title: Exploring high-resolution chromatin interaction changes and functional enhancers of myogenic marker genes during myogenic differentiation

first: Xiaokai

state: Sichuan

address: Huiming road #211

institute: Sichuan Agricultural University

summary: Skeletal muscle differentiation (myogenesis) is a complex and highly coordinated biological process regulated by a series of myogenic marker genes. Chromatin interactions between gene’s promoters and their enhancers have an important role in transcriptional control. However, the high-resolution chromatin interactions of myogenic genes and their functional enhancers during myogenesis remain largely unclear. Here, we used circularized chromosome conformation capture coupled with next-generation sequencing (4C-seq) to investigate eight myogenic marker genes in C2C12 myoblasts (C2C12-MBs) and C2C12 myotubes (C2C12-MTs). We revealed dynamic chromatin interactions of these marker genes during differentiation, and identified 163 and 314 significant interaction sites (SISs) in C2C12-MBs and C2C12-MTs, respectively. The interacting genes of SISs in C2C12-MTs were mainly involved in muscle development, and histone modifications of the SISs changed during differentiation. Through functional genomic screening, we also identified 25 and 41 putative active enhancers in C2C12-MBs and C2C12-MTs, respectively. Using luciferase reporter assays for putative enhancers of Myog and Myh3, we identified eight activating enhancers. Furthermore, dCas9-KRAB epigenome editing and RNA-seq revealed a role for Myog enhancers in the regulation of Myog expression and myogenic differentiation in the native genomic context. Taken together, this study lays the groundwork for understanding 3D chromatin interaction changes of myogenic genes during myogenesis and provides insights that contribute to our understanding of the role of enhancers in regulating myogenesis.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of dCas9-KRAB cells and Myog-En5 cells on days 5 of differentiation

first: Keren

last: Long

first: Sha

last: Zeng

first: Duo

last: Su


title: Foxa2 and Pet1 direct and indirect synergy drive serotonergic neuronal differentiation [ChIP-Seq]

status: Public on Jun 09 2022

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

country: USA

institute: Penn State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Neuronal programming by forced expression of transcription factors (TFs) holds promise for clinical applications of regenerative medicine. However, the mechanisms by which TFs coordinate their activities on the genome and control distinct neuronal fates remain obscure. Using direct neuronal programming of embryonic stem cells, we dissected the contribution of a series of TFs to specific neuronal regulatory programs. We deconstructed the Ascl1-Lmx1b-Foxa2-Pet1 TF combination that has been shown to generate serotonergic neurons and found that stepwise addition of TFs to Ascl1 canalizes the neuronal fate into a diffuse monoaminergic fate. The addition of pioneer factor Foxa2 represses Phox2b to induce serotonergic fate, similar to in vivo regulatory networks. Foxa2 and Pet1 appear to act synergistically to upregulate serotonergic fate. Foxa2 and Pet1 co-bind to a small fraction of genomic regions but mostly bind to different regulatory sites. In contrast to the combinatorial binding activities of other programming TFs, Pet1 does not strictly follow the Foxa2 pioneer. These findings highlight the challenges in formulating generalizable rules for describing the behavior of TF combinations that program distinct neuronal subtypes.

overall_design: ChIP-seq was used to characterize the genomic binding of induced transcription factors when various combinations of Ascl1, Lmx1b, Pet1, and Foxa2 were expressed in mouse embryonic stem cells.

first: Begüm

last: Aydin

first: Michael

last: Sierk

first: Mireia

last: Moreno-Estelles

first: Link

last: Tejavibulya

first: Nikathan

last: Kumar

first: Nuria

last: Flames

first: Esteban

middle: O

last: Mazzoni


title: Regulation of fin regeneration by a voltage-gated sodium channel

city: Madison

first: Junsu

last: Kang

state: WI

address: 1111 Highland Avenue

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

type: Expression profiling by high throughput sequencing

summary: We compare the brain and fin RNA-seq profiles of wild-type and scn8ab mutant zebrafish, which exhibit locomotion and fin regeneration defects.

overall_design: Biological duplicate brain and fin profiles of adult wild-type sibling and scn8ab(temca) mutant zebrafish. Corresponding sample pools include: whole brain of wild-type siblings and temca mutants and uninjured and 36 hpa fins of wild-type siblings and temca mutants at the restrictive temperature (33 degrees)

first: Daniel

last: Osorio-Mendez


title: Direct tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules

status: Public on Jun 12 2022

city: New Haven

first: Li-Tao

last: Guo

state: Connecticut

address: 260 Whitney Ave

institute: Yale University

summary: We combined electrophoresis and nanopore sequencing to analyze MarathonRT velocity over the heterogeneous sequences and structures of HOTAIR RNA template and reveal that the local sequences and structures of the template have negligible effect to MarathonRT, and MarathonRT can copy the long RNA in a single turnover, which leads to unusually synchronized primer extension at a constant speed of 25 nt/sec. We further demonstrate that ultra-stable RNA structure insertions do not obstruct MarathonRT, suggesting that MarathonRT can immediately disrupt any RNA structures within the template.

overall_design: MarathonRT velocity was determined using the cDNA samples generated at different reaction times (from 5 to 70 sec with 5 sec increment). The RT stops were confirmed using two replicates.

first: Sara

last: Olson

first: Shivali

last: Patel

first: Brenton

middle: R

last: Graveley

first: Anna

middle: M

last: Pyle


title: Regulatory architecture of the RCA gene cluster captures a novel intragenic boundary and enhancer elements in B cells

city: Berlin

first: Rafael

middle: Domínguez

last: Acemel

state: Berlin

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

summary: The Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes which share functions in the innate immune system. We aimed to investigate the structural organisation of the RCA gene cluster to identify key regulatory elements that influence the expression of CR2 and other genes in this important immunomodulatory region. Using 4C-seq, we captured extensive CTCF-mediated chromatin looping across the RCA gene cluster in B cells and showed these were organised into two topological associated domains (TADs). Interestingly, the inter-TAD boundary was located within the CR1 gene at a well-characterised segmental duplication. Additionally, we mapped numerous gene-gene and gene-enhancer interactions across the region, revealing extensive co-regulation. Importantly, we uncovered an intergenic enhancer and functionally demonstrated this element upregulates two RCA members (CR2 and CD55) in B cells simultaneously. Here, we highlight novel, long-range mechanisms whereby SLE susceptibility may be influenced by genetic variants, and the important contribution of chromatin topology to gene regulation and complex genetic disease.

overall_design: 4C-seq experiments using CTCF binding sites as baits in B lymphoblastoid cell lines

first: Jessica

last: Cheng

first: Joshua

middle: S

last: Clayton

middle: D

first: José

middle: L

last: Gómez-Skarmeta

first: Rhonda

last: Taylor

first: John

middle: B

last: Harley

first: Elizabeth

last: Quail

first: Daniela

last: Ulgiati


title: The E3 Ubiquitin Ligase AFF1 targets ARF19 to the proteasome

city: Saint Louis

first: Ryan

middle: Joseph

last: Emenecker

state: MO

address: 660 S Euclid Ave

department: Biochemistry and Molecular Biophysics

institute: Washington University School of Medicine

summary: Auxin critically regulates nearly every aspect of plant growth and development. Auxin-driven transcriptional responses are mediated through the AUXIN RESPONSE FACTOR (ARF) family of transcription factors. Although ARF protein stability is regulated via the 26S proteasome, molecular mechanisms underlying ARF stability and turnover are unknown. Here, we report the identification and functional characterization of an F-Box E3 ubiquitin ligase, which we have named AUXIN RESPONSE FACTOR F-BOX1 (AFF1). AFF1 directly interacts with ARF19 and regulates its accumulation. Mutants defective in AFF1 display ARF19 protein hyperaccumulation, mild auxin resistance, and developmental defects. Together, our data suggest a new mechanism, namely control of ARF protein stability, in regulating auxin responsiveness.

overall_design: This RNAseq experiment examined 3 genotypes (Col-0, aff1-1, aff1-2) of 4 day old Arabidopsis thaliana seedlings under two conditions (mock treated or 2 hour treatment with 10mM indole-3-acetic acid (IAA)). The RNA was isolated from whole seedlings. There were three replicates carried out for each genotype/treatment combination yeilding a total of 18 samples. The aff1-2 line is Salk_083453.

first: Hongwei

last: Jing

first: Lucia

last: Strader


title: Gene expression profiling of epithelial ovarian cancer by bulk RNA-seq

status: Public on Jun 08 2022

city: Yayoi, Bunkyo-ku

first: Tomoatsu

last: Hayashi

state: Tokyo

country: Japan

institute: The University of Tokyo

summary: Ovarian cancer has one of the worst prognoses among gynecologic malignancies. About 60% of ovarian cancer cases are diagnosed at Stages III and IV, and their five-year survival rate is less than 30%. Ovarian cancer is classified into four major histological subtypes; serous, clear cell, endometrioid and mucinous. Ovarian clear cell carcinoma (OCCC) is less sensitive to conventional platinum-based chemotherapy and has worse prognosis than other subtypes. In this study, we attempted to identify novel molecular targets critical for the proliferation and tumorigenicity of OCCC using the CRISPR/Cas9 system, and identified some genes as important candidates. Some of these candedates were upregulated in ovarian cancer tissue, especially OCCC. Our results suggest that not only may be these candedates a promising diagnostic maker for OCCC, drugs against these candedates would be useful for the therapeutic treatment of OCCC.

overall_design: Profiling of gene expression in primary ovarian cancer specimens (Clear cell (CCC); n = 11, High-grade serous (HGSC); n = 8, Endometrioid (EC); n= 4).

first: Ayako

last: Kawabata

first: Yoko

last: Nagayoshi

first: Naoko

last: Yokota

first: Ryuichiro

last: Nakato

first: Aikou

last: Okamoto

first: Tetsu

last: Akiyama


title: Integrated analysis of expression profile and potential pathogenic mechanism of temporal lobe epilepsy with hippocampal sclerosis

city: ChangSha

first: ZhaoQian

last: Liu

state: China

address: xiangya road 110

country: China

institute: Xiangya Hospital, Central South University

type: Methylation profiling by genome tiling array

summary: To investigate the potential pathogenic mechanism of temporal lobe epilepsy with hippocampal sclerosis (TLE+HS), we have employed analyzing of the expression profiles of microRNA/ mRNA/ lncRNA/ DNA methylation in brain tissues of hippocampal sclerosis (TLE+HS) patients. Brain tissues of six patients with TLE+HS and nine of normal temporal or parietal cortices (NTP) of patients undergoing internal decompression for traumatic brain injury (TBI) were collected. The total RNA was dephosphorylated, labeled, and hybridized to the Agilent Human miRNA Microarray, Release 19.0, 8x60K. The cDNA was labeled and hybridized to the Agilent LncRNA+mRNA Human Gene Expression Microarray V3.0，4x180K. For methylation detection, the DNA was labeled and hybridized to the Illumina 450K Infinium Methylation BeadChip. The raw data was extracted from hybridized images using Agilent Feature Extraction, and quantile normalization was performed using the Agilent GeneSpring. We found that the disorder of FGFR3, hsa-miR-486-5p, and lnc-KCNH5-1 plays a key vital role in developing TLE+HS.

first: Zhi-Bin

last: Wang

first: Jian

last: Qu

first: Zhuan-Yi

last: Yang

first: Ding-Yang

first: Shi-Long

last: Jiang

first: Ying

last: Zhang

first: Zhi-Quan

first: Xiao-Yuan

last: Mao

first: Zhao-Qian


title: Transcriptional changes to cytotoxic stresses are driven by HSF-activated genes and enhancers.

status: Public on Jun 10 2022

city: Turku

first: Samu

middle: Valtteri

last: Himanen

state: Varsinais-Suomi

address: Tykistökatu 6A

department: Cell Biology

country: Finland

institute: Åbo Akademi University

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

overall_design: Refer to individual Series


title: A dual-activity topoisomerase complex regulates mRNA translation and turnover

city: Baltimore

first: Weidong

state: MD

address: 251 Bayview Blvd

department: National Institute on Aging

institute: Shuaikun Su

summary: Topoisomerase 3β (TOP3B) and TDRD3 form a dual-activity topoisomerase complex that interacts with FMRP and can change the topology of both DNA and RNA.  Here, we investigated the post-transcriptional influence of TOP3B and associated proteins on mRNA translation and turnover.  First, we discovered that in human HCT116 colon cancer cells, knock-out (KO) of TOP3B had similar effects on mRNA turnover and translation as did TDRD3-KO, while FMRP-KO resulted in rather distinct effects, indicating that TOP3B had stronger coordination with TDRD3 than FMRP in mRNA regulation.  Second, we identified TOP3B-bound mRNAs in HCT116 cells; we found that while TOP3B did not directly influence the stability or translation of most TOP3B target mRNAs, it stabilized a subset of target mRNAs but had a more complex effect on translation--enhancing for some mRNAs whereas reducing for others.  Interestingly, a point mutation that specifically disrupted TOP3B catalytic activity only partially recapitulated the effects of TOP3B-KO on mRNA stability and translation, suggesting that the impact of TOP3B on target mRNAs is only in part linked to its ability to change topology of mRNAs.  Collectively, our data suggest that TOP3B-TDRD3 can regulate mRNA translation and turnover by mechanisms that are dependent and independent of topoisomerase activity.

overall_design: To identify the functions of the TOP3B-TDRD3 complex on post-transcriptional regulation in HCT116 cells, total 62 samples were uploaded, including PRO-seq, RNA-seq, Ribo-seq and eCLIP-seq samples from WT and KO/KI cells. Most of them contain two or three replications. For TOP3B eCLIP-seq, TOP3B-KO cells  were used as negative controls separately. For PRO-seq, RNA-seq and Ribo-seq, wild type cells were used as controls.

first: Shuaikun

last: Su

first: Yutong

last: Xue

first: Alexei

last: Sharov

first: Yongqing

first: Seung

middle: K

last: Lee

first: Jennifer

last: Martindale

first: Wen

last: Li

first: Wai

last: Ku

first: Keji

last: Zhao

first: Supriyo

last: De

first: Weiping

last: Shen

first: Payel

last: Sen

first: Myriam

last: Gorospe

first: Dongyi

last: Xu


title: Foxa2 and Pet1 direct and indirect synergy drive serotonergic neuronal differentiation

first: Shaun

last: Mahony


title: Foxa2 and Pet1 direct and indirect synergy drive serotonergic neuronal differentiation [ATAC-Seq]

overall_design: ATAC-seq was used to characterize chromatin accessibility when various combinations of Ascl1, Lmx1b, Pet1, and Foxa2 were expressed in mouse embryonic stem cells.

first: Begüm

last: Aydin

first: Michael

last: Sierk

first: Mireia

last: Moreno-Estelles

first: Link

last: Tejavibulya

first: Nikathan

last: Kumar

first: Nuria

last: Flames

first: Esteban

last: Mazzoni


title: Immune responses to Coronavirus disease-19 with Thymosin α 1 intervention: an observational cohort study

city: Xian

first: chengsheng

last: zhang

state: Shaanxi

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

department: precision medicine center

institute: First Affiliated Hospital of Xi 'an Jiaotong University

summary: Background   Coronavirus disease-19 (COVID-19) pandemic has posed a serious threat to global health. Thymosin α 1 (Tα1) was considered being applied in COVID-19 therapy. However, there were limited clinical evidence to support. We aimed to study the immune and inflammation response to COVID-19 under Tα1 treatment and confirm its clinical benefit.  Methods   We did a cohort study including COVID-19 patients and healthy volunteers with or without Tα1 treatment. We obtained peripheral blood mononuclear cells (PBMCs) samples. Single cell RNA-sequencing (ScRNA-seq) and T cell receptor-sequencing (TCR-seq) was done to test for  immune responses.  Findings   The proportion of CD3+KLRD1+ NKT, TBX21+CD8+ NKT was significant higher in Health controls with Tα1 treatment (HCT) than those without Tα1 (HC) (p=0.016; p=0.031). The proportion of CD3+KLRD1+ NKT, TBX21+CD8+ NKT was also observed increase in COVID-19 patients with Tα1 treatment (COVT) than those without Tα1 (COV) (p=0.024; p=0.010). The proportion of CD33-HLA-DMA-CD14+ classical monocyte was significant lower in COVT in comparison with COV. Those cell sets were significantly associated with thymosin intervention (CD3+KLRD1+ NKT, p=0.028; TBX21+CD8+ NKT, p=0.003; CD33-HLA-DMA-CD14+ classical monocyte, p=0.047).  Interpretation   The increased T cell and decreased monocyte response might support the prevention and therapy effect of Tα1 treatment. These data might also serve as a rich resource for designing cellular immunity therapies for this pandemic disease.

overall_design: 53 peripheral blood mono-nuclear cell (PBMC) samples including 42 COVID-19 patients derived samples and 11 healthy controls (HCs) derived samples

first: Chengsheng

last: Zhang


title: Direct reprogramming of adult adipose-derived regenerative cells toward cardiomyocytes using six transcriptional factors I

status: Public on Jun 07 2022

city: Showa-ku, Nagoya

first: Shingo

last: Narita

state: Aichi

address: 65 Tsurumai-cho

department: Cardiology

institute: Nagoya University Graduate School of Medicine

summary:
It is widely accepted that adipose-derived regenerative cells (ADRCs) can differentiate into mesodermal lineage cells. However, reprogramming adult ADRCs into mature cardiomyocytes is challenging. We investigated the induction of myocardial differentiation in ADRCs via direct reprogramming using lentiviral gene transfer.
We compared gene expression profiling from RNA sequencing of culture ADRCs and embryonic heart organ, and examined candidate transcriptional factors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for culture ADRCs from adult mouse adipose tissue, and heart tissue from embryonic (E11.5) mouse.

first: Kazumasa

last: Unno


title: Epiblast inducers capture mouse Trophectoderm Stem Cells in vitro and pattern blastoids for implantation in utero. [bulk RNA-Seq]

city: Vienna

first: Giovanni

last: Sestini

address: Dr.-Bohr-Gasse 3, 1030 Wien

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

summary: The embryo instructs the allocation of cell states to spatially regulate growth and functions. In the blastocyst, the formation and divergence of the trophoblast lineage ensures successful implantation and placental development. Here, we defined an optimal set of molecules secreted by the inner epiblast cells (inducers) that captures stable, highly self-renewing, pre-implantation-like mouse trophectoderm stem cells (TESCs). When exposed to suboptimal inducers, these stem cells form interconvertible subpopulations with reduced self-renewal, known as trophoblast stem cells (TSCs), and resembling peri-implantation progenitors. TECSs have an enhanced capacity to form blastoids that implant more efficiently in utero. We find that this enhanced capacity is due to epiblast inducers not only controlling trophoblast growth but also trophoblast secretion of WNT6/7B that stimulates uterine decidualization. Thus, the embryo leverages epiblast inductions to drive both the growth and decidualization potential of trophoblasts required for implantation and development.

overall_design: For each sample, we analyzed three thecnical replicates except for the sorted populations (in the sample description, H correspond to "high" whereas L to "low"). C3.1 cell line was cultured in TX condition and used as a non-treated control.

first: Nicolas

last: Rivron

first: Jinwoo

last: Seong

first: Javier

last: Frias-Aldeguer

first: Viktoria

last: Holzmann

first: Harunobu

last: Kagawa

first: Heidar

middle: H

last: Khoei

first: Yvonne

last: ReimerOp

first: Maarten

last: Kip

first: Lucas

last: Verwegen

first: Judith

last: Vivié

first: Linfeng

last: Li

first: Anna

last: Alemany

first: Jeroen

last: Korving

first: Frank

last: Darmis

first: Alexander

last: van Oudenaarden

first: Derk

last: ten Berge

first: Niels

last: Geijsen


title: Epiblast inducers capture mouse Trophectoderm Stem Cells in vitro and pattern blastoids for implantation in utero. [scRNAseq]

first: Giovanni

last: Sestini

overall_design: To delineate the trophoblast stem cells (TSCs) heterogenity, single cell RNA seq analysis was performed. After the removal of FGF4 and TGFβ1, TSCs were let to differentiate. Samples were collected at different time points (0, 4, 12, 24, 48 and 36 hours) and subsequentially sequenced. Library preparation was performed by following CEL-Seq2 protocol.

first: Nicolas

last: Rivron


title: Real-time quantitative PCR analysis of Rag1-/- knockout and Rag1-/- Tbx21-/- double knockout mouse liver in a diet- and ischemia-reperfusion injury (IRI)-specific manner.

city: Washington, DC

last: Kroemer

state: DC

address: 3800 Reservoir Road NW, Pasquerilla Healthcare Center (PHC), 2nd Floor,

department: Center for Translational Transplant Medicine (CTTM)

institute: MedStar Georgetown Transplant Institute

summary: Differential gene expression of mouse cytokines and chemokines in Rag1 knockout (Rag1-/- or Rag1-KO) and Rag1-/- Tbx21-/- double knockout (Rag1-Tbet-DKO) was tested in fatty liver ischemic-reperfusion injury (IRI). C57BL/6 mice harboring Rag1-/- or Rag1-/- Tbx21-/- deletions were fed with a normal chow diet (ND, 4.09 kcal/gram,13.4% kJ/fat) or a high-fat diet (HFD, 5.10 kcal/gram, 60% kJ/fat). To induce liver ischemic-reperfusion injury in mice, an atraumatic micro clip was placed across the hepatic hilus, which interrupted the blood supply to the left and median lobes of the liver for 45-minutes of partial warm ischemia time. After 24 hours of liver IRI, the affected left lobe of the liver was harvested and stored in Allprotect Tissue Reagent (Qiagen). We used Qiagen RT² Profiler™ PCR Array for mouse cytokines & chemokines to distinguish immunologically related and diet-specific gene signatures specific to liver IRI in Rag1-KO and Rag1-Tbet-DKO mice.

overall_design: qPCR gene expression profiling. Liver tissue specimens from IRI and a non-IRI group from mice (n=3) were used and treated separately, as indicated in summary. An equal amount of total RNA from mice was pooled prior to gene expression analysis.


title: IgG from systemic sclerosis patients induce a profibrosing and serotype-dependent phenotype in normal dermal fibroblast: a multi-omics study

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: This study explored the effect of purified IgG from SSc patients on the phenotype and function of healthy dermal fibroblast (FB) using an innovative multi-omics approach.

overall_design: Normal dermal FB were cultured in the presence of purified IgG from patients with diffuse cutaneous SSc (dcSSc), limited cutaneous SSc or healthy controls (HC). FB proteome and transcriptome were explored using mass spectrometry coupled with liquid chromatography (LC-MS/MS) and microarray assays, respectively

first: Vincent

last: Sobanski


title: Expression data from hiPSC derived WT and ISG15 KO endothelial cells stimulated with interferon-a and treated with itaconic acid, dimethyl itaconate, 4-octyl itaconate and ruxolitinib

city: Hannover

last: Pessler

state: Niedersachsen

address: Feodor Lynen Str. 7

institute: Twincore

summary: Analysis of gene expression in WT and ISG15 KO endothelial cells, stimulated with IFNa and treated with Itaconic acid (IA), Dimethyl itaconate (DI), 4-octyl itaconate (4OI) and ruxolitinib (RUX) to investigate the effects of treatments on transcriptional response in the cells.

overall_design: WT and ISG15 KO endothelial cells were differentiated from hiPSCs. Endothelial cells were stimulated with interferon-a for 8 hours. Cells were then treated with itaconic acid, dimethyl itaconate, 4-octyl itaconate and ruxolitinib for 16 hours. RNA was extracted, and subjected to transcriptome profiling array  Clariom™ S Assay, human.

first: Robert

last: Geffers


title: 10x single-cell RNAseq profiling of hiPSC derived WT and ISG15 KO macrophages stimulated with interferon-a and treated with itaconic acid, 4-octyl itaconate and ruxolitinib

summary: WT and ISG15 KO macrophages were stimulated with interferon-a and treated with itaconic acid and 4-octyl itaconate as they are known for anti-inflammatory effects.  In this experiment, we further explored how itaconic acid and 4-octyl itaconate can play its role keeping ruxolitinib as a positive control in order to inhibit JAK/STAT pathway

overall_design: WT and ISG15 KO macrophages were differentiated from hiPSCs, stimulated with interferon-a and treated with itaconic acid, 4-octyl itaconate and ruxolitinib.


title: RECEPTOR LIKE PROTEIN KINASE 2 constrains proximal secondary vein branching in the Arabidopsis thaliana embryo

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

summary: Over time, plants have evolved flexible self-organizing patterning mechanisms to adapt tissue functionality to continuous organ growth. A clear example of this process is the multicellular organization of vascular cells into narrow and elongated conductive channels in foliar organs of Arabidopsis thaliana such as cotyledons. The establishment of a closed vascular network is achieved through the coordinated specification of newly recruited procambial cells by means of their proliferation and elongation. An important and yet poorly understood component of this process is secondary vein branching; a mechanism employed to extend vascular tissues throughout cotyledon surface. Here we revise the directionality of the formation of vascular tissues in the embryonic cotyledon of Arabidopsis and show that distal veins arise from the bifurcation of cell files contained in the midvein. Instead, proximal veins emerge from the division of provascular cells, a process partially constrained by RECEPTOR LIKE PROTEIN KINASE 2 (RPK2). Utilizing genetic, transcriptomic and live-cell imaging analyses, we show that RPK2 function is antagonized by COTYLEDON VASCULAR PATTERN 2 and its homologous CVP2 LIKE 1. Whilst RPK2 expression at the cotyledon margin prevents the branching of secondary proximal veins, the divergence of the midvein into distal veins appears to be auxin-dependent and follows a distinct regulatory mechanism. Our work supports a model in which RPK2 modulates vascular complexity independently of cell-to-cell auxin-propagation to adapt the spatial configuration of vascular tissues to organ growth.

overall_design: 3 samples examined: embryo (torpedo stage) from Arabidopsis thaliana Col0 wild type, cvp2cvl1 double mutant and cvp2cvl1 containing a transgene expressing a artificial miRNA targeting RPK2

first: Elizabeth

last: Kastanaki

first: Noel

last: Blanco-Touriñá

first: Alessandra

last: Sturchler

first: Antia

last: Rodriguez-Villalon


title: Evaluation of Transcriptomic Responses in Livers of Mice Exposed to the Short-Chain PFAS Compound HFPO-DA

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

institute: ToxStrategies

summary: HFPO-DA (ammonium 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate; CASRN 62037-80-3; trade name “GenX”) is an alternative to environmentally persistent per- and poly-fluorinated alkyl substances (PFAS). The liver is the primary target of toxicity for HFPO-DA in rodents and previous examination of hepatic transcriptomic responses in mice following oral exposure to HFPO-DA for 90 days showed induction of peroxisome proliferator-activated receptor (PPAR) signaling pathways, predominantly by PPAR alpha, as well as increased gene expression of both peroxisomal and mitochondrial fatty acid metabolism. To further investigate the mechanism of liver toxicity, transcriptomic analysis was conducted on liver tissue from mice orally exposed to 0, 0.1, 0.5 or 5 mg/kg-bw/day HFPO-DA in a reproduction/developmental toxicity study. Hepatic gene expression changes were consistent with the previous 90-day mouse study, demonstrating activation of the PPAR alpha signaling pathway. Peroxisomal and mitochondrial fatty acid beta-oxidation gene sets were enriched at lower HFPO-DA concentrations, and complement cascade, cell cycle and apoptosis related gene sets were enriched at higher HFPO-DA concentrations. These results support the reported histopathological findings in livers of mice from this study and indicate that these effects are mediated through rodent-specific PPAR alpha signaling mechanisms.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from FFPE liver tissue of male and female CD1 mice orally exposed to 0, 0.1, 0.5 or 5 mg/kg-bw/day HFPO-DA (n= 5 per treatment group) once daily for a total of 84 – 85 or 53 – 65 doses in male or female mice, respectively.

first: Grace

middle: A

last: Chappell

first: Chad

last: Thompson

first: Laurie

middle: C

last: Haws


title: A genome-wide CRISPR/Cas9 screen identifies therapeutic targets required for  the tumorigenesis of ovarian clear cell carcinoma (OCCC).

first: Tomoatsu

last: Hayashi

summary: To identify genes critical for the proliferation of ovarian clear cell carcinoma (OCCC), we performed CRISPR/CAS9 screens against the OCCC cell lines OVICE, ES2, TOV21G and JHOC5 using the TKOv3 sgRNA library.

overall_design: Genome-wide CRISPR/Cas9  screen of OVISE, TOV21G, ES2 and JHOC5 (ovarian cancer cell) using the Toronto KnockOut (TKO) CRISPR Library (TKOv3). 2 biological replicates (OVISE, TOV21G, ES2) and 1 biological replicate (JHOC5).

first: Ayako

last: Kawabata

first: Yoko

last: Nagayoshi

first: Naoko

last: Yokota

first: Ryuichiro

last: Nakato

first: Aikou

last: Okamoto

first: Tetsu

last: Akiyama


title: Transcriptomic and phenomic investigations reveal elements in biofilm repression and formation in the cyanobacterium Synechococcus elongatus PCC 7942 [RNA-seq]

status: Public on Jun 06 2022

city: La Jolla

first: Ryan

last: Simkovsky

state: California

address: 9500 Gilman Drive

institute: University of California San Diego

summary: Biofilm formation by photosynthetic organisms is a complex behavior that serves multiple functions in the environment. Biofilm formation in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 is regulated in part by a set of small secreted proteins that promotes biofilm formation and a self-suppression mechanism that prevents their expression. Little is known about the regulatory and structural components of the biofilms in PCC 7942, or response to the suppressor signal(s). We performed transcriptomics (RNA-Seq) and phenomics (RB-TnSeq) screens that identified four genes involved in biofilm formation and regulation, more than 25 additional candidates that may impact biofilm formation, and revealed the transcriptomic adaptation to the biofilm state. In so doing, we compared the effectiveness of these two approaches for gene discovery.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Expression profiling by high throughput sequencing (RNA-seq) comparing WT and the pilB::Tn5 biofilm forming mutant strain over time

first: Rami

last: Parnasa

first: Jingtong

last: Wang

first: Elad

last: Nagar

first: Eli

last: Zecharia

first: Shiran

last: Suban

first: Yevgeni

last: Yegorov

first: Boris

last: Veltman

first: Eleonora

last: Sendersky

first: Rakefet

last: Schwarz

first: Susan

last: Golden


title: mRNAseq profiling of interferon-a stimulated WT and ISG15 KO- Human-iPSC derived macrophages

first: Frank

last: Pessler

summary: ISG15 KO cells are hyperinflammatory in phenotype. In this experiment, we further explored how they respond to interferon-a stimulation and how they differ from WT cells

overall_design: WT and ISG15 KO macrophages were differentiated from hiPSCs and stimulated with interferon-a

first: Robert

last: Geffers


title: Transcriptomic and phenomic investigations reveal elements in biofilm repression and formation in the cyanobacterium Synechococcus elongatus PCC 7942

platform_organism: Synechococcus elongatus PCC 7942 = FACHB-805


title: Synovial inflammatory pathways characterize anti-TNF-responsive rheumatoid arthritis patients

city: Worcester

first: Jing

state: MA

address: 100 Research Drive

institute: AbbVie

summary: Objectives: This study was undertaken to understand the mechanistic basis of response to anti-TNF therapies and determine if transcriptomic changes in the synovium are reflected in peripheral protein markers. Methods: Synovial tissue from 46 RA patients was profiled with RNA sequencing before and 12 weeks after treatment with anti-TNF therapies.  Pathway and gene signature analyses were performed on RNA expression profiles of synovial biopsies to identify mechanisms that could discriminate among EULAR good, moderate and non-responders.  Serum proteins encoded by synovial genes differentially expressed between EULAR response groups were measured in the same patients. Results: The gene signatures were able to predict good responder patients and pathway analysis identified elevations in immune pathways including chemokine signaling, Th1 and Th2 cell differentiation, and Toll-like receptor signaling uniquely in good responders. These inflammatory pathways were correspondingly down-modulated by anti-TNF therapy only in good responders.  Based on cell signature analysis, lymphocyte, myeloid and fibroblast cell populations were elevated in good responders relative to non-responders, consistent with the increased inflammatory pathways.  Cell signatures which decreased following anti-TNF treatment were predominately associated with lymphocytes and fewer were associated with myeloid and fibroblast populations. Following anti-TNF treatment and only in good responders, several peripheral inflammatory proteins decreased consistent with corresponding synovial gene changes. Conclusions: Collectively, these data suggest that RA patients with robust responses to anti-TNF therapies are characterized at baseline by immune pathway activation, which decreases following anti-TNF treatment.  Understanding mechanisms that define patient responsiveness to anti-TNF may assist in development of predictive markers of patient response and earlier treatment options.

overall_design: Forty-six RA patients fulfilling 2010 ACR/EULAR RA Classification Criteria were enrolled at the Centre for Experimental Medicine and Rheumatology, Barts and The London School of Medicine, Queen Mary University of London, UK. The study received ethical approval from the local UK Health Research Authority (10/H0801/47) and all patients gave written informed consent. Patients had clinically defined synovitis and were eligible to start anti-TNF according to UK NICE guidelines (failure of at least 2 csDMARDs and DAS28 >= 5.1). Upon enrolment and acquisition of demographics, current medications and clinical disease parameters, including CRP, ESR, RF/ACPA positivity/titer and DAS28, patients underwent minimally invasive US-guided synovial biopsy (17) of the most inflamed joint (ultrasound synovial thickening score >=2) (17) at baseline and 12 weeks after treatment with anti-TNF (19 etanercept, 27 certolizumab pegol).  Duration of treatment was ensured up to primary endpoint and there were no treatment interruptions.

first: Melanie

last: Ruzek


title: Transcription factor-driven coordination of cell cycle exit and lineage-specification in vivo during granulocytic differentiation

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

overall_design: Refer to individual Series


title: From Bench to Bedside and Back: Improving the Safety of GalNAc-siRNA Conjugates Using GNA-Destabilized Seed-Pairing

city: Cambridge

first: Joseph

last: Barry

address: 675 West Kendall St

institute: Alnylam Pharmaceuticals

summary: Preclinical mechanistic studies have pointed towards RNAi-mediated off-target effects as a major driver of hepatotoxicity for GalNAc-siRNA conjugates. Here we demonstrate that a single glycol nucleic acid (GNA) modification can substantially reduce siRNA seed-mediated binding to off-target transcripts while maintaining on-target activity. In siRNAs with established off-target effects leading to hepatotoxicity, these Enhanced Stabilization Chemistry plus (ESC+) designs exhibit a substantially improved therapeutic window in rat. We utilized this strategy to improve the safety of ALN-HBV, which exhibited dose-dependent, transient, and asymptomatic alanine aminotransferase elevations in healthy volunteers.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: The increased specificity of GNA-containing GalNAc-siRNAs is demonstrated in vitro and in vivo using measures of differential expression derived from RNA-seq data.

first: Mark

last: Schlegel

first: Maja

last: Janas

first: Yongfeng

last: Jiang

first: Wendell

last: Davis

first: Saket

last: Agarwal

first: Daniel

last: Berman

first: Christopher

last: Brown

first: Adam

last: Castoreno

first: Sarah

last: LeBlanc

first: Abigail

last: Liebow

first: Tara

last: Mayo

first: Stuart

last: Milstein

first: Tuyen

last: Nguyen

first: Svetlana

last: Shulga-Morskaya

last: Solomon

first: John

last: Szeto

first: Lauren

last: Woods

first: Vedat

last: Yilmaz

first: Muthiah

last: Manoharan

first: Klaus

last: Charisse

first: Laura

last: Sepp-Lorenzino

first: Patrick

last: Haslett

first: Kevin

last: Fitzgerald

first: Vasant

last: Jadhav

first: Martin

last: Maier


title: Direct reprogramming of adult adipose-derived regenerative cells toward cardiomyocytes using six transcriptional factors III

first: Shingo

last: Narita

summary:
It is widely accepted that adipose-derived regenerative cells (ADRCs) can differentiate into mesodermal lineage cells. However, reprogramming adult ADRCs into mature cardiomyocytes is challenging. We investigated the induction of myocardial differentiation in ADRCs via direct reprogramming using lentiviral gene transfer.
We ultimately confirmed that the combination of six unique factors (Baf60c, Gata4, Gata6, Klf15, Mef2a, and Myocd) could efficiently express enhanced green fluorescent protein (GFP) in ADRCs isolated from adult alpha-myosin heavy chain promoter-driven GFP transgenic mice.

overall_design: The ADRCs three weeks after transduction with six factors were collected and analyzed using scRNAseq.

first: Kazumasa

last: Unno


title: Transcrpitomic analysis of Oral lichen planus with immumosuppressive therapy

status: Public on Jun 05 2022

city: Chengdu

first: Hao

last: Xu

address: No.17 section3 renmin south road, chengdu

institute: Sichuan university

summary: We compared the transcriptomes of tissues from Oral lichen planus patients with immunosuppressive  therapy to reveal the biological mechanism of oral lichen planus treatment.

overall_design: Expression profiling by high throughput sequencing

first: Qianming

last: Chen


title: Protein levels in Human CD8+ T cells treated with melanoma small extracellular vesicles

city: Philadelphia

first: lei

last: guan

address: 433 S University Ave.

department: Biology

institute: university of pennsylvania

summary: Human healthy donor CD8+ T cell lysates were analyzed by RPPA

overall_design: Healthy donor Human CD8 T cells from healthy donor treated with Vehicle or small extracellular vesicles derived form HRSWT-FLAG, HRSS345A-FLAG or HRSS345D-FLAG WM9 cell lines

first: Lei

last: Guan

first: Bin

last: Wu

first: Wei

last: Guo

first: Ting

last: Li

first: Gordon

last: Mills

first: Meenhard

last: Herlyn


title: Direct reprogramming of adult adipose-derived regenerative cells toward cardiomyocytes using six transcriptional factors II

overall_design: Comparative gene expression profiling analysis of RNA-seq data for culture ADRCs from adult mouse adipose tissue, and the GFP-positive ADRCs (6F-ADRCs) induced by six factors collected three weeks after transduction by fluorescence-activated cell sorting (FACS)


title: Conjunctival epithelial cells resist productive SARS-CoV-2 infection

city: NEWCASTLE

first: Megan

middle: Saphana Rose

last: Hasoon

address: Newcastle University

country: United Kingdom

institute: Newcastle University

summary: Although tropism of SARS-CoV-2 for respiratory tract epithelial cells is well established, an open question is whether the conjunctival epithelium is also a target for SARS-CoV-2. Conjunctival epithelial cells, which express viral entry receptors ACE2 and TMPRSS2, constitute the largest exposed epithelium of the ocular surface tissue, and may represent a relevant viral entry route. To address this question, we generated an organotypic air-liquid-interface model of conjunctival epithelium, composed of progenitor, basal and superficial epithelial cells and fibroblasts, which could be maintained successfully up to day 75 of differentiation. Using single cell RNA-Seq, with complementary imaging and virological assays, we observed that while all conjunctival cell types were permissive to SARS-CoV-2 genome expression, a productive infection did not ensure. The early innate immune response to SARS-CoV-2 infection in conjunctival cells was characterised by a robust NF-Kβ activity, alongside evidence of suppression of antiviral interferon signalling. Collectively these data enrich our understanding of SARS-CoV-2 infection at the human ocular surface, with potential implications for the design of preventive strategies such as personal protective equipment.

overall_design: Problem: Respiratory viruses including SARS-CoV-2, responsible for the COVID-19 pandemic, enter via the respiratory tract epithelium, however they can also use the eye surface as an additional en-try point. The conjunctiva has a large unexposed surface area with mucus producing cells. Clinical reports have shown that some of COVID-19 patients suffer from conjunctivitis in the early stages of infection. To date it is not fully established if the conjunctiva can be used as an additional entry and propagation portal for SARS-CoV-2.  Results: To assess whether conjunctiva can be infected by SARS-CoV-2, we generated an in vitro model by culturing human conjunctival cells under special conditions, which promote cell differen-tiation and layer stratification through air-liquid contact. In this manuscript, we show that the ex vivo model contains all cells found in the native conjunctiva and moreover expresses the two key viral entry factors, ACE2 and TMPRSS2. Infection of the model with SARS-CoV-2 shows that while all conjunctival cells can be infected with the virus,  new viral particles that are necessary for propaga-tion cannot be generated. Importantly, the conjunctival cells responded to viral infection by up-regulating a key signalling pathway, NF-κB, which is often the first line of defence upon viral infec-tion of eye cells.  Impact: Our data indicate that the risk of SARS-CoV-2 transmission from a conjunctival organ trans-plant is low. The lack of viral propagation in conjunctiva should also be informative on provision of protective personal equipment used by medical staff and carers of COVID-19 patients.

first: Robert

last: Jackson

first: Catherine

middle: F

last: Hatton

first: Jarmila

last: Spegarova

first: Maria

last: Georgiou

first: Joseph

last: Collin

first: Emily

last: Stephenson

first: Bernard

last: Verdon

first: Iram

middle: J

last: Haq

first: Rafiqul

last: Hussain

first: Jonathan

last: Coxhead

first: Hardeep

last: Mudhar

first: Tracey

last: Davey

first: Paul

last: Rooney

first: Anjam

last: Khan

first: Chris

last: Ward

first: Malcolm

last: Brodlie

first: Muzlifah

last: Haniffa

first: Sophie

last: Hambleton

first: Lyle

last: Armstrong

first: Bart

last: Wagner

first: Francisco

last: Figueiredo

first: Rachel

last: Queen

first: Christopher

last: Duncan

first: Majlinda

last: Lako


title: Comprehensive RNA-Seq Reveals Molecular Changes in Kidney Malignancy Among People Living with HIV

city: Shanghai

first: jin

last: wang

address: 2901 Caolang Road, Jinshan District,

institute: Shanghai Public Health Clinical Center, Fudan University,

summary: To heighten the awareness of kidney malignancy in patients with HIV infection to facilitate the early diagnosis of kidney cancer, the differentially expressed mRNAs were analyzed in this malignant tumor using RNA sequencing (RNA-seq). We identified 2962 protein-coding transcripts in HIV-associated kidney cancer. KISS1R, CAIX, and NPTX2 mRNA expression levels were specifically increased in HIV-associated kidney cancer, and UMOD and TMEM213 mRNA were decreased in most cases based on real-time PCR analyses. These findings were similar to those noted for the general population with renal cell carcinoma. Immunohistochemical staining analysis also showed that a total of 16 of 18 malignant kidney cases among PLWH exhibited positive staining for KISS1R and CAIX. Pathway analysis of the differentially expressed mRNAs in HIV-associated kidney cancer revealed that several key pathways were involved, including vascular endothelial growth factor-activated receptor activity, IgG binding, and lipopolysaccharide receptor activity. Altogether, our findings reveal the identified molecular changes in kidney malignancy, which may offer a helpful explanation for cancer progression and open up new therapeutic avenues that may decrease mortality after a cancer diagnosis among PLWH.

overall_design: To identify the responsible mechanisms, we investigated the differentially expressed mRNAs  in kidney malignancy in patients with HIV infection to facilitate the early diagnosis of kidney cancer, using RNA sequencing (RNA-seq). KISS1R, CAIX, and NPTX2 mRNA expression levels were specifically increased in HIV-associated kidney cancer, and UMOD and TMEM213 mRNA were decreased in most cases based on real-time PCR analyses. Immunohistochemical staining analysis also showed that a total of 16 of 18 malignant kidney cases among PLWH exhibited positive staining for KISS1R and CAIX.

first: Jin

last: Wang


title: Inactivation of the splicing factor RBM10 limits EGFR targeted therapy response in EGFR mutant lung cancer

status: Public on Jun 04 2022

city: San Francisco

first: Wei

last: Wu

state: CA

address: 600 16th street

department: Department of Medicine

institute: University of California, San Franciso

summary: Oncogene-driven lung cancers such as those with activating mutations in the epidermal growth factor receptor (EGFR) often harbor additional co-occurring genetic alterations. The significance of most alterations co-occurring with mutant EGFR remains unclear. We report the impact of loss of the mRNA splicing factor RBM10 in human EGFR mutant lung cancer. RBM10 loss decreased EGFR inhibitor efficacy in patient-derived EGFR mutant tumor models. RBM10 regulated mRNA splicing of the mitochondrial apoptotic regulator Bcl-x. Genetic inactivation of RBM10 diminished EGFR inhibitor-mediated apoptosis by altering Bcl-x splicing, decreasing Bcl-xS (pro-apoptotic) and increasing Bcl-xL (anti-apoptotic) levels. Co-inhibition of Bcl-xL and mutant EGFR overcomes resistance induced by RBM10 loss. RBM10 loss was a biomarker of poor response to EGFR inhibitor treatment in clinical samples. Inactivation of the splicing factor RBM10 is a key co-occurring genetic alteration in EGFR mutant tumors that limits EGFR inhibitor efficacy and a potential biomarker of Bcl-xL inhibitor response.

overall_design: Examination of 2 different shRBM10 KD in lung cancer PC9 cells.

first: Shigeki

last: Nanjo


title: The effects of abundant nematode-derived miRNAs on the transcriptome of mouse differentiating Th2 cells

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

institute: ETH Zurich / University of Zurich

summary: Four microRNAs(miRNAs) highly abundantly secreted by the parasitic nematode Heligmosomoides polygyrus were synthesized (miRVana, Ambion) and transfected repeatedly into differentiating Th2 cells in vitro, individually or in combination. The effects of the different transfection regimens were assessed by RNA sequencing (Illumina).

overall_design: The spleen and lymph nodes from wild-type C57BL/6 female mice were used to isolate naïve CD4+ T cells (magnetic beads). Cells were put in culture and allowed to differentiate into Th2 cells over 4 days, in the presence of α-CD28 and α-CD3, IL-4, IL-2, and α-IFN-γ. Cells were transfected every 24 h with 10 nM miRNA(s), 4 times consecutively, or only once at experiment start (0 h), with 50 nM miRNA(s). Controls included the transfection reagent (Lipofectamine), no treatment, or a commercial universal negative control. After 4 days in culture, cells were restimulated with α-CD3 and total RNA was extracted for transcriptome analysis. The experiment was repeated 3 times independently.

first: Lucienne

last: Tritten

first: Julien

last: Soichot

first: Nathalie

last: Guttmann


title: Lipolysis regulates major transcriptional programs in brown adipocytes [DOX exp]

status: Public on Jun 03 2022

city: Odense M

first: Lasse Kruse

last: Markussen

address: Campusvej 55

department: BMB

institute: University of Southern Denmark

summary: β-Adrenergic signaling is a core regulator of brown adipocyte function stimulating both lipolysis and transcription of thermogenic genes, thereby expanding the capacity for oxidative metabolism. Here we have used pharmacological inhibitors and a novel direct activator of lipolysis to acutely modulate the activity of lipases, thereby enabling us to uncover lipolysis-dependent signaling pathways downstream of β-adrenergic signaling in brown adipocytes. We show that induction of lipolysis leads to acute induction of several gene programs and is required for transcriptional regulation by β-adrenergic signals. Using machine-learning algorithms to infer causal transcription factors, we show that PPARs are key mediators of lipolysis-induced activation of genes involved in lipid metabolism and thermogenesis. Importantly, lipolysis also activates the unfolded protein response and regulates the core circadian transcriptional machinery independently of PPARs. Our results demonstrate that lipolysis generates important metabolic signals that exert profound pleiotropic effects on brown adipocyte transcription and function.

overall_design: Brown adipocytes with stable knockdown of ABHD5 stimulated with ISO ( 10 nm) or SR-3420 (20 uM) for 3hrs.

first: Lasse

first: Susanne

last: Mandrup


title: Lipolysis regulates major transcriptional programs in brown adipocytes [Lipase Inh. Exp]

overall_design: Immortalized mouse brown adipocytes (D7) treated +/- Lipase inhibitors for 1hr and subsequently stimulated with either vehicle, isoproterenol or SR-3420 for 3hrs.


title: Transcriptomic and phenomic investigations reveal elements in biofilm repression and formation in the cyanobacterium Synechococcus elongatus PCC 7942 [RB-TnSeq]

first: Ryan

last: Simkovsky

first: Rami

last: Parnasa

first: Jingtong

first: Elad

last: Nagar

first: Eli

last: Zecharia

first: Shiran

last: Suban

first: Yevgeni

last: Yegorov

first: Boris

last: Veltman

first: Eleonora

last: Sendersky

first: Rakefet

last: Schwarz

first: Susan

last: Golden


title: Monocytic-Myeloid Derived Suppressor Cells Suppress T-Cell Responses in Recovered SARS CoV2-Infected Individuals

first: Nadejda

middle: S.

last: Beliakova-Bethell

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary:
The goal of this study was to determine changes in the expression of genes in monoctic myleoid derived suppressor cells (M-MDSC) as a result of SARS CoV2 infection. The study aimed to investigate if M-MDSC are functionally active and inhibit T cell function in response to SARS CoV2 antigens 5 months after first detection of the virus.
Methods: Peripheral blood mononuclear cells (PBMC) were collected from CoV2 (-) and CoV2 (+) donors (N=5 each group). M-MDSC were isolated by flow cytometry, and RNA extracted for RNA-seq studies. Filtering low quality reads and removal of the 3’ adapter sequences were performed using the Trim Galore tool. Reads were mapped to the latest version of the human genome (build hg38) using HISAT2. Mapped reads were counted against the human GENCODE annotation (v37) using HT-Seq. The EdgeR library in the R computing environment was used for quality control of the RNA-Seq data, and ComBat-seq method for correction of batch effects. Differential gene expression analysis was conducted using EdgeR. Pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8.
Results: An average of 34 million reads per sample were acquired and mapped to the human genome (build hg38). After applying filtering criteria, 9,217 human genes were identified with the HISAT2 and HTSeq workflow. Differential expression analysis was performed between CoV2 (+) and CoV2 (-) samples using EdgeR. A total of 188 differentially expressed genes (DEGs) were identified with nominal p-value <0.05; of which 63 were up- and 125 downregulated in CoV2 (+) samples. A total of 12 DEGs were identified with false discovery rate corrected p-value <0.05, of which 2 were up- and 10 downregulated. Pathway enrichment analysis identified pathways involved in immune response and innate immune signaling.
Conclusion: The study demonstrated that CoV2 infection modulated the expression of genes involved in immune response and innate immune signaling. Most of the genes remained downregulated even after 5 months of first detection of SARS CoV2.

overall_design: Transcriptomic profiling of monocytic myeloid derived suppressor cells isolated from SARS CoV2 (+) (N=5) individuals, after 5 months after infection was first detected, and SARS CoV2 (-) (N=5) individuals.

first: Kthirvel

last: Maruthai

first: Ruilie

last: Xu

first: Liliana

last: Salvador

first: Ankita

last: Garg


title: RUNX2-specific human Natural Killer (NK) cells

city: Ghent

first: Wouter

last: Van Loocke

state: East Flanders

address: C. Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

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


title: nCounter analysis of Leishmania-infected macrophages and  LT-HSC

city: Leuven

first: Johan

last: Van Weyenbergh

state: VL BR

address: Herestraat 49

department: Microbiology, Immunity and Transplantation

institute: KU Leuven

summary: Given the discontinuation of various first-line drugs for visceral leishmaniasis (VL), large-scale in vivo drug screening, establishment of a relapse model in rodents, immunophenotyping and transcriptomics were combined to study persistent infections and therapeutic failure. Double bioluminescent/fluorescent Leishmania infantum and L. donovani reporter lines enabled the identification of long-term hematopoietic stem cells (LT-HSC) as a niche with remarkably high parasite burdens, a feature confirmed for human hematopoietic stem cells (hHSPC). LT-HSC are more tolerant to antileishmanial drug action and serve as source of relapse. A unique transcriptional “StemLeish” signature in these cells was defined byupregulated TNF/NF-kB and RGS1/TGF-β/SMAD/SKIL signalling, and a downregulated oxidative burst.Cross-species analyses demonstrated significant overlap with human VL and HIV co-infected blood transcriptomes. In summary, the identification of LT-HSC as a drug- and oxidative stress-resistant niche,undergoing a conserved transcriptional reprogramming underlying Leishmania persistence and treatment failure, may open new therapeutic avenues for leishmaniasis.

overall_design: Cell lysates (from approximately 10,000 LT-HSC or macrophages, triplicates for both infected and uninfected conditions) for nCounter (NanoString) analysis were prepared using RNeasy Lysis buffer (RLT buffer, Qiagen). Cell lysates were hybridized to unique capture/reporter pairs (50 bp each) targeting 784 transcripts (734 murine transcripts and 20 housekeeping genes present in the Nanostring Myeloid/Innate Immunity Panel, complemented with 20 murine and 10 Leishmania spp. transcripts from a customized   panel) as well as 6 positive and 8 negative control probes (all from NanoString). 7

first: Guy

last: Caljon


title: The role of GCN2 kinase in amino acid dependent longevity and feeding behaviour in Drosophila

city: Cologne

first: Dennis

middle: Said

last: Gadalla

state: NRW

address: Joseph-Stelzmann-Straße 26

department: Systems Biology

institute: CECAD Research Center

summary: Dietary amino acids restriction extends lifespan in diverse species ranging from flies to mammals. The evolutionarily conserved serine/threonine kinase General Control Nonderepressible 2 (GCN2) is a key sensor of amino acid deficiency and has been implicated in lifespan regulation upon dietary restriction. However, the role of individual essential amino acids (EAA) in modulating organismal lifespan and the underlying molecular mechanisms through which EAA mediate these effects are only partially understood. We generated a novel Drosophila GCN2 null mutant and systematically analyzed its response to individual amino acid deficiency.

overall_design: Transcriptional profiling of control and GCN2 null mutant flies feeding with the Yaa control diet or diets with arginine (R), methionine (M), or all amino acid (All) deprived. RNA was extracted from head and thorax, with three replicates for each sample. RNA sequencing was performed using the HiSeq 2500 platform.

first: Anchal

last: Srivastava

first: Sebastian

last: Grönke

first: Linda

last: Partridge


title: Transcriptome analysis of human Natural Killer (NK) cells overexpressing the transcription factor RUNX2-I isoform.

summary: Research has already gained much insight into the roles of various members of the RUNX family of transcription factors in the development of human T- and B-cells, however the importance in human NK cell development remains unclear. In this study we discovered that NK cells predominantly express the shorter of the two principal isoforms of RUNX2, also referred to as RUNX2-I. Therefore, we overexpressed the RUNX2-I isoform in human umbilical cord blood-derived hematopoietic progenitor cells (HPC) and cultured them in vitro in an NK cell differentiation model. On day 14 of culture (CD56+CD94+) NK cells from RUNX2-I overexpression and control cultures were sorted, after which mRNA was isolated and transcriptome analysis was performed by RNA sequencing. Evaluation of the transcriptome in these NK cells could reveal the molecular mechanisms of the RUNX2-I isoform.

overall_design: mRNA profile of RUNX2-I overexpressing NK cells from d14 of culture in comparison to control transduced NK cells.

first: Sigrid

last: Wahlen

first: Georges

last: Leclercq


title: Pervasive translation of circular RNAs driven by short IRES-like elements

first: Xiaojuan

last: Fan

address: 320 Yue Yang Road

institute: CAS-MPG Partner Institute of Computational Biology

summary: Circular RNAs (circRNAs) are a class of abundant RNAs with ambiguous function. Although some circRNAs can be translated through IRES driven mechanisms, the scope and functions of circRNA translation are unclear because endogenous IRESs are rare. To determine the prevalence and mechanism of circRNA translation, we developed a cell-based system to screen random sequences and identified 97 overrepresented AU-rich hexamers (>2% of all hexamers) that drive cap-independent translation of circRNAs. These IRES-like short elements are significantly enriched in circRNAs and sufficient to drive circRNA translation. We further identified multiple trans-acting factors that bind these IRES-like short elements to initiate translation. Using mass-spectrometry data, hundreds of circRNA-coded peptides were identified, most of which have low abundance due to rapid degradation. As judged by mass-spectrometry, 50% of translatable endogenous circRNAs undergo rolling circle translation, several of which were experimentally validated by western blotting.  Consistently, the mutation of the IRES-like short element in one circRNA reduced its translation.  Collectively, our findings suggest a pervasive translation of circRNAs, providing profound implications in circRNA function.

overall_design: A library of random 10-nt sequences was inserted before the start codon of circRNA-coded GFP, which was transfected into 293T cells to generate circRNAs that can be translated into intact GFP.  The cells with active circRNA translation (i.e. green cells) can be recovered with fluorescence activated cell sorting (FACS), and the inserted decamers can be subsequently sequenced to identify the IRES-like elements that drive circRNA translation.

first: Yun

last: Yang

first: Chuyun

last: Chen

first: Zefeng

last: Wang


title: RUNX2-specific ChIP of human peripheral blood NK cells

summary: Research has already gained much insight into the roles of various members of the RUNX family of transcription factors in the development of human T- and B-cells, however the importance in human NK cell development remains unclear. We performed a ChIP-Seq analysis with a RUNX2-specific antibody on sorted human peripheral blood NK cells (CD3- CD19- CD56+) to shed more light onto the genes that are under control of RUNX2 in this cell type.

overall_design: ChIP analysis of human peripheral blood NK cells (CD3- CD19- CD56+).


title: Transcriptome analysis of human Natural Killer (NK) cells expressing a RUNX2-specific shRNA.

summary: Research has already gained much insight into the roles of various members of the RUNX family of transcription factors in the development of human T- and B-cells, however the importance in human NK cell development remains unclear. Therefore, we transduced a shRNA that specifically binds to all known RUNX2 isoforms in human umbilical cord blood-derived hematopoietic progenitor cells (HPC) and cultured them in vitro in an NK cell differentiation model. On day 21 of culture (CD56+CD94+) NK cells from shRNA and control cultures were sorted, after which mRNA was isolated and transcriptome analysis was performed by RNA sequencing. Evaluation of the transcriptome in these NK cells could reveal the molecular mechanisms of RUNX2.

overall_design: mRNA profile of RUNX2 shRNA-expressing NK cells from d21 of culture in comparison to control transduced NK cells.


title: The Origin of Bladder Cancer from Mucosal Field Effects [I]

city: Houston

first: David

middle: Earl

last: Cogdell

state: Tx

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

summary: Whole-organ histologic and genomic mapping (WOHGM) approach to analyze the molecular profile of bladder cancer evolution from mucosal field effects on a whole-organ scale

overall_design: Multiple samples from one basal, one luminal cystectomies profiled on 4 genomic platforms

first: Jolanta

last: Bondaruk

first: Roman

last: Jaksik

first: Ziqiao

first: Hui

last: Yao

first: Sangkyou

last: Lee

first: Li

last: Zhang

first: Neema

last: Navai

first: Colin

last: Dinney

first: Christopher

last: Logothetis

first: John

middle: N

last: Weinstein

first: Shaolong

last: Cao

first: Charles

last: Guo

first: Wenyi

first: Peng

last: Wei

last: McConkey

first: Marek

last: Kimmel

first: Bogdan

last: Czerniak


title: The Origin of Bladder Cancer from Mucosal Field Effects

first: David

overall_design: Refer to individual Series


title: The role of phagocitized ferroptotic cargo in regulating dendritic cell transcriptome

status: Public on Jun 02 2022

city: Zwijnaarde

first: Bartosz

last: Wiernicki

address: Technologiepark 71

institute: Ugent

summary: The objective is to understand how the transcriptome of dendritic cells changes after the uptake of ferroptotic cells.

overall_design: Bone marrow derived dendritic cells (4 samples) and bone marrow derived dendritic cells co-cultured with ferroptotic Jurkats and futher sorted, so only dendritic cells that phagocitized the ferroptotic cells are subjected to the analysis.

first: Sophia

last: Maschalidi


title: Host Cell-Dependent Late Entry Step As Determinant of Hepatitis B Virus Infection

city: Hershey

first: Xupeng

last: Hong

state: PA

address: 1230 York Ave

department: Laboratory of Virology and Infectious Disease

institute: The Rockefeller University

summary: In search for potential host factors that may be responsible for the difference in HBV cccDNA formation during infection between WC3-huNTCP and WCH-17-huNTCP cells, we did RNA-seq analysis on these two woodchuck hepatic cell lines.

overall_design: Total 4 samples (2 replicates of each cell line) were analyzed;

first: Yuka

last: Imamura Kawasawa

first: Stephan

last: Menne

first: Jianming

last: Hu


title: Multiomics Analyses Reveal the Central Role of Pentose Phosphate Pathway in Resident Thymic Macrophages to Cope with Efferocytosis-Associated Stress

city: Taipei

first: Chia-Lin

last: Hsu

address: R309, Biomedical Building, NYCU, No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Tissue-resident macrophages (TRMs) are heterogeneous cell populations found throughout the body. Depending on their location, they perform diverse functions maintaining tissue homeostasis and providing immune surveillance. To survive and function within, TRMs adapt metabolically to the distinct microenvironments. However, little is known about the metabolic signatures of TRMs. The thymus provides a nurturing milieu for developing thymocytes yet efficiently removes those that failed the selection, relying on the TRMs – resident thymic macrophages (TMφs). This study harnesses multiomics analyses to characterize TMφs and unveils their unique metabolic features. We find that the pentose phosphate pathway (PPP) is preferentially activated in TMφs, responding to the reduction-oxidation demands associated with the efferocytosis of dying thymocytes. The blockade of PPP in Mφs leads to decreased efferocytosis, which can be rescued by ROS scavengers. Our study reveals the key role of PPP in TMφs and underscores the importance of metabolic adaptation in supporting Mφ efferocytosis.

overall_design: Bone-marrow-derived macrophages generated from C57BL mice were treated with or without dexamethasone-induce apoptotic thymocytes at the ratio of 1:40. After 24 hr, the apoptotic cells were removed and the macrophages were harvested for RNA extraction. Each sample represents a biological replicate. The library was prepared by using Illumina TruSeq Stranded mRNA Sample Prep Kit and sequenced by Illumina NextSeq High Output Kit v2.5-75 cycles on the NextSeq 550 platform. The sequence was annotated according to Mus musculus GRCm38 mm10.

first: Tsung

last: Tsai

first: Yu

middle: T

last: Hsieh

first: Chia


title: 24 chemicals exposure to hESCs at different doses and time points

city: Kyoto

first: Junko

last: Yamane

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

institute: Kyoto University

summary: We obtained data about the expression of genes that were perturbed by the 24 chemicals.

overall_design: We analyzed gene expression profile of 24 chemicals to human ESCs.

first: Kenta

last: Kobayashi

first: Wataru

last: Fujibuchi


title: scRNA-seq and scTCR-seq of autoreactive CD8 T cells from NOD mice

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

summary: Type 1 diabetes (T1D) is an autoimmune disorder defined by CD8 T cell-mediated destruction of pancreatic β cells. Our previous work has shown that diabetogenic CD8 T cells in the islets of the non-obese diabetic (NOD) mouse model of T1D are phenotypically heterogenous, but CD8 T cell clonal heterogeneity in this model remains relatively unexplored. Here, we use paired single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) to characterize autoreactive CD8 T cells from the islets and spleens of NOD mice. Clonal analysis of scTCR-seq data demonstrates that CD8 T cells targeting the immunodominant β cell epitope IGRP206-214 exhibit highly restricted TCR gene usage, with over 70% of IGRP206-214-reactive cells utilizing the same TCR V alpha, J alpha, and V beta genes. Despite this, we observe only 5% overlap of IGRP206-214-reactive CD8 T cell clones between two groups of 10 NOD mice, demonstrating the immense TCR heterogeneity generated by junctional diversity during V(D)J recombination. scRNA-seq identifies two new clusters of autoreactive CD8 T cells in the islets and six clusters of diabetogenic CD8 T cells in the spleen, including multiple memory-like clusters and a population of exhausted cells. Strong clonal overlap between IGRP206-214-reactive CD8 T cells in the islets and spleen suggests that these cells may exit the islets and enter the peripheral circulation. Finally, we identify correlations between TCR J beta gene usage, which is less restricted than that of other TCR genes, and CD8 T cell clonal expansion as well as effector fate. Collectively, our work demonstrates that IGRP206-214-specific CD8 T cells are phenotypically heterogeneous but clonally similar, raising the possibility of selectively targeting either conserved or divergent TCR structures of these cells for therapeutic benefit.

overall_design: scRNA-seq and scTCR-seq of IGRP+ and IGRP- CD8 T cells from islets and IGRP+ CD8 T cells from spleens of NOD mice

first: Moujtaba

middle: Y

last: Kasmani

first: Yi-Guang

last: Chen


title: The Origin of Bladder Cancer from Mucosal Field Effects [III]

first: David

last: Cogdell

summary: Whole-organ histologic and genomic mapping (WOHGM) approach to analyze the molecular profile of bladder cancer evolution from mucosal field effects on a whole-organ scale.

overall_design: Multiple samples from one basal, one luminal cystectomies profiled on 4 genomic platforms.

first: Jolanta

last: Bondaruk

first: Roman

last: Jaksik

first: Ziqiao

last: Wang

first: Hui

last: Yao

first: Sangkyou

last: Lee

first: Li

last: Zhang

first: Neema

last: Navai

first: Colin

last: Dinney

first: Christopher

last: Logothetis

first: John

last: Weinstein

first: Shaolong

last: Cao

first: Charles

last: Guo

first: Wenyi

first: Peng

last: Wei

last: McConkey

first: Marek

last: Kimmel

first: Bogdan


title: Transcriptomics profiling of white adipose tissue of macrophage-specific Gja1 Knockout mice fed a normal chow diet (NCD) and high fat diet (HFD)

status: Public on Jun 01 2022

city: Seoul

first: CheolJun

last: Choi

address: 1, Gwanak-ro, Gwanak-gu, 29-310

country: South Korea

institute: Seoul National University

summary: Adipose mRNA profiles of wild-type and Gja1 knockout (tamoxifen-induced Csf1r-CreER/ Gja1(floxed/floxed)) mice were generated by deep sequencing.

overall_design: White adipose tissue mRNA profiles of wild-type (WT) and Macrophage specific Gja1 KO (KO) mice after feeding NCD and HFD were generated by deep sequencing. Three biological replicates were analyzed for each of four conditions.

first: Yun-Hee

first: Yoon

last: Cho


title: Crosstalk between CYP2E1 and PPARα substrates and agonists modulate adipose browning and obesity

city: Beijing

first: Youbo

state: China

address: Xueyuan Road No. 38

institute: Peking University

summary: We report the discrepancy of hepatic mRNA expression in Cyp2e1 widetype and knockout mice by application of RNA-seq technology.

overall_design: Hepatic mRNA profiles of Cyp2e1 wt and ko mice after fed with High-fat diet for 14 weeks

first: Tingting

last: Yan

first: Frank

last: Gonzalez

first: Xiuwei

last: Yang


title: Transcriptomic changes associated with deletion of Rv3143 from Mycobacterium tuberculosis H37Rv in relation to wild-type strain grown in 7H9/OADC medium

city: Lodz

first: Przemyslaw

last: Plocinski

address: Lodowa 106

country: Poland

institute: Institute of Medical Biology of the Polish Academy of Sciences

summary: RNA-Seq results accompanying submission of a manuscript: "The orphan response regulator Rv3143 modulates the activity of the NADH dehydrogenase complex (Nuo) in Mycobacterium tuberculosis via protein-protein interactions" describing the function of the Rv3143 "orphan" response regulator of the two-component signal transduction systems family, which enable mycobacterial cells to quickly adapt and adequately respond to adverse environmental conditions encountered at various stages of host infection. We identified the Rv3143 protein as an interaction partner for NADH dehydrogenase complex involved in oxidative phosphorylation. We propose that the regulatory protein Rv3143 is a component of the complex and modulates its activity.

overall_design: Next generation sequencing results are provided in three independent biological replicates for each strain growing in standard 7H9/10% OADC medium. The effect of Rv3143 removal on M. tuberculosis transcriptome was analysed on 7H9/10% OADC medium. The bacteria were grown to mid-logarythmic phase of growth, when they were collected and total RNA was isolated. The resulting RNA was subjected to ribodepletion with RiboZero Bacteria kit (Illumina, San Diego, CA, USA) and used for preparation of sequencing libraries,generated with a KAPA-stranded RNA Seq kit according to the manufacturer’s protocol (Roche Diagnostics, Rotkreuz, Switzerland). The resulting adapter-ligated, PCR-amplified cDNA libraries were subjected to sequencing on a NextSeq500 sequencer using the NextSeq500/550 v.2 sequencing kit (Illumina, San Diego, CA, USA), and approximately 5 to 10 million paired-end reads were sequenced for each sample.

first: Renata

last: Płocińska

first: Karolina

last: Wasik

first: Przemysław

last: Płociński

first: Ewelina

last: Lechowicz

first: Magdalena

last: Antczak

last: Błaszczyk

first: Bożena

last: Dziadek

first: Marcin

last: Słomka

first: Anna

last: Rumijowska-Galewicz

first: Jarosław


title: Lipolysis regulates major transcriptional programs in brown adipocytes [TC ETO exp]

first: Lasse Kruse

last: Markussen

summary: β-Adrenergic signaling is a core regulator of brown adipocyte function stimulating both lipolysis and transcription of thermogenic genes, thereby expanding the capacity for oxidative metabolism. Here we have used pharmacological inhibitors and a novel direct activator of lipolysis to acutely modulate the activity of lipases, thereby enabling us to uncover lipolysis-dependent signaling pathways downstream of β-adrenergic signaling in brown adipocytes. We show that induction of lipolysis leads to acute induction of several gene programs and is required for transcriptional regulation by β-adrenergic signals. Using machine-learning algorithms to infer causal transcription factors, we show that PPARs are key mediators of lipolysis-induced activation of genes involved in lipid metabolism and thermogenesis. Importantly, lipolysis also activates the unfolded protein response and regulates the core circadian transcriptional machinery independently of PPARs. Our results demonstrate that lipolysis generates important metabolic signals that exert profound pleiotropic effects on brown adipocyte transcription and function.

overall_design: Immortalized mouse brown adipocytes (D7) pretreated for 1hr with etiher etomoxir (50uM) or triascin C (5uM) and subsequently stimulated +/-  SR-3420 (10uM) for 3hrs.

first: Lasse

first: Susanne

last: Mandrup


title: The Origin of Bladder Cancer from Mucosal Field Effects [II]

first: David

last: Cogdell

first: Jolanta

last: Bondaruk

first: Roman

last: Jaksik

first: Ziqiao

last: Wang

first: Hui

last: Yao

first: Sangkyou

last: Lee

first: Li

last: Zhang

first: Neema

last: Navai

first: Colin

last: Dinney

first: Christopher

last: Logothetis

first: John

last: Weinstein

first: Shaolong

last: Cao

first: Charles

last: Guo

first: Wenyi

first: Peng

last: Wei

last: McConkey

first: Marek

last: Kimmel

first: Bogdan

last: Czerniak


title: Targeted protein expression analysis of skewed or drug-treated mouse T cells, and of serum from first disease vs flare in a model of Cutaneous Lupus Erythematosus

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed targeted protein expression analysis on cultured Th0, Th1 and Th2 cells, and on T cells treated with known drug triggers of cutaneous lupus erythematosus (CLE). In tandem, we performed targeted protein expression analysis on serum from first vs flare Th2-injected mice in the CLE model.

overall_design:
DO.11 T cells were skewed in vitro towards Th0, Th1 or Th2. In tandem, Th0 were treated with known drug triggers of CLE, specifically 5' fluorouracil, terbinafine and hydrochlorothiazide, or vehicle. Culture supernatants were frozen for later analysis. We also measured inflammatory proteins in serum from mice in the first course of disease (approximately 4 weeks) or at flare (approximately 12 weeks). All samples were analyzed using Ray Biotech Quantibody Mouse Th1/Th2/Th17 Array (QAM-TH17-1-2).

Please note that the 'STD1' (in the slide_* raw data files) represents 'standard 1', which is recombinant protein standard mixture provided by RayBiotech.

first: Ann

last: Marshak-Rothstein


title: circRNA expression profile from three Parkinson's disease(PD) patients and  three healthy controls

city: Nanning

first: Jiajia

last: Liao

address: Shuangyong road

institute: Guangxi Medical University

summary: To explore the involvement of circular RNAs in PD development, we analyzed levels of circular RNAs in human peripheral blood from PD patients and healthy patients. 10,145 expressed circRNAs were identified.

overall_design: three patients with PD(D1,D2,D3) and three healthy controls (C1,C2,C3) were selected for investigation into the expression of circRNAs

first: Jin

first: Yousheng

last: Xiao


title: Translational regulation of T follicular helper cell differentiation

city: New York

first: Robert

last: Schneider

address: 450 E29th Str

institute: NYUSOM

summary: We report the translational regulation of murine TFH cells, showing that they contain high levels of translation initiation factor eIF4E, which we show is essential for translation of TFH cell differentiation and function mRNAs.

overall_design: Examination of transcriptomics and translatomics in mouse CD4+ T cells and derived TFH cells.

first: Preeyam

middle: S

last: Patel

first: Sandra

last: Perez-Baos

first: Beth

last: Walters


title: Gene expression and Targeted protein expression analysis of skewed or drug-treated mouse T cells, and of serum from first disease vs flare in a model of Cutaneous Lupus Erythematosus

type:
Expression profiling by array
Protein profiling by protein array

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


title: Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases [RNA-Seq]

city: Boston

first: Ilya

last: Korsunsky

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

summary: Pro-inflammatory fibroblasts are critical to pathogenesis in rheumatoid arthritis, inflammatory bowel disease, interstitial lung disease, and Sjögren’s syndrome, and represent a novel therapeutic target for chronic inflammatory disease. However, the heterogeneity of fibroblast phenotypes, exacerbated by the lack of a common cross-tissue taxonomy, has limited the understanding of which pathways are shared by multiple diseases. To investigate, we profiled patient-derived fibroblasts from inflamed and non-inflamed synovium, intestine, lung, and salivary glands with single-cell RNA-sequencing. We integrated all fibroblasts into a multi-tissue atlas to characterize shared and tissue-specific phenotypes. Two shared clusters, CXCL10+CCL19+ immune-interacting and SPARC+COL3A1+ vascular-interacting fibroblasts were expanded in all inflamed tissues and additionally mapped to dermal analogues in a public atopic dermatitis atlas. We further confirmed these human pro-inflammatory fibroblasts in animal models of lung, joint, and intestinal inflammation. This work represents the first cross-tissue, single-cell fibroblast atlas revealing shared pathogenic activation states across four chronic inflammatory diseases.

overall_design: We generated a novel time-course RNA-seq dataset of DSS mice, profiling RNA from flow sorted fibroblasts rather than from whole tissue. At days 2, 4, 7, 9, 11, and 14 of the model, we sacrificed 6 mice with DSS-induced colitis and 1 healthy control mouse, flow-sorted Epcam-Cd45-Cd31-Pdpn+Pdgfra+ disaggregated colon cells, and profiled 1000 sorted fibroblasts from each mouse with RNA-sequencing.

first: Korsunsky

last: Ilya


title: Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases


title: Gene expression analysis of skewed mouse T cells pre- vs post-injection, and ex vivo skin T cells from first disease vs flare, in a model of Cutaneous Lupus Erythematosus

summary: We performed gene expression analysis on cultured Th0, Th1 and Th2 cells pre-injection, and on enriched T cells from lesional skin of cutaneous lupus erythematosus (CLE) mice post-injection, to compare differences in transcription that could predict skin tropism and flare

overall_design: DO.11 T cells were skewed in vitro towards Th0, Th1 or Th2. A portion of the cells were saved for RNA analysis and the remainder were injected into recipient mice. Only Th2 cells induced skin disease. To analyze gene expression post-injection, we enriched for T cells from lesional skin of mice in the first course of disease (approximately 4 weeks) or at flare (approximately 12 weeks) using Miltenyi CD3 bead isolation kits. All extracted RNA samples were analyzed using NanoString mouse Immunology panel (C2269).


title: Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases [scRNA-Seq]

overall_design: Single cell profiles of CD45-negative joint cells from 3 mice with collagen induced arthritis and 3 control mice.


title: Monocytic HLA-DR density in renal transplant recipients

city: Oxford

first: Matthew

last: Bottomley

state: Oxfordshire

address: Old Road Campus

department: Nuffield Department of Medicine

institute: University of Oxford

summary: Cohort study of 137 renal transplant recipients and 29 non-immunosuppressed controls, looking at clinical influences upon monocytic HLA-DR density (mHLA-DRd) and associated clinical outcomes (namely, malignancy development)

overall_design: Monocytes enriched from PBMC by negative selection using magnetic beads from 12 transplant recipients with high and low mHLA-DRd, matched by age and prednisolone use, analysed using Nanostring nCounter 'Human Myeloid Immunity' panel


title: Copper acts synergistically with fluconazole in Candida glabrata by compromising drug efflux, zinc homeostasis and sterol metabolism

city: OEIRAS

first: Catarina

last: Pimentel

state: LISBOA

address: Av. da República

department: MOSTMICRO

country: Portugal

institute: ITQB-NOVA

summary: In this study we used a transcriptomic approach to study the molecular determinants of the synergy between copper and fluconazole, in Candida glabrata, the second most frequent cause of invasive candidiasis. We demonstrate that copper acts together with fluconazole by downregulating three distinct pathways: azole efflux, ergosterol biosynthesis and zinc homeostasis. Coincidently, all these pathways are important for C. glabrata to cope with fluconazole stress. Therefore, when copper and fluconazole are combined cells fail to detoxify this drug and accumulate toxic methylated intermediates of sterol metabolism. This accumulation, possibly together with copper-induced lipid damages, should affect the activity of plasma membrane transporters, which impedes zinc uptake, leading to zinc depletion

overall_design: RNA-Seq of Candida glabrata ATCC2001 strain exposed to Fluconazole, CuSO4 or both compounds when compared to untreated cells was perfomed on a Illumina NextSeq500 platform

first: A

last: Gaspar-Cordeiro

first: C

last: Amaral

first: V

last: Pobre

first: W

last: Antunes

last: Petronilho

last: Rodrigues-Pousada


title: Latent HIV infection disrupts cell-intrinsic innate immunity [scRNA-seq]

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Single Cell RNA Sequencing in Primary CD4 T-Cells infected with HIV, suppressed with ART, and treated with IFNb

overall_design: Primary CD4 T cells from human donors cultured with homeostatic cytokines then mock-infected or infected with NanoLuc HIV, supressed with ART for 7 days and then treated with media or IFNB for 8 hours

first: Rebecca

last: Olson

first: Leanne

last: Whitmore

first: Daniel

last: Newhouse

first: Elise

last: Smith

first: Jennifer

last: Tisoncik-Go

first: German

last: Gornalusse

first: Christina

last: Ochsenbauer

first: Florian

last: Hladik

last: Gale Jr


title: RNAseq Quantitative Analysis of Arabidopsis Wild Type versus transcription factor dof4-1 mutant

status: Public on May 31 2022

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

summary: Transcriptome of seeds at nine days after polinization were compared between wild type and loss-of-function mutant in the transcription factor DOF4.1 gene

overall_design: wild-type versus mutant seeds


title: ID2 and HIF-1α collaborate to Protect Quiescent Hematopoietic Stem Cells from Activation, Differentiation and Exhaustion [scRNA-seq]

city: Frederick

first: Kristbjorn

middle: Orri

last: Gudmundsson

state: MD

address: 1050 Boyles St.

department: MCGP

institute: NCI

summary: Defining mechanism(s) that maintain tissue stem quiescence is important for improving tissue regeneration, cell therapies, aging, and cancer. We report here that genetic ablation of Id2 in adult hematopoietic stem cells (HSCs) promotes increased HSC activation and differentiation, which results in HSC exhaustion and bone marrow failure over time. Id2Δ/Δ HSCs show increased cycling, reactive oxygen species (ROS) production, mitochondrial activation, ATP production, and DNA damage compared to Id2+/+ HSCs, supporting the conclusion that Id2Δ/Δ HSCs are less quiescent. Mechanistically, HIF-1α expression is decreased in Id2Δ/Δ HSCs, and stabilization of HIF-1α in Id2Δ/Δ HSCs restores HSC quiescence and rescues HSC exhaustion. ID2 promotes HIF-1α expression by binding to the Von Hippel-Lindau (VHL) protein and interfering with proteasomal degradation of HIF-1α. HIF-1α promotes Id2 expression and enforces a positive feedback loop between ID2 and HIF-1α to maintain HSC quiescence. Thus, sustained ID2 expression could protect HSCs during stress, and improve HSC expansion for gene editing and cell therapies.

overall_design: 1000 ID2+/+ and 1000 ID2Δ/Δ HSCs were sorted and subjected to single cell RNA-Seq using 10X genomics technology

first: Brad

middle: L

last: Jakubison

first: Tanmoy

last: Sarkar

middle: O

first: Jonathan

middle: R

last: Keller


title: ID2 and HIF-1α Collaborate to Protect Quiescent Hematopoietic Stem Cells from Activation, Differentiation and Exhaustion [RNA-seq]

summary: Defining mechanism(s) that maintain tissue stem quiescence is important for improving tissue regeneration, cell therapies, aging, and cancer. We report here that genetic ablation of Id2 in adult hematopoietic stem cells (HSCs) promotes increased HSC activation and differentiation, which results in HSC exhaustion and bone marrow failure over time. Id2Δ/Δ HSCs show increased HSC cycling, reactive oxygen species (ROS) production, mitochondrial activation, and DNA damage supporting the conclusion that Id2Δ/Δ HSCs are less quiescent. Mechanistically, HIF-1α expression is decreased in Id2Δ/Δ HSCs, and stabilization of HIF-1α in Id2Δ/Δ HSCs restores HSC quiescence and rescues HSC exhaustion. ID2 promotes HIF-1α expression by binding to the Von Hippel-Lindau (VHL) protein and interfering with proteasomal degradation of HIF-1α. HIF-1α promotes Id2 expression and enforces a positive feedback loop between ID2 and HIF-1α to maintain HSC quiescence. Thus, sustained ID2 expression could protect HSCs during stress, and improve HSC expansion for gene editing and cell therapies.

overall_design: ID2+/+ and ID2Δ/Δ HSCs were sorted from 8-16 week old mice followed by subsequent RNA-Seq Analysis

first: Lei

last: Sun


title: Effects of IsovalerylspiramycinⅠ(ISP-I) on gene expression profile of NSCLC cells

city: Shanghai

first: Tao

last: Ren

address: No. 600, Yi Shan Road

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

summary: To explore the possible mechanisms of ISP-I-induced NSCLC cell death, we performed RNA-seq comparisons of H460 and A549 after ISP-I treatment for 48h.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for non-treated as well as ISP-I treated NSCLC cells (3 replicates per group)

first: Liu

last: Zeyu

first: Ren

last: Tao


title: Whole transcriptome sequencing of peripheral blood from opioid use disorder [RNA-seq]

city: Wuhan

first: Yong

last: Wu

address: Gongnongbing road 89#

institute: Wuhan Mental Health Center

summary: 7 male OUD patients and 7 male health controls with demographic and clinical data matched were enrolled in this study. rRNA removed library and small RNA library were constructed using peripheral blood RNA. RNA-seq was used to investigate the peripheral transcriptomic changes between the two groups.

overall_design: transcriptome profile of 7 male OUD patients and 7 male health controls

first: Shan-Shan

last: Pu

first: Xiao-Bo

last: Liu

first: Yi

last: Li


title: Extracellular vesicle (EV) miRNome profiling in hiPSC-cardiomyocyte differentiation reveals a stemness-maintenance miRNA cluster driving hiPSC-EV bioactivity

city: Oeiras

first: Ana

middle: Filipa

last: Louro

address: Av. República, Qta. do Marquês Edifício iBET/ITQB

department: Animal Cell Technology Unit

institute: iBET

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular Vesicles (EV) are an attractive therapy to boost cardiac regeneration. Nevertheless, identification of EV and corresponding cell platform(s) suitable for therapeutic application, is still a challenge. Here, we isolated EV from key stages of the human induced pluripotent stem cell-cardiomyocyte (hiPSC-CM) differentiation and maturation, i.e., from hiPSC (hiPSC-EV), cardiac progenitors (CPC-EV), immature (CMi-EV) and mature (CMm-EV) cardiomyocytes, with the aim of identifying a promising cell biofactory for EV production, and pinpoint the genetic signatures of bioactive EV.  EV were characterized in terms of expression of specific markers, yield, and size. Bioactivity was assessed in human umbilical vein endothelial cells (HUVEC) and hiPSC-CM. Small RNA-Seq was performed to identify the differentially expressed miRNA in the four EV groups. Bioactivity assays showed increased tube formation and migration in HUVEC treated with hiPSC-EV compared to EV from committed cell populations. hiPSC-EV also significantly increased hiPSC-CM proliferation. Global miRNA expression profiles corroborated an EV-miRNA pattern indicative of stem cell to cardiomyocyte specification. A stemness maintenance miRNA cluster upregulated in hiPSC-EV was found to target the PTEN/PI3K/AKT pathway. Moreover, hiPSC-EV treatment mediated PTEN suppression and increased AKT phosphorylation.  Overall, our findings validate hiPSC as suitable cell biofactories for EV production for cardiac regenerative applications.

overall_design: Analysis of the extracellular vesicle (EV) miRNA content of four EV groups, each with three independent biological replicates, corresponding to different extracellular vesicle preparations from three independent cell cultures.

first: Marta

last: Paiva

last: Oliveira

first: Patrícia

last: Gomes-Alves

first: Paula

last: Alves

first: Margarida

last: Serra


title: Cytokines and lipid mediators of inflammation in lungs of SARS-CoV-2 infected mice

status: Public on May 30 2022

city: Quebec

first: Julien

last: Prunier

state: QC

address: 1030 av. de la medecine

department: Forestry

country: Canada

institute: Université Laval

summary: We investigared the gene expression response of K18-ACE2 mices to Sars-Cov-2 infection. We compared gene expression profiles of control and infected mices at different time points as well as the infection from the Wuhan and Delta strains

overall_design: Comparison of gene expression profiles between non-infected (control), Wuhan infected and Delta infected mices at days 5 and 7 past infection.

first: Isabelle

last: Dubuc

first: Émile

last: Lacasse

first: Annie

last: Gravel

first: Florian

last: Puhm

first: Isabelel

last: Allaeys

first: Anne-Sophie

last: Archambault

first: Leslie

last: Gudimard

first: Arnaud

last: Droit

first: Nicolas

last: Flamand

first: Éric

last: Boilard

first: Louis


title: 3D landscape of Hepatitis B virus interactions with human chromatins [RNA-seq]

first: Xiong

last: Ji

address: Yiheyuan Road

department: School of life science

summary: We employed a highly sensitive technology, 3C-HTGTS (3C-high-throughput genome-wide sequencing), to globally identify HBV DNA-host DNA contacts in cellular models of HBV infection.  We found that HBV cccDNA does not randomly position in host genome, but instead preferentially establishes contacts with the host DNA at active chromatin regions.  In contrast, the organization of integrated HBV DNA is largely regulated by the local genome epigenetic environment, which particularly forms chromosome loop with host genome where gene promoters together with active histone modifications are enriched. Our study provides a high throughput 3D landscape for the spatial organizations of cccDNA and integrated HBV DNA within the human genome, and provides a foundation to further understand the mechanisms of HBV modulation of liver disease development and progression in the future.

overall_design:
Examination of 2 different HBV DNAs in 2 HBV cell models using two different primer.
HepAD38 replicates human hepatitis B virus (HBV) under conditions that can be regulated with tetracycline.

first: Bo

last: Yang

first: Boyuan

last: Li


title: RNA Sequencing Facilitates Quantitative Analysis of Cont/Dicer KO/Scx HT mice Achilles Tendon Transcriptome

city: Hiroshima

first: Shigeru

last: Miyaki

state: Hiroshima

address: 1-2-3, kasumi Minami-ku

department: Medical Center for Translational and Clinical Research

institute: Hiroshima University

summary: To investigate which mRNA and miRNA are involved in Dicer KO mouse tendon hypoplasticity, we performed RNA-seq and small RNA-seq using RNA from Achilles tendon of Cont (Dicer f/f), Scx HT (ScxCre/+ Knock In:Dicer +/+) and Dicer KO (ScxCre/+ Knock In:Dicer f/f) mice at 4 weeks of age. Achilles tendon from 4-week-old female mice was harvested, RNA was isolated using an RNA extraction kit. RNA libraries were generated and sequenced by K. K. DNAFORM (Tokyo, Japan). The libraries were sequenced by Illumina HISEQ4000 using Illumina provided protocol. Differential gene expression was analyzed with R Bioconductor DESeq2. We found that a large portion of tendon-fibroblast characteristic genes was downregulated in Dicer KO mice Achilles tendon compared to Cont and Scx HT.

overall_design: mRNA and miRNA profiles of 4-week-old wild-type, Dicer KO and Scx HT Achilles tendon tissue

first: Chenyang

last: Ding