title: Distinctive properties of endothelial cells from tumor and normal tissue in human breast cancer

status: Public on Jul 05 2022

city: Warsaw

first: Klaudia

last: Brodaczewska

address: Szaserow 128

country: Poland

institute: Military Institute of Medicine

summary: Tumor microenvironment shapes aggressiveness and is largely maintained by the conditions of angiogenesis formation. Thus endothelial cells (ECs) biological reactions are crucial to know and control the design of efficient therapies. Here we used a model of ECs representative for the breast cancer tumor site and the same but healthy organ. Cells characterization was performed at the transcriptome, protein expression levels and assessment of their functional biological responses: angiogenesis and permeability. We showed that the expression of proteins specific for ECs (ACE+, VWF+), their differentiation (CD31+, CD 133+, CD105+, CD34-), adhesion properties (ICAM-1+, VCAM-1+, CD62-L+), barrier formation (ZO-1+) were down-regulated in tumor-derived ECs. The NGS-based differential transcriptome analysis confirmed CD31-lowered expression and pointed to the increase of Ephrin-B2 and SNCAIP indicative for dedifferentiation. Functional assays confirmed these differences as angiogenesis was impaired while permeability increased in tumor-derived ECs, further validated by the distinct enhanced VEGF production in response to hypoxia, reflecting the tumor conditions. This work shows that endothelial cells differ highly significantly, both phenotypically and functionally in the tumor site vs. the normal corresponding tissue, influencing the tumor microenvironment.

overall_design: RNA-Seq for normal cells (2 replicates) and breast cancer cells (2 replicates)

first: Kinga

last: Wilkus

first: Arkadiusz

last: Kajdasz

first: Claudine

last: Kieda


title: Predicting off-target effects of antisense oligomers targeting bacterial mRNAs with the MASON webserver

status: Public on Jul 01 2022

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

department: Institute of Molecular Infection Biology (IMIB)

country: Germany

institute: University of Würzburg

type: Expression profiling by high throughput sequencing

summary: Antisense oligomers (ASOs) such as peptide nucleic acids (PNAs), designed to inhibit the translation of essential bacterial genes, have emerged as attractive sequence- and species-specific programmable RNA antibiotics. Yet, potential drawbacks include unwanted side effects caused by their binding to transcripts other than the intended target. To facilitate the design of PNAs with minimal off-target effects, we developed MASON (Make AntiSense Oligomers Now), a webserver for the design of PNAs that target bacterial mRNAs. MASON generates PNA sequences complementary to the translational start site of a bacterial gene of interest and reports critical sequence attributes and potential off-target sites. We based MASON’s off-target predictions on experiments in which we treated Salmonella enterica serovar Typhimurium with a series of 10mer PNAs derived from a PNA targeting the essential gene acpP but carrying two serial mismatches. Growth inhibition and RNA-sequencing (RNA-seq) data revealed that PNAs with terminal mismatches are still able to target acpP, suggesting wider off-target effects than anticipated. Comparison of these results to an RNA-seq dataset from uropathogenic Escherichia coli (UPEC) treated with eleven different PNAs confirmed our findings are not unique to Salmonella. We believe that MASON’s off-target assessment will improve the design of specific PNAs and other ASOs.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: RNA profiles of Salmonella after short-term treatment with peptide nucleic acids. All samples are in duplicate, except the control samples, which contain 5 replicates.

first: Linda

last: Popella

first: Phuong

middle: T

last: Do

first: Patrick

last: Pfau

first: Jörg

last: Vogel

first: Lars

last: Barquist


title: Transcriptomic analysis of the effects of CDK8 and CDK19 knockout and re-expression and selective CDK8/19  kinase inhibitor Senexin B treatment on gene expression in HEK293 cells

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

country: USA

institute: University of South Carolina

summary: RNA-Seq analysis was carried out to investigate the effects of selective CDK8/19 inhibitor Senexin B (different treatment period) and knockout/re-expression of CDK8 and CDK19 proteins) on gene transcription in HEK293 cells

overall_design: Parental HEK293 cells (WT), CDK8/CDK19 single-knockout derivatives (8KO, 19KO), CDK8/19 double-knockout (dKO), and dKO-reexpression derivatives (dKO-V, dKO-8, dKO-19) were treated with Vehicle control (XXX.C) or 1μM Senexin B (XXX.S) for different period of time (3hr, 5hr, 24hr, 3d and 15d). Each treatment condition was done in biological triplicate.

first: Hao

last: Ji

first: Igor

middle: B

last: Roninson


title: Effect of SOX9 depletion on active chromatin marks in hESC-derived cranial neural crest cells [ChIP-seq]

status: Public on Jul 04 2022

city: Stanford

first: Sahin

last: Naqvi

state: CA California

address: 265 Campus Drive, Lokey Stem Cell Research Building/SIM1

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To assess the effects of SOX9 depletion on active chromatin marks in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of the degrader molecule dTAGV-1 results in SOX9 depletion. We then profiled the active chromatin mark H3K27ac by ChIP-Seq in undepleted CNCCs or CNCCs in which SOX9 was depleted for 3h or 24h. We also titrated SOX9 to four distinct levels with dTAGV-1 and assessed SOX9 binding by V5 ChIP-seq, as well as TWIST1 and TFAP2A binding by ChIP-seq.

overall_design: Genome-wide chromatin mark and TF binding profiling (H3K27ac, V5, TWIST1, TFAP2A ChIP-seq) of WT and SOX9-tagged H9 hESC-derived cranial neural crest cells (CNCCs)


title: Single-nucleus RNA sequencing of mouse brown adipose tissue

status: Public on Jul 03 2022

city: Daejeon

first: JUNGMO

last: KIM

state: -- None selected --

address: 291 Daehak-ro, Yuseong-gu

department: Center for Vascular Research

country: South Korea

institute: Institute for Basic Science

summary: Here, we performed single nucleus RNA sequencing on mouse brown adipose tissues to investigate the gene expression patterns relative to BAT thermogenesis mechanism using denervation model.

overall_design: Single nuclear from mouse brown adipose tissues were isolated and single-nucleus transcriptome libraries were generated

first: Gou

middle: Y

last: Koh

first: JungMo

last: Kim

first: Hyeok

middle: J

last: Lee


title: Assessing the role of TPL2 in TauP301S mice

status: Public on Jul 16 2022

city: Mississauga

first: Alyaa

middle: M

last: Mohamed

state: Ontario

address: 7070 Mississauga Road Mississauga, ON L5N 5M8 Canada

country: Canada

institute: Hoffman La Roche

summary:
ScRNAseq analysis shows
•TPL2 KD (kinase dead) reduced TauP301S dependent IEG and MHCII activation states in microglia
•TPL2 KD reduced peripheral immune cell infiltration in TauP301S mouse brain

overall_design:
Single cell suspensions of mouse hippocampi were obtained by FACS from ~ 9-month-old TPL2 KD mice crossed with TauP301S mice and littermate control mice.
Samples analyzed:
1. Tpl2 wt/wt, Tau P301S -/-, n = 3
2. Tpl2 kd/kd, Tau P301S -/-, n = 3
3. Tpl2 wt/wt, Tau P301S +/-, n = 6
4. Tpl2 kd/kd Tau P301S +/-, n = 6

first: Yuanyuan

last: Wang

first: Jesse

last: Hanson

first: Brad

last: Friedman

first: Mitchell

last: Rezzonico

first: Zora

last: Modrusan


title: De novo inference of thermodynamic binding energies using deep learning models of in vivo transcription factor binding

status: Public on Jun 29 2022

first: Amr

middle: Mohamed

last: Alexandari

state: CA

address: 240 Pasteur Dr

summary: We introduce Affinity Distillation (AD), a method for extracting thermodynamic affinities de-novo from in-vivo immunoprecipitation experiments using deep learning. We show that neural networks modeling base-resolution in-vivo binding profiles of yeast and mammalian TFs can accurately predict energetic impacts of varying underlying DNA sequence on TF binding. Systematic comparisons between Affinity Distillation predictions and other predictive algorithms consistently show that Affinity Distillation more accurately predicts affinities across a wide range of TF structural classes and DNA sequences. Affinity Distillation relies on in-silico marginalization against many sequence backgrounds, resulting in a higher dynamic range and more accurate predictions than motif discovery algorithms. Moreover, we show that Affinity Distillation can learn differential paralog-specific affinities, thereby making it possible to more accurately reconstruct regulatory networks in cells.

overall_design: Chromatin immunoprecipitation (ChIP-nexus) data for Pho4 and Cbf1 in Saccharomyces cerevisiae

first: Connor

middle: A

last: Horton

first: Avanti

last: Shrikumar

first: Nilay

last: Shah

first: Eileen

last: Li

first: Melanie

last: Weilert

first: Miles

last: Pufall

first: Julia

last: Zeitlinger

first: Polly

last: Fordyce

first: Anshul

last: Kundaje


title: Precise modulation of transcription factor levels reveals drivers of dosage sensitivity

first: Sahin

last: Naqvi

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

overall_design: Refer to individual Series


title: Effect of SOX9 depletion on transcription mRNA in hESC-derived cranial neural crest cells [SLAM-seq]

summary: To assess the effects of SOX9 depletion on transcription in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of the degrader molecule dTAGV-1 results in SOX9 depletion. We then profiled transcription by metabolic labeling of RNA (SLAM-Seq) in undepleted CNCCs or CNCCs in which SOX9 was depleted for 3h or 24h

overall_design: Genome-wide transcription profiling (SLAM-Seq) of WT and SOX9-tagged H9 hESC-dervied cranial neural crest cells (CNCCs)


title: Effect of SOX9 dosage changes on gene expression in hESC-derived cranial neural crest cells [RNA-seq]

summary: To assess the effects of quantitative SOX9 dosage changes on gene expression in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of differing concentrations of the degrader molecule dTAGV-1 results in different SOX9 concentrations, as measured by flow cytometry. We then profiled gene expression profiling in each of these SOX9 concentrations

overall_design: Genome-wide gene expression profiling (RNA-Seq) of WT and SOX9-tagged H9 hESC-dervied cranial neural crest cells (CNCCs)


title: Effect of SOX9 dosage changes on chromatin accessibility in hESC-derived cranial neural crest cells [ATAC-seq]

summary: To assess the effects of quantitative SOX9 dosage changes on chromatin accessibility in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of differing concentrations of the degrader molecule dTAGV-1 results in different SOX9 concentrations, as measured by flow cytometry. We then profiled chromatin accessibility in each of these SOX9 concentrations

overall_design: Genome-wide chromatin accessibility profiling (ATAC-Seq) of WT and SOX9-tagged H9 hESC-derivied cranial neural crest cells (CNCCs)


title: Single cell preparations of Mycobacterium tuberculosis damage the mycobacterial envelope and disrupt macrophage interactions

status: Public on Jun 23 2022

city: St. Louis

first: Jennifer

last: Philips

state: MO

address: 660 S. Euclid Avenue, Campus Box 8051

department: Department of Medicine, Division of Infectious Diseases

institute: Washington University School of Medicine

summary: In order to investigate the impact of using in vitro techniques to generate single cell suspensions of Mycobacterium tuberculosis (Mtb) on macrophage gene expression, we compared uninfected bone marrow derived macrophages to macrophages infected with Mtb that was prepared using gentle sonication followed by low-speed centrifugation (so/sp)  or passage through a 5 µm syringe filter (5µmF).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type murine macrophages were uninfected or infected with Mtb H37Rv at a multiplicity of infection of 5 followed by RNA sequencing at 72 hours post infection. 5 experimental replicates were performed for each group.

first: Ekansh

last: Mittal

first: Andrew

last: Roth


title: Molecular and cognitive signatures of ageing partially restored through synthetic delivery of IL2 to the brain

city: Cambridge

first: Samar

middle: Hayat Khan

last: Tareen

address: Babraham Hall, Babraham

country: United Kingdom

institute: Babraham Institute

summary: Cognitive decline is a common pathological outcome during aging, with an ill-defined cellular or molecular basis. Among the cellular changes observed with age are alterations to neuronal plasticity, changes in the glial compartment and the decline of the neurogenic niche. In the recent years, the concept of inflammaging, defined as a low-grade inflammation increasing with age, has emerged as a nexus for age-related diseases. This increase of basal inflammation is also observed in the central nervous system. While not classically considered a neurological cell type, infiltrating T cells increase in the brain with age, and may be responsible for amplification of inflammatory cascades and disruptions to the neurogenic niche. Recently, a small resident population of regulatory T cells has been identified in the brain, and the capacity of IL2-mediated expansion of this population to counter neuroinflammatory disease has been demonstrated. Here we test a brain-specific IL2 delivery system for the prevention of neurological decline in aging mice. We identify the molecular hallmarks of aging in the brain glial compartments, and identify partial restoration of this signature through IL2 treatment. At a behavioral level, brain IL2 delivery prevented the age-induced defect in learned memory formation during maze tests, without improving the general decline in motor skill or novelty-seeking behavior. These results identify immune modulation as a potential path to preserving cognitive function for healthy ageing.

overall_design: C57BL/6 mice were treated at ages 2 months and 22 months with either control vector PHP.GFAP-GFP or the treatment vector PHP.GFAP-IL2. Two months later, astrocytes, microglia, oligodendrocytes and oligodendrocyte precursors were sort-purified from the mouse brains for 10x single cell transcriptomics analysis.

middle: H

first: Emanuela

last: Pasciuto

first: Pierre

last: Lemaitre

first: Matthew

last: Holt

first: Lidia

last: Yshii

first: Adrian

last: Liston


title: Lovastatin Promotes the Self-renewal of Murine and Primate Spermatogonial Stem Cells

status: Public on Jun 10 2022

city: Guangzhou

first: Xiuling

last: Song

address: 1038 Shatai South Road

country: China

institute: Southern Medical University

summary: The spermatogonial stem cells (SSCs) niche is critical for SSC maintenance and the subsequent spermatogenesis. Numerous reproductive hazards impair the SSC niche, thereby result in aberrant SSC self-renewal and male infertility. However, promising agents targeting the impaired SSC niche to promote SSC self-renewal are still limited. Here, we screen out and assess the effects of Lovastatin on the self-renewal of mouse spermatogonial stem cells (mSSCs). Mechanistically, Lovastatin promotes the self-renewal of mSSCs and inhibits its inflammation and apoptosis through the regulation of isoprenoid intermediates. Likewise, other statins  exhibit similar effects on SSC self-renewal. Remarkably, the treatment by Lovastatin could promote the self-renewal of mSSCs in the male gonadotoxicity model generated by busulfan injection. Noteworthy, we demonstrate that Lovastatin could significantly enhance the self-renewal of in vitro cultured primate SSCs. Collectively, our findings uncover that lovastatin could promote the self-renewal of both murine and primate SSCs and have implications for the treatment of certain male infertility using small compounds.

overall_design: We screen out and assess the effects of Lovastatin on the self-renewal of mouse spermatogonial stem cells (mSSCs). To investigate how lovastatin functioned in mSSC self-renewal, we performed bulk RNA-Seq using cell samples from PTC, LOVA, and NTC groups. Mechanistically, Lovastatin promotes the self-renewal of mSSCs and inhibits its inflammation and apoptosis through the regulation of isoprenoid intermediates.

first: Chaohui

first: Fang

last: Lou

first: Zhaokai

last: Yao


title: Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages

status: Public on Jun 24 2022

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

summary: We developed ONT-cappable-seq, a specialized long-read RNA sequencing technique that allows end-to-end sequencing of primary prokaryotic transcripts using the Nanopore sequencing platform. We applied ONT-cappable-seq to study the transcriptional landscape of Pseudomonas aeruginosa phage LUZ7, leading to a comprehensive genome-wide map of viral transcription start sites, terminators and complex operon structures that fine-regulate gene expression. At the same time, it provides new insights in the RNA biology of LUZ7 and paves the way for more in depth transcription studies that can help unveil the complex layers of phage-host interactions.

overall_design: Full-length transcriptional profiling of P. aeruginosa US449 infected with phage LUZ7 at different time points (0, 5, 10 and 20 minutes) using ONT-cappable-seq.

first: Leena

last: Putzeys

first: Maarten

last: Boon

first: Eveline-Marie

last: Lammens

first: Konstantin

last: Kuznedelov

last: Severinov


title: Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer (ChIP-Seq)

status: Public on Jun 17 2022

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: Activating estrogen receptor alpha (ER) mutations are present in primary endometrial and metastatic breast cancers, promoting estrogen-independent activation of the receptor. Functional characterizations in breast cancer have established unique molecular and phenotypic consequences of the receptor, yet the impact of ER mutations in endometrial cancer has not been fully explored. In this study, we used CRISPR-Cas9 to model the clinically prevalent ER-Y537S mutation and compared results to ER-D538G to discover allele-specific differences between ER mutations in endometrial cancer. We found that constitutive activity of mutant ER resulted in changes in the expression of thousands of genes, stemming from combined alterations to ER binding and chromatin accessibility. The unique gene expression programs resulted in ER mutant cells developing increased cancer associated phenotypes, including migration, invasion, anchorage independent growth, and growth in vivo. To uncover potential treatment strategies, we identified ER associated proteins via Rapid Immunoprecipitation and Mass Spectrometry of Endogenous Proteins (RIME) and interrogated two candidates, CDK9 and NCOA3. Inhibition of these regulatory protein resulted in decreased growth and migration, representing potential novel treatment strategies for ER mutant endometrial cancer. Taken together, this study provides insight into ER mutant activity in endometrial cancer and identifies potential therapies for women with ER mutant endometrial cancer.

overall_design: ChIP-seq was used to study the effects of mutant ER-Y537S on ER genomic binding and the effects of wildtype or mutant ER (ER-Y537S and ER-D538G) on CDK9 genomic binding.

first: Zannel

last: Blanchard

first: Craig

last: Rush


title: Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin structures

city: Tianjin

first: Zhou

last: Sijie

address: No.135 Yaguan road

institute: Tianjin Unversity

summary: To investigate the mechanisms underlying the rearrangement patterns,we compared the rearrangement map with local chromatin structures and the three-dimensional genome architecture via assay for transposase-accessible chromatin using sequencing (ATAC-seq) and genome-wide chromosome conformation capture (Hi-C), respectively

overall_design: ATAC-seq and Hi-C of synthetic strain yZSJ025

first: Ying-Jin

last: Yuan

first: Yi

last: Wu

first: Sijie

last: Zhou


title: Time course expression pattern during neural crest cells (NCCs) differentiation from iPSCs

status: Public on Jun 18 2022

city: Fujisawa

first: Daisuke

last: Kamiya

state: Kanagawa

address: 26-1 Muraoka-Higashi 2-chome

department: CiRA

country: Japan

institute: Kyoto University

summary: To clarify the changes in cell properties during the differentiation process from iPSCs into NCCs, we sampled each cell during the differentiation process and compared gene expression patterns.

overall_design: During the 10-day NCC differentiation process from iPSC, we sampled every 2 days and compared gene expression patterns. On day 10, FACS sorting was performed with the NCC marker CD271, and the expression patterns of CD271 high and low expression cells were also compared.

first: Teppei

last: Akaboshi

first: Makoto

last: Ikeya


title: Effects of CDK8/19 Mediator Kinase inhibition by Senexin B in HEK293 cells treated with or without Interferon-gamma

first: Mengqian

last: Chen

summary: RNA-Seq analysis was carried out to investigate the effects of selective CDK8/19 inhibitor Senexin B on gene transcription mediated by IFN-γ signaling pathway in HEK293 cells

overall_design: HEK293 cells were treated with Vehicle control (293.C), 1μM Senexin B (293.S), 10ng/mL IFN-γ (293.I) or Senexin B/IFN-γ combination (293.IS) for 5 hours. Each treatment condition was done in biological triplicate.

first: M

first: H

last: Ji

first: I

last: Roninson


title: Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer


title: Human skin specific long noncoding RNA HOXC13-AS regulates keratinocyte differentiation by inferfering with Golgi-ER retrograde transport

status: Public on Jun 15 2022

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

summary:
In an RNAseq analysis, we have identified the HOXC13-AS significantly downregulated in wound biopsies and epidermal cells compared to skin counterparts.
To study the genes regulated by HOXC13-AS, we transfected HOXC13-AS siRNA pool into human primary epidermal keratinocytes to knockdown HOXC13-AS and induced cell differentiation for 3 days by 1.5 mM calcium. We performed a global transcriptome analysis of keratinocytes upon the HOXC13-AS knockdown using Affymetrix arrays.

overall_design: Gene expression profiling of differentiated keratinocytes transfected with either siRNA control (n = 3) or si-HOXC13-AS (n = 3) was carried out by using human Clariom™ S assay (ThermoFisher Scientific) at the Bioinformatics and Expression Analysis (BEA) core facility at Karolinska Institutet.

middle: X

last: Landén

first: Letian

last: Zhang


title: Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer (RNA-Seq)

overall_design: RNA seq was used to study the effects of mutant ER-Y537S on gene expression


title: Malpighian tubules (MT) gene expression between control and yki3SA gut-tumor-bearing flies.

status: Public on May 29 2022

city: Boston

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

state: Massachusetts

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

summary: To investigate the function of Malpighian tubules on host wasting, we established a fly model of tumor-induced wasting  by activation of an oncogene Yki in adult intestinal stem cells (ISCs) for 8 days to cause gut-tumor formation and systemic organ wasting and metabolic abnormalities. We then performed RNA-seq and gene expression analysis in Malpighian tubules from control and yki3SA tumor-bearing flies

overall_design: Comparative species composition and diversity analysis, gene expression profiling analysis of meta-seq data for control and yki3SA tumor-bearing flies.


title: Allele-specific gene regulation, phenotypes, and therapeutic vulnerabilities in estrogen receptor alpha mutant endometrial cancer (ATAC-Seq)

first: Jason

last: Gertz

overall_design: ATAC seq was used to study the effects of mutant ER-Y537S on chromatin accessibility


title: Activation of TnSmu1, an integrative and conjugative element, is lethal to Streptococcus mutans

status: Public on May 18 2022

city: Jonesboro

first: Robert

middle: Colquhoun

last: Shields

state: Arkansas

address: Lab Science East

department: Biological Sciences

institute: Arkansas State University

summary: RNA-seq was utilized to compare the transcriptomes of a CRISPRi control strain and a CRISPRi strain targeting/repressing SMU_218

overall_design: Streptococcus mutans mRNA profiles were generated for a CRISPRi control strain and a CRISPRi strain targeting/repressing SMU_218 by deep sequencing, in triplicate

middle: C


title: Rapid 3D Bioprinting of Multicellular Model Recapitulating Pterygium Microenvironment

status: Public on Jun 01 2022

city: La Jolla

first: ZHENG

last: ZHONG

state: California

address: 9500 Gilman Dr

department: Nanoengineering

institute: University of California, San Diego

summary: Pterygium is an ocular surface disorder with high prevalence that can lead to vision impairment. As a pathological outgrowth of conjunctiva, pterygium involves neovascularization and chronic inflammation, but its pathogenesis remains largely unknown. Over the last decade, various types of disease models have been built to study pterygium. Here, we developed a 3D multicellular in vitro pterygium model using the digital light processing (DLP)-based 3D bioprinting of human conjunctival stem cells (hCjSCs). A novel feeder-free culture system was adopted and efficiently expanded the primary hCjSCs with homogeneity, stemness and differentiation potency. The DLP-based 3D bioprinting was able to fabricate hydrogel scaffolds that support the viability and biological integrity of the encapsulated hCjSCs. The bioprinted 3D pterygium model was fabricated with hCjSCs, immune cells and vascular cells to recapitulate the disease microenvironment. Transcriptomic analysis using RNA sequencing (RNA-seq) identified a distinct profile correlated to inflammation response, angiogenesis, and epithelial mesenchymal transition in the bioprinted 3D pterygium model. In addition, the pterygium signatures and disease relevance of the bioprinted model were validated with the public RNA-seq data from patient-derived pterygium tissues. By integrating the stem cell technology and 3D bioprinting, this is the first reported 3D in vitro disease model for pterygium that can be utilized by future studies towards the personalized medicine and the drug screening.

overall_design: RNA seq was carried out on the 3D Bioprinting of Multicellular Model and 2D culture as control

first: Zheng

last: zhong


title: Placental transcriptome analysis of hypertensive pregnancies identifies distinct gene expression profiles of preeclampsia superimposed on chronic hypertension

status: Public on May 30 2022

city: Ann Arbor

first: Ashley

last: Hesson

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

summary: The pathogenesis of preeclampsia superimposed on chronic hypertension is poorly understood relative to preeclampsia occurring in pregnant people without chronic hypertension. Placental transcriptomes in pregnancies complicated by de novo preeclampsia and superimposed preeclampsia have not been previously compared.

overall_design:
The goal of this study is to investigate the transcriptomes of placentas from different types of hypertensive pregnancies.
We identified pregnant people in the University of Michigan Biorepository for Understanding Maternal and Pediatric Health with hypertensive disorders affecting singleton, euploid gestations (N=36) along with non-hypertensive control subjects (N=12). Subjects were grouped as: (1) normotensive (N=12), (2) chronic hypertensive (N=13), (3) preterm preeclampsia with severe features (N=5), (4) term preeclampsia with severe features (N=11), (5) preterm superimposed preeclampsia (N=3), or (6) term superimposed preeclampsia (N=4). Bulk RNA sequencing of paraffin-embedded placental tissue was performed.

first: Elizabeth

last: Langen

first: Plazyo

last: Olesya

first: Johann

last: Gudjonsson

first: Santhi

last: Ganesh


title: Patterns of oncogene co-expression at single-cell resolution influence clinical outcome in Diffuse Large B-Cell Lymphoma.

status: Public on May 23 2022

city: Singapore

first: Michal

middle: Marek

last: Hoppe

address: 14 Medical Dr

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

summary: Intratumor heterogeneity (ITH) in oncogene expression is common in cancer, but it is not known if oncogenes exert combinatorial effects at the single cell level to influence clinical outcome. We address this question using quantitative spectral imaging to simultaneously measure the cellular co-expression of the oncogenes MYC, BCL2 and BCL6 in clinically annotated cohorts of Diffuse Large B-Cell Lymphoma (DLBCL). Unlike in non-malignant lymphoid tissue, where the co-expression of these oncogenes is spatially constrained, DLBCL samples show multiple permutations of oncogenic co-expression at the single cell level. Oncogene co-expression follows clustered and non-random spatial distribution, and is typically stable across different regions of a tumour. Interestingly, we noted that the extent of cells with the unique oncogene combination MYC+BCL2+BCL6- (M+2+6-) associates consistently with patient survival across three independent DLBCL cohorts. We then show that the fraction of M+2+6- co-expressing cells can be inferred from quantitative single oncogene data, as the overall frequencies of co-expression of these oncogenes are stochastic. Predicted values of M+2+6- cellular co-expression frequency from immunohistochemistry of MYC/BCL2/BCL6 (n=316) and multiple independent gene expression datasets (n=2522; 8 cohorts) consistently correlate with survival after R-CHOP chemotherapy, offering a novel strategy for identification of high-risk DLBCL. Finally, we use comparative RNAseq analysis of patient-derived M+2+6+ and M+2+6- B-cells to identify cyclin D2 as a potential BCL6-repressed mediator of the aggressive behavior of M+2+6- population. Overall, our work demonstrates that patterns of oncogene co-expression analyzed at single-cell resolution are clinically relevant, with implications for both diagnostics and target discovery in other cancer types.

overall_design: Primary germinal centre B-cells derived from fresh tonsil of independent donors were isolated (Caeser et al. 2019 Nat Commun) and either MYC and BCL2 or MYC, BCL2 and BCL6 were overexpressed. Four samples of each condition were assessed for gene-expression by RNA sequencing.

first: Rebecca

last: Caeser

first: Daniel

last: Hodson

first: Anand

middle: D

last: Jeyasekharan


title: Transcript analysis of hESC-derived neurons treated with maturation promoting compounds

status: Public on Jun 03 2022

city: New York

first: Emiliano

last: Hergenreder

state: NY

institute: Memorial Sloan Kettering Cancer Center

summary: High-content screening identified compounds that promote maturation of human neurons derived from pluripotent stem cells. We sequenced total RNA from neurons treated with these drugs to detemrine their effect at the transcriptome level.

overall_design: Bulk RNA-seq from neurons treated with maturation factors or DMSO for 7 days. 3 Biologial replicates from independent differentiations.

first: Lorenz

last: Studer


title: Single-cell comparative transcriptomics of control and MK-886-treated sea urchin primary mesenchyme cells

first: Cynthia

middle: A.

last: Bradham

state: MA

address: 24 Cummington Mall

department: Biology

institute: Boston University

summary: We report the single-cell transcriptional profiling of sea urchin primary mesenchyme cells isolated from embryos treated with DMSO or with 5-lox activating protein (FLAP) inhibitor MK-886. We find that inhibition of LOX activity with MK-886 prior to PMC isolation induces shifts in gene expression within the PMC population. We further demonstrate that control PMCs cluster into four transcriptionally-defined subsets, and MK-886-treated PMCs cluster into five distinct subsets. These data highlight novel transcriptional paradigms in the diversification of PMCs, and the requirement of ectodermal LOX activity for proper PMC transcriptional diversification.

overall_design: Examination of sea urchin primary mesenchyme cell transcriptional diversity and its regulation by ectodermally-expressed 5-lipoxygenase

first: Dakota

last: Hawkins

first: James

last: Huth

last: Zuch


title: Limitations of a submerged culture system

status: Public on May 06 2022

city: Magdeburg

first: Constanze

last: Nossol

address: Leipziger Str. 44

department: Medical Faculty

institute: Otto-von-Guericke University

summary: in vitro microarray study of transcriptional changes of jejunal cells

overall_design: three samples per experimental group were used for expression profiling

first: Klaus

last: Wimmers

first: Michael

last: Oster


title: Regulatory T cells in skin promote hair follicle stem cell activation and hair growth through glucocorticoid signaling (RNA-Seq)

status: Public on May 02 2022

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: The maintenance of tissue homeostasis in steady state or under stress is dependent on the proper communication between tissue-resident stem cells (SCs) and immune cells in their microenvironment or “niche”. In addition to promoting immune tolerance, regulatory T cells (Tregs) have recently emerged as a critical component of stem cell niche in the hair follicle (HF), injured muscle, bone marrow and intestine to support stem cell differentiation. How Treg cells sense the dynamic signals in the niche environment and communicate with stem cells during tissue regeneration is largely unknown. Here, by using HF as a model, we uncover a hitherto unrecognized function of glucocorticoid receptor (GR) signaling pathway in skin-resident Treg cells to facilitate hair follicle stem cell (HFSC) activation and HF regeneration. Ablation of GR signaling in Tregs blocked HFSCs activation and proliferation after hair depilation and during the natural hair growth cycle. Mechanistically, GR signaling induces skin-resident Tregs to produce TGF-b3, which activates Smad2/3 in HFSCs and promotes HFSC proliferation and hair growth. Our study identifies a novel crosstalk between skin-resident Tregs and HFSCs mediated by the GR/TGF-b3 axis, highlighting a new avenue to manipulate Tregs to support tissue regeneration.

overall_design: mRNA profiles of skin Treg cells in glucocorticoid receptor knock out (GR KO) and wile type (GR WT) one day after hair dipilation (HD). GR WT has three replicates while GR KO has five replicates. mRNA profiles of hair follicle stem cell (HFSC) in GR KO and GR WT four days after hair depilation. Each condition has three replicates.

first: Zhi

last: Liu

first: Xianting

last: Hu

first: Yuqiong

last: Liang

first: Ye

last: Zheng


title: A CRISPR-engineered Isogenic Model Reveals Altered Neuronal Phenotypes of the 22q11.2 A-B Syndromic Deletion

city: San Francisco

first: Arun

middle: P

last: Wiita

state: CALIFORNIA

address: 185 Berry St, Ste 290/Rm 2410

institute: University of California San Francisco

summary: The 22q11.2 deletion syndrome (22q11.2DS) is the most common copy number variant (CNV)-associated syndrome, leading to congenital, cognitive, and neuropsychiatric anomalies in patients. The clinical presentation of the disease phenotypes is variable, posing significant challenges for prognosis of inheritance risk and clinical outcomes for the CNV carriers. ~85% of patients and almost all available human-centered models of this condition reflect the ~2.7 Mb “A-D” deletion at this locus. Leveraging a CRISPR/Cas9-based engineering strategy and induced pluripotent stems cells, we generated novel isogenic models for the smaller, commonly inherited 1.5 Mb “A-B” deletion found in ~5-10% of 22q11.2DS patients. The bulk RNA-seq data included here reflects paired-end 100 bp sequencing of iPSC-derived neuronal progenitor cells and excitatory neurons. These data reflect three independent clones either carrying the designed 22q11.2 deletion or control comparators (2 clones nucleofected with same sgRNA but with no deletion generated; 1 clone derived from the parental Cas9-expressing iPSC line). We anticipate that these novel, isogenic models will carry significant utility for the study of 22q11.2 deletion syndrome.

overall_design: RNA sequencing of iPS derived NPCs and neurons (control and those harboring CRISPR engineered 22qAB deletions) in biological triplicates to study RNA level changes in control vs deletion NPCs and neurons and also across stages

first: Neha

last: Paranjape

first: Yu-Hsui

last: Lin

first: Quetzal

last: Flores-Ramirez

first: Vishesh

last: Sarin

first: Amanda

last: Johnson

first: Julia

last: Chu

first: Mercedes

last: Paredes


title: Regulatory T cells in skin promote hair follicle stem cell activation and hair growth through glucocorticoid signaling

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

overall_design: Refer to individual Series


title: A Yap-dependent transcriptional program directs cell migration for embryo axis assembly

status: Public on May 01 2022

city: Heidelberg

first: Javier

last: Vázquez-Marín

state: Baden-Württemberg

address: Im Neuenheimer Feld 230, 5th floor

department: Centre for Organismal Studies (COS)

institute: Heidelberg University

summary: The assembly of the embryo’s primary axis is a fundamental landmark to establish the vertebrate body plan. Although the morphogenetic movements directing cell convergence towards the midline have been described extensively, little is known on how gastrulating cells interpret mechanical cues. Yap proteins are well-known transcriptional mechanotransducers, yet their role in gastrulation remains elusive. Here we show that the double knockout of yap and its paralog yap1b in medaka results in an axis assembly failure, due to reduced displacement and migratory persistence in mutant cells. We identified genes involved in cytoskeletal organization and cell-ECM adhesion, rather than in germ layers specification, as direct Yap targets. Dynamic analysis of live sensors and downstream targets reveal that Yap is acting in migratory cells, in which promotes cortical actin and focal adhesions recruitment. Our results indicate that Yap coordinates a mechano-regulatory loop essential to maintain the directed cell migration sustaining embryo axis development.

overall_design: RNA-seq profile of wild type, yap-/- and yap-/- yap1b-/- mutant embryos at stage 16.

first: Ana

last: Sousa-Ortega

first: Juan

middle: R

last: Martínez-Morales

first: María

last: Almuedo-Castillo


title: Inflammatory stress signaling via NF-kB alters accessible cholesterol to upregulate SREBP2 transcriptional activity in endothelial cells

status: Public on Apr 28 2022

city: New Haven

first: Joseph Wayne

middle: Montano

last: Fowler

state: CT

address: 10 Amistad St.

department: Pharmacology

institute: Yale University

summary: There is a growing appreciation that a tight relationship exists between cholesterol homeostasis and immunity in leukocytes, however, this relationship has not been deeply explored in the vascular endothelium. Endothelial cells (ECs) rapidly respond to extrinsic signals, such as tissue damage or microbial infection, by upregulating factors to activate and recruit circulating leukocytes to the site of injury and aberrant activation of ECs leads to inflammatory based diseases, such as multiple sclerosis and atherosclerosis. Here, we studied the role of cholesterol and its master regulator, SREBP2, in the EC responses to inflammatory stress. Treatment of ECs with pro-inflammatory cytokines upregulates SREBP2 cleavage and cholesterol biosynthetic gene expression within the late phase of the acute inflammatory response. Furthermore, SREBP2 activation was dependent on NF-kB DNA binding and canonical SCAP-SREBP2 processing. Mechanistically, inflammatory activation of SREBP was mediated by a reduction in accessible cholesterol, leading to heightened sterol sensing and downstream SREBP2 cleavage. Detailed analysis of NF-kB inducible genes that may impact sterol sensing resulted in the identification of a novel RELA-inducible target, STARD10, that mediates accessible cholesterol homeostasis in ECs. Thus, this study provides an in-depth characterization of the relationship between cholesterol homeostasis and the acute inflammatory response in EC.

overall_design: Comparative gene expression of early passage HUVECs treated with either siRNA to CTRL or RELA and treated with TNF for 0, 4, and 10 hours

first: Joseph

middle: W

first: Rong

last: Zhang

first: Bo

last: Tao

first: Nabil

middle: E

last: Boutagy

first: William

last: Sessa


title: Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

institute: University of Würzburg

summary: Antisense peptide nucleic acids (PNAs) that target mRNAs of essential bacterial genes exhibit specific bactericidal effects in several microbial species, but our mechanistic understanding of PNA activity and their target gene spectrum is limited. Here, we present a systematic analysis of PNAs targeting eleven essential genes with varying expression levels in uropathogenic Escherichia coli (UPEC). We demonstrate that UPEC is susceptible to killing by peptide-conjugated PNAs, especially when targeting the widely-used essential gene acpP. Our evaluation yields three additional promising target mRNAs for effective growth inhibition, i.e., dnaB, ftsZ, and rpsH. The analysis also shows that transcript abundance does not predict target vulnerability and that PNA-mediated growth inhibition is not universally associated with target mRNA depletion. Global transcriptomic analyses further reveal PNA sequence-dependent but also -independent responses, including the induction of envelope stress response pathways. Importantly, we show that the growth inhibitory capacity of 9mer PNAs is generally as effective as their 10mer counterparts. Overall, our systematic comparison of a range of PNAs targeting mRNAs of different essential genes in UPEC suggests important features for PNA design, reveals a general bacterial response to PNA conjugates and establishes the feasibility of using PNA antibacterials to combat UPEC.

overall_design: Bacterial overnight cultures were diluted 1:100 in fresh MHB and grown to an OD600 of 0.5. Subsequently, obtained cultures were again diluted 1:100 in fresh MHB to adjust a cell concentration of approximately 106 cfu/mL. After transferring 1.9 mL of the bacterial solution into 5 mL low-binding tubes (LABsolute), 100 µL of 20x PPNA stock solutions were added to reach a final concentration of 5 µM for all KFF-conjugated PNAs. In parallel, an equal amount of cells was treated with the respective volume of sterile nuclease-free water, which was used as solvent for the test compounds, and served as negative control. After incubating the samples for 15 min at 37 °C, RNAprotect Bacteria (Qiagen) was added according to the manufacturer’s instructions. Following a 10-min incubation, cells were pelleted at 4 °C and 21,100 xg for 20 min. The supernatant was discarded and pellets were either directly used or stored at – 20 °C (< 1 day) for subsequent bacterial RNA isolation.

first: Linda

last: Popella

first: Phuong

middle: T

last: Do

first: Regan

last: Hayward

first: Lars

last: Barquist

first: Jörg

last: Vogel


title: Regulatory T cells in skin promote hair follicle stem cell activation and hair growth through glucocorticoid signaling (ChIP-Seq)

first: Jingting

last: Yu

overall_design: Chromatin immunoprecipitation and sequencing (ChIP-seq) in skin Treg and Tcon cells treated with ETOH and DEX using antiodies against Foxp3 and GR.

first: Zhi

last: Liu

first: Xianting

last: Hu

first: Yuqiong

last: Liang

first: Ye

last: Zheng


title: An ectopic primate RNA in mouse neurons promotes activity and CREB function

status: Public on Apr 29 2022

first: Priit

last: Pruunsild

address: INF 364

department: Neurobiology

institute: University of Heidelberg

summary: The expression of the primate-specific LINC00473 (Lnc473) gene is decreased in the brains of schizophrenics as well as female depression patients. It is not clear, however, what is the function of Lnc473 in neurons. We introduced the human Lnc473 RNA into mouse primary neurons and show that this resulted in a transcriptomic shift comprising downregulation of epilepsy-associated genes and a rise in the transcriptional output of CREB activity. Moreover, ectopic Lnc473 expression increased neuronal as well as network excitability.

overall_design: mRNA expression profile in mouse hippocampal primary neurons supplemented with human Lnc473 compared to EGFP expression.


title: CHD-associated enhancers direct human cardiomyocyte lineage commitment.

status: Public on May 15 2022

city: Dallas

first: Daniel

last: Armendariz

state: TX

address: 5323 Harry Hines Boulevard

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

summary: Enhancers orchestrate gene expression programs that drive multicellular development and lineage commitment. Thus, genetic variants at enhancers are thought to contribute to developmental diseases by altering cell fate commitment. However, while many variant-containing enhancers have been identified, systematic studies to endogenously test the impact of these enhancers on lineage commitment have been lacking. We performed a single-cell CRISPRi screen to directly assess the roles of 25 enhancers and putative cardiac target genes implicated in genetic studies of congenital heart defects (CHD). We identified 16 enhancers whose repression leads to delayed differentiation of human cardiomyocytes. A focused analysis on 6 TBX5 enhancers showed that TBX5 enhancer perturbation delays the transcriptional switch from mid-CM to late-CM states. Knockout of two TBX5 enhancers resulted in X and Y, which phenocopy expected CHD phenotypes. Together, these results identify critical enhancers of cardiac development and suggest that misregulation of these enhancers could contribute to cardiac defects in human patients.

overall_design: Single cell sequencing of differentiated cardiomyocytes from H9 hESC comprised of three separate conditions. Large screen lentivirally transduced hESCs, validation screen lentivirally transduced hESCs, and hESCs in which either a TBX5 enhancer or the TBX5 promoter were knocked out.

first: Gary

last: Hon


title: A cryptic transcription factor regulates Caulobacter crescentus adhesion [ChIP-seq]

status: Public on Apr 27 2022

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: Alphaproteobacteria commonly produce a polar adhesin that is anchored to the exterior of the cell envelope. In Caulobacter crescentus, this adhesin enables permanent attachment to solid surfaces and is known as the holdfast. An ensemble of two-component signal transduction (TCS) proteins control C. crescentus holdfast biogenesis by indirectly regulating expression of HfiA, a potent holdfast inhibitor. We designed a genetic screen to identify regulators of hfiA that function downstream of the TCS adhesion regulatory system. This screen identified a hypothetical protein that we have named RtrC. Though the primary structure of RtrC does not match any defined sequence family, we demonstrate that RtrC directly binds and regulates dozens of sites on the C. crescentus chromosome via a pseudo-palindromic motif. Among these binding sites is the hfiA promoter where RtrC functions to repress transcription and thereby activate holdfast biogenesis. RtrC forms an OR-gated type I coherent feedforward loop with the DNA-binding response regulator SpdR and the adhesion regulator RtrB. This type of network motif is known to buffer gene expression against transient loss of regulating signals. We further demonstrate that, in addition to promoting adhesion, RtrC expression influences cell motility in soft agar. We conclude that the formerly hypothetical gene, rtrC, encodes a transcription factor that functions downstream of the C. crescentus TCS adhesion control system to regulate holdfast biogenesis and motility.

overall_design: Chromatin Immunoprecipitation sequencing (ChIP-seq) for 3xFLAG-tagged rtrC

first: Aretha

last: Fiebig

first: Maeve

last: McLaughlin

first: David

middle: M

last: Hershey

first: Leila

last: Reyes Ruiz


title: Dynamic mode decomposition of transcriptome dynamics and optimal sensor placement for discovery of genetic reporters

status: Public on Apr 21 2022

city: Santa Barbara

first: Aqib

last: Hasnain

address: UCEN Road

institute: University of California Santa Barbara

summary: Accelerating the design of synthetic biological circuits for biosensing requires expanding the currently available genetic toolkit. Although whole-cell biosensors have been successfully engineered and deployed, particularly in applications such as environmental and medical diagnostics, novel sensing applications necessitate the discovery and optimization of novel biosensors. Here we develop a data-driven approach that combines dynamic mode decomposition and observability analysis to extract salient, endogenous genetic sensors for analytes of interest from dynamic gene expression profiles. We show that relatively few dynamic modes are required to capture the transcriptome dynamics. The concept of system observability is then used to rank genes based on their ability to reconstruct the cell state. Genes which contribute to the system's observability are dubbed encoder genes. As a demonstration of our method, we extract, construct, and characterize 15 genetic reporters for the organophosphate malathion in the host bacterium \textit{Pseudomonas fluorescens} SBW25. Furthermore, we demonstrate how the distinct responses of each genetic reporter can be used to construct a single-input, single-output virtual sensor network, approximating a pair of reference trajectories. This library of living malathion sensors can be optimized for use in environmental diagnostics while the developed machine learning tool can be applied to discover genetic reporters in the compendium of host organisms and environmental conditions.

overall_design: Comparative time-series gene expression profiling analysis of RNA-seq data for the bacterium P. fluorescens SBW25 with and without induction of malathion.

first: Shara

last: Balakrishnan

first: Dennis

last: Joshy

first: Steven

middle: B

last: Haase

first: Jen

last: Smith

first: Enoch

last: Yeung


title: A cryptic transcription factor regulates Caulobacter crescentus adhesion [RNA-seq]

overall_design: RNA-sequencng from cells overexpressing rtrC


title: Single-cell sequencing reveals homogeneity and heterogeneity in the molecular cytopathological mechanisms of AKI caused by different etiologies

status: Public on Apr 30 2022

city: Fuzhou

first: Zhimin

last: Chen

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

summary: We constructed single-cell atlases of AKI induced by different etiologies, revealed potential homogeneity of injury patterns and heterogeneity between models in AKI. Extensive cell death and cytoskeletal remodeling events in proximal tubular cells (PTCs) as well as aberrant proliferation and inflammation of endothelial cells (ECs) in AKI are common injury patterns across different AKI models. However, there are differences in injury outcomes in PTCs with different etiologies, and ECs also have distinct transcriptional profiles.

overall_design:
Single-cell sequenceing of AKI induced by different etiologies:
cisplatin (CP), folic acid (FA), sodium oxalate (SO), ischemia reperfusion injury (IRI), and unilateral ureteral obstruction (UUO).

first: Yinshuang

last: Li

first: Ying

last: Yuan

first: Ruilong

last: Lan

first: Kunmei

last: Lai

first: Hong

first: Yanfang

last: Xu


title: Guanosine-7 tRNA methylation steers tRNA-derived fragment biogenesis and translational control in prostate cancer

status: Public on Apr 12 2022

city: Salamanca

first: Sandra

last: Blanco

address: Campus Miguel de Unamuno

country: Spain

institute: Cancer Research Institute (CIC) - Instituto de Biología Molecular y Celular  del Cáncer (IBMCC-CSIC)

summary: mRNAs from WT and METTL1 KO cells were subjected to expression profiling using Gene Chip Human Geome U133 Plus 2.0  to unveil transcriptional changes ocurring on these cells.

overall_design: total RNA from prostate cancer cells PC3 were extrated using NZYTECH RNA extration kit. Cells were either control CRIPSR (WT) or METTL1KO (using CRISPR). Three replicates were used per condition. A total of 6 samples were analysed.

first: Alejandro

last: Paniagua


title: Single Nucleus RNA Sequencing of Pre-Malignant Liver Reveals Disease-Associated Hepatocyte State with HCC Prognostic Potential

city: Bentley

first: Rodrigo

last: Carlessi

state: WA

address: Kent St

department: Curtin Medical School

country: Australia

institute: Curtin University

summary: Current approaches to stage chronic liver diseases have limited utility to directly predict liver cancer risk. Here, we employed single nucleus RNA sequencing (snRNA-seq) to characterize the cellular microenvironment of healthy and chronically injured pre-malignant livers using two distinct mouse models. Analysis of 40,748 hepatic nuclei unraveled a previously uncharacterized disease-associated hepatocyte transcriptional state (daHep). These cells were absent in healthy livers, but were increasingly prevalent as chronic liver disease progressed towards hepatocarcinogenesis. Gene expression deconvolution of 1,439 human liver transcriptomes from publicly available datasets revealed that daHep frequencies highly correlate with current histopathological liver disease staging systems. Importantly, we show that high daHep levels precede carcinogenesis in mice and humans and predict a higher risk of hepatocellular carcinoma (HCC) development. This novel transcriptional signature with diagnostic and, more importantly, prognostic significance has the potential to change the way chronic liver disease patients are staged, surveilled and risk-stratified.

overall_design: To identify and characterize cell states associated with the chronically injured pre-malignant liver, we employed a droplet-based (10x chromium) single nucleus transcriptomics approach. Hepatic nuclei were isolated and profiled from (a) healthy mice fed normal chow, (b) mice subjected to a choline-deficient, ethionine-supplemented (CDE) diet, and (c) mice provided with thioacetamide (TAA) in the drinking water. We obtained a total of 40,748 single nucleus transcriptomes (16,222 healthy; 14,507 CDE; and 10,019 TAA) from three mice per condition.

first: Elena

last: Denisenko

first: Ebru

last: Boslem

first: Julia

last: Koehn-Gaone

first: Nathan

last: Main

first: Nur

last: Abu Bakar

first: Gayatri

last: Shirolkar

first: Matthew

last: Jones

first: Daniel

last: Poppe

first: Benjamin

middle: J

last: Dwyer

first: Connie

last: Jackaman

first: Mark

last: Tjiam

first: Ryan

last: Lister

first: Michael

last: Karin

first: Jonathan

middle: A

last: Fallowfield

first: Timothy

last: Kendall

first: Stuart

last: Forbes

first: John

middle: K

last: Olynyk

first: George

last: Yeoh

first: Alistair

last: Forrest

first: Grant

last: Ramm

last: Febbraio

first: Janina

last: Tirnitz-Parker


title: Novel genetically engineered mouse models for clear cell renal cell carcinoma with somatic mutations in Bap1, Pbrm1 and Setd2

status: Public on Apr 06 2022

first: Johannes

middle: C.

last: van der Mijn

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Kidneys from our advanced GEMMs of early stage cancer renal cancers contain low frequent somatic mutations in Bap1, Pbrm1 and Setd2, enhanced immune clearance and activation of the DNA damage response

overall_design: We performed RNAseq on kidney cortex samples from transgenic mice with constitutive activation of HIF1A and gene edits in Bap1,Pbrm1 and compared gene expression to kidneys from wild type mice

first: Lorraine

last: Gudas


title: CryoGrid-PIXUL-RNA:  High throughput RNA isolation platform for tissue transcript analysis

status: Public on Mar 31 2022

city: Seattle

first: Karol

last: Bomsztyk

address: 850 Republican St

department: UW Medicine South Lake Union

institute: University of Washington

summary: We compared proteinase K buffer (PKBuffer) vs TRIzol vs column-based (PureLink RNA Micro kit) RNA isolation on frozen mouse organs methods using the high throughput CryoGrid system integrated with PIXUL sonicator. Mice were treated with intraperiteal injection of LPS (model of endotoxin  induced sepsis) or PBS (control).  After 12 hours mice were euthanized and  brains, hearts, kidneys, and livers were harvested, immediately placed on ice, and then frozen in CryoTrays.

overall_design: For each isolation method (Trizol vs PIXUL PK Buffer vs PureLink RNA column): 1 pair of tissue sample replicates was taken for each type of tissue treatment (LPS VS PBS) and each organ type.  Replicates are from different mice but with the same LPS/PBS treatment. For 2 isolation methods with 2 replicates of 2 treatment conditions across 4 types of organs = 48 total tissue samples

first: Scott

last: Schactler

last: Mar


title: GPR183 mediates the capacity of the novel CD47-CD19 bispecific antibody TG-1801 to heighten ublituximab-umbralisib (U2) anti-lymphoma activity

status: Public on Mar 30 2022

city: Badalona

first: Marcelo

middle: Lima

last: Ribeiro

state: Barcelona

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

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: Targeted therapies have considerably improved the survival rate of B-cell non-Hodgkin lymphoma (B-NHL) patients in the last decade; however, most subtypes remain incurable. TG-1801, a bispecific antibody that targets CD47 selectively on CD19+ B-cells, is under clinical evaluation in relapsed/refractory B-NHL patients either as a single-agent or in combination with ublituximab, a CD20 antibody, which is also being combined with the PI3Kδ/CK1e inhibitor, umbralisib (“U2”-regimen). In this study, we demonstrated that TG-1801 potentiates ublituximab-mediated antibody-dependent cell death (ADCC) and antibody-dependent cell phagocytosis (ADCP), leading to an additive anti-tumour effect of the TG-1801/U2 combination in B-NHL co-cultures. Accordingly, in a B-NHL xenotransplant model, the triplet achieved a 93% tumour growth inhibition, with 40% of the animals remaining tumour-free 35 days after the last dosing. Transcriptomic analysis further uncovered the upregulation of the G protein-coupled receptor, GPR183, as a crucial event associated with TG-1801/U2 synergism, while pharmacological blockade or genetic depletion of this factor impaired ADCP initiation, as well as cytoskeleton remodelling and cell migration, in B-NHL cultures exposed to the drug combination. Thus, our results set the preclinical rationale and support a combination strategy of TG-1801 with PI3Kδ- and CD20-targeting agents in patients with B-NHL.

overall_design: We used RNA-seq to uncover the mechanisms underlying the triplet combination (TG-1801 + U2) activity in Burkitt lymphoma. RNA-seq was performed in two Burkitt lymphoma (BL) cell lines (Daudi and Raji), two BL primary samples subjected to the following treatments for 24h: TG-1801 (10 ng/mL ),  U2 (umbralisib 1 µM + ublituximab 10 µg/mL) and the triplet combinationand. Additionally we also included two representative bulk Raji xenografts from the following treatment arms : TG-1801 (5 mg/kg, qw), Ublituximab (5 mg/kg, qw) + Umbralisib (150 mg/kg, bid), the triplet (U2 + TG-1801).

middle: L

first: Núria

last: Profitós-Pelejà

first: Juliana

middle: C

last: Santos

first: Pedro

last: Blecua

first: Diana

last: Garau

first: Marc

last: Armengol

first: Miranda

last: Fernández-Serrano

first: Emmanuel

last: Normant

first: Gaël

last: Roué


title: RNA-seq analysis of CaSki/SiHa/HeLa cell lines

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

summary: We perfomed RNA-seq analysis using HPV16-postive CaSki and SiHa cells and HPV18-postive HeLa cells for HPV integration and gene expression analyses

overall_design: Examination of HPV integration and expression in three cervical cancer cell lines

first: Lulu

last: Yu

first: Vladimir

last: Majerciak

first: Alexei

last: Lobanov

first: Sameer

last: Mirza

first: Vimla

last: Band

first: Haibin

last: Liu

first: Maggie

last: Cam


title: E3 ubiquitin ligase NEDD4-1  suppresses acetaminophen-induced liver injury in mouse by targeting the degradation of VDAC1

status: Public on Mar 29 2022

city: Changchun

first: Lin

last: Lei

address: 5333 Xi’an Road, Changchun, Jilin, China

department: State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Veterinary Medicine

institute: Jilin University

summary: Acetaminophen (APAP) overdose provokes various degrees of liver injury, whose pathogenesis involves multiple pathological events, such as mitochondrial damage and necrosis. E3 ubiquitin ligase neural precursor cell expressed developmentally downregulated 4-1 (NEDD4-1) plays vital roles in regulating a wide spectrum of physiological processes, and has been implicated in the pathogenesis of numerous liver disease. However, studies about the regulation of NEDD4-1 on APAP-induced liver injury (AILI) is still deficient. Thus, the aim of this study is to determine whether and how NEDD4-1 plays a role in AILI. Thus, we performed transcriptomic studies comparing liver samples of APAP-treated Flox or APAP-treated hepatocyte-specific Nedd4-1 (HepKO) deficiency mice,

overall_design: RNA-seq was conducted on total RNA isolated from livers of Flox or HepKO mice treated with 300 mg/kg APAP for 24 h; n = 3 per group.

first: Xinwei

last: Li

first: Yiwei

last: Zhu

first: Guowen


title: Nanoparticles-mediated TRPV1 channel blockade amplifies cancer thermo-immunotherapy via heat shock factor 1 modulation

status: Public on Mar 24 2022

city: su zhou

first: Ting

state: jiang su

address: Ren ai road 199

department: college of pharmaceutical science

institute: Soochow university

summary: Survival of malignant tumours is highly relevant to their intrinsic self-defense pathways such as heat shock protein (HSP) during cancer therapy, yet precisely dismantling self-defenses to amplify antitumour potency remains unexplored. Herein, we demonstrate that nanoparticles-mediated transient receptor potential vanilloid member 1 (TRPV1) channel blockade selectively modulates heat shock factor 1 to suppress dual self-defense pathways for potentiating thermo-immunotherapy. TRPV1 blockade is identified to inhibit calcium influx and subsequent nuclear translocation of HSF1 upon hyperthermia, leading to selective suppression of stressfully overexpressed HSP70 for enhancing thermotherapeutic efficacy against a variety of primary, metastatic and recurrent tumours. Particularly, the suppression of HSF1 translocation further restrains TGFβ pathway to apparently degrade extracellular matrix in tumour for improving the infiltration of antitumour therapeutics and immune cells into highly fibrotic and immunosuppressive pancreatic cancers, ultimately synergizing with anti-PD-L1 antibody to retrieve thermo-immunotherapy with tumour-eradicable and immune memory effects. The nanoparticles-mediated TRPV1 blockade represents as an effective and universal approach to selectively dismantle self-defenses for potent cancer therapy.

overall_design: Examination of TRPV1 blockade and thermotherapy on A549 cancer cells.

first: Shuhui

last: Jiang

first: Ying

last: Zhang

first: Jie

last: Luo

first: Ming

first: Hengte

last: Ke

first: Yibin

last: Deng

first: Tao

last: Yang

first: Xiaohui

last: Sun

first: Huabing

last: Chen


title: CLIP-seq of E. coli YhgF

status: Public on Mar 18 2022

city: Uppsala

first: Erik

last: Holmqvist

state: Uppland

address: Husargatan 3, Box 596, Uppsala University, Dept. of Cell and Molecular Biology

institute: Uppsala University

summary: YhgF is an uncharacterized protein in E. coli. We have shown through RNA interactome capture and other methods that it interacts with RNA. The aim of this study was to indentify in vivo RNA-targets of YhgF by using CLIP-seq.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: CLIP-seq

first: Thomas

last: Søndergaard Stenum

first: Jonas

last: Kjellin


title: The uncharacterized gene Rnf149 is a regulator of cardiopharyngeal development

status: Public on Mar 07 2022

city: New York

first: Burcu

last: Vitrinel

address: 100 Washington Sq E

institute: New York University

summary: To assay Rnf149 function during early cardiopharyngeal specification, bulk RNAseq was performed to profile the FACS-purified cardiopharyngeal lineage cells isolated from20 hpf Ciona larvae with CRISPR/Cas9-mediated Rnf149 mutagenesis.

overall_design: Examination of CRISPR/Cas9-mediated Rnf149 mutagenesis in the cardiopharyngeal lineage at 20 hpf.

first: Christine

last: Vogel

first: Lionel

last: Christiaen


title: Directionality Of Developing Skeletal Muscles Is Set By Mechanical Forces

first: Louis

last: Faure

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

summary: Formation of oriented myofibrils is a key event in the development of a functional musculoskeletal system. However, the mechanisms that control orientation of myocytes, their fusion and the resulting directionality of adult muscles remain enigmatic. Here, we utilized in vivo and in vitro live imaging, CAS9/CRISPR-mediated mutagenesis in fish, genetic experiments in mice and single cell transcriptomics to demonstrate that individual myocyte polarization and subsequent orientation depend on cell stretch imposed by skeletal expansion. Our data revealed that upon migration, individual facial myocytes form unpolarized clusters corresponding to future muscle groups. These clusters undergo oriented stretch and alignment during embryonic growth. Experimental in vivo perturbations of cartilage shape, size and distribution caused disruptions in directionality and number of myofibrils. Controlled in vitro 2D and 3D experiments applying continuous tension via artificial attachment points demonstrated a sufficiency for mechanical forces to instruct coherent polarization of myocyte populations. Consistently, perturbations of cartilage extension revealed a role of the developing skeleton in the directional outgrowth of non-muscle soft tissues during limb and facial morphogenesis.

overall_design: We performed bulk RNA seq to confirm single cell transcriptomic analysis of cells collected daily from soft and hard culture conditions.

first: Kazunori

last: Sunadome

first: Delf

last: Kah

first: Ben

last: Fabry

first: Csaba

last: Adori

first: Alek

last: Erickson

first: Polina

last: Kameneva

first: Shigeaki

last: Kanatani

first: Marketa

last: Kaucka

first: Ivar

last: Dehnisch

last: Tesarova

first: Tomáš

last: Zikmund

first: Jozef

last: Kaiser

first: Steven

last: Edwards

first: Kaj

last: Fried

first: Igor

last: Adameyko


title: Identifying target genes for the long noncoding RNA, GATA2-AS1

status: Public on Feb 25 2022

city: Toronto

first: Philip

last: Marsden

address: 209 Victoria Street, Room 522

department: Medicine

institute: University of Toronto

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

summary: We have identified a set of endothelial-enriched long noncoding RNAs (lncRNAs) in another experiment. In this experiment, we aim to identify genes that are regulated by the GATA2-AS1 lncRNA. We have depleted GATA2-AS1 using  two distinct siRNA in  human umbilical vein endothelial cells (HUVEC)

overall_design: In this experiment, we use total cellular RNA from HUVEC  treated with either a non-targeting (Ctl) siRNA or one of two siRNAs targeting GATA2-AS1. We have paired comparisons of Ctl siRNA versus two distinct siRNAs in three biological lines of HUVEC.

first: H

last: Man

first: Noeline

last: Subramaniam


title: Nox4 effect on mouse articular chondrocytes

status: Public on Mar 01 2022

city: Suwon

first: Jimin

last: Jeon

address: 206, World cup-ro, Yeongtong-gu

department: Biomedical Sciences

institute: Ajou University Graduate School of Medicine

summary:
Gene expression profiling of mouse articular chondrocytes infected with Ad-C or Ad-Nox4
In this study, we have attempted to explore the effects of Nox4 and have identified numerous genes which are involved in osteoarthritis pathogenesis.

overall_design: mouse articular chondrocytes were isolated from mouse femoral condyles and tibial plateaus cartilage tissue and infected with Ad-C(control) or Ad-Nox4 for 36 hours. Total RNA was extracted from primary mouse articular chondrocytes cultured with Ad-C (2 biological replicates) or Ad-Nox4 for 36 hours (2 biological replicates) and subjected to microarray analysis.

first: Siyoung

last: Yang


title: ActivinA effect on mouse articular chondrocytes

summary:
Gene expression profiling of mouse articular chondrocytes infected with Ad-C or Ad-Activin A
In this study, we have attempted to explore the effects of Activin A and have identified numerous genes which are involved in osteoarthritis pathogenesis.

overall_design: mouse articular chondrocytes were isolated from mouse femoral condyles and tibial plateaus cartilage tissue and infected with Ad-C(control) or Ad-ActivinA for 36 hours. Total RNA was extracted from primary mouse articular chondrocytes cultured with Ad-C (2 biological replicates) or Ad-activinA for 36 hours (2 biological replicates) and subjected to microarray analysis.


title: Molecular dissection unveiling dwarfing effects of plant growth retardants on pomegranate

status: Public on Feb 13 2022

city: Guangzhou

first: Yuchen

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

summary: Dwarfed stature is a desired trait for modern orchard production systems. One effective strategy of dwarfing is exogenously applying plant growth retardants (PGRs) to plants. However, for many economic fruit trees, the current knowledge on the regulatory mechanisms underlying the dwarfing effect of PGRs were limited, which largely restricts their agricultural application. In this study, we exogenously applied three kinds of PGRs (paclobutrazol, B9 and mannitol) to the seedlings of pomegranate (Punica granatum L.) and performed comparative transcriptome analysis to elucidate the molecular features of PGR-induced dwarfing in pomegranates. Our results showed that all the three PGRs could significantly suppress auxin biosynthetic and metabolic processes, as well as auxin-mediated shoot development, which may be the main reason for the dwarfing. Besides, different PGRs were also found to induce dwarfing via specially mechanisms. Cellular response to strigolactone were downregulated by the application of paclobutrazol, while carbohydrate homeostasis and metabolism were specifically suppressed in conditions of either B9 or mannitol treatments. Furthermore, exogenous PGR application was supposed to causes adverse impacts on the normal physiological process of pomegranate seedlings, which may bring extra burden to stress adaptation of pomegranate plants. These novel findings unveiled the genetic basis underlying the dwarfing in pomegranates.

overall_design: To investigate the molecular mechanisms underlying plant growth retardants (PGRs)-induced dwarfing in pomegranates, we exogenously applied three kinds of PGRs (paclobutrazol, B9 and mannitol) to the seedlings of pomegranate for 90 days and conducted transcriptome-wide bulk RNA-seq of the treated and untreated pomegranate plants.

first: Jingjing

last: Qian


title: Interleukin-10 contributes to reservoir establishment and persistence in antiretroviral therapy-treated, SIV-infected macaques

status: Public on Feb 09 2022

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Interleukin (IL)-10 is an immunosuppressive cytokine that signals through STAT3 to regulate T follicular helper cell (TFH) differentiation and germinal center formation. In SIV-infected macaques, levels of IL-10 in plasma and lymph node (LN) are induced by infection and not normalized with ART. During chronic infection, plasma IL-10 and transcriptomic signatures of IL-10 signaling were significantly correlated with the cell-associated SIV-DNA content within LN CD4+ memory subsets, including TFH, and predicted the frequency of CD4+ TFH and their cell- associated SIV-DNA content during ART, respectively. Notably, in ART-treated RMs, cells harboring SIV-DNA by DNAscope were preferentially found in the LN B-cell follicle in close proximity to IL-10. Finally, we demonstrate that the in vivo neutralization of soluble IL-10 in ART-treated, SIV-infected macaques significantly reduces B cell follicle maintenance and, by extension, cellular sites of viral persistence, including LN TFH and memory CD4+ T-cells expressing PD-1 and CTLA-4. Thus, these data support a role for IL-10 in maintaining a pool of target cells in lymphoid tissue that serve as a niche for viral persistence. Targeting IL-10 signaling to impair CD4+ T-cell survival and improve antiviral immune responses may represent a novel approach to limit viral persistence in ART-suppressed people living with HIV.

overall_design: 16 female Indian-origin, specific-pathogen-free (SPF) rhesus macaques were infected with SIVmac239 and at day 60 post-infection (p.i.) began a 5-drug, oral antiretroviral therapy. Starting at d60 and d203 p.i., seven RMs began 6-dose, weekly cycle of subcutaneous rhesus IL-21-IgFc (IL-21)

first: Justin

last: Harper

first: Susan

last: Ribeiro

first: Chi

middle: N

last: Chan

first: Malika

last: Aid

first: Claire

last: Deleage

first: Luca

last: Micci

first: Maria

last: Pino

first: Barbara

last: Cervasi

first: Gopalan

last: Raghunathan

first: Eric

last: Rimmer

first: Gulesi

last: Ayanoglu

first: Guoxin

last: Wu

first: Neeta

last: Shenvi

first: Richard

last: Barnard

middle: D

last: Prete

first: Kathleen

last: Busman-Sahay

last: Bosinger

first: Kirk

last: Easley

first: Bonnie

last: Howell

first: Dan

last: Gorman

first: Daria

last: Hazuda

first: Jacob

last: Estes

first: Rafick-Pierre

last: Sekaly

first: Mirko

last: Paiardini


title: Whole blood transcriptome from Covid-19 patients in India

status: Public on Feb 22 2022

city: Bangalore

first: Nagasuma

last: Chandra

state: Karnataka

address: C V Raman Road

department: Biochemistry

country: India

institute: IISC

summary: High throughput sequencing is performed on mRNA isolated from whole blood of adult Covid-19 patients, bacterial coinfection with Covid-19 and healthy controls in a South Indian cohort. Samples were collected from individuals at the time of hospitalization or visit to clinic. The Covid-19 samples are categorized by severeity.

overall_design: Gene expression profiling of Covid-19 patients, bacterial superinfection with Covid-19 and healthy controls.

first: Ushashi

last: Banerjee

first: Sneha

last: Chunchanur

first: Pragathi

last: Rao

first: Megha

last: Reddy

first: Amit

last: Singh


title: Alpha7 Nicotinic Acetylcholine Receptor Mediates Chronic Nicotine Inhalation-Induced Cardiopulmonary Dysfunction

status: Public on Feb 08 2022

city: New Orleans

first: Xinping

last: Yue

state: Louisiana

address: 1901 Perdido Street, MEB 7205

institute: LOUISIANA STATE UNIVERSITY HEALTH SCIENCES CENTER - N.O.

summary:
Purpose: The goal of this study is to compare the effects of inhaled nicotine on aortic gene expression and the role of the alpha7 nicotinic acetylcholine receptor (alpha7-nAChR) in mediating the nicotine effects.
Methods: WT and alpha7-nAChR knockout (KO) mice at 5-month of age were exposed to nicotine vapor or room air for a total of 12 weeks. Total RNA was extracted from thoracic aortas using RNeasy Plus mini kit followed by library preparation using SMART-Seq v4 Ultra Low Input RNA Kit. Illumina next generation sequencing was performed using the NextSeq 500 system with the high output flow cell (up to 800 M paired end reads).
Results:  A total of 179 differentially expressed genes (149 upregulated and 30 downregulated, adjusted P-value < 0.1) were found in thoracic aortas from WT mice exposed to nicotine vapor compared to those exposed to room air. In contrast, only 7 non-overlapping genes were found to be differentially expressed in alpha7-nAChR KO mice exposed to nicotine compared to the air controls.
Conclusions: Our study suggests that nicotine-induced changes in vascular gene expression is largely mediated by the alpha7-nAChR.

overall_design: Thoracic aorta gene expression of 8-month old WT and alpha7-nAChR KO mice with prior exposure to nicotine vapor or room air for 12 weeks.

first: Anna

last: Whitehead


title: The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis [ChIRP-seq]

status: Public on Feb 12 2022

city: Frederiksberg C

first: Yu

last: Jin

address: Thorvaldsensvej 40, 2nd floor

country: Denmark

institute: University of Copenhagen

summary: We identified differentially expressed genes in flail mutants linked to the regulation of flowering through stranded RNA-seq. A genomic rescue fragment of FLAIL (pFLAIL:gFLAIL) introduced in flail mutants can complement expression defects and early flowering, consistent with trans-acting effects of the FLAILRNA. We determined the genomic binding regions of FLAIL by ChIRP-seq. FLAIL binding to chromatin regions promotes the expression of selected flowering repressors.

overall_design: ChIRP-seq was used to determine chromatin binding regions of FLAIL.

first: Maxim

last: Ivanov

first: Sebastian

last: Marquardt


status: Public on Feb 19 2022

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

institute: City of Hope

summary: Colorectal cancer (CRC) is one of the most frequently diagnosed and lethal malignancy. Several key factors including poor dietary habits, smoking, alcohol consumption, genetic predisposition, obesity, diabetes mellitus, and sedentary lifestyle – all result in a significantly increased risk for developing CRC. Current treatment modalities for patients with CRC include surgery, which is often followed with adjuvant chemotherapy, especially in patients with a stage II and III disease. Most patients with advanced CRC are generally treated with the chemotherapeutic drug, 5-fluorouracil (5-FU) – either given alone or in combination with oxaliplatin and other molecularly-targeted drugs. While such treatment regimens are effective at improving disease outcomes, their clinical usefulness is often hampered due to the considerable toxicity associated with these treatments, which often causes severe nausea, vomiting, weight loss, and risk of infectious complications due to immunosuppression. Furthermore, their therapeutic efficacy is limited due to the emergence of chemotherapeutic drug resistance. In this study we performed genomewide transcriptomic analysis of parental and 5-FU resistant cells to identify differentially expressed genes and its associated pathways in promoting chemoresistance in CRC.

overall_design: RNA-seq profiles between human parental and 5-FU drug resistant HCT116 and SW480 colorectal cancer cell lines.

first: Souvick

last: Roy

first: Yinghui

last: Zhao

first: Yate

first: Ajay

last: Goel


title: Analysis of gene expression profile and T cell and B cell receptor diversities in the fetuses and trafficked maternal cells following murine in-utero transplantation of semi-allogenic bone marrow-derived hematopoietic stem cells

status: Public on Feb 03 2022

city: SINGAPORE

first: Karthikeyan

last: Kandasamy

state: SINGAPORE

address: 10 Medical Drive

department: Obstetrics & Gynaecology

institute: National University of Singapore

summary: We investigated the immune responses in the fetuses and trafficked maternal cells following in-utero transplantation (IUT) of maternal (mIUT) and paternal (pIUT) bone marrow donor mononuclear cells (MNC). Fetal cells and trafficked maternal cells were isolated from the 1 week old neonates by magnetic and FACS sorting and subjected to bulk RNA-sequencing. The gene expression profile in maternal and recipient cells of mIUT and pIUT show enriched clusters for RNA and protein metabolism, hemopoiesis and immune system development.  In recipients of DT+ pIUT recipient clusters additionally represented T-cell regulation. Upregulated pIUT and DT+pIUT maternal clusters represented mitogen-activated protein kinases (MAPK) cascades, T-cell activation, and immune system development. All groups shared common genes represented for cytokine stimulus response, immune system regulation, B-cell mediated immunity and adaptive immune response.  Analysis of receptor clonotypes reveals, the retrieval frequency of maternal-derived clonotypes increased and clonotypes diversity was reduced following mIUT and pIUT compared to uninjected controls. In DT+pIUT, decreased maternal clonotype retrieval and increased diversity towards baseline. In contrast, mIUT and pIUT recipient-derived clonotypes showed increased diversity while decreased frequency in DT+pIUT recipients.  Maternal-derived top 5 clonotypes in each group were expanded with IUT and diminished with DT+, while recipient-derived top 5 clonotypes were most abundant in uninjected pups. We observed a large number of public maternal-derived clonotypes between DT+pIUT and controls, and a substantial number of public recipient-derived clonotypes between mIUT, pIUT and DT+pIUT.  Complementarity-determining region 3 (CDR3) of naïve and antigen-experienced clonotypes are longer and shorter respectively, reflecting antigen driven selection. We also observed uniqueness in V/J-segment usage between uninjected control, mIUT and pIUT clonotypes. Our data indicate that both maternal and recipient immune cells respond to donor cells and that only maternal TCR and BCR diversity is affected by maternal DC depletion.

overall_design: Analysis of maternal and fetal immune responses following in-utero transplantation of hematopoietic stem cells

first: Citra

last: Mattar


title: Prevalent aberrant condensates of onco-fusion transcription factors and their dissolution as potential cancer therapy

status: Public on Jan 28 2022

city: Beijing

first: Chunyu

last: Yu

address: Xueyuan Road 38#

institute: Peking University

summary: Cancer-associated chromosomal rearrangements can result in the expression of numerous pathogenic fusion proteins. The mechanisms via which the fusion proteins contribute to oncogenesis are largely unknown and effective therapies for fusion-associated cancers are lacking. Here, we comprehensively scrutinized fusion proteins found in various cancers. We found that many fusion proteins are composed of phase separation-prone domains (PS) and DNA-binding domains (DBD), and these fusions have strong correlation with aberrant gene expression patterns. Furthermore, we established a high-throughput screening method, named DropScan, to screen drugs capable of modulating aberrant condensates. One of the drugs identified via DropScan, LY2835219, effectively dissolved the condensates in reporter cells lines expressing Ewing sarcoma fusions and partially rescued the abnormal expression of target genes. Our results indicate that aberrant phase separation is likely a common mechanism for these PS-DBD fusion-related cancers, and suggest that modulating aberrant phase separation is a potential route to treat these diseases.

overall_design: Wild type U2OS, U2OS integrated with mCherry-EWS-FLI1, and A673 cell lines were cultured in DMEM (HyClone) supplemented with 10% FBS (Gibco) and 100 units/mL penicillin and 100 μg/mL streptomycin (HyClone) at 37℃ with 5% CO2 in a humidified incubator (Above 10^7 cells in 10cm dish). Each replicate was treated with 7.5μM LY2835219 for 0(untreated), 3 and 6 hours.

first: Yuan

last: Wang

first: Gaofeng

last: Pei

first: Tingting

last: Li

first: Pilong


title: Whole transcriptome-sequencing of CD1c+ conventional type 2 dendritic cells of human non-infectious uveitis patients [Replication cohort]

status: Public on Jan 29 2022

city: Utrecht

first: Jonas

last: Kuiper

address: Heidelberglaan 100

department: Ophthalmology

country: Netherlands

institute: Universitair Medisch Centrum Utrecht

summary: RNA-sequencing data from flow cytometry-sorted primary HLA-DR+ Lin-(CD19-CD3-CD14-) CD1c+ cDC2s purifed from frozen peripheral blood mononuclear cells from patients with anterior, intermediate, and posterior non-infectious uveitis and healthy controls.

overall_design: This cohort was used as a replication cohort for GSE194060 (see also: https://www.biorxiv.org/content/10.1101/2021.11.16.468816v1). Nitrogen-stored PBMCs were thawed and subjected to cDC2 purification by flow cytometry and subjected to RNA-sequencing by NextSeq.

first: J


title: Single cell RNA sequencing of peripheral retina in control and FGF signaling mutant mouse embryonic tissue

status: Public on Jan 27 2022

first: Revathi

last: Balasubramanian

state: NY

address: 635 West 165th street

institute: Columbia University

summary: The goal of the study is to identify changes in gene expression and cell distribution in the ciliary margin upon loss of FGF signaing. Neural retinal cells from embryonic day E14 were isolated from control and mutant eyes. Dissociated cells were sorted based on GFP and TdTomato reporter expression in the control and mutant retina respectively. Flow-sorted single cells were processed by the core facility at Columbia University on a 10x platform.

overall_design: 3 control and 3 mutant embryos were pooled and sorted based on reporter expression for single cell sequencing

first: Xin

last: Zhang


title: Hyperactivation of YAP/TAZ drives alterations in mesangial cells through stabilization of N-MYC in diabetic nephropathy

status: Public on Feb 01 2022

city: Daejeon

first: Seunghyeok

last: Choi

address: Daehakro 291

institute: KAIST

summary: Mesangial cells (MCs) in the kidney are central to maintaining glomerular integrity, and their impairment leads to major glomerular diseases including diabetic nephropathy (DN). Although high blood glucose elicits abnormal alterations in MCs, the underlying molecular mechanism is poorly understood. Here, we show that YAP and TAZ, the final effectors of the Hippo pathway, are highly increased in MCs of patients with DN and of Zucker diabetic fatty rats. Moreover, high glucose directly induces activation of YAP/TAZ through the canonical Hippo pathway in cultured MCs. Hyperactivation of YAP/TAZ in mouse model MCs recapitulates the hallmarks of DN, including excessive proliferation of MCs and extracellular matrix deposition, endothelial cell impairment, glomerular sclerosis, albuminuria, and reduced glomerular filtration rate. Mechanistically, activated YAP/TAZ bind and stabilize N-Myc protein, one of the Myc family of oncogenes. N-Myc stabilization leads to aberrant enhancement of its transcriptional activity and eventually to MC impairments and DN pathogenesis. Together, these findings shed light on how high blood glucose in diabetes mellitus leads to DN and support a rationale that lowering blood glucose in diabetes mellitus could delay DN pathogenesis.

overall_design: 8 samples were analyzed, 5 for control mice and 3 for Last1/2 k/o mice.

first: Sang

middle: H

last: Suh

first: Hosung

last: Bae


title: Single-cell transcriptomics of dynamic cell behaviors

status: Public on Jan 25 2022

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

summary: Despite advances in spatial transcriptomics, linking dynamic behavior of cells in their native environment to molecular profiling remains a major challenge. We present a method, termed behavioral transcriptomics, that allows us to couple physiological behaviors of single cells in an intact tissue to deep molecular profiling of individual cells. This method enables us to establish a novel molecular signature for a striking migratory cellular behavior following tissue injury.

overall_design: In order to visualize the airway epithelium at high resolution over days, we explant a mouse trachea and secure it in a custom imaging platform, which minimizes sample movement during imaging and maintains a constant supply of nutrients from below the explant without disrupting the air-liquid interface. To determine the molecular signatures of cells with directional movement compared to regenerating non-moving cells, we marked epithelial regions by photoconversion at 24 hours after injury, imaged every 6 hours, screened for “movers” with >50 μm displacement (>3 μm/hr) at 18 hours after photoconversion, and then isolated photoconverted epithelial cells for plate-based single cell sequencing (scSeq). Dimensionality reduction revealed that cells from “moving” region (M) and a “non-moving” (NM) region cluster separately.

first: Sheldon

last: Kwok

first: Daniel

last: Montoro

first: Seok-Hyun

last: Yun

first: Vladimir

last: Vinarsky


title: Transcriptomic signatures of flight muscle, brain and leg tissues during Drosophila pupal development

city: Martinsried-Planegg

first: Maria

middle: Lynn

last: Spletter

address: Großhaderner Str. 9

department: Physiological Chemistry

institute: Ludwig-Maximilians-University München, Biomedical center

summary: Alternative splicing produces multiple, distinct mRNA transcripts from the same gene locus. To explore tissue-type specific gene expression and alternative splicing, we generated mRNA-Seq data from pupal tissues dissected from Drosophila. This allowed us to compare expression between dissected, highly enriched brain and indirect flight muscle (IFM) samples as well as whole legs. Bioinformatic analysis allowed us to characterize tissue-specific differences in gene expression as well as alternative splicing among the three tissues, as well as to identify a multitude of novel splicing events that are not currently contained in the Drosophila annotation. This suggests that tissue or cell-type specific sequencing at multiple timepoints during the fly life cycle will help extend existing annotations, and novel splice junction discovery is an important consideration in mRNA-Seq data analysis.

overall_design: Analysis of differential gene expression and exon use among Drosophila wildtype (w1118) tissues at 72h APF, including brain, indirect flight muscle (IFM) and whole leg.

first: Shao-Yen

last: Kao

first: Keshika

last: Ravichandran

first: Luka

last: Borozan

first: Stefan

last: Canzar

first: Domagoj

last: Matijevi

first: Tobias

last: Straub


title: Change in lncRNA and mRNA content of brain-derived extracellular vesicles following chronic intermittent ethanol vapor exposure in male mice

status: Public on Jan 23 2022

city: Pittsburgh

first: Annalisa

last: Baratta

state: PA

address: 3501 Fifth Ave

institute: University of Pittsburgh

summary: To understand how chronic intermittent ethanol vapor exposure changes the RNA content of brain-derived extracellular vesicles, we isolated total RNA and used lncRNA/mRNA microarray analysis to examine differential expression following CIE exposure in male animals

overall_design: Adult, male C57BL/6J mice were exposed to ethanol vapor or room air for 8h a day, 5 days a week, for 4 weeks. Animals were euthanized immediately following the final day of exposure and brains collected. Extracellular vesicles were isolated from whole brain by differential ultracentrifugation and total RNA isolated from extracellular vesicles for analysis of lncRNA and mRNA content

first: Baratta

last: Annalisa


title: Change in lncRNA and mRNA content of brain-derived extracellular vesicles following chronic intermittent ethanol vapor exposure in mice

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

overall_design: Refer to individual Series


title: Whole transcriptome-sequencing of CD1c+ conventional type 2 dendritic cells of human non-infectious uveitis patients

first: Jonas

last: Kuiper

summary: RNA-sequencing data from MACS-sorted primary CD19-CD303-CD1c+ cDC2s purifed from fresh peripheral blood mononuclear cells from patients with anterior, intermediate, and posterior non-infectious uveitis.

overall_design: PBMCs were isolated from heparin blood and subjected to MACS isolation to purify CD1c+ cDC2 cells. Purity was evaluated by flow cytometry and cell fraction subjected to RNA-sequencing by NovaSeq.


title: Change in lncRNA and mRNA content of brain-derived extracellular vesicles following chronic intermittent ethanol vapor exposure in female mice

summary: To understand how chronic intermittent ethanol vapor exposure changes the RNA content of brain-derived extracellular vesicles, we isolated total RNA and used lncRNA/mRNA microarray analysis to examine differential expression following CIE exposure in female animals

overall_design: Adult, female C57BL/6J mice were exposed to ethanol vapor or room air for 8h a day, 5 days a week, for 4 weeks. Animals were euthanized immediately following the final day of exposure and brains collected. Extracellular vesicles were isolated from whole brain by differential ultracentrifugation and total RNA isolated from extracellular vesicles for analysis of lncRNA and mRNA content


title: The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis.

status: Public on Jan 10 2022

first: Yu

last: Jin


title: Peanut oral immunotherapy suppresses clonally distinct subsets of T helper cells

status: Public on Dec 31 2021

city: Cambridge

first: Ang

middle: Andy

last: Tu

state: MA

address: 500 Main Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: Food allergy affects an estimated 8% of children in the US, with increasing severity and global prevalence. Using single-cell RNA sequencing and paired TCR sequencing, we assessed the transcriptomes of CD154+ and CD137+ peanut-reactive T helper cells from 12 peanut-allergic patients longitudinally throughout peanut oral immunotherapy. These results demonstrate a differential response to OIT among subsets of peanut-reactive T helper cells, and indicate that non-Th2 activation signatures may be associated with clinical outcomes.

overall_design:
Single-cell RNA and TCR sequencing of human samples via Seq-Well.

***Human raw data will be uploaded to dbGaP for controlled access

first: Brinda

last: Monian

first: Bert

last: Ruiter

first: Duncan

last: Morgan

first: Patrick

last: Petrossian

first: Neal

middle: P

last: Smith

first: Todd

last: Gierahn

first: Julia

last: Ginder

first: Wayne

middle: G

last: Shreffler

first: J

last: Love


title: The trans-acting long noncoding RNA FLAIL represses flowering in Arabidopsis [RNA-seq]

overall_design: RNA-seq was used to determine differentially expressed genes in wild type, flail mutant and complementation line.

first: Maxim

last: Ivanov

first: Sebastian

last: Marquardt


title: RNA-Seq of early passage wild type and short telomere G1 G4 Terc-/- ESCs.

status: Public on Jan 04 2022

city: tianjin

first: nannan

last: zhao

state: --- Select a state ---

address: nankai

institute: nankai university

summary: We aimed to investigate the retrotranspositon expression after telomere shortening.

overall_design: The Wild type and G1, G4 Terc-/- ESCs

first: Lin

last: Liu

first: Xinyi

last: Lv

first: Nannan

last: Zhao

first: Chun