated cellular toxicity (AAV9 with human a-syn 3K model)

overall_design: Transcriptional profiling of rat cortical neuron cultures overexpressing human aSyn 3K or empty vector at 6, 12, and 19 days post AAV

first: Joost

last: Groot

first: Thomas

last: Carlile

first: Lori

last: Hrdlicka


title: DMRT1-mediated reprogramming drives development of cancer resembling human germ cell tumors with features of totipotency

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

type: Methylation profiling by high throughput sequencing

summary: In vivo reprogramming provokes a wide range of cell fate conversion. Here, we discover that in vivo induction of higher levels of OSKM in mouse somatic cells leads to increased expression of primordial germ cell (PGC)-related genes and provokes genome-wide erasure of genomic imprinting, which takes place exclusively in PGCs. Moreover, the in vivo OSKM reprogramming results in development of cancer that resembles human germ cell tumors. Like a subgroup of germ cell tumors, propagated tumor cells differentiate into trophoblasts. Moreover, these tumor cells give rise to induced pluripotent stem cells (iPSCs) with expanded differentiation potential into trophoblasts. Remarkably, the tumor-derived iPSCs are able to contribute to non-neoplastic somatic cells in adult mice. Mechanistically, DMRT1, which is expressed in PGCs, drives the reprogramming and propagation of the tumor cells in vivo. Furthermore, the DMRT1-related epigenetic landscape is associated with trophoblast competence of the reprogrammed cells and provides a therapeutic target for germ cell tumors. These results reveal an unappreciated route for somatic cell reprogramming and underscore the impact of reprogramming in development of germ cell tumors.

overall_design: Analyzing transcriptional profiles and DNA methylation profiles by RNA-seq, WGBS and Methyl-seq in OSKM-induced cellular reprogramming in vitro and in vivo

first: Mio

last: Kabata

first: Takuya

last: Yamamoto


title: TCF7L2 lncRNA: A Link between Bipolar Disorder and Body Mass Index through Glucocorticoid Signaling

first: Thanh Thanh

last: Nguyen


title: CometChip® and TempO-Seq®: A high-throughput 96-well platform to measure and classify DNA damaging agents in human HepaRG™ Cells [HCC3]

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary:
Introduction: Higher-throughput mode-of-action-based assays provide a valuable approach to expedite chemical evaluation for human health risk assessment. In this study, we combined the high-throughput alkaline CometChip® assay with the TGx-DDI transcriptomic biomarker (DDI = DNA damage-inducing) using high-throughput TempO-Seq® as an integrated genotoxicity testing approach.
Objective: To determine if the high-throughput CometChip® assay and TGx-DDI biomarker analysis can be combined using human HepaRG™ cells to provide an efficient next-generation genotoxicity screening approach to identify DNA damage-inducing (DDI) chemicals.
Methods: Metabolically competent human HepaRG™ cell cultures were exposed to increasing concentrations of 12 chemicals (9 DDI and 3 non-DDI) using a repeat exposure design (0 hr, 24 hr, 48 hr) in 96-well plates to measure and classify chemicals based on their ability to damage DNA. After a 4 hr recovery period, exposed cells were used to perform the Trevigen CometChip assay to assess DNA damage or used for TempO-Seq® S1500+ Targeted  Transcriptome Sequencing for TGx-DDI classification purposes. Bioinformatics and statistical tools were used to classify chemicals as DDI or non-DDI using three separate analyses. Benchmark concentration analysis was also conducted for both assays for the purposes of potency ranking.
Results: In combination, the CometChip® assay and the TGx-DDI were 100% accurate in identifying chemicals that induce DNA damage. Quantitative benchmark concentration (BMC) modeling was applied to evaluate chemical potencies for both assays. The BMCs for the CometChip® assay and the TGx-DDI for all 12 chemicals were highly concordant (within four-fold) and resulted in identical potency rankings.
Conclusions: These results suggest that these two assays can be integrated for efficient, high-throughput identification of DNA damage in HepaRG™ cells. This study provides evidence for the complementarity of the high-throughput CometChip® assay with TGx-DDI biomarker analysis. Integration of these two tests provides an effective and high-throughput approach to identify DDI agents. This work is a first step in accomplishing a more integrated genotoxicity testing strategy to derive mechanistic information to better inform human health risk assessment in a high-throughput manner.

overall_design: Examination of the complementarity of two high-throughput genotoxicity tests, the CometChip assay to assess DNA damage and TGx-DDI biomarker analysis for chemical classification, following exposure to 9 DNA-damage inducing (DDI) chemicals and 3 non-DDI chemicals  in human HepaRG ™ cells.

first: Julie

middle: K

last: Buick

first: Andrew

last: Williams

middle: J

first: Carol

middle: D

last: Swartz

first: Leslie

last: Recio

first: Rémi

last: Gagné

first: Stephen

middle: S

last: Ferguson

first: Bevin

middle: P

last: Engelward

first: Carole

last: Yauk


title: Gene expression data of CD8+ T cells from C57BL/6 mouse

status: Public on Jul 18 2021

first: Chungyong

last: Han

summary:
Anti-CD4 monoclonal antibody, a prominent immunomodulatory agent, elicits robust anti-tumor immunity in various cancers by increasing tumor-infiltrating lymphocytes and promoting CD8+ T cell reactivity against tumor cell-derived antigens.
We used microarrays to investigate anti-CD4-induced gene-expression change of CD8+ T cells.

overall_design: The model of mouse melanoma (B16F10) was used to study anti-CD4-induced change of endogenous CD8+ T cells. We designed a regimen that utilizes cyclophosphamide treatment, adoptive transfer of tumor-specific T cells, and anti-CD4 treatment, a combination that synergistically increases the efficacy of adoptive T cell therapy. Three days after the B16F10 challenge, C57BL/6 mice sequentially received cyclophosphamide, ex vivo-primed Pmel-1 cells (melanoma-specific TCR-transgenic CD8+ T cells), and IL-2. A transient treatment (on day 10, 17, and 24) of anti-CD4 started seven days after cyclophosphamide treatment. Twenty-five days after the tumor challenge, endogenous CD8+ T cells isolated from lymphoid tissues of the mice were subjected to microarray analysis. Two groups (5 mice each) received cyclophosphamide/Pmel-1 or cyclophosphamide/Pmel-1/anti-CD4.  For each group, endogenous CD8+ T cells from five mice were pooled and used in the analysis.

first: Seon-Hee

last: Kim


title: Gene expression in non-perfused liver samples from endotoxemic Sus scrofa in context of deoxynivalenol contaminated diets

city: Braunschweig

first: Fabian

last: Billenkamp

address: Bundesallee 37

country: Germany

institute: Friedrich-Loeffler-Institute

summary:
It has been proposed that chronic exposure to deoxynivalenol modulates hepatic gene expression and that sensivity to xenobiotics like deoxynivalenol is modulated by inflammation.
We used microarrays to evaluate whether chronic deoxynivalenol exposure influences the hepatic gene expression of Sus scrofa in vivo and whether interaction between chronic deoxynivalenol exposure and systemic inflammation occur.

overall_design: Sus scrofa liver samples were collected at slaugthering 195 minutes after inducing endotoxemia via pre-hepatic or post-hepatic LPS infusion. Animals were subjected to chronic deoxynivalenol exposure via diet (4.59 mg deoxynivalenol/kg diet) or to a control diet (0.12 mg deoxynivalenol/kg diet) for 29 days before LPS infusions. RNA of nin-perfused liver samples was isolated and subjected to Affymetrix microarrays

first: Susanne

last: Bühler

first: Michael

last: Oster

first: Ann-Katrin

last: Heymann


title: The pesticide chlorpyrifos promotes obesity by inhibiting diet-induced thermogenesis in brown adipose tissue

city: Hamilton

first: Gregory

middle: R

last: Steinberg

address: 1200 Main St W

department: Medicine

institute: McMaster University

summary: Obesity results from a caloric imbalance between energy intake, absorption and expenditure. In both rodents and humans, diet-induced thermogenesis contributes to energy expenditure and involves the activation of brown adipose tissue (BAT). We hypothesized that environmental toxicants commonly used as food additives or pesticides might reduce BAT thermogenesis through suppression of uncoupling protein 1 (UCP1) and this may contribute to the development of obesity. Using a step-wise screening approach, we discovered that the organophosphate insecticide chlorpyrifos suppresses UCP1 and mitochondrial respiration in BAT at concentrations as low as 1 pM.  In mice housed at thermoneutrality and fed a high-fat diet, chlorpyrifos impaired BAT mitochondrial function and diet-induced thermogenesis, promoting greater obesity, non-alcoholic fatty liver disease (NAFLD) and insulin resistance. This was associated with reductions in cAMP; activation of p38MAPK and AMPK; protein kinases critical for maintaining UCP1 and mitophagy, respectively in BAT. These data indicate that the commonly used pesticide chlorpyrifos, suppresses diet-induced thermogenesis and the activation of BAT, suggesting its use may contribute to the obesity epidemic.

overall_design: Total RNA was isolated from 6 replicates of immortalized murine brown adipocyte cells treated with either 1pM Chlorpyrifos or Vehicle (DMSO) for 4h. A total of 12 samples were analyzed.

first: Bo

last: Wang

first: Evangelia

last: Tsakiridis

first: Shuman

last: Zhang

first: Andrea

last: Llanos

first: Eric

last: Desjardins

first: Julian

last: Yabut

first: Alexander

last: Green

first: Emily

last: Day

first: Brennan

last: Smith

first: James

last: Lally

first: Jianhan

last: Wu

first: Amogelang

last: Raphenya

first: Krishna

last: Srinivasan

middle: G

last: McArthur

first: Shingo

last: Kajimura

first: Jagdish

last: Patel

last: Wade

first: Katherine

last: Morrison

first: Alison

middle: C

last: Holloway


title: Intra- and extra-cellular environments contribute to the fate of HIV-1 infection

status: Public on Jul 16 2021

city: Boston

first: Sean

last: Lawler

state: MA

address: 75 Francis St

institute: Brigham and Women's Hospital

summary: We used an HIV-1-based reporter viruses to study the fate of HIV-1 infection in primary human CD4+ T cells

overall_design: Primary human CD4+ T cells (i.e., target cells) were isolated and infected with HI.fate (reporter) viruses. Cell populations were sorted by flow cytometry according to those supporting viral latency, active viral transcription, or control uninfected cells and their transcriptome was analyzed.

first: Alon

last: Herschhorn

first: Joseph

last: Sodroski

first: Zachary

last: Herbert


title: Persistent JunB Activation in Fibroblasts Disrupts Stem Cell Niche Interactions Enforcing Skin Aging

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm


title: Visualization of individual cell division history in complex tissues

city: Zürich

first: Baptiste

middle: N

last: Jaeger

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zürich

summary: The division potential of individual stem cells and the molecular consequences of successive rounds of proliferation remain largely unknown. Here, we developed an inducible cell division counter (iCOUNT) that reports cell division events in human and mouse tissues in vitro and in vivo. Analysing cell division histories of neural stem/progenitor cells (NSPCs) in the developing and adult brain, we show that iCOUNT can provide novel insights into stem cell behaviour. Further, we used single cell RNA-sequencing (scRNA-seq) of iCOUNT-labelled NSPCs and their progenies from the developing mouse cortex and forebrain-regionalized human organoids to identify molecular pathways that are commonly regulated between mouse and human cells, depending on individual cell division histories. Thus, we developed a novel tool to characterize the molecular consequences of repeated cell divisions of stem cells that allows an analysis of the cellular principles underlying tissue formation, homeostasis, and repair.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNA sequencing of i) single cells isolated from human iCount forebrain organoids, ii) single nuclei isolated from embryonic cortices of iCount mice and iii) bulk WT and iCount mouse ESCs.
For the human single cell dataset, human forebrain organoids were injected with Cre (1μg/μl) and electroporated using the AMAXA Nucleofector device. 4 and 7 days after electroporation (39 days in culture), cells were dissociated. Single cells were isolated by flow cytometry and prepared for scRNA-seq according to the Smart-Seq2 protocol.
For the mouse single nuclei dataset, tamoxifen (180mg/kg) was injected into pregnant H3.1-iCOUNT x ROSA26:CreERT2 mice at E13.5. 38h later, embryonic cortices were dissected and the nuclei were dissociated. Single nuclei were isolated by flow cytometry and prepared for snRNA-seq according to the Smart-Seq2 protocol.
For the mouse bulk RNA-seq dataset, three independent biological replicates of WT and iCount mESCs were collected using TrypLE washed and resuspended in DPBS containing RNAse inhibitor. RNA extraction was performed using the PureLink RNA Mini Kit according to the manufacturer’s protocol. PolyA selection was performed and libraries were prepared with the TruSeq RNA library prep kit (Illumina).

first: Annina

last: Denoth-Lippuner

first: Tong

last: Liang

first: Lars

last: Royall

first: Stefanie

last: Chie

first: Kilian

last: Buthey

first: Diana

last: Machado

first: Vladislav

middle: I

last: Korobeynyk

first: Merit

last: Kruse

first: Clara

last: Munz

last: Gerbaulet

first: Benjamin

last: Simons

first: Sebastian

last: Jessberger


title: Persistent JunB Activation in Fibroblasts Disrupts Stem Cell Niche Interactions Enforcing Skin Aging [RNA-seq]

summary: Fibroblasts residing in the connective tissue of all organs constitute the stem cell niche particularly in connective tissue rich organs like skin. Though the impact of the connective tissue resident fibroblasts on stem cell niches and organ aging is an emerging concept, the underlying mechanisms are largely unresolved. Here, we report a novel mechanism of redox-dependent activation of the transcription factor JunB, which through concomitant upregulation of cyclin dependent kinase inhibitor p16INK4A and repression of IGF-1 dependent cell growth and protein translation initiates the installment of irreversible fibroblast senescence. Fibroblast senescence in turn profoundly disrupts the metabolic and structural niche and its essential interactions with different stem cells thus enforcing depletion of stem cells pools and skin tissue decline. In fact, silencing of JunB in a fibroblast niche-specific knock out mouse - by the reinstatement of IGF-1 and p16 levels - fully restored skin stem cell pools and overall tissue integrity of the skin.  We here uncovered a previously unreported role of JunB in the control of the endogenous connective tissue niche and identified promising targets to combat skin aging and associated pathologies.

overall_design: For RNA-Seq analysis, 1-5 µg of total RNA from total skin was first rRNA depleted using either Ribominus Eukaryotic system v2 kit (ThermoFisher Scientific) or Ribo-Zero kit (Illumina). rRNA depleted RNA was subjected to preparation of Illumina compatible RNA-seq libraries using NEXTFLEX Rapid Directional RNA-Seq kit (Bioo Scientific). RNA-seq libraries were quality controlled through Qiaxcel advanced system (Qiagen) and Bioanalyzer (Agilent) and finally measured by Qubit fluorimeter (ThermoFisher Scientific). Validated libraries were sequenced on Illumia Nextseq 500 system (Microsynth GmbH) using NextSeq v2 chemistry (1 ´ 75 cycles).


title: Persistent JunB Activation in Fibroblasts Disrupts Stem Cell Niche Interactions Enforcing Skin Aging [ATAC-seq]

summary: ATAC-seq was performed in control murine dermal fibroblasts (MDF) in the absence and presence of rotenone at a concentration of 250µM for 3 hrs), and in freshly isolated control (Co) and Sod2 cKO MDF.

overall_design: In brief, 50000 MDFs were lysed in Nuclei lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) for 2 min, followed by nuclei isolation using centrifugation (500 ´ g for 10 min at 4°C). Isolated nuclei were subjected to tagmentation reaction with Tn5 transposase (Illumina) for 30 min at 37°C. Tagmented DNA was then purified using MinElute kit (Qiagen) and used for PCR amplification to add the i5 and i7 dual barcodes. The PCR amplified products were purified by two times 1.8´ AMPure XP bead cleanup (Beckman Coulter). The purified library was then quality controlled by Qiaxcel advanced system (Qiagen) and Bioanalyzer (Agilent) and finally measured by Qubit fluorimeter (ThermoFisher Scientific). Thereafter, libraries were sequenced on Illumina NextSeq 500 platform (Microsynth GmbH) using NextSeq v2 chemistry (2 ´ 75 cycles).


title: Next-generation sequencing facilitates quantitative analysis of T1-T4 sympathetic ganglia transcriptomes from TRKC+/-, AdNTF3-Tg and their respective wild type control mice after 1 day cold exposure at 5℃

status: Public on Jul 15 2021

first: Bingzhong

last: Xue

state: Georgia

address: 50 Decatur St SE

department: Biology

institute: Georgia State University

summary: Activation of brown fat thermogenesis increases energy expenditure and alleviates obesity. Sympathetic nervous system (SNS) is important in brown/beige adipocyte thermogenesis. Here we discover a novel fat-derived “adipokine” neurotrophic factor neurotrophin 3 (NTF3) and its receptor Tropomyosin receptor kinase C (TRKC) as key regulators of SNS growth and innervation in adipose tissue. NTF3 is highly expressed in brown/beige adipocytes, and potently stimulates sympathetic neuron neurite growth. NTF3/TRKC regulates a plethora of pathways in neuronal axonal growth and elongation. Adipose tissue sympathetic innervation is significantly increased in mice with adipocyte-specific NTF3 overexpression, but profoundly reduced in mice with TRKC haploinsufficiency (TRKC+/-). Increasing NTF3 via pharmacological or genetic approach promotes beige adipocyte development, enhances cold-induced thermogenesis and protects against diet-induced obesity (DIO); whereas TRKC+/- mice or SNS TRKC deficient mice are cold intolerant and prone to DIO. Thus, NTF3 is an important fat-derived neurotrophic factor regulating SNS innervation, energy metabolism and obesity.

overall_design: T1-T4 sympathetic ganglia (which innervate into iBAT) mRNA profiles of 12-week-old WT and TrkC+/- as well as WT and AdNTF3-Tg mice after 1 day cold exposure at 5℃

first: Hang

last: Shi


title: Human Placental Trophoblasts infected by Listeria monocytogenes Undergo a Pro-Inflammatory Switch Associated with Poor Pregnancy Outcomes

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

summary: The bacterial pathogen Listeria monocytogenes breaches the placental barrier and infects the placental/fetal unit resulting in poor pregnancy outcomes. L. monocytogenes is thought to enter the placenta by infection of trophoblasts at the maternal/fetal interface. Trophoblasts are fetal epithelial cells that delineate the maternal/fetal interface and ensure critical functions by promoting all nutritional and waste exchanges between maternal and fetal bloods and by forming a protective immune barrier. In this work, we report the first transcriptomic analysis of L. monocytogenes-infected trophoblasts  by RNA sequencing. Primary human trophoblasts (PHT) and BeWo (fused and non-fused) were infected for 5 h with WT L. monocytogenes and highly purified RNA was extracted from infected and control cells. A 200 ng total RNA sample was used for sequencing on Illumina NovaSeq SP flowcell in paired-end 150 bp format to a read yield between 70-80 million reads. Pathway analysis showed that infection upregulated TLR2-, NOD-like, and cytosolic DNA sensing pathways, as well as downstream pro-inflammatory circuitry (NF-KB, AP-1, IRF4, IRF7) leading to the production of mediators known to elicit the recruitment and activation of maternal leukocytes (IL8, IL6, TNFA, MIP-1). Signature genes associated with poor pregnancy outcomes were also upregulated upon infection. Measuring the release of 54 inflammatory mediators confirmed the transcriptomic data and revealed sustained production of tolerogenic factors (IL-27, IL-10, IL-1RA, TSLP) despite infection. Both the SYN and mononuclear trophoblasts produced cytokines, but surprisingly, some cytokines were predominantly produced by the SYN (IL-8, IL-6) or by non-fused trophoblasts (TNFA). Collectively, our data support that trophoblasts act as placental gatekeepers that limit and detect L. monocytogenes infection resulting in a pro-inflammatory response, which may contribute to the poor pregnancy outcomes if the pathogen persists.

overall_design: Primary human trophoblasts from 3 placentas along with fused and non-fused cells from 3 BeWo cultures were infected or not with L. monocytogenes in duplicate

last: Webb

first: Siavash

last: Azari

first: Lauren

last: Johnson

first: Stephanie

last: Seveau


title: Transcriptomes of evolved Pseudomonas putida KT2440 on non-native sugars

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

summary: Efficient utilization of lignocellulosic biomass-derived sugars is essential to improve the economics of biorefinery. While Pseudomonas putida is a promising microbial host, its usage is limited because this strain cannot utilize xylose or galactose as a sole carbon source. To address this issue, we heterologously introduced a xylose utilizing gene (xylD) from Caulobacter crescentus and a galactose operon (galETKM) from E. coli MG1655. To improve the utilization further, we evolved the engineered strains in minimal medium conditions. After the evolution, they acquired better fitnesses on the non-native sugars. To understand transcriptional changes after the evolution, the transcriptomes of few evolved isolates were analyzed.

overall_design: 4 evolved KT2440-xylD isolates and 3 evolved KT2440-galETKM isolates were grown on the minimal media supplemented with either xylose or galactose as a sole carbon source. The cultures were conducted with two biological duplicates.

first: Hyungyu

last: Lim

first: Adam

last: Feist


title: Identification of abscisic acid-associated known and novel miRNAs and their target genes in Arabidopsis thaliana

city: Poznań

first: Agnieszka

last: Ludwików

address: Uniwersytetu Poznańskiego 6

department: Faculty of Biology

country: Poland

institute: Adam Mickiewicz University in Poznan

type: Non-coding RNA profiling by high throughput sequencing

summary: Using RNA-Seq, we identified miRNAs in the WT Col-0 strain of Arabidopsis and its abi1td, mkkk17 and mkkk18 mutant lines that are differentially expressed in response to ABA treatment. Both known and novel miRNAs were characterized and the expression profiles of a subset were validated by qRT-PCR; we also verified the potential target genes of selected novel miRNAs by 5′ RLM-RACE. GO annotation revealed that the top-ranked miRNA target genes were involved in diverse biological processes, including regulation of transcription, response to stress, biosynthetic processes, and signaling pathways.

overall_design: Seeds of WT Arabidopsis thaliana, Columbia ecotype (Col-0), as well as abi1td, mapkkk17td, and mapkkk18td mutants were used in this study. After two days of stratification at 4°C, the plants were grown in Half Murashige and Skoog Basal Medium supplemented with sucrose. Seedlings were grown weeks for two weeks, then treated with ABA (±100 µM) for 4 hours. The harvested plant materials were freezed in liquid nitrogen and stored in -80°C freezer until further use. For each condition (mock and ABA treated), three independent biological replicates were used and small RNA was extracted using Tri-reagent according to the manufacturer’s protocol (Direct-zol RNA Miniprep; ZYMO Research Corporation). And samples were used for miRNA sequencing.

first: Syed

last: Mehdi

first: Sivakumar

last: Krishnamoorthy

first: Michał

last: Szcześniak


title: Identification of mRNA clients of SYNJ2BP by RIP-seq

city: San Francisco

first: Wei

last: Qin

address: 550 Gene Friend Way Apt509

institute: Stanford University

summary: We discovered SYNJ2BP is an OMM-localized RNA binding protein. We identified the potential mRNA clients of SYNJ2BP by RIP-seq and validated by CLIP-qPCR.

overall_design: The SYNJ2BP RIP was performed using the GenSeqTM RIP Kit and a SYNJ2BP antibody (HPA000866-100UL, Sigma-Aldrich) along with an IgG negative control. RNA-seq libraries were generated using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions and the library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150 bp paired-end reads.


title: RNA sequencing of BAT from Ox1RΔSERT and control mice fed a HFD

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

summary: We report differences in gene expression between Ox1RΔSERT and control mice.

overall_design: BAT was dissected at the end of hyperinsulinemic-euglycemic clamp experiments. RNA was extracted and sequenced. n = 4 vs. 4.

first: Xing

last: Xiao

first: Paul

last: Klemm


title: Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

summary: Many genes in bacterial genomes are of unknown function, often referred to as y-genes. Recently, the analytic methods have divided bacterial transcriptomes into independently modulated sets of genes (iModulons). Functionally annotated iModulons that contain y-genes lead to testable hypotheses to elucidate y-gene function. The inversely correlated expression of a putative transporter gene, ydhC, relative to purine biosynthetic genes, has led to the hypothesis that it encodes a purine-related transporter and revealed a LysR-family regulator, YdhB, with a predicted 23-bp palindromic binding motif. RNA-Seq analysis of a ydhB knockout mutant confirmed the YdhB-dependent activation of ydhC in the presence of adenosine. The deletion of either the ydhC or the ydhB gene led to a substantially decreased growth rate for E. coli in minimal medium with adenosine, inosine, or guanosine as the nitrogen source. Taken together, we provide clear evidence that YdhB activates the expression of the ydhC gene that encodes a purine transporter in E. coli. We propose that the genes ydhB and ydhC be re-named as punR and punC, respectively.

overall_design: Identification of genome-wide bindings for novel transcription factor YdhB in E. coli K-12 MG1655, using ChIP-exo technology


title: Role of a cryptic tRNA gene operon in the recovery from translation stress

status: Public on Jul 14 2021

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

summary: As compared to Eukaryotes, Bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs, which are thought to act in concert for the maintenance of gene translation. Here we show that in some bacteria the tRNA gene set may be partitioned in a housekeeping sub-set that sustains translation, and an inducible one that is generally silent but can be largely induced to provide functionality under particular conditions. In the model cyanobacterium Anabaena sp. PCC 7120, the inducible set forms an operon encoding 23 functional tRNAs. Transcription of these tRNAs is induced by translation stress, i.e. by insults that impair translation, including antibiotics that target the ribosome. The operon is co-regulated with genes encoding proteins like the tRNA ligase RtcB and the stress-specific protein DpsA, probably involved in a response directed to protect the cell and recover translation. Common regulation suggests participation of operonic tRNAs in this response, although mechanistic issues remain to be determined. Similar long tRNA gene operons were found in species across major bacterial phyla and are shown to be distinct in many aspects from other operons that evolved by gene accretion.

overall_design: Cultures of Anabaena (Nostoc) sp. PCC 7120 were grown in triplicate in BG11 medium, treated with 40 µg ml-1 chloramphenicol and incubated under culture conditions. Alliquots were taken 0, 3 ,9 and 24 hours after treatment to extract RNA.

first: Ignacio

last: Luque

first: Ana

middle: B

last: Romero-Losada


title: mRNA sequencing analysis on cardiofibroblasts exposed to reduced graphene oxide (rGO) Nanomaterials

city: xi'an

first: Dengfeng

address: NO.157 Xiwu Rd,Xi'an City

country: China

institute: The Second Affiliated Hospital, Xi’an Jiaotong University

summary: In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to rGO on cardiofibroblasts (CFs) cells. We performed mRNA sequencing experiments using CFs cells exposed to rGO for 24h.

overall_design: 24h rGO exposed CFs cells were used for total RNA extraction and sequenced on Illumina HiSeq instrument.

first: Yanjing

last: Feng


title: Meningioma methylation analysis.

city: Toronto

first: Yasin

last: Mamatjan

address: 610 University Ave.

institute: Princess Margaret Cancer Center

type: Methylation profiling by genome tiling array

summary:
Methylation analysis of meningioma samples.
Genomic DNA isolated directly from fresh-frozen human meningioma specimens.

overall_design: Meningioma samples n = 121,  No technical replicates performed.

first: Nassiri

last: Farshad


title: Effect of early-life plane of nutrition on the transcriptional profile of the hypothalamic arcuate nucleus region in heifer calves

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

summary: The aim of this study was to examine alterations in the transcriptional profile of the arcuate nucleus region of the hypothalamus between heifer calves offered varying planes of nutrition during early life. Angus X Holstein-Friesian heifer calves (19 ± 5 days of age, BW: 51.2 ± 7.8 kg, mean ± SD) were offered a high (HP, n=14) or moderate plane of nutrition (MP, n=15) from 3 to 21 weeks of age to achieve a target growth rate of 1.2 kg/d and 0.5 kg/d, respectively. At 21 weeks of age, all calves were euthanized and the arcuate nucleus region of the hypothalamus of each calf recovered. RNA was extracted transcriptional profiles examined using RNAseq. Compared with calves on the moderate plane of nutrition, a High plane of nutrition altered the expression of 80 genes within the arucate nucleus. Functional analysis of differentially expressed genes revealed functions including organismal development, behaviour, endocrine system development and function, lipid metabolism, molecular transport, small molecule biochemistry, cellular development, cellular growth and proliferation, and nervous system development and function to be affected by early life plane of nutrition in the arucate nucleus of heifer calves.

overall_design: 29 arcuate nuclues RNA samples were analysed in total. 14 samples were derived from calves fed the High plane of nutrition (HP, n=14) and 15 samples were derived from the claves fed the Moderate plane of nutrition (MP, n=15). Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase, the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks. All samples were collected at the same time-point (21 weeks of age) all differentially expressed genes reported were up- or down-regulated in HP calves compared to MP calves.

first: Jose

last: Sanchez

first: Alan

last: Kelly

first: Colin

last: Byrne

first: Pat

last: Lonergan

first: David

middle: A

last: Kenny


title: Effect of early-life plane of nutrition on the transcriptional profile of the hypothalamus in heifer calves

summary: The objective of this study was to examine changes in hypothalamic gene expression of heifer calves offered varying planes of nutrition during early life. Angus X Holstein-Friesian heifer calves (19 ± 5 days of age, BW: 51.2 ± 7.8 kg, mean ± SD) were offered a high (HP, n=14) or moderate plane of nutrition (MP, n=15) from 3 to 21 weeks of age to achieve a target growth rate of 1.2 kg/d and 0.5 kg/d, respectively. At 21 weeks of age, all calves were euthanized and the hypothalamus of each calf recovered. RNA was extracted and hypothalamic gene expression examined using RNAseq. Compared with calves on the moderate plane of nutrition, a HP of nutrition altered the expression of 39 transcripts in the hypothalamus. Biological pathway analysis revealed these differentially expressed genes to be involved in pathways including acute phase response signalling, STAT3 pathway, and tight junction signalling. Additionally, biological functions affected by early life plane of nutrition included  cell-to-cell signalling and interaction, molecular transport, small molecule biochemistry, behaviour, nervous system development and function, nucleic acid metabolism, and cellular function and maintenance.

overall_design: 29 hypothalamus RNA samples were analysed in total. 14 samples were derived from calves fed the High plane of nutrition (HP, n=14) and 15 samples were derived from the claves fed the Moderate plane of nutrition (MP, n=15). Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase, the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks. All samples were collected at the same time-point (21 weeks of age) all differentially expressed genes reported were up- or down-regulated in HP calves compared to MP calves.


title: Single-cell RNA-seq Analysis of Pancreatic and Hepatic Progenitor Cells from Tg(Prox1-EGFP) Transgenic Mouse Embryos

status: Public on Jul 13 2021

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

country: United Kingdom

institute: King's College London

summary:
Formation of the hepato-pancreato-biliary organ system in mammals is a paradigm for organogenesis, whereby a small progenitor population of the ventral foregut gives rise to a multitude of different adult tissues, including liver, pancreas, gallbladder, and extra-hepatic bile ducts. The multipotent ventral foregut cell population undergoes an initial fate segregation into hepatic and pancreato-biliary progenitors in response to signaling cues from surrounding mesodermal tissues. Subsequently, pancreato-biliary progenitors give rise to ventral pancreatic and gallbladder progenitors.
In this study, we used single-cell RNA sequencing to molecularly characterize progenitor populations in the ventral foregut that contribute to the formation of hepatic, pancreatic, and biliary organ rudiments throughout organogenesis.

overall_design: 452 single cells isolated from foregut, pancreatic and hepatic progenitor cells of Tg(Prox1-EGFP) transgenic mouse embryos at embryonic day (E) 8.5, 10.5, and E14.5 were processed for single-cell RNA sequencing using SmartSeq2 method. Only samples that passed the QC check are included in this submission.

last: Willnow

first: Uwe

last: Benary

first: Anca

last: Margineanu

first: Maria

middle: L

last: Vignola

first: Igor

last: Pongrac

first: Zahra

last: Karimaddini

first: Fabian

last: Konrath

first: Alessandra

last: Vigilante

first: Jana

last: Wolf


title: Addiction-associated genetic variants implicate brain cell type- and region-specific cis-regulatory elements in addiction neurobiology

city: Pittsburgh

first: BaDoi

middle: Nguyen

last: Phan

state: PA

address: 5000 Forbes Ave

department: Computational Biology

institute: Carnegie Mellon University

summary: Recent large genome-wide association studies (GWAS) have identified multiple confident risk loci linked to addiction-associated behavioral traits. Genetic variants linked to addiction-associated traits lie largely in non-coding regions of the genome, likely disrupting cis-regulatory element (CRE) function. CREs tend to be highly cell type-specific and may contribute to the functional development of the neural circuits underlying addiction. Yet, a systematic approach for predicting the impact of risk variants on the CREs of specific cell populations is lacking. To dissect the cell types and brain regions underlying addiction-associated traits, we applied LD score regression to compare GWAS to genomic regions collected from human and mouse assays for open chromatin, which is associated with CRE activity. We found enrichment of addiction-associated variants in putative regulatory elements marked by open chromatin in neuronal (NeuN+) nuclei collected from multiple prefrontal cortical areas and striatal regions known to play major roles in reward and addiction. To further dissect the cell type-specific basis of addiction-associated traits, we also identified enrichments in human orthologs of open chromatin regions of mouse neuron subtypes: cortical excitatory, PV, D1, and D2. Lastly, we developed machine learning models from mouse cell type-specific regions of open chromatin to further dissect human NeuN+ open chromatin regions into cortical excitatory or striatal D1 and D2 neurons and predict the functional impact of addiction-associated genetic variants. Our results suggest that different neuron subtypes within the reward system play distinct roles in the variety of traits that contribute to addiction.

overall_design: Examination of bulk and cell type specific ATAC-seq in mouse cortex and striatum. Cell type-specific ATAC-seq was performed using cSNAIL (cre-specific Sun1-GFP nuclear anchored independent label) paired with cre-mouse lines for PV, SST, D1, and D2(Adora2a) lines.

first: Srinivasan

last: Chaitanya

first: Lawler

last: Alyssa

first: Pfenning

last: Andreas


title: Transcriptome analysis studying the role of ZEB1 in Th1 and Th17 differentiation [RNA-seq]

status: Public on Jul 12 2021

city: Chicago

first: Yuan

last: Qian

state: ILLINOIS

address: 303 E Superior St

institute: Northwestern University

summary: We performed bulk-RNAseq to study the role of ZEB1 in human and mouse Th1 and Th17 cells differentiation.

overall_design: In vitro differentiated Th0, Th1 and Th17 cells with or without ZEB1.

first: Jaehyuk

last: Choi


title: scRNA-seq analysis of tumor infiltrating lymphocytes in PTENα-expressing tumors

city: Beijing

first: Yizhe

last: Sun

state: Beijing

address: No.38, Xueyuan Road ,Haidian District

institute: Peking University Health Science Center

summary: As a tumor suppressor, PTEN is frequently mutated in human cancers and PTEN mutants promote tumor progression and metastasis. PTEN mutations have been implicated in immune regulation, but the underlying mechanism is largely unknown. We report that PTENα, the isoform of PTEN, remains active in cancer bearing stop-gained PTEN mutations. Through counteraction of CD8+ T cell-mediated cytotoxicity, presence of PTENα leads to T cell dysfunction and accelerates immune-resistant cancer progression. Clinical analysis further uncovers that PTENα-active mutations suppress host immune responses and result in poor prognosis in cancer as relative to PTENα-inactive mutations. Furthermore, germline deletion of Ptenα in mice increases cell susceptibility to immune attack through augmenting stress granule formation and limiting synthesis of peroxidases, leading to massive oxidative cell death and severe inflammatory damage. We propose that PTENα protects tumor from T cell killing and thus PTENα is a potential target in antitumor immunotherapy.

overall_design: Study of  tumor infiltration lymphocytes in Mock or PTENα expressing B16 Pten-/- tumors using 10x scRNA-seq technologies.

first: Dan

last: Lu

first: Xin

last: Zhang


title: Generation of ovarian follicles from mouse pluripotent stem cells

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Oocytes mature in a specialized fluid-filled sac, the ovarian follicle, which provides signals needed for meiosis and germ cell growth. Methods have been developed to generate functional oocytes from pluripotent stem cell–derived primordial germ cell–like cells (PGCLCs) when placed in culture with embryonic ovarian somatic cells. In this study, we developed culture conditions to recreate the stepwise differentiation process from pluripotent cells to fetal ovarian somatic cell–like cells (FOSLCs). When FOSLCs were aggregated with PGCLCs derived from mouse embryonic stem cells, the PGCLCs entered meiosis to generate functional oocytes capable of fertilization and development to live offspring. Generating functional mouse oocytes in a reconstituted ovarian environment provides a method for in vitro oocyte production and follicle generation for a better understanding of mammalian reproduction.

overall_design: Examination of single-cell transcriptomes in the in vivo gonad somatic cells and the in vitro induced ES cell-derived gonad smatic cells.

first: Katsuhiko

last: Hayashi

first: Takashi

last: Yoshino


title: Assessing the impact of Ccnc or Cdk8 loss +/- ATR inhibition on mRNA gene transcription using RNA-seq

city: Cambridge

first: Rebecca

last: Lloyd

address: Tennis Court Road

department: University of Cambridge

institute: Wellcome/CRUK Gurdon Institute

summary: We have found that loss of Ccnc or Cdk8 (members of the RNAPII mediator complex) provide ATRi resistance. As part of invesitgations into the mechanism of this suppression, we probed for specific changes in the transcriptome by performing RNA-seq in WT, Cdk8 KO and Ccnc KO mESCs following DMSO or ATRi (AZD6738) treatment. However, this did not identify any transcripts that were significantly differentially regulated following AZD6738 treatment in both Ccnc and Cdk8 KO, but not WT, cells. Similarly, pathway analyses of proteins whose transcripts were up- or down-regulated in a treatment-independent manner in both Cdk8 and Ccnc KO clones compared to WT mESCs did not provide a clear explanation why the Ccnc/Cdk8 KO cells are ATRi resistant.

overall_design: Two WT mESC biological replicates, three independent Ccnc KO mESC clones (D1, G2, H5) and three independent Cdk8 KO mESC clones (B9, H4, C8) were treated for 4h with DMSO or 900 nM AZD6738. The same WT samples were independently multiplexed with Ccnc KO samples, and again with Cdk8 KO samples, due to limitations on the number of samples that could be multiplexed, and to eliminate the impact of sequencing-run bias. The corresponding WT samples were used in downstream analysis.

first: Inigo

last: Ayestaran

first: Stephen

last: Jackson


title: microRNA-seq analysis studying the role of ZEB1 in Th0 and Th17 differentiation [miRNA-seq]

summary: We performed microRNA-seq to study the role of ZEB1 in human Th17 cells differentiation.

overall_design: In vitro differentiated Th17 cells with or without ZEB1.


title: A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome

city: Seoul

first: Daehyun

last: Baek

address: Rm 402, Bldg 504, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul

department: School of Biological Sciences

institute: Seoul National University

summary: COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infected >200 million people resulting in >4 million deaths. However, temporal landscape of the SARS-CoV-2 translatome and its impact on the human genome remain unexplored. Here, we report a high-resolution atlas of the translatome and transcriptome of SARS-CoV-2 for various time points after infecting human cells. Intriguingly, substantial amount of SARS-CoV-2 translation initiates at a novel translation initiation site (TIS) located in the leader sequence, termed TIS-L. Since TIS-L is included in all the genomic and subgenomic RNAs, the SARS-CoV-2 translatome may be regulated by a sophisticated interplay between TIS-L and downstream TISs. TIS-L functions as a strong translation enhancer for ORF S, and as translation suppressors for most of the other ORFs. Our global temporal atlas provides compelling insight into unique regulation of the SARS-CoV-2 translatome and helps comprehensively evaluate its impact on the human genome.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: mRNA-seq, RPF-seq, QTI-seq, and sRNA-seq experiments at uninfected state and at 0, 1, 2, 4, 12, 16, 24, 36, and 48 hpi upon SARS-CoV-2 infection in human Calu-3 cell lines.

first: Doyeon

last: Kim


title: Off-the-shelf proximity labeling

status: Public on Jul 09 2021

city: Lausanne

first: Guido

last: van Mierlo

address: Route Cantonale

institute: EPFL

summary: In this study we developed a new assay to perform proximity biotinylation in cells without the requirement for genetic manipulation or transfection to fuse a biotin ligase to a protein of interest. We show the specificity by targeting H3K9me3 and performing ChIP-seq for the biotin modification. Targeting IgG was used as a control. By doing so, we identified flywch1 as a new protein binding to H3K9me3 regions, which we validated using ChIP-seq (IgG ChIP was used as a control)

overall_design: ChIP-seq profiling of biotin after H3K9me3 or IgG targeting and ChIP-seq for Flywch1 or IgG

first: Irene

last: Barriopedro

first: Michiel

last: Vermeulen


title: Pten's function in regulating cardiomyocyte differentiation

city: Hong Kong

first: Wuming

last: Wang

address: Sha Tin

institute: The Chinese University of Hong Kong

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

overall_design: Refer to individual Series


title: RNA-seq analysis of Igf2's function in the differentiation of mouse embryonic stem cells

summary: We report the function of IGF2 in regulating the differentiation of ESCs, and then we performed RNA-seq for the wild-type and Igf2 knockout ESCs and embryoid bodies collected at different time points to analyze the transcriptomes. The results showed a significant difference between wild-type and Igf2 knockout groups in transcriptomes, and we performed a series experiments to study the function of Igf2 in the differentiation of ESCs.

overall_design: Examination of RNA-seq for wild-type and Igf2 knockout embryonic stem cells and embryoid bodies and exploration of the role of Igf2 in ESC differentiation.

first: Gang

first: Wai-Yee

last: Chan


title: Genome-wide DNA methylation pattern in whole blood associated with primary intracerebral hemorrhage

status: Public on Jul 10 2021

city: Changsha

first: hy

last: long

address: xiangya road

institute: xiangya hospital

summary: To reveal the role of DNA methylation in peripheral blood from primary intracerebral hemorrhage(ICH) ,DNAs from 30 ICH patients and 34 matched controls were analyzed by methylation microarray.  In total, we identified 1377 hypomethylated and 153 hypermethylated differentially  methylated positions (DMPs) in  peripheral blood from ICH patients compared to healthy controls.

overall_design: Peripheral blood samples from 30 patients with ICH and 34 matched controls were analyzed by Illumina Infinium HumanMethylation850K BeadChip.

first: Yupeng

first: Hongyu

last: Long

first: Sai

first: Wenbiao

last: Xiao

first: Meishan

last: Xiong

first: Jianyi

last: Liu

first: Lei

last: Chen

first: Ruijuan

first: Xueli

last: Wei

first: Yi

last: Shu

last: Zeng

first: Le


title: Comparative analysis of gene expression in tomato leaves during mild and severe potato spindle tuber viroid infection [leaf RNA-seq].

city: Warszawa

first: Aneta

last: Więsyk

address: Pawinskiego 5a

institute: Institute of Biochemistry and Biophysics, PAS

summary: Comparative analysis of gene expression in tomato leaves during mild and severe potato spindle tuber viroid infection.

overall_design:
Mild (PSTVd-M) and severe (PSTVd-S23) strains were used to inoculate Solanum lycopersicum cv Rutgers plants. Leaf samples were collected  at 17 days post inoculation (dpi), i.e. at early stage of symptoms. Three independent biological replicates of PSTVd-M, PSTVD-S23 and pUC9 were analised. Totally 18 samples of RNA were analysed.

Please note that the *Gene_counts* file was updated on Sep 22, 2021.

first: Anna

last: Góra-Sochacka

first: Maciej

last: Lirski


title: RNA-seq analysis of Pten's function in regulating cardiomyocyte differentiation

first: Wuming

summary: We report the function of Pten in regulating the cardiomyocyte differentiation, and then we performed RNA-seq for the wild-type and Pten knockout cardiomyocytes to analyze the transcriptomes. The results showed a significant difference between wild-type and Pten knockout groups in transcriptomes, and we performed a series experiments to study the function of Pten in cardiogenesis.

overall_design: Examination of RNA-seq for wild-type and Pten knockout cardiomyocytes and Whole-genome bisulfite sequencing for wild-type and Pten knockout embryoid bodies and cardiomyocytes

first: Gang

last: Lu


title: Direct and indirect transcriptional effects of abiotic stress in Zea mays plants defective in RNA-directed DNA methylation

status: Public on Jul 08 2021

city: Bothell

first: Thelma

middle: F

last: Madzima

state: WA

address: 18115 Campus Way NE

department: Division of Biological Sciences

institute: University of Washington Bothell

summary:
MOP1-mediated regulation of gene expression of plant responses to early ABA induction has transcriptionally and physiologically relevant roles. Homozygous mop1-1 plants are compromised in their ability to recover from water deprivation.
Purpose: Genome-wide identification of immediate and direct MOP1-dependent ABA transcriptional responses
Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 1 hour. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR.
Results: we mapped ~33 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 1,856 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a log2FC ≥ 0.95 and FDR <0.05, 1,119 DEGs were found to be unique to one genotype/treatment comparison.
Conclusions: MOP1-mediated regulation of gene expression in maize seedlings in the RdDM (mop1-1) mutant has relevant transcriptional and physiological roles in plants subjected to stress. Our study generated by RNA-seq technology identified genes and biological processes regulated by RdDM and ABA-mediated stress responses, including MOP1-dependent and immediate response genes (MIMs).

overall_design: RNA-seq was preformed on homozgyous Mop1 wildtype and mop1-1 mutant V3 seedling shoots with and without exogenous 50 µM ABA treatment for 1 hour.

first: Karen

middle: M

last: McGinnis

first: Stefania

last: Vendramin

first: Jason

last: Lynn

first: Phebe

last: Lemert

first: Katherine


title: Targeted T cell receptor gene editing provides predictable T cell product function for immunotherapy

city: Munich

first: Thomas

last: Müller

state: Bavaria

address: Trogerstr. 30

department: MIH

institute: TUM

summary: Adoptive transfer of T cells expressing a transgenic T cell receptor (TCR) has the potential to revolutionize immunotherapy of infectious diseases and cancer. However, the generation of defined TCR-transgenic T cell medicinal products with predictable in vivo function still poses a major challenge and limits broader and more successful application of this ‘living drug’. Here, by studying 51 different TCRs, we show that conventional genetic engineering by viral transduction leads to variable TCR expression and functionality as a result of variable transgene copy numbers and untargeted transgene integration. In contrast, CRISPR/Cas9-mediated TCR replacement enables defined, targeted TCR transgene insertion into the TCR gene locus. Thereby, T cell products display more homogenous TCR expression similar to physiological T cells. Importantly, increased T cell product homogeneity after targeted TCR gene editing correlates with predictable in vivo T cell responses, which represents a crucial aspect for clinical application in adoptive T cell immunotherapy.

overall_design: mRNA profiles from TCR-engineered T cells comparing retroviral transduction and CRISPR/Cas9-mediated replacement

first: Sebastian

last: Jarosch

first: Monika

last: Hammel

first: Justin

last: Leube

first: Simon

last: Grassmann

first: Bettina

last: Bernard

first: Manuel

last: Effenberger

first: Immanuel

last: Andrä

first: M

middle: Z

last: Chaudhry

first: Theresa

last: Kaeuferle

first: Antje

last: Malo

first: Luka

last: Cicin-Sain

first: Peter

last: Steinberger

first: Tobias

last: Feuchtinger

first: Ulrike

last: Protzer

first: Kathrin

last: Schumann

first: Michael

last: Neuenhahn

first: Kilian

last: Schober

first: Dirk

middle: H

last: Busch


title: Whole-genome bisulfite sequencing analysis of Pten's function in regulating cardiomyocyte differentiation

first: Wuming

last: Wang

summary: We report the function of Pten in regulating the cardiomyocyte differentiation, and then we performed whole-genome bisulfite sequencing for the wild-type and Pten knockout embryoid bodies and cardiomyocytes to analyse the methylomes. The results showed a significant difference between wild-type and Pten knockout groups in methylomes, and we performed a series of experiments to study the function of Pten in cardiogenesis.

overall_design: Examination of RNA-seq for wild-type and Pten knockout cardiomyocytes and whole-genome bisulfite sequencing for wild-type and Pten knockout embryoid bodies and cardiomyocytes.

first: Gang

last: Lu

first: Wai

middle: Y

last: Chan


title: 10X single-cell RNASeq profiling of human in vitro differentiated Th17 cell [scRNA-seq]

first: Yuan

last: Qian

summary: We performed single-cell RNAseq to study the role of ZEB1 in human Th17 cells differentiation.

overall_design: Different timepoint (Day 1 and Day 5) in vitro differentiated Th17 cells with or without ZEB1.

first: Jaehyuk

last: Choi


title: Neuro-mesenchyme units control ILC2 and obesity via a brain-adipose circuit

status: Public on Jul 07 2021

city: Lisboa

first: Ana

middle: Filipa Ribeiro

last: Cardoso

state: Lisboa

address: Avenida  Brasília, Fundação champalimaud, Immunophysiology lab

country: Portugal

institute: Fundação Champalimaud


title: A novel intronic circular RNA antagonizes influenza virus by absorbing a miRNA that degrades CREBBP and accelerating IFN-β production

status: Public on Jul 06 2021

city: Harbin

first: Zhiyuan

last: Qu

address: Haping road 678

department: State Key Laboratory of Veterinary Biotechnology

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

summary: Virus-host interactions are complicated processes, and multiple cellular proteins have been reported to promote or inhibit viral replication through different mechanisms. Recent progress has implicated circular RNAs (circRNA) in cancer biology and progression; however, the role of circRNAs in viral infection remains largely unclear. Here, we detected 11,620 circRNAs in A549 cells and found that 411 of them were differentially expressed in influenza virus-infected A549 cells. We characterized a novel intronic circRNA, AIVR, that was upregulated in influenza virus-infected A549 cells, and found that silencing of AIVR significantly promoted influenza virus replication in A549 cells. We further found that AIVR predominantly localizes in the cytoplasm and works as a microRNA (miRNA) sponge. One of the miRNAs absorbed by AIVR binds the mRNA of CREBBP, which is an important component of the large nucleoprotein complex IFN-β enhanceosome that accelerates IFN-β production. AIVR-overexpression significantly increased the mRNA and protein levels of INF-β in the influenza virus-infected A549 cells. Therefore, the upregulation of AIVR is a cellular antiviral strategy, with AIVR exerting its antiviral effect by absorbing miRNA and promoting the expression of CREBBP to facilitate IFN-β production. Our study provides new insights into the roles of circRNAs in the cellular innate antiviral response.

overall_design: To investigate the differential expression of circRNAs in influenza virus-infected cells, human alveolar epithelial cells (A549) were mock-infected or infected with an H9N2 avian influenza virus, A/chicken/Jiangsu/C4258/12 (H9N2) (H9N2 virus). At 12 h post-infection (p.i.), total RNA was extracted from the cells, and the circRNAs, miRNAs, and mRNAs were deep-sequenced and computationally analyzed.

first: Fei

last: Meng

first: Hualan

last: Chen


title: Single cell imaging of T cell immunotherapy responses in vivo

first: Qian

last: Qin

address: 24 Peabody Terrace, Unit 2002

department: Molecular Pathology Unit

institute: Massachusetts General Hospital

summary: T cell immunotherapies have revolutionized treatment for a subset of cancers. Yet, a major hurdle has been the lack of facile and predicative preclinical animal models that permit dynamic visualization of T cell immune responses at single cell resolution in vivo. Here, optically-clear immunocompromised zebrafish were engrafted with fluorescent-labelled human cancers along with chimeric antigen receptor T (CAR T) cells, bispecific T cell engagers (BiTEs), and antibody peptide epitope conjugates (APECs), allowing real-time single cell visualization of T cell-based immunotherapies in vivo. This work uncovered important differences in the kinetics of T cell infiltration, tumor cell engagement and killing between these immunotherapies and established early endpoint analysis to predict therapy responses. We also established EGFR-targeted immunotherapies as a powerful approach to kill rhabdomyosarcoma muscle cancers, providing strong preclinical rationale for assessing a wider array of T cell immunotherapies in this disease.

overall_design: Blood Lineage analysis of zebrafish kidney marrow samples from WT, rag2∆/∆ and rag2∆/∆, il2rga-/- immunocompromised zebrafish

first: Chuan

last: Yan

first: Sowmya

last: Iyer

first: David

last: Langenau


title: Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome compaction and individualization

city: Worcester

first: Bastiaan

last: Dekker

address: 368 Plantation street

department: Systems Biology

institute: University of Massachusetts Medical School

summary: Hi-C on reconstituted mitotic chromosomes in Xenopus system in IGG or specific depleted egg extracts to study to role of condensin and linker histone in chromosome condensation

first: Pavan

last: Choppakatla

first: Erin

middle: E

last: Cutts

first: Alessandro

last: Vannini

first: Job

first: Hironori

last: Funabiki


title: Neuro-mesenchyme units control ILC2 and obesity via a brain-adipose circuit [GAT MSCs]

summary: Signals from sympathetic neurons and immune cells regulate adipocytes contributing to fat tissue biology. Interactions between the nervous and immune systems have recently emerged as major regulators of host defence and inflammation1-4. Nevertheless, whether neuronal and immune cells cooperate in brain-body axes to orchestrate metabolism and obesity remains elusive. Here we report a novel neuro-mesenchyme unit that controls group 2 innate lymphoid cells (ILC2), adipose tissue physiology, metabolism and obesity via a brain-adipose circuit. We found that sympathetic nerve terminals act on neighbouring adipose mesenchymal cells via the beta-2 adrenergic receptor to control the expression of the glial-derived neurotrophic factor (GDNF) and the activity of ILC2 in gonadal fat. Accordingly, ILC2-autonomous manipulation of the GDNF receptor machinery led to altered ILC2 function, energy expenditure, insulin resistance and propensity to obesity. Retrograde tracing, chemical, surgical and chemogenetic manipulations identified a sympathetic aorticorenal circuit that modulates gonadal fat ILC2 and connects to high-order brain areas, including the paraventricular nucleus of the hypothalamus (PVH). Our work decodes a neuro-mesenchymal unit that translates long-range neuronal circuitry cues into adipose-resident ILC2 function, shaping the host metabolism and obesity.

overall_design: GAT MSCs from mice treated with 6-OHDA and vehicle treated controls.

first: Filipa


title: Transcriptomics analysis of KB-3-1 xenograft mice treated with cisplatin

status: Public on Jul 05 2021

city: GAINESVILLE

first: Lingtao

last: Jin

state: FL

address: 2033 Mowry Rd, UF CGRC 356

institute: University of Florida

summary: This study was designed to evaluate the transcriptomic alterations mediated by cisplatin exposure in a human cancer xenograft mouse model. The tumor samples from xenograft mice with or without cisplatin treatment were applied to transcriptomic analysis.

overall_design: 6-week-old athymic nude mice were subcutaneously injected with 1x10e6 human carcinoma cell line KB-3-1. The xenograft mice were randomly divided into 2 groups (10 mice/group) and were either treated with 0.5 mg/kg of cisplatin or PBS at day 5 and 5 mg/kg of cisplatin or PBS at day 10 after the xenograft. Tumors were collected at the experimental endpoint at day 20, and three tumors from each group were randomly selected and applied for RNA isolation and poly-(A) RNA sequencing.

first: Chaoyun

last: Pan

first: Sumin

last: Kang


title: Neuro-mesenchyme units control ILC2 and obesity via a brain-adipose circuit [GAT ILC2s]

first: Ana

overall_design: GAT ILC2 from RetDVav1, RetMEN2B  and their littermate controls


title: Integrative Transcriptomic, Lipidomic, and Metabolomic Analysis Reveals Potential Biomarkers of Basal and Luminal Muscle Invasive Bladder Cancer Subtypes

city: Nanning

first: Zhenxing

last: Wang

state: Guangxi

address: Zhongshan Street

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medicla University

summary: Muscle invasive bladder cancer (MIBC) is a heterogeneous disease with a high recurrence rate and poor clinical outcomes. Molecular subtype provides a new framework for the study of MIBC heterogeneity. Clinically, MIBC can be classified as basal and luminal subtypes, they display different clinical and pathological characteristics, but the molecular mechanism is still unclear. Lipidomic and metabolomic molecules have recently been considered to play an important role in the genesis and development of tumors, especially as potential biomarkers. Their different expression profiles in basal and luminal subtypes provide clues for the molecular mechanism of basal and luminal subtypes and the discovery of new biomarkers. Herein, we stratified MIBC patients into basal and luminal subtype using a MIBC classifier based on transcriptome expression profiles. We qualitatively and quantitatively analyzed the lipids and metabolites of basal and luminal MIBC subtypes, and identified differential lipid and metabolite profiles of them. Our results suggest that free fatty acids (FFA) and sulfatides (SL), which are closely associated with immune and stromal cell types, can contribute to the diagnosis of basal and luminal subtypes of MIBC. Moreover, we showe that glycerophosphocholine (GCP)/imidazoles and nucleosides/imidazoles ratios can accurately distinguish the basal and luminal tumors. Overall, by integrating transcriptomic, lipidomic, and metabolomic data, our study reveals specific biomarkers to differentially diagnose basal and luminal MIBC subtypes and may provide a basis for precision therapy of MIBC.

overall_design: We stratified MIBC patients into basal and luminal subtype using a MIBC classifier based on transcriptome expression profiles. We then qualitatively and quantitatively analyzed the lipids and metabolites of basal and luminal MIBC subtypes, and identified differential lipid and metabolite profiles of them.

first: Chao

last: Feng

first: Lixin

first: Shaomei

last: Tang

first: Liangyu

last: He


title: Ectopic expression of the homeobox gene Cdx2 in hematopoietic stem cells

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

summary: This dataset describes the transcriptomic profiling by mRNA-seq of the bone marrow of mice either wild type or ectopically expressing the homeobox gene Cdx2 in hematopoietic stem cells. Each condition was analyzed in triplicates to address the role of Cdx2 in leukemogenesis.

overall_design: Bone marrow samples from wild type mice and mice engineered for inducible expression of Cdx2 in hematopoietic stem cells were tested by RNASeq in triplicates, resulting in a total of 6 samples. All the mice, aged 3 months, were administrated 3 times intraperitoneally pI:pC at 10µg/g in NaCl and analyzed 6 weeks later.

first: Claire

last: Domon-Dell

first: Jean-Noel

last: Freund


title: Mapping the Cellular Origin and Early Evolution of Leukemia in Down Syndrome

city: Toronto

first: Elvin

last: Wagenblast

state: ON

address: 101 College Street

department: Princess Margaret Cancer Centre

institute: UHN


title: Tumor-initiating stem cell shapes its microenvironment into an immunosuppressive barrier and pro-tumorigenic niche

status: Public on Jul 02 2021

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

institute: Stowers Institute for Medical Research

summary: Tumor-initiating stem cells (TSCs) are critical for drug resistance and immune escape. However, the mutual regulations between TSC and tumor microenvironment (TME) remain unclear. Using DNA-label retaining, single-cell RNA sequencing (scRNA-seq), and other approaches, we investigated intestinal adenoma in response to chemoradiotherapy (CRT), thus identifying therapy-resistant TSCs (TrTSCs). We find bidirectional crosstalk between TSCs and TME using CellPhoneDB analysis. An intriguing finding is that TSCs shape TME into a landscape that favors TSCs for immunosuppression and propagation. Using adenoma-organoid co-cultures, niche-cell depletion, and lineaging tracing, we characterize a functional role of cyclooxygenase-2 (Cox-2)-dependent signaling, predominantly occurring between tumor-associated monocytes and macrophages (TAMMs) and TrTSCs. We show that TAMMs promote TrTSC proliferation through prostaglandin E2 (PGE2)-PTGER4(EP4) signaling, which enhances β-catenin activity via AKT phosphorylation. Thus, our study shows that the bidirectional crosstalk between TrTSC and TME results in a pro-tumorigenic and immunosuppressive contexture.

overall_design: We separate MC and EP from intesitines according to different time point traetment. For APCmin MC/EP, we have replicates. Control EP/MC are B6 wild type mice.

first: Xi

first: Linheng

last: Li


title: Comparison of the Pseudomonas aeruginosa PA2504 deficient strain and the PAO1161 wild type strain

status: Public on Jul 01 2021

city: Warsaw

first: Joanna

last: Drabinska

state: Masovian

institute: Institute of Biochemistry and Biophysics PAS

summary: Pseudomonas aeruginosa is an ubiquitous gram-negative bacterium that may colonize a wide range of organisms, including bacteria, plants, and animals. It is a human opportunistic pathogen which shows a great threat to immunocompromised patients. P. aeruginosa displays intrinsic resistance to many antibiotics, and has a high ability to develop novel mechanisms of resistance which forms a threat in hospital environments and makes it extremely hard to eradicate. Additionally over half of the genes of this bacteria have no described function, so it is urgent to search for proteins related to its pathogenicity and antibiotic resistance. The aim of this study was to characterise the P. aeruginosa PA2504 protein of unknown function. Basic phenotypic analysis did not indicate the role of PA2504 in the cell, thus, in order to recognize transcripts affected by the lack of PA2504 transcriptomes of the ΔPA2504 and the wild-type PAO1161 strains were compared using high-throughput RNA sequencing (RNA-seq). Using qRT-PCR method we determined that the level of PA2504 transcript is higher in the stationary phase of growth as compared to the exponential phase of bacterial growth (Log2 FC = 2,77) thus the samples for the RNA-seq experiments were withdrawn from this phase of growth.The RNA-seq revealed that the expression of 42 transcripts was changed in the ΔPA2504 mutant as compared to the parental PAO1161 strain and that the majority of them were connected to the sulphur transport/metabolism.

overall_design: Pseudomonas aeruginosa PAO1161 (leu-, r-, RifR) derivative of PAO1 was used in the experiment (Kawalek et al., 2020; BMC Genomics, 21:14). To determine the effect of the lack of the PA2504 protein on the transcriptome, the RNA-seq analysis was performed on RNA isolated from Pseudomonas aeruginosa PAO1161 wild type strain control (later referred to as PAO1161) and the PAO1161 ΔPA2504 strain (later reffered to as PA2504). The strains where grown in the L-broth rich medium in 37°C with shaking. The samples for the RNA extraction were withdrawn from the stationary phase of bacterial growth, after 18 h. Three independent biological replicates of total RNA were isolated for each strain.

first: Elzbieta

last: Kraszewska


title: The Negative Effect of Protein Phosphatase Z1 Deletion on the Oxidative Stress Tolerance of Candida albicans Is Synergistic with Betamethasone Exposure

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary: The glucocorticoid betamethasone (BM) has potent anti-inflammatory and immunosuppressive effects; however, it increases the susceptibility of patients to superficial Candida infections. Previously we found that this disadvantageous side effect can be counteracted by menadione sodium bisulfite (MSB) induced oxidative stress treatment. The fungus specific protein phosphatase Z1 (CaPpz1) has a pivotal role in oxidative stress response of Candida albicans and was proposed as a potential antifungal drug target. The aim of this study was to investigate the combined effects of CaPPZ1 gene deletion and MSB treatment in BM pre-treated C. albicans cultures. We found that the combined treatment increased redox imbalance, enhanced the specific activities of antioxidant enzymes, and reduced the growth in cappz1 mutant (KO) strain. RNASeq data demonstrated that the presence of BM markedly elevated the number of differentially expressed genes in the MSB treated KO cultures. Accumulation of ROS, increased iron content and fatty acid oxidation, as well as the inhibiting ergosterol biosynthesis and RNA metabolic processes explain, at least in part, the fungistatic effect caused by the combined stress exposure. We suggest that the synergism between MSB treatment and CaPpz1 inhibition could be considered in developing of a novel combinatorial antifungal strategy accompanying steroid therapy.

overall_design: Transcriptional responses of eight different cultures such as untreated, betamethasone sodium phosphate (BM), menadione sodium bisulfite (MSB) and BM+MSB treated Candida albicans QMY23 and ΔCaPPZ1 strains, were studied. Three independent cultures were used for RNAseq experiments.

first: István

last: Pócsi

first: Ágnes


title: Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals virus-snoRNA interactions

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

summary: SARS-CoV-2 coronavirus is one of the largest RNA viruses (26-32kb) and has emerged as a major threat to global public health. The resulting pandemic has caused global societal and economic disruptions. Here, we investigate the intramolecular and intermolecular RNA interactions of wildtype and a 382 deletion SARS-CoV-2 virus inside cells. We identified twelve potentially functional structural elements along the SARS-CoV-2 genome and observed that subgenomic viral RNA (sgRNAs) contains different structures that could be important for their functions using direct RNA sequencing. Proximity ligation sequencing experiments identified hundreds of intramolecular and intermolecular pair-wise interactions within the virus genome and between virus and host cellular RNAs. SARS-CoV-2 binds strongly to mitochondrial and nucleolar RNAs including COX1 and SNORD27, and contains 130 2’O-methylation sites along its genome. 2’O-methylation sites along the virus RNA are enriched in the UTRs and associated with increased pair-wise interactions. SARS-CoV-2 infection also results in a global decrease of 2’O-methylation sites on host mRNAs, suggesting that binding of SARS-CoV-2 to snoRNAs could be a pro-viral mechanism to sequester methylation machinery away from host RNAs to methylate the virus genome.  Collectively, these studies deepen our understanding of the molecular basis of SARS-CoV-2 pathogenicity, its cellular host factors and provides a platform for targeting the virus.

overall_design: SHAPE-MaP, Pore-Cupine, SPLASH & Nmseq of 2 strains of SARS-CoV-2 in E6 Vero cells

first: Siwy

last: Yang

first: Louis

last: DeFalco Jr

first: Danielle

last: Anderson

first: Yu

last: Zhang

first: Ashley

last: Aw

first: Su

last: Lim

first: Lim

middle: X

last: Ni

first: Kiat

last: Tan

first: Tanu

last: Chawla

first: Yan

last: Su

first: Alexander

last: Lezhava

first: Paola

last: deSessions

first: Adres

last: Mertis

first: Linfa

first: Yue

last: Wan


title: scRNA sequencing uncovers a TCF4-dependent transcription factor network regulating commissure development in mouse

status: Public on Jul 04 2021

city: Erlangen

first: Marie-Theres

last: Wittmann

address: Schwabachanlage 10

department: Institute of Human Genetics

institute: Universitätsklinikum Erlangen

summary: The bHLH transcription factor TCF4 plays an important role in neurodevelopment highlighted by its association with schizophrenia and Pitt-Hopkins-Syndrome. Here we demonstrate that TCF4 function is essential for forebrain commissure formation in mice. Single-cell RNA sequencing of TCF4 knockout neocortices revealed dysregulation of multiple gene regulatory networks. We provide evidence that TCF4 controls the underlying regulons by interaction with the regulators, transcription factors surprisingly not belonging to the known canonical interactors of the bHLH family. In-depth analysis of the interplay between TCF4 and SOX11 showed a synergistic effect on commissural formation. Mice haploinsufficient for Sox11 or Tcf4 showed no commissural phenotype or only a mild callosal shortening, respectively, whereas Tcf4/Sox11 double haploinsufficient mice display aggravated corpus callosum dysgenesis and anterior commissure agenesis. Moreover, TCF4 and SOX11 synergistically induce the expression of common target genes. Collectively, these findings illuminate how TCF4 dysregulation influences brain development and contributes to neurodevelopmental diseases.

overall_design: Single-cell RNA sequencing from E18.5 neocortices of wildtype and Tcf4 knock out mice.

first: Sayako

last: Katada

first: Elisabeth

last: Sock

first: Philipp

last: Kirchner

first: Arif

last: Ekici

first: Michael

last: Wegner

first: Kinichi

last: Nakashima

first: Chichung

middle: D

last: Lie

first: André

last: Reis


title: Retinoblastoma SNP array data

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

summary: Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, genomic  profiling of primary retinoblastoma samples. Most of the patients whose tumors were studied had received no treatment prior to surgical enucleation.

overall_design:
Immediately following enucleation, a needle was inserted through the eye?s anterior chamber to extract a tumor sample by aspiration; the tumor specimen was then snap frozen. For these arrays, DNA was extracted from these snap frozen samples.
We used  Affymetrix CytoScan HD Array arrays to study the genome alteration patterns of 28 primary retinoblastoma tumors
We used  Illumina 370K SNP arrays to study the genome alteration patterns of 44 primary retinoblastoma tumors
We used  Illumina 610 0K SNP arrays to study the genome alteration patterns of 22 primary retinoblastoma tumors

first: François

last: Radvanyi

first: Meriem

last: Sefta

first: Jing

last: Liu

last: Chapeaublanc

first: Celine

last: Desbrousses

first: Daniela

last: Ottaviani


title: Retinoblastoma gene expression data

summary: Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, genomic profiling of primary retinoblastoma samples. Most of the patients whose tumors were studied had received no treatment prior to surgical enucleation.

overall_design: Gene expression of 63 samples retinoblastomas tumor and 3 fetal retina were assesed using the Hg-U133 Plus 2.0 Affymetrix array


title: Nopp140-chaperoned 2’-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity

city: Bronx

first: Thomas

last: Meier

state: New York

address: 1300 Morris Park Avenue

department: Department of Anatomy & Structural Biology

institute: Albert Einstein College of Medicine, INC

summary: Spliceosomal small nuclear RNAs (snRNAs) are modified by small Cajal body (CB) specific ribonucleoproteins (scaRNPs) to ensure snRNP biogenesis and pre-mRNA splicing. However, the function and subcellular site of snRNA modification are largely unknown. We show that CB localization of the protein Nopp140 is essential for concentration of scaRNPs in that nuclear condensate; and that phosphorylation by casein kinase 2 (CK2) at some 80 serines targets Nopp140 to CBs. Transiting through CBs, snRNAs are apparently modified by scaRNPs. Indeed, Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2’-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Additionally, alternative splicing patterns change indicating that these modifications in U1, U2, U5, and U12 snRNAs safeguard splicing fidelity. Given the importance of CK2 in this pathway, compromised splicing could underlie the mode of action of small molecule CK2 inhibitors currently considered for therapy in cholangiocarcinoma, hematological malignancies, and COVID-19.

overall_design: Total RNA-Seq from HeLa cells with and without Nopp140 knockdown

first: Jonathan

last: Bizarro

first: Svetlana

last: Deryusheva

first: Ludivine

last: Wacheul

first: Varun

last: Gupta

first: Felix

last: Ernst

first: Denis

last: Lafontaine

first: Joseph

last: Gall

first: U

middle: T


title: A human liver cell-based system modeling a clinical prognostic liver signature combined with single-cell RNA-Seq for discovery of liver disease therapeutics

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

summary: Abstract: Chronic liver disease and hepatocellular carcinoma (HCC) are life-threatening with limited treatment options. The lack of clinically relevant/tractable experimental models hampers therapeutic discovery. We developed a simple and robust human liver cell-based system modeling a clinical prognostic liver signature (PLS) predicting long-term liver disease progression toward HCC. Using the PLS as a readout, followed by validation in NASH-HCC animal models and patient-derived tumorspheroids, we identified nizatidine, a histamine receptor H2 (HRH2) blocker, for treatment of advanced liver disease and HCC chemoprevention. Perturbation studies combined with scRNA-Seq analyses of patient liver tissues uncovered HRH2+, CLEC5Ahigh, MARCOlow liver macrophages and hepatocytes as nizatidine targets. The PLS model combined with scRNA-Seq of patient tissues enables discovery of urgently needed targets and therapeutics for treatment of advanced liver disease and cancer prevention.

overall_design: To investigate the functional effects of nizatidine on liver immune cells, we isolated CD45+ leucocytes from liver tissues of patients with advanced liver disease and HCC and treated the immune cell population with nizatidine or vehicle control. We then analyzed the effect of the compound by scRNA-Seq.

first: Emilie

last: Crouchet

first: Antonio

last: Saviano

first: Clara

last: Ponsolles

last: Baumert


title: Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

institute: Keio University School of Medicine

summary: Many animals have a conserved adaptive genome defense system known as the Piwi-interacting RNA (piRNA) pathway which is essential for germ cell development and function. Disruption of individual mouse Piwi genes results in male but not female sterility, leading to the assumption that PIWI genes do not play a role in mammalian oocytes. Contrary to this, PIWIL1- and PIWIL3-defective golden hamsters we have produced show defects in production of functional oocytes. Mechanisms involved,  however, vary between the two PIWI genes; lack of PIWIL1 has a strong impact on gene expression including hamster-specific young transposon de-silencing, while PIWIL3 deficiency has little impact on gene expression in oocytes, although DNA methylation of chromosomes was reduced to some extent. Our findings serve as the foundation for developing useful models to study the piRNA pathway in mammalian oocytes including humans, which cannot be possible with mice.

overall_design: small RNA sequencing, RNA sequencing, and whole genome bisulfite sequencing of PiwiL1 and/or PiwiL3 mutant hamsters.

first: H

last: Hasuwa

first: Y

middle: W

first: W

middle: K

last: Au Yeung

last: Sasaki

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