title: High-throughput transcriptomics assessment of 24 per- and polyfluoroalkyl substances (PFAS) in human liver spheroids

city: Ottawa

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary: Per- and polyfluoroalkyl substances (PFAS) are some of the most prominent organic contaminants in human blood that have the potential to disrupt biological processes and pathways in the liver. Although the toxicological implications from human exposure to perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) are well established, data on other, lesser-understood PFAS are limited. A challenge for regulatory authorities is to determine acceptable levels of human exposure to large, diverse classes of environmental contaminants. New approach methodologies (NAMs) that apply bioinformatics tools to interpret biological data are being increasingly considered to inform risk assessment when traditional toxicology methodologies are not amenable. The aim of the current investigation was to identify the biological responses relevant to PFAS mode of action as the concentration (benchmark dose) that these effects take place in order to utililze this information to inform/facilitate read-across for risk assessment of data-poor PFAS. A TempO-Seq platform (BioSpyder) measured gene expression changes in human liver microtissues (i.e., spheroids) after 1-day and 10-day exposures to increasing concentrations of PFAS. A bioinformatics framework was applied to 23 PFAS sub-classed into carboxylates (PFCAs), sulfonates (PFSAs), or PFAS precursors that were analyzed for the total altered transcripts, the concentration where effects take place, and identifying target genes of interest. Both PFCAs and PFSAs exhibited a trend toward increased transcriptional changes with carbon chain-length. Specifically, longer-chain compounds (7 to 10 carbons) were more likely to surpass liver-toxic transcriptomic thresholds established from previous studies than shorter chain PFAS. Longer-chain PFAS were also more potent, inducing transcriptional effects at lower concentrations. However, PFOS was the most potent PFAS and of all precursors, only PFOSA (a PFOS precursor) induced a response. The combined high-throughput transcriptomic and bioinformatics analyses revealed the capability of NAMs to assess the effects of PFAS in liver microtissues; such data improves our understanding of PFAS-related effects in humans and facilitates the use of read-across in human health risk assessment for other data-poor chemicals.

overall_design: PFAS TempO-Seq Experiment  : Sequencing data from 6 treatment concentrations and 1 control in DMSO over 2 time points (1-day and 10-day exposure) for  PFBA, PFPeA, PFHxA, PFHpA, PFOA, PFNA, PFDA, PFUnA, PFTeA, PFBS, PFHxS, PFHpS, PFOS, PFDS, PFOSA, 8:2 monoPAP, 6:2 monoPAP, 8:2 FtS, 6:2 FtS, 4:2 FtS, 8:2 FtOH, 6:2 FtOH, 5:3 acid, GenX (4 replicates)

first: Anthony

last: Reardon

first: Andrea

last: Rowan-Carroll

first: Stephen

last: Ferguson

first: Remi

last: Gagne

first: Byron

last: Kuo

first: Karen

last: Leingartner

first: Andrew

last: Williams

first: Christine

last: Lemieux

first: Luigi

last: Lorusso

last: Levicki

first: Julie

last: Bourdon-Lacomb

first: Russell

last: Carrier

first: Ivy

last: Moffat

first: Carole

last: Yauk

first: Ella

last: Atlas


title: SUMOylation of Linker Histone H1 Drives Chromatin Condensation and Restriction of Embryonic Cell Fate Identity [SMART-Seq]

status: Public on Nov 05 2021

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

type: Expression profiling by high throughput sequencing

summary: The fidelity of the early embryonic program is underlined by tight regulation of the chromatin. Yet, our understanding of how the chromatin is organized to prohibit the reversal of the developmental program remains limited. Specifically, the totipotency to pluripotency transition marks one of the most dramatic events to the chromatin, yet the nature of histone changes and regulation underlying this process are only partly characterized. Here we show that linker histone H1 is post-translationally modulated by SUMO2/3, which facilitates its fixation onto ultra-condensed heterochromatin in embryonic stem cells (ESCs). Upon SUMOylation depletion, the chromatin becomes de-compacted and H1 is evicted, leading to totipotency reactivation. Further, we show that H1 and SUMO2/3 jointly mediate the repression of totipotent elements. Lastly, we demonstrate that preventing SUMOylation on H1 abrogates its ability to repress totipotency in ESCs. Collectively, our findings unravel a critical role for SUMOylation of H1 in mediating chromatin repression and desolation of the totipotent identity.

overall_design: RNA-seq was performed to measure changes in mRNA expression between UBC9-inhibited and DMSO-control morula mouse embryos. The selected embryos in this experiment were morphologically matched.

first: Daoud

last: Sheban

first: Tom

last: Shani

first: Yifat

last: Merbl

first: Jacob

last: Hanna


title: The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epstein-Barr virus (EBV) establishes life-long latency in human B-cells by maintaining its chromatinized episomes within the nucleus. These circularized mini-chromosomes do not integrate into the host genome. Therefore, it is essential for EBV to organize its chromatin in a manner suitable for genomic stability, DNA replication, and efficient gene expression. Poly [ADP-ribose] polymerase 1 (PARP1) activity is significantly higher in B-cells infected with EBV than those without, and considerably higher in the transcriptionally active type III latency compared to the immunoevasive type I. In addition to its role in DNA damage response, PARP1 has been implicated in transcriptional regulation and structural maintenance of both the human and EBV genome at specific regions. To better understand PARP1's role in the regulation of the EBV episome, we have functionally characterized the effect of PARP enzymatic inhibition on total episomal structure through in situ Hi-C mapping, generating the first complete 3D structure of the EBV genome. We have also mapped intragenomic contact changes after PARP inhibition to global binding of the chromatin looping factors CTCF and cohesin across the EBV genome.  Additionally, PARP inhibition was shown to alter gene expression at the regions where chromatin looping was most effected. Finally, we have identified a novel function of PARP, which regulates cohesin complex chromatin binding. In conclusion, PARP1 inhibition does not alter the location of cohesin binding but does increase its frequency of binding at these regions. Despite this, there are fewer overall unique intragenomic interactions after PARP inhibition, while some areas have new chromatin loops not seen in the untreated EBV episome, leading us to conclude that PARP does have an essential role in the regulation of global EBV chromatin structure. The altered expression profile after the structural rearrangement induced by PARP inhibition also supports the idea that PARP1 helps maintain EBV latency programs.

overall_design:
HiC in Mutu I and Mutu LCL cell lines under control and olaparib-treated conditions

CHIP-seq of CTCF in Mutu I and Mutu LCL cell lines with IgG control

first: Italo

last: Tempera

first: Sarah

last: Johnson


title: BACH2 inhibition reverses β-cell failure in type 2 diabetes models

status: Public on Nov 11 2021

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

institute: University of Arizona

summary: Type 2 diabetes is associated with defective insulin secretion and reduced β-cell mass. Available treatments provide a temporary reprieve, but secondary failure rates are high, making insulin supplementation necessary. Reversibility of b-cell failure is a key translational question. Here, we reverse-engineered and interrogated pancreatic islet-specific regulatory networks to discover T2D-specific subpopulations characterized by metabolic-inflexibility and endocrine-progenitor/stem cell features. Single-cell gain- and loss-of-function and glucose-induced Ca++ flux analyses of top candidate MR in islet cells validated transcription factor BACH2 and associated epigenetic effectors as a key driver of T2D cell states. BACH2 knockout in T2D islets reversed cellular features of the disease, restoring a non-diabetic phenotype. BACH2-immunoreactive islet cells increased ~4-fold in diabetic patients, confirming the algorithmic prediction of clinically relevant subpopulations. Treatment with a BACH inhibitor lowered glycemia and increased plasma insulin levels in diabetic mice, and restored insulin secretion in diabetic mice and human islets. The findings suggest that T2D-specific populations of failing b-cells can be reversed and indicate pathways for pharmacological intervention, including via BACH2 inhibition.

overall_design: Obtain 9600 scRNA-Seq profiles from human inlet cells

first: Jinsook

last: Son

first: Andrea

last: Califano

first: Domenico

last: Accili


title: Single cell sequencing of the nodose ganglia

city: Durham

first: Winston

last: Liu

state: NC

address: MSRB1 217, 203 Research Drive

department: Neurobiology

institute: Duke University

summary: Guided by gut sensory cues, humans and animals prefer nutritive sugars over non-caloric sweeteners. But how the gut differentiates such stimuli to rapidly guide preferences remains unknown. In the intestine, innervated enteroendocrine cells synapse with the vagus nerve to convey luminal sugar stimuli to the brain within seconds. Here, we sequenced individual vagal nodose neuron cells from the left and right nodose to assess their relative contribution to sugar signaling from the gut.  The neurons lack expression of sugar receptors and transporters, but do express receptors for neurotransmitters and neuropeptides secreted by intestinal sensory epithelial cells.

overall_design: Single cell transcriptomes of the left and right sensory nodose ganglia

middle: W

first: Diego

last: Bohórquez

first: M

middle: M

last: Kaelberer


title: RNASeq profiles from two distinct F4/80+VCAM1+ sorted bone marrow populations are consistent with non-macrophage cells coated with macrophage fragments

city: Woolloongabba

first: Susan

last: Millard

state: QLD

address: 37 Kent St

department: Translational Research Institute

country: Australia

institute: Mater Research Institute - The University of Queensland

summary: The objective of this study was to characterise macrophage subsets in bone marrow (BM) isolated from Csf1r-EGFP mice. A concurrent imaging flow cytometry study conducted by our team unexpectedly revealed macrophage surface marker staining emanates from membrane-bound subcellular remnants associated with unrelated cells. Expression data from sorted BM “macrophage” populations was found to be consistent with macrophage fragments associated with non-macrophage cells. Granulocyte-specific genes were enriched within the CD11b+ “macrophage” (CD11b+F4/80+Ly6G-GFPloVCAM1+) populations, whereas CD11b- “macrophages” (CD11b-F4/80+GFP+VCAM1+) were consistent with a mixed cell population including both plasma cells and erythroblasts. This data demonstrates how fragmentation of hematopoietic tissue macrophages can result in misattribution of macrophage identity to non-macrophage populations, thereby undermining accuracy of macrophage ex vivo molecular profiles.

overall_design: mRNA profiles of two distinct sorted bone marrow cell populations (CD11b+ "macrophages" and CD11b- "macrophages") isolated from Csf1r-EGFP mice. Four biological replicates were analysed for each population.

first: Simranpreet

last: Kaur

first: Andy

middle: C

last: Wu

first: Graham

last: Magor

first: Andrew

last: Perkins

first: Allison

middle: R

last: Pettit


title: RNA sequencing (RNA-Seq) of multi-drug resistant (MDR) cancer cells and MDR persister cancer cells.

status: Public on Nov 04 2021

city: Chengdu

first: Chen

last: Haining

address: Renminnan Road

country: China

institute: Sichuan University

summary: To gain insight into the alterations of gene expression profile in the course of non-mutationally acquired resistance, we performed RNA-seq comparing MDR persister cells to MDR cancer cells.

overall_design: Screened differentially expressed genes by statistical significance based on gene expression profiles of MCs and MPCs

first: Zhe

last: Zhang

first: Hai-Ning

last: Chen


title: Expression pattens of long non-coding RNAs in peripheral blood mononuclear cells of non-segmental vitiligo

city: nanchang

first: shulan

last: zhang

state: Jiangxi

address: NO.1 minde Road

institute: The Second Affiliated Hospital of Nanchang University

type: Non-coding RNA profiling by high throughput sequencing

summary: Objective: We explored the patterns of long non-coding RNA (lncRNA) expression in peripheral blood mononuclear cells (PBMCs) from patients with non-segmental vitiligo. Methods: We used high-throughput RNA sequencing technology to generate sequence data from five patients with non-segmental vitiligo alongside five normal healthy individuals, and then performed bioinformatics analyses to detect the differential expression of lncRNA in PBMCs. Gene Ontology (GO) and pathway analyses were performed for functional annotation, and quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify gene expression. Target miRNAs and mRNAs of differentially expressed lncRNAs were predicted using bioinformatics analysis. Results: A total of 292 lncRNAs were differentially expressed in non-segmental vitiligo (fold change≥2.0, P<0.05), of which 171 were upregulated and 121 were downregulated. Six differentially expressed lncRNAs were selected , namely ENST00000460164.1, ENST00000393264.2, NR-046211.1, NR-135491.1, NR-135320.1, and ENST00000381108.3, for validation by qRT-PCR. The results showed that ENST00000460164.1 and NR-046211.1 were highly expressed in PBMCs of non-segmental vitiligo. An lncRNA-miRNA-mRNA network containing two lncRNAs, 17 miRNAs, and 223 mRNAs was constructed. Conclusion: Our results revealed patterns of differentially expressed lncRNAs in the PBMCs of non-segmental vitiligo individuals. ENST00000460164.1, and NR-046211.1 may be potential biomarkers and drug targets for the treatment of non-segmental vitiligo.

first: Shulan

first: Xinyue

last: Yang

first: Zhibin

first: Yifeng

last: Xiong

first: Yingpeng

first: Chunming

last: Li

first: Ougen

first: Xiaoyan

last: Wang

first: Yating

last: Peng


title: Pre-neoplastic somatic mutations including MYD88L265P in lymphoplasmacytic lymphoma

city: Pamplona

first: Ibai

last: Goicoechea

state: Navarra

address: Centro de Investigación Médica Aplicada (CIMA) Avenida Pío XII, 55

country: Spain

institute: Universidad de Navarra

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Pre-neoplastic somatic mutations including MYD88L265P in lymphoplasmacytic lymphoma [scRNA-seq]

summary: Normal-cell counterparts of solid and myeloid tumors accumulate mutations years before disease onset; whether this occurs in B-lymphocytes prior to lymphoma remains uncertain. We sequenced multiple stages of the B-lineage in elderly individuals and patients with lymphoplasmacytic lymphoma, a singular disease for studying lymphomagenesis because of high-prevalence of mutated MYD88. We observed similar accumulation of random mutations in B-lineages from both cohorts and, unexpectedly, found MYD88L265P in normal precursor and mature B-lymphocytes from lymphoma patients. We uncovered genetic and transcriptional pathways driving malignant transformation and leveraged these to model lymphoplasmacytic lymphoma in mice, based on mutated MYD88 in B-cell precursors and BCL2 overexpression. Thus, MYD88L265P is a pre-neoplastic event, which challenges current understanding of lymphomagenesis and may have implications for early detection of B-cell lymphomas.

overall_design: single-cell RNA and BCR sequencing (scRNA/BCRseq) in a total of 40,169 B cells and PCs from three patients with IgM MGUS and two with LPL/WM

first: Sara

last: Rodriguez

first: Bruno

last: Paiva


title: Pre-neoplastic somatic mutations including MYD88L265P in lymphoplasmacytic lymphoma [WES]

overall_design: Whole Exome Sequencing (WES) in B cells from 8 M88Ym/M88Yc mice and 15 M88BCRm/M88B2m mice

first: Jon

last: Celay

first: Jose

middle: A

last: Martinez-Climent


title: Integrative phenotypic and genomic analyses reveal strain-dependent responses to acute ozone exposure and their associations with airway macrophage transcriptional activity [ATAC-seq]

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

summary: Acute ozone (O₃) exposure is associated with multiple adverse cardiorespiratory outcomes, the severity of which varies across human populations and rodent models from diverse genetic backgrounds. However, molecular determinants of response, including biomarkers that distinguish which individuals will develop more severe injury and inflammation (i.e., high responders), are poorly characterized. Here, we exposed adult, female and male mice from 6 strains, including 5 Collaborative Cross (CC) strains, to filtered air (FA) or 2 ppm O₃ for 3 hours, and measured several inflammatory and injury parameters 21 hours later. Additionally, we collected airway macrophages and performed RNA-seq analysis to investigate influences of strain, treatment, and strain-by-treatment interactions on gene expression as well as transcriptional correlates of lung phenotypes. Animals exposed to O₃ developed airway neutrophilia and lung injury, with varying degrees of severity. We identified many genes that were altered by O₃ exposure across all strains, and examination of genes whose expression was influenced by strain-by-treatment interactions revealed prominent differences in response between the CC017/Unc and CC003/Unc strains, which were low- and high-responders, respectively (as measured by cellular inflammation and injury). Further investigation of this contrast indicated that baseline gene expression differences likely contribute to their divergent post-O₃ exposure transcriptional responses. We also observed alterations in chromatin accessibility that differed by strain and with strain-by-treatment interactions, lending further plausibility that baseline differences can modulate post-exposure responses. Together, these results suggest that aspects of the respiratory response to O₃ exposure may be mediated through altered airway macrophage transcriptional signatures, and further confirms the importance of gene-by-environment interactions in mediating differential responsiveness to environmental agents.

overall_design: We compared chromatin accessibility across two CC strains, representative of low and high responses to ozone as measured by lung injury and inflammation: CC017/Unc and CC003/Unc, respectively.

first: Wesley

middle: L

last: Crouse

first: Terrence

middle: S

last: Furey

first: Samir

middle: N

last: Kelada


title: Integrative phenotypic and genomic analyses reveal strain-dependent responses to acute ozone exposure and their associations with airway macrophage transcriptional activity [RNA-seq]

overall_design: We profiled transcriptomes from adult, male and female mice representing 6 different strains (C57BL/6J and 5 CC strains) collected from airway macrophages 21 hours after a 3 hour exposure to filtered air or 2 ppm ozone.


title: RNA-seq in Harpegnathos ovaries after Kr-h1 knockdown in the brain

first: Roberto

last: Bonasio

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: We injected mature (4-months-old) workers and gamergates with siRNAs against Kr-h1 or, as a control, GFP and performed RNA-seq on their ovaries 24 h later

overall_design: At least four biological replicates (ovaries from an individual ant) per sample

first: Karl

last: Glastad

first: Janko

last: Gospocic


title: Integrative phenotypic and genomic analyses reveal strain-dependent responses to acute ozone exposure and their associations with airway macrophage transcriptional activity


title: RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes

city: Edinburgh

last: Buonomo

address: Alexander Crum Brown Road

department: Institute of Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: We have investigated the effect acute deletion of Rif1 has on the transcriptome in mESC and during early stage differentiation.

overall_design: 4 female mESC cell lines in total  (2 Rif1+/+ and 2 Rif1 F/F). 3 conditions (mESC no OHT treatment , mESC with 2days of OHT treatment and 2days embryoid bodies with pre OHT treatment), 1 technical replicate

first: Elin

last: Enervald

first: Lynn Marie

last: Powell

first: Lora

last: Boteva

first: Rossana

last: Foti

first: Nerea

last: Blanes Ruiz

first: Gözde

last: Kibar

first: Agnieszka

last: Piszczek

first: Fatima

last: Cavaleri

first: Martin

last: Vingron

first: Andrea

last: Cerase

first: Sara B C


title: Identifying biomarkers predicting response to chemotherapy in Stage II and Stage III colorectal cancer patients

city: MIAMI

first: Xi

last: CHEN

state: FL

address: 1120 NW 14th Street

institute: University of Miami

summary: Defining molecular features that can predict the response to chemotherapy for stage II-III colorectal cancer (CRC) patients remains challenging in cancer research. Most available clinical samples are Formalin-Fixed and Paraffin-Embedded (FFPE). Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA) is one platform marketed for high-throughput gene expression profiling for FFPE tissue samples. In this study, we analyzed the whole transcriptom gene expression of 156 CRC patient samples measured by this platform to identify biomarkers predicting the response to chemotherapy for stage II-III CRC patients.

overall_design:
In this study, we measured the whole transcriptom gene expression of 156 CRC patient samples (Stage I to Stage IV) based on HTA platform.

The disease status was provided in each sample characteristics field as following;
no evidence of disease (NED)
alive with disease (AWD)
dead of disease (DOD)
dead of unrelated causes (DOC)

The values 0 and 1 for the sample characteristics represent NO and YES, respectively.

first: Jing

last: Zhu

first: Natasha

middle: G

last: Deane

first: Keeli

middle: B

last: Lewis

first: Chandrasekhar

last: Padmanabhan

first: M

middle: K

last: Washington

first: Chanjuan

last: Shi

first: Kristen

last: Ciombor

first: Cynthia

last: Timmers

first: Richard

last: Goldberg

last: Chen

first: R

middle: D

last: Beauchamp


title: RNA-seq in Harpegnathos central brains after hormone injection

first: Roberto

last: Bonasio

summary: We injected 10-day-old workers wth 20E or JH3 or DMSO as control and performed RNA-seq from the central brain 10 hours later

overall_design: 7 biological replicates each for 20E and JH3 and 5 biological replicate for the DMSO control

first: Karl

last: Glastad

first: Janko

last: Gospocic


title: RNA-seq in primary Harpegnathos neuronal cultures stimulated with 20E or JH3

summary: We cultured primary Harpegnathos neurons in a medium containing 20E or JH3 and then switched the hormones. RNA-seq was performed 30 minutes, 6 hours, or 24 hours after the switch. To determine baseline expression in the cultures before the switch we also performed RNA-seq on the 6-day-old cultures 30 minues after addition of vehicle (DMSO).

overall_design: At least 3 independent cultures (biological replicates) per condition and time point


title: ChIP-seq for Kr-h1 in Harpegnathos brains

summary: We performed ChIP-seq with a new Kr-h1 antibody in the central brains of in established gamergates (day 120) and age-matched workers

overall_design: Three biological replicates for ChIP from workers or gamergates and matching input chromatin controls


title: RNA-seq in Harpegnathos central brains after Kr-h1 knockdown

summary: Central brain RNA-seq after control and Kr-h1 knockdown in d10 worker or gamergate.

overall_design: At least seven biological replicates (individual ant brains) per sample


title: Functional genomic analyses on the role of Kr-h1 in the 20E/JH3 pathways in Harpegnathos ants


title: Hepatocyte-specific knockout of Nicotinamide phosphoribosyltransferase increases susceptibility for liver fibrosis in mice

status: Public on Nov 03 2021

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Nicotinamide adenine dinucleotide (NAD+) supplementation has been suggested as a therapy against non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH). We investigated whether hepatocyte-specific knockout of nicotinamide phosphoribosyltransferase (Nampt) caused increased susceptibility towards liver damage in mice fed a low-methionine, choline-free 60% high-fat (MCD) diet. Knockout mice (HNKO) accumulated less hepatic triglyceride than WT littermates after 3 weeks of MCD, but had increased scores for liver inflammation, necrosis, and fibrosis. We found that fibrosis, necrosis, and portal inflammation was also present in HNKO mice on a purified control diet (PD) but not in chow-fed HNKO mice due to a higher content of NAD+ precursors in the diet. The PD induced fibrosis within 3 days of exposure could be prevented by supplementation with the NAD+ precursor nicotinamide riboside (NR). When NR was supplied after fibrosis induction, hepatic NAD+ levels markedly increased, and portal inflammation was attenuated. The fibrosis phenotype was associated with a decreased abundance of proteins involved in oxidation and reduction processes, particularly for proteins in oxidative phosphorylation (OXPHOS). NR supplementation increased abundance of these proteins. High-resolution respirometry revealed that PD-fed HNKO mice had decreased oxygen consumption when stimulated with succinate, and a decrease in maximal uncoupled respiratory capacity. Conclusions: We show that HNKO mice have increased susceptibility towards liver fibrosis when dietary NAD+ content is restricted, and that low NAD+ levels can affect hepatic mitochondrial function. Furthermore, our data suggest NR treatment has potential for preventing liver damage and NASH progression.

overall_design: Total RNA-seq of mus musculus liver in wild-type (WT) and hepatocyte specific NAMPT knockout (KO) mice on a purified diet. Samples were taken at 3, 6, 12 and 21 days of age.

first: Morten

last: Dall

first: Anna

last: Hassing

first: Lili

last: Niu

first: Thomas

last: Nielsen

first: Karolina

last: Sulek

first: Samuel

last: Trammel

first: Matthew

middle: P

last: Gillum

first: Romain

last: Barrés

first: Steen

last: Larsen

last: Poulsen

first: Matthias

last: Mann

first: Cathrine

last: Ørskov

first: Jonas

middle: T

last: Treebak


title: Epigenetic adaptation of stickleback to sea and freshwater conditions: RNA-seq

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

summary: Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation  to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment. This is the RNA-seq experiment, DNA methylation data (bisulfite-seq) is provided under accession number GSE82310.

overall_design: The following sample groups were studied: 1) marine sticklebacks kept in marine water, their natural habitat (M@M); 2) freshwater sticklebacks kept in freshwater (F@F); 3) marine sticklebacks incubated in fresh water for 4 days (M@F); 4) freshwater sticklebacks incubated in marine water for 4 days (F@M). In each gruop, 4-5 individual fish were profiled.

first: Nikolai

last: Mugue

first: Sergey

last: Rastorguev

first: Alexander

last: Mazur

first: Svetlana

last: Tsygankova

first: Eugenia

last: Boulygina

last: Nedoluzhko

first: Yulia

last: Medvedeva

first: Egor

last: Prokhortchouk


title: RNA-seq in central brains from Harpegnathos castes

first: Roberto

last: Bonasio

summary: We performed RNA-seq in central brains from adults of different ages and different castes as well as late pupae

overall_design: At least 4 replicates each for d10 and d20 workers, d10 duelers, d20 gamergates, d120 dominant gamergates and hunting workers, and late pupae

first: Karl

last: Glastad

first: Janko

last: Gospocic


title: Single-nucleus sequencing of liver cells from hepatocyte-specific Nampt knockout mice and WT littermates reveals major changes to the hepatocyte transcriptome in mice with necrosis

city: Copenhagen N

first: Morten

last: Dall

address: BLEGDAMSVEJ 3B, BLDG. 7.7

institute: University of Copenhagen

summary: Single-nucleus RNAseq was performed to investigate whether transcriptomics changes observed in bulk RNAseq could be attributed to specific hepatic cell populations.

overall_design: We isolated nuclei from 3 hepatocyte-specific Nampt knockout (HNKO) mice and 3 WT littermates, and sequenced 4,250 nuclei/sample

first: Anna

last: Hassing


title: Single cell RNA-seq data of human hESCs comparing experiments with cDNA library equalization

city: Gainesville

first: Rhonda

last: Bacher

address: 2004 Mowry Rd.

institute: University of Florida

summary: Considerable effort has been devoted to refining experimental protocols having reduced levels of technical variability and artifacts in single-cell RNA-sequencing data (scRNA-seq). We here present evidence that equalizing the concentration of cDNA libraries prior to pooling, a step not consistently performed in single-cell experiments, improves gene detection rates, enhances biological signals, and reduces technical artifacts in scRNA-seq data.  In this submission the original single-cell cDNA is from GSE75748 cells labelled EC2 and TB2 in which the cDNA was not equalized prior to library preparation. We performed a set of experiments with the equalization step and provide three count matrices - 1) EQ (equalized cDNA prior to pooling in equal amounts); 2) EQ Vary (same as EQ but pooled at unequal amounts); 3) EQ-75% (equalized cDNA and pooled equally, sequeced to lower total depth).

first: Li-Fang

last: Chu


title: Extracellular adenine released by the cardiac muscle cell disrupts pyrimidine biosynthesis in non-muscle cells to regulate tissue repair after heart injury

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Organ metabolism is spatio-temporally regulated at the cellular and tissue level to link metabolic pathways with key homeostatic processes, but little is known about the cellular regulation of metabolism during tissue repair after acute injury. In a murine model of ischemic cardiac injury, we demonstrate that the cardiac muscle cell regulates pyrimidine biosynthesis of non-muscle cells to affect cardiac repair. We demonstrate that the ectonucleotidase ENPP1 hydrolyzes extracellular ATP released after cardiac injury to form AMP, which then induces the cardiomyocyte to release adenine and specific ribonucleosides that disrupt pyrimidine biosynthesis, cause genotoxic stress and induce a p53 mediated cell death of non-myocyte cells such as fibroblasts, macrophages, endothelial and smooth muscle cells. As non-myocyte cells play a critical role in mediating heart repair, we demonstrate that rescue of pyrimidine biosynthesis by administration of uridine after cardiac injury or by genetic targeting of ENPP1/AMP pathway enhances repair and post infarct heart function. We establish a high through- put assay to screen a large library of small molecules to identify small molecule ENPP1 inhibitors and demonstrate that systemic administration of ENPP1 inhibitors following heart injury rescues pyrimidine biosynthesis in non-myocyte cells and augments tissue repair and function. We determine specific biochemical steps of pyrimidine biosynthesis that are disrupted and identify the critical pyrimidine metabolite orotidine as a serum biomarker for monitoring the metabolic control of tissue repair. These observations demonstrate that the cardiac muscle cell by releasing adenine regulates pyrimidine metabolism in non-muscle cells via paracrine mechanisms and provide insight into how inter-cellular regulation of pyrimidine biosynthesis can be targeted and monitored for augmenting tissue repair.

overall_design: Bulk RNA-seq and scRNA-seq in non-muscle cells in tissue repair after heart injury

first: Shen

last: Li

first: Matteo

last: Pellegrini

first: Arjun

last: Deb


title: Next generation sequencing of unstimulated and TNF-alpha-stimulated WT and DREAM-null neutrophils

city: Austin

first: Mijeong

last: Kim

state: Texas

address: 2500 Speedway

institute: The University of Texas at Austin

summary: To investigate the role of DREAM (a transcriptional repressor) in regulating gene transcription in neutrophils under inflammatory conditions, we conducted the next generation sequencing using unstimulated and TNF-alpha-stimulated neutrophils isolated from WT and DREAM KO mice.

overall_design: WT and DREAM-null neutrophils were treated without or with TNF-alpha for 30 or 120 minutes, followed by the next generation sequencing.

first: Jaehyung

last: Cho

first: Jonghwan


title: Cardoon (Cynara cardunculus var. altilis L.) RNA-seq

city: Milano

first: Raul

last: Pirona

address: Via Alfonso Corti 12

country: Italy

institute: IBBA-CNR

summary: Calluses RNA-seq experiments from wild type and three line over-expressing the Arabidpsis thaliana MYB4 gene

overall_design: Undifferentiated wild type (WT) friable calluses were induced from leaves of cardoon plants  (“Spagnolo” genotype), following the method described in (Figueiredo et al., 1987), and gently provided for this study from Dr. M. De Palma (CNR-IBBR).

first: Dario

last: Paolo

first: Franca

last: Locatelli

first: Eleonora

last: Cominelli

first: Sara

last: Pozzo

first: Giulia

last: Graziani

first: Alberto

last: Ritieni

first: Monica

last: De Palma

first: Teresa

last: Docimo

first: Marina

last: Tucci

first: Francesca

last: Sparvoli


title: α6β2* nAChR Antagonist TxIB Changed Gene Expression in Zebrafish (Danio rerio) brain Induced by Alcohol Withdrawal

city: Haikou

first: Kailin

last: Mao

state: Hai Nan

address: Hai Dian Campus of Hainan University, No.58 of Ren Min Road, Mei Lan District, Haikou, Hainan Province,China

department: School of Life Sciences

institute: Hainan University

summary: Background and Purpose: Alcohol use disorder (AUD) is a serious public health issue and affects the lives of numerous people. Previous studies have shown a link between nicotinic acetylcholine receptors (nAChR) and alcohol addiction. However, the role of α6β2* nAChR in alcohol addiction remains obscure and whether α6β2* nAChR can be used as a potential drug target for alcohol withdrawal need to be studied.  Methods: Zebrafish (Danio rerio) were exposed to 0.2% alcohol for 14 days followed by 7 days of repeated withdrawal and then retro-orbitally injected with α-conotoxin TxIB (a selective α6β2* nAChR antagonist). RNA-sequencing (RNA-seq) and subsequent bioinformatics analysis were applied to explore the potential network regulation by blocking α6β2* nAChR using TxIB after alcohol withdrawal.   Results: RNA sequencing of zebrafish brain indicated a total of 657 genes showed aberrant expression and among which 225 were reversed after TxIB injection. These reversed genes were significantly enriched in cardiac muscle contraction and calcium signaling pathways and the gene expression profile was further validated by RT-PCR.   Conclusion: Our finding suggests α6β2* nAChR antagonists have the potential to modulate alcohol withdrawal.

overall_design: Three groups were divided into normal, alcohol-withdrawal, and TxIB. Each group has 3 biological replicates.

first: Xiaodan

first: Zongde

last: Chen

first: Xiaoqian

last: Dong

first: Dongting

last: Zhangsun

first: Xiaopeng

last: Zhu

first: Sulan

last: Luo


title: Giardia lamblia WB:  5pac_5n control vs 15279  (5pac_5n also know as 5'∆5N-Pac) (15279 also know as pPSpo11)

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

country: Taiwan

summary: Transcriptional profiling of Giardia lamblia WB comparing control 5pac_5n cells with 15279 cells.  (5pac_5n also know as 5'∆5N-Pac) (15279 also know as pPSpo11)

overall_design: Two-condition experiment 5pac_5n cells with 15279 cells.  (5pac_5n also know as 5'∆5N-Pac) (15279 also know as pPSpo11)


title: PRMT5 deficiency enforces the transcriptional and epigenetic programs of Klrg1+CD8+ terminal effector T cells [scRNA-seq]

status: Public on Nov 02 2021

city: Shanghai

first: zheyi

last: chen

address: 1665 Kong Jiang Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Protein arginine methyltransferase 5 (PRMT5) participates in symmetric dimethylation of arginine residues of proteins and contributes to a wide range of biological processes. But how PRMT5 affects the transcriptional and epigenetic programs involved in the establishment and maintenance of T cell subsets differentiation and roles in antitumor immunity are still incompletely understood. Here, using the single cell RNA sequencing, CHIP-sequencing and bulk RNA sequencing, we found that mice T cell-specific deletion of PRMT5 had greater effects on CD8+ than CD4+ T cells development, enforcing CD8+ T cells differentiation into Klrg1+ terminal effector cells. Mechanically, T cells deficiency of PRMT5 activated Prdm1 by decreasing H4R3me2s and H3R8me2s deposition on its loci, which promote differentiation of Klrg1+CD8+ T cells. Furthermore, effector CD8+ T cells that transited into memory precursor cells were decreased in PRMT5 deficiency T cells thus caused dramatic CD8+ T cells death.

overall_design: CD3+ T cells were isolated from control (WT) (n=3) and PRMT5 CKO (CRE) (n=3) mice spleens and used for single cell RNA sequencing.

first: Yingxia

last: Zheng

first: Zheyi


title: PRMT5 deficiency enforces the transcriptional and epigenetic programs of Klrg1+CD8+ terminal effector T cells [CHIP-seq]

overall_design: CD8+ T cells were isolated from control (n=5) and PRMT5 CKO (n=5) mice spleens and analyzed by ChIP-seq using antibodies to H4R3me2s and H3R8me2s.


title: Hepatocyte-specific perturbation of the NAD+ biosynthetic pathways in mice promotes reversible NASH-like phenotypes

first: Morten

last: Dall

summary: We report that the decreased expression of mitochondrial genes we observe in hepatocyte-specific Nampt knockout mice is normalized in primary hepatocytes, and that hepatocyte isolations causes major changes to the hepatocyte transcriptome for both knockouts and wildtype mice.

overall_design: We isolated primary hepatocytes from wildtype and hepatocyte-specific Nampt knockout mice, and sequenced RNA from 1. a liver biopsy following perfusion with saline (L), 2. from washed hepatocytes prior to seeding (CS) and 3. from primary hepatocytes following 24h of culturing (PH) for both genotypes and compared transcriptomes

first: Anna

last: Hassing

first: Jonas

last: Treebak


title: PRMT5 deficiency enforces the transcriptional and epigenetic programs of Klrg1+CD8+ terminal effector T cells [RNA-seq]

overall_design: Thymus T cells (CD4+CD8+ T cells (DP), CD4+CD8- (CD4+ SP) and CD8+CD4- (CD8+ SP) T cells) and spleen T cells (CD4+ SP and CD8+ SP T cells) were isolated from control (n=3) and PRMT5 CKO mice (n=3) and used for bulk RNAseq.


title: Trans-esophageal pacing induced changes in cardiac gene expression

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

summary: To investigate if a maximally physiologic exercise-similar pattern of heart rate acceleration delivered by a pacing approach can beneficially impact downstream cellular adaptations, thereby acting as a trigger for desired molecular remodeling that underlies cardiac stress resistance.

overall_design: Total RNA was sequenced after isolation from ventriclar tissue from 8-10 week old male C57-Bl6 mice (3 per group, 2 groups) after undergoing 8 days of atrial pacing vs. sham intervention.

first: Duane

last: Hall

first: Leonid

last: Zingman


title: Genome-wide mRNA targets of CPEB1 in muscle stem cells

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: We performed CPEB1 RIP-seq on freshly isolated muscle stem cells. We found that CPEB1 associated genes are enriched in translational regulation pathways.

overall_design: Two biological replicates of CPEB1 RIP-seq compared with two sets of input RNA-seq. Illumina Nextseq 500 platform. 2X75 sequencing kit.

middle: H

first: Wenshu

last: Zeng


title: Comprehensive DNA methylation analysis of human neuroblastoma cells treated with haloperidol and risperidone

city: Kumamoto

first: Kazuya

last: Iwamoto

address: 1-1-1 Honjo, Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

summary: This work reveals the effect of antipsychotics on DNA methylation using the cell model. After the treatment of antipsychotics, haloperidol and risperidone, DNA methylation profiles obtained by Illumina HumanMethylation450 beadchip were examined.

overall_design: We conducted a comprehensive DNA methylation analysis of human neuroblastoma cells (SK-N-SH) cultured with antipsychotics. The cells were cultured with low and high concentrations of haloperidol or risperidone based on their effective blood concentrations for 8 days. DNA methylation assay was performed with the Illumina HumanMethylation450 BeadChip. Three independent samples were prepared for each experimental group (n=18 in total).

first: Du

last: Jianbin

first: Nakachi

last: Yutaka

first: Kiyono

last: Tomoki

first: Fujii

last: Shinya

first: Kasai

last: Kiyoto

first: Miki

last: Bundo


title: Transcriptomic analysis of orthotopic pancreatic tumors treated by Axl inhibitor TP-0903 or combination with chemo/immunotherapy using the nCounter PanCancer Immune Profiling panel (Nanostring Technologies) [mouse]

status: Public on Nov 01 2021

city: Dallas

first: Yuqing

last: Zhang

state: TX

address: 6000 Harry Hines Blvd

department: Surgery

institute: UTSouthwestern Medical Center

summary: RNA isolated from KPfC orthotopic tumors was analyzed using Mouse PanCancer Immune Profiling Panel (NanoString Technologies).

overall_design: KPfC tumor tissues from orthotopic endpoint experiment were lysed in RLT lysis buffer and purified according to the manufacturer’s instructions (QIAGEN). RNA was sent to the Microarray Core Facility in UTSouthwestern and analyzed using a preassembled nCounter PanCancer Immune Profiling Panel (mouse) and the nCounter system (NanoString Technologies) according to the manufacturer’s instructions. Samples were then normalized based on the geometric means of the supplied positive controls and the panel of housekeeping genes, as recommended by the manufacturer.

first: Emily

last: Arner


title: Sulfonamide functional head group drives developmental toxicity of short-chain per- and polyfluorolkyl substances

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

summary:
Purpose: The goals of this study are to investigate developmental toxicity and hazard potential of a short-chain PFAS homologous series in zebrafish, specifically interrogating the impact of different functional head groups. Developmental toxicity findings were supplemented with investigations into transcriptom-wide effects of body burdens following PFAS exposures.
Methods: For developmental toxicity assessments, dechorionated embryonic zebrafish were statically exposed at 8 hours post fertilization (hpf) to either vehicle control (0.5% methanol) or to FBSA, PFBS, PFPeA, or 4:2 FTS across a range of concentrations (1-100 µM, normalized to 0.5% methanol) in 96-well plate format. Morphological and Behavior endpoints were assessed at 24 and 120 hpf. For investigations into transcriptomic effects and body burdens, embryos were exposed to vehicle control or 47 µM of each PFAS and then sampled at 48 hpf, before morphological effects were observable.  Transcriptomic effects of FBSA exposure were phenotypically anchored to abnormal morphology at 120 hpf as 47 µM was the concentration at which morphological effects were observed in 80% of the exposure group. At 48 hpf, 10 embryos were pooled per replicate, euthanized via ice bath, and total RNA extracted using a Zymo Research Direct-zol RNA MiniPrep kit and then sequenced on the BGISEQ-500 platform (Beijing Genomics Institute; BGI) for the transcriptomic investigation. Data analysis and visualization was conducted by BGI and their Dr. Tom platform. Briefly, sequencing data was filtered using SOAPnukes to remove adaptor sequences, N content greater than 5%, and low-quality reads. Clean reads were mapped to the reference genome (Danio rerio GRCz11) using HISAT2. Gene fusions and differential splicing were detected using Ericscript and rMATS, clean read alignments using Bowtie2 and expression level calculations using RSEM. Differential expression analysis was performed using DESEq2 (q-value ≤ 0.05), followed by gene ontology enrichment analysis using Phyper and transcription factor enrichment analysis using MetaCore. For body burden measurments, 4 replicates of 40 embryos were pooled per exposure group, euthanized on ice, homogenized, and analyzed by high pressure liquid chromatography and triple quadrupole mass spectrometry.
Results: Across the 4-fluorinated carbon short-chain PFAS series, all chemicals induced larval behavior effects, but only FBSA caused morphological, behavioral and large-scale transcriptomic disruptions (specifically at 47 µM). Notably, exposures at concentrations shown to induce only behavior effects resulted in a small number of differentially expressed genes. Biological processes enriched following FBSA exposure at 47 µM were related to lipid metabolism and biosynthesis, cellular homeostasis, brain and nervous system development, and immune processes. The bioaccumulative potential of the series at 47 µM was FBSA > PFBS > 4:2 FTS > PFPeA.

overall_design: Investigating developmental toxicity in zebrafish (n=36), transcriptome-wide effects with RNA-seq (3 replicates of 10 pooled 48 hpf embryos), and body burden measurements (4 replicates of 40 pooled 48 hpf embryos) following exposures to 4 PFAS.

first: Yvonne

last: Rericha

first: Dunping

last: Cao

first: Lisa

last: Truong

first: Micheal

last: Simonich

first: Jennifer

last: Field

first: Robyn

last: Tanguay

first: Chris


title: RNA-seq analysis of NIL-TT2HJX and NIL-TT2HPS32 aerial organs of 12-day-old seedlings under normal and heat treatment

first: Yi

last: Kan

address: Fenglin

institute: Center for Excellence in Molecular Plant Sciences ,CAS

summary: We observed that the differentially expressed genes were enriched in wax-related pathway

overall_design: mRNA profiles of NILs aerial organs (12-day-old)  were sequenced


title: PRMT5 deficiency enforces the transcriptional and epigenetic programs of Klrg1+CD8+ terminal effector T cells

first: zheyi

last: chen

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

overall_design: Refer to individual Series


title: Pathogenic CLP1 p.R140H mutation alters mRNA processing in human motor neurons (tRNA-seq)

city: Cleveland

first: Ashleigh

last: Schaffer

state: OH

address: 2109 Adelbert Road

department: Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics

institute: Case Western Reserve University

summary: Pontocerebellar Hypoplasia Type 10 (PCH10) is a childhood neurodegenerative disease caused by bi-allelic p.R140H variants in CLP1, a multifunctional RNA kinase, by unknown pathophysiological mechanisms. Here, we combine novel patient data with mutation-specific in vivo and in vitro models to define motor neuron dysfunction as a penetrant, prominent feature of  PCH10 and uncover a previously unrecognized mRNA misprocessing signature in motor neurons that likely contributes to pathology.

overall_design: Induced pluripotent stem cells reprogrammed from primary fibroblasts of an affected PCH10 patient ("Affected", CLP1 R140H/R140H) and their unaffected parent ("Unaffected", CLP1 R140H/+) were differentiated into mature motor neurons using an established protocol (Markmiller et al., Cell, 2018). For total RNA sequencing, 3 Affected clonal replicates and 2 Unaffected clonal replicates were used; for Poly(A)-Click sequencing and tRNA sequencing, 2 Affected clonal replicates and 2 Unaffected clonal replicates were used.

first: Geneva

last: LaForce

first: Jordan

last: Farr

first: Eric

middle: J

last: Wagner

first: Ping

last: Ji

first: Cydni

last: Akesson

first: Otis

last: Pinkard

first: Jeff

last: Coller

first: Thomas

last: Sweet

middle: E


title: Pathogenic CLP1 p.R140H mutation alters mRNA processing in human motor neurons


title: A stress-induced error prone 3’ flap-based Okazaki fragment maturation pathway creates internal tandem duplications for cell survival (WGS)

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Faithful and efficient Okazaki fragment maturation is the key to maintain the genome integrity. In addition, this process is coupled with deposition of histone proteins. Therefore, functional deficiency in Okazaki fragment maturation may cause genome instablities as well and epigenetic alterations. We conduct WGS of WT and rad27 knockout yeast strains to define the DNA mutations caused by defective Okazaki fragment muturaton and conduct RNA-seq to define the changes in gene expression profiling due to defetive Okazaki fragment muturations..

overall_design: We conduct WGS of WT and rad27 knockout yeast strains (n=1 for each sample) to define the genome-wide DNA mutation frequence and spectrum caused by defective Okazaki fragment muturaton. We conduct RNA-seq (n = 2 for each sample) to define the changes in gene expression profiling due to defetive Okazaki fragment muturations..

first: Haitao

last: Sun

first: Amanpreet

last: Singh

first: Li

last: Zheng

first: Binghui

last: Shen


title: A stress-induced error prone 3’ flap-based Okazaki fragment maturation pathway creates internal tandem duplications for cell survival (RNA-seq)


title: RNA structure probing to characterize RNA-protein interations on a low abundance pre-mRNA in living cells

first: Maurice

last: Swanson

address: 2033 Mowry Road,, Cancer & Genetics Research Complex, Swanson Lab, Room 220G

summary: We develop an enrichment strategy to enriched for low abundance RNAs of interest before reverse transcription for RNA struture probing experiments

overall_design:
Mbnl1-/-,Mbnl2-/- double knockout mouse embryonic fibroblasts were treated with 2'-methylnicotinic acid imidazolide (NAI) or DMSO only and used SHAPE-MaP to examine the structure of regulatory region of a low abundance pre-mRNA.

Target gene chromosome coordinates (mm10):

Rn7SK: chr9:78175303-78175633
Rpph1: chr14:50807449-50807767
Mbnl1: chr3:60614481-60614939

first: Jodi

last: Bubenik

first: Melissa

last: Hale

first: Ona

last: McConnell

last: Wang

first: Robert

middle: C

last: Spitale

first: J

middle: A

last: Berglund


title: Genome-wide small RNA sequencing analysis of KSHV long-term-infected endothelial (LTC) and parental uninfected TIVE cells [miRNA-seq]

city: Boston

first: Soo Mi

last: Lee

state: MA

address: 3 BLACKFAN CIRCLE, CLS 417

department: Pathology

institute: BIDMC/Harvard Medical School

summary:
Purpose: To characterize genome-wide microRNA (miRNA) expression profiles in the context of Kaposi’s sarcoma-associated herpesvirus (KSHV)-induced oncogenesis using isogenic cell lines for a Kaposi's sarcoma (KS) xenograft model: KSHV-infected human endothelial cells (LTC) that form tumors with properties closely resembling KS lesions in nude mice and uninfected parental (TIVE) cells.
Methods: miRNA expression profiles of LTC and TIVE cells were generated by deep sequencing using Illumina HiSeq 2500. The mappable reads were aligned to the human genome and miRBase using Bowtie.
Results: We show, through global cellular miRNA transcriptome analysis, that KSHV infection has a profound impact on the host miRNA expression landscape, up-regulating multiple miRNAs with oncogenic roles while down-regulating many tumor suppressive miRNAs, thereby contributing to KS oncogenesis. In particular, we identify miR-127-3p as one of the most significantly down-regulated miRNAs in LTC and restoring this miRNA inhibits KSHV-induced transformation, proliferation and tumorigenesis.
Conclusions: This study provides a detailed analysis of the cellular miRNA transcriptome in LTC and TIVE cells using small RNA sequencing technology. We identify significant dysregulation of cellular miRNAs with important oncogenic or tumor-suppressive functions that may be physiologically relevant to KSHV oncogenesis. Moreover, our results identify a previously unrecognized tumor suppressor function for miR-127-3p in KS, indicating that its restoration offers potential as a therapeutic intervention for KS.

first: Frank

last: Slack


title: Exploring transcriptome-wide changes in the brain-localized immune cells in a mouse model of Parkinson's Disease

city: Wuerzburg

first: Rhonda

last: McFleder

address: Josef-schneider-strasse 11

country: Germany

institute: Neurologische Klinik und Poliklinik des Universitaetsklinikum Wuerzburg

summary: In this study we identify the gene expression changes that occur in the brain-localized immune cells in a mouse model of Parkinson's Disease. A mouse model of Parkinson's Disease was created as previously described by stereotacticaly injecting an AAV-expressing the human A53T_mutated form of a-Synuclein into the Substantia Nigra of adult mice, while control mice were injected with empty vector (EV). These mice exhibit neurodegeneration in the Substantia Nigra and Parkinson-like behaviour phenotypes. Sixteen weeks after the injection, the Substantia Nigra and Srtiatum were micro-dissected and a Percoll gradient was used to enrich for the immune cells present in these tissues. The immune cells were also isolated from the Substantia Nigra and Striatum of same-age WT uninjected mice (WT). RNA was isolated from these cells and single-end 75nt high throughput sequencing were performed on libraries prepared from the RNA. We identified over 400 genes that were differentially expressed between control and Parkinson's mice with a log2 fold-change > |0.75|. These genes were enriched for terms related to immune activation such as: cytokine processing, leukocyte activation, and antigen presentation. The genes associated with these GO terms tended to be up-regulated in the Parkinson's mice suggesting that brain-localized immune cells are more activated in Parkinson's disease.

overall_design: We sequenced tissues from five mice per condition at ~35 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) with the High Output Kit v2.5

first: Chi

middle: W

last: lp

middle: L

first: Thorsten

last: Bischler

first: Tobias

last: Heckel


title: Plasma extracellular vesicle miR-483-3p and let-7d-3p as potential biomarkers for sepsis

status: Public on Oct 31 2021

city: shaoxing

first: guanguan

last: qiu

state: zhejiang

address: Yanan Road123

institute: shaoxing second hospital

summary: Recent literature has documented the use of microRNAs (miRNAs) from circulating extracellular vesicles (EVs) as biomarkers for a plethora of diseases. The aim of this prospective study was to identify the diagnostic value of plasma EV-miRNAs in sepsis.Sepsis patients and healthy controls were matched for age and gender. EVs were separated from plasma of sepsis patients at admission as well as healthy controls. The expression of EV-miRNAs was evaluated by microarray and qRT-PCR.

overall_design: Sepsis patients and healthy controls were matched for age and gender. EVs were separated from plasma of sepsis patients at admission as well as from healthy controls.

first: Guanguan

last: Qiu

first: Jiajie

last: Fan

first: Guoping

first: Jiangping

last: He

first: Fangping

last: Lin

first: Menghua

last: Ge

first: Jiangmei

first: Jie

last: Xia

first: Ruoqiong

last: Huang

first: Qiang

last: Shu

first: Jianguo

last: Xu


title: Pathogenic CLP1 p.R140H mutation alters mRNA processing in human motor neurons (total RNA-seq)

first: Ashleigh

last: Schaffer

first: Geneva

middle: R

last: LaForce

first: Jordan

middle: S

last: Farr

first: Eric

last: Wagner

first: Ping

last: Ji

first: Cydni

last: Akesson

first: Otis

last: Pinkard

first: Jeff

last: Coller

first: Thomas

last: Sweet


title: Pathogenic CLP1 p.R140H mutation alters mRNA processing in human motor neurons (PAC-seq)


title: AGATA: First nationwide molecular screening program in Spain for patients with advanced breast cancer

city: Barcelona

first: Jordi

last: Canes

address: C/ Balmes 89 3º 7ª

institute: SOLTI

summary:
The SOLTI-1301 AGATA study aimed to assess the feasibility of a multi-institutional molecular screening program to better characterize the genomic landscape of advanced breast cancer (ABC) and to facilitate patient access to matched-targeted therapies in Spain.
Between September 2014 and July 2017, 305 patients with ABC from 10 institutions were enrolled.

overall_design: DNA sequencing of 74 cancer-related genes was performed using FFPE tumor samples in three different laboratories with three different gene panels. A multidisciplinary advisory board prospectively recommended potential targeted treatments. The primary objective was to determine the success of matching somatic DNA alteration to an experimental drug/drug class.

first: Sonia

last: Pernas

first: Patricia

last: Villagrasa

first: Ana

last: Vivancos

first: Maurizio

last: Scaltriti

last: Rodón

first: Octavio

last: Burges

first: Paolo

last: Nuciforo

first: Laia

last: Paré

first: Marta

last: Dueñas

first: María

last: Vidal

first: Juan

middle: M

last: Cejalvo

first: Antonia

last: Perelló

first: Antonio

last: Llombart

first: Joan

last: Dorca

first: Álvaro

last: Montaño

first: Tomas

last: Pascual

first: Mafalda

last: Oliveira

first: Gloria

last: Ribas

first: Inmaculada

last: Rapado

first: Aleix

last: Prat

first: Eva

last: Ciruelos


title: MicroRNA profiling of psoriatic skin identifies 11 miRNAs associated with disease severity

city: Trondheim

first: Mari

last: Løset

state: Sør-trøndelag

address: Håkon Jarls gate 11

department: Department of Public Health and Nursing

country: Norway

institute: NTNU

summary: MicroRNAs (miRNAs) are small non-coding RNAs that have emerged as central regulators of gene expression and powerful biomarkers of disease. Much is yet unknown about their role in psoriasis pathology. To globally characterize the miRNAome of psoriatic skin, skin biopsies were collected from psoriatic cases (n = 75) and non-psoriatic controls (n = 57) and RNA sequenced. Count data was meta-analyzed with a previously published dataset (cases, n = 24, controls, n = 20), increasing the number of psoriatic cases four-fold from previously published studies. Differential gene expression analyses were performed comparing lesional psoriatic (PP), non-lesional psoriatic (PN) and control (NN) skin. Further, functional enrichment and cell-specific analyses were performed. Across all contrasts, we identified 439 significantly differentially expressed miRNAs (DEMs), of which 127 were novel for psoriasis and 11 were related to disease severity. Meta-analyses identified 20 DEMs between PN and NN, suggesting an inherent change in the constitution of all skin in psoriasis. By integrating the miRNA transcriptome with mRNA target interactions, we identified several functionally enriched terms, including ‘thyroid hormone signaling’, ‘insulin resistance’ and various infectious diseases. Cell specific expression analyses revealed that the upregulated DEMs were enriched in epithelial and immune cells. This study provides the most comprehensive overview of the miRNAome in psoriatic skin to date and identifies a miRNA signature related to psoriasis severity. Our results may represent molecular links between psoriasis and related comorbidities and have outlined potential directions for future functional studies to identify biomarkers and treatment targets.

overall_design:
Differential gene expression analyses were performed comparing lesional psoriatic (PP), non-lesional psoriatic (PN) and control (NN) skin.
NOTE from submitter: It is sensitive human sequencing data and the raw data can not be provided due to patient privacy concerns.

first: Åshild

middle: O

last: Solvin

first: Konika

last: Chawla

first: Lene

last: Olsen

first: Kjersti

last: Danielsen

first: Marita

last: Jenssen

first: Anne-Sofie

last: Furberg

first: Marit

last: Saunes

first: Kristian

last: Hveem

first: Pål

last: Sætrom


title: A stress-induced error prone 3' flap-based Okazaki fragment maturation pathway creates internal tandem duplications for cell survival

first: Xiwei

last: Wu


title: Canonical Wnt signaling exerts bidirectional control on choroid plexus epithelial development

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

summary: The choroid plexus (CP) secretes cerebrospinal fluid and is critical for the development and function of the brain. In the telencephalon, the CP epithelium (CPe) arises from the Wnt- and Bmp- expressing cortical hem. We examined the role of canonical Wnt signaling in CPe development and report that the mouse and human embryonic CPe expresses molecules in this pathway. Either loss of function or constitutive activation of β-catenin, a key mediator of canonical Wnt signaling, causes a profound disruption of mouse CPe development. Loss of β-catenin results in a dysmorphic CPe, while constitutive activation of β-catenin causes a loss of CPe identity and a transformation of this tissue to a hippocampal-like identity. Aspects of this phenomenon are recapitulated in human embryonic stem cell (hESC)-derived organoids. Our results indicate that canonical Wnt signaling is required in a precisely regulated manner for normal CP development in the mammalian brain.

overall_design: Wnt Gain of function Chorid plexus and hippocampus were dissected and processed for RNA seq

first: Orly

last: Reiner

first: Aditya

last: Khsirsagar

first: Arpan

last: Parichha


title: Genome-wide transcriptome analysis of KSHV long-term-infected endothelial (LTC) and parental uninfected TIVE cells [RNA-seq]

first: Soo Mi

last: Lee

summary:
Purpose: To characterize genome-wide mRNA expression profiles in the context of Kaposi’s sarcoma-associated herpesvirus (KSHV)-induced oncogenesis using isogenic cell lines for a Kaposi's sarcoma (KS) xenograft model: KSHV-infected human endothelial cells (LTC) that form tumors with properties closely resembling KS lesions in nude mice and uninfected parental (TIVE) cells.
Methods: mRNA expression profiles of LTC and TIVE cells were generated by deep sequencing using Illumina. In addition, mRNA profiles of LTC transfected with miR-127-3p or negative control (NC) mimic were generated by deep sequencing.
Results: We analyzed global transcriptome changes in LTC compared to TIVE cells and identified significant upregulation of many cell cycle and oncogenic signaling pathways. In addition, we assessed global transcriptome changes in LTC transfected with miR-127-3p mimic and found a significant decrease in the levels of E2F and Myc targets, indicating that miR-127-3p suppresses E2F and Myc transcriptional activities.
Conclusions: This study provides a detailed analysis of the cellular transcriptome in LTC and TIVE cells using RNA sequencing technology. Our study identifies miR-127-3p as a potent tumor suppressor miRNA that acts as a negative regulator of the CDK-RB-E2F cell cycle signaling pathway and the oncogenic Myc network in the context of KSHV oncogenesis and establishes a strong rationale for developing this miRNA as a therapeutic agent against KS.

overall_design: mRNA profiles of LTC and TIVE cells were generated by deep sequencing using Illumina. In addition, mRNA profiles of LTC treated with miR-127-3p or NC mimic were generated using deep RNA-seq.

first: Frank

last: Slack


title: Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer [ATAC-Seq]

status: Public on Oct 28 2021

city: Ann Arbor

first: Pushpinder

middle: Singh

last: Bawa

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: This study profiles chromatin accessibility, gene expresison, transcription factor binding, and three-dimensional DNA-DNA contact changes upon rapid SWI/SNF ATPase inactivation in prostate cancer cells. SWI/SNF ATPases activity was disabled using a novel PROTAC degrader compound targeting the SMARCA2, SMARCA4 and PBRM1 subunits of the SWI/SNF remodeling complex.

overall_design: Distinct prostate cancer cells were treated in vitro with the SMARCA2/4 degrader (AU-15330, abbreviated as AU) for indicated durations (ranging from 4 to 24h) and dosages (ranging from 0.1 - 1uM), and processed for multi-omic characterization.

first: Abhijit

last: Parolia

first: Lanbo

last: Xiao

first: Yuping

last: Zhang

first: Arul

last: Chinnaiyan


title: Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer


title: MARS Seq and total RNA seq data from human choroid plexus organoids

city: Rehovot

address: 234, Herzl Street,

department: Molecular Genetics

institute: Weizmann Institute of Science

summary: We analyze gene expression data of human choroid plexus organoid development

overall_design: Two developmental time points and two CHIR concentrations were examined

last: Kshirsagar

last: Paricha


title: Porphyromonas gingivalis alters gene expressions in the liver and brown adipose tissue, and induces gestational obesity and underweight of fetus in pregnant mice [BAT]

city: Tokyo

first: Sayaka

last: Katagiri

institute: Tokyo Medical and Dental University

summary: The aim of this study was to evaluate the effect of oral and intravenous administration of sonicated P.gingivalis to the liver and brown adipose tissue tissueof pregnant mice

overall_design: Intravenous injection and oral administration of P. gingivalis and saline was conducted three times a week during pregnancy, and the liver and brown adipose tissuewas measured on gestational day 18.


title: Porphyromonas gingivalis alters gene expressions in the liver and brown adipose tissue, and induces gestational obesity and underweight of fetus in pregnant mice [Liver]


title: Intracellular Staphylococcus aureus perturbs the host cell Ca2+-homeostasis to promote cell death

first: Martin

last: Fraunholz

address: Theodor-Boveri-Weg

department: Chair of Microbiology

institute: University of Wuerzburg

summary: The pathogen Staphylococcus aureus can invade and survive within human cells. There,  the intracellular bacterium induces host cell death, which may facilitate spread of infection and tissue destruction.  We here conducted a shRNA screen and infected the library of knock-down cells with S. aureus. We identified calcium signaling pathways to play a role in S. aureus invasion and cytotoxicity. For latter, the intracellular bacteria induce a cytoplasmic and mitochondrial Ca2+-overload, which results in host cell death.

overall_design: HeLa shRNA Screen

first: Kathrin

last: Stelzner

first: Ann-Cathrin

last: Winkler

first: Liang

last: Chunguang

first: Carsten

last: Ade

first: Thomas

last: Dandekar

last: Rudel


title: 3D Adipose Tissue Culture Links the Organotypic Microenvironment to Improved Adipogenesis

status: Public on Oct 27 2021

city: Solna

first: Joanne

last: Shen

state: Stockholm

address: Solnavägen 9 (Biomedicum)

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: Understanding the molecular underpinnings of adipogenesis is of fundamental importance for the development of novel therapeutics against metabolic disorders. However, translational approaches are hampered as current models do not accurately recapitulate adipogenesis. Here, a scaffold-free versatile 3D adipocyte culture platform with chemically defined conditions is presented in which primary human preadipocytes accurately recapitulate adipogenesis. Following differentiation, multi-omics profiling and functional tests demonstrate that 3D adipocyte cultures feature mature molecular and cellular phenotypes similar to freshly isolated mature adipocytes. Spheroids exhibit physiologically relevant gene expression signatures with 4704 differentially expressed genes compared to conventional 2D cultures (false discovery rate < 0.05), including the concerted expression of factors shaping the adipogenic niche. Furthermore, lipid profiles of >1000 lipid species closely resemble patterns of the corresponding isogenic mature adipocytes in vivo (R^2 = 0.97). Integration of multi-omics signatures with analyses of the activity profiles of 503 transcription factors using global promoter motif inference reveals a complex signaling network, involving YAP, Hedgehog, and TGFβ signaling, that links the organotypic microenvironment in 3D culture to the activation and reinforcement of PPARγ and CEBP activity resulting in improved adipogenesis.

overall_design: RNA sequencing by poly(A) capture was performed for adipocyte spheroid cultures developed from primary human adipocyte progenitors from the stromal vascular fraction and for corresponding freshly isolated mature adipocytes with seven donors in total.

first: Volker

last: Lauschke

middle: X

first: Morgane

last: Couchet

first: Jérémy

last: Dufau

first: Thais

last: deCastro Barbosa

first: Maximilian

last: Ulbrich

last: Helmstädter

first: Aurino

last: Kemas

first: Reza

last: ZandiShafagh

first: Marie-Adeline

last: Marques

first: Jacob

middle: B

last: Hansen

first: Niklas

last: Mejhert

first: Dominique

last: Langin

first: Mikael

last: Rydén


title: Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer [ChIP-Seq]

first: Pushpinder

last: Bawa

first: Abhijit

last: Parolia

first: Lanbo

last: Xiao

first: Yuping

last: Zhang

first: Arul

last: Chinnaiyan


title: Chromatin remodeler Brahma safeguards canalization in cardiac mesoderm differentiation [ChIP-seq]

city: San Francisco

first: Benoit

last: Bruneau

address: 1650 Owens Street

institute: Gladstone Institute of Cardiovascular Disease

summary: We used antibody against REST protein (Sigma, 17-10456) to chromatin IP  REST at D4 and D6 of  cardiac differentiation from WT and BRM KO cells.

overall_design: REST ChIPseq  were performed in WT and BRM KO cells during D4 and D6 stages of cardiac differentiation

middle: G

first: Swetansu

last: Hota


title: Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer [HiChIP-Seq]


title: Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer [RNA-Seq]


title: Comprehensive expression profiles of mRNAs, lncRNAs and miRNAs in Kashin-Beck Disease identified by RNA-sequencing

city: Xi′an

first: Xiaoxia

last: Dai

state: Shaanxi

address: No.76 Yanta West Road, Xi′an, Shaanxi 710061, China

institute: Xi′an Jiaotong University

summary: RNA‐seq technology to detect the differentially expressed mRNAs, lncRNAs and miRNAs in KBD patients. The database of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEEG) were employed to conduct functional annotation and pathway enriched analysis for differential expression.

overall_design: Examination of  differentially expressed mRNAs, lncRNAs and miRNAs in two different group.

first: Yu


title: Chromatin remodeler Brahma safeguards canalization in cardiac mesoderm differentiation [ATAC-seq]

summary: We performed ATAC-seq  on WT and BRM KO ESCs and D2 EBs in 3 biological replicates follwing Corces et al., 2017 paper.

overall_design: ATACSeq was performed for each samples with 50, 000 viable cells, libraries were sequenced with NEB nextSeq system using high throuput V2 150 cycle kit.


title: Chromatin remodeler Brahma safeguards canalization in cardiac mesoderm differentiation [scRNA-seq]

summary: We investigated the transcriptional consequences of BRM loss in mouse embryonic stem cells

overall_design: single cell RNAseq of WT and BRM KO cells in ESCs


title: WT and BRM KO scRNAseq at D10

summary:
We investigated the transcriptional consequences of BRM loss in cardiomyocytes
Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization How robust canalization is established or maintained is unclear. Here we show that deletion of the BRG1/BRM-associated factor (BAF) chromatin remodeling complex ATPase gene Brm (encoding Brahma) results in a radical identity switch during directed cardiogenesis of mouse embryonic stem cells (ESCs). Despite establishment of well-differentiated precardiac mesoderm, Brm-null cells subsequently shifted identities, predominantly becoming neural precursors, violating germ layer assignment. Trajectory inference showed sudden acquisition of non-mesodermal identity in Brm-null cells, consistent with a new transition state inducing a saddle-node bifurcation. Mechanistically, loss of Brm prevented de novo accessibility of cardiac enhancers while increasing expression of the neurogenic factor POU3F1 and preventing expression of the neural suppressor REST.  Brm mutant identity switch was overcome by increasing BMP4 levels during mesoderm induction, repressing Pou3f1 and re-establishing a cardiogenic chromatin landscape. Our results reveal BRM as a compensable safeguard for fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory that must be safeguarded.

overall_design: single cell RNAseq of WT and BRM KO cells during D10 of cardiac differentiation

middle: K


title: Single cell RNAseq of WT and BRG1 conditional KO at D4 and D10 of cardiac differentiation

summary:
We invetigated the transcriptional consequences of BRG1 loss at D4 and D10 stages of cardiac differentiation
Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization How robust canalization is established or maintained is unclear. Here we show that deletion of the BRG1/BRM-associated factor (BAF) chromatin remodeling complex ATPase gene Brm (encoding Brahma) results in a radical identity switch during directed cardiogenesis of mouse embryonic stem cells (ESCs). Despite establishment of well-differentiated precardiac mesoderm, Brm-null cells subsequently shifted identities, predominantly becoming neural precursors, violating germ layer assignment. Trajectory inference showed sudden acquisition of non-mesodermal identity in Brm-null cells, consistent with a new transition state inducing a saddle-node bifurcation. Mechanistically, loss of Brm prevented de novo accessibility of cardiac enhancers while increasing expression of the neurogenic factor POU3F1 and preventing expression of the neural suppressor REST.  Brm mutant identity switch was overcome by increasing BMP4 levels during mesoderm induction, repressing Pou3f1 and re-establishing a cardiogenic chromatin landscape. Our results reveal BRM as a compensable safeguard for fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory that must be safeguarded.

overall_design: single cell RNAseq of WT and BRG1 conditional KO cells during D4 and D10 of cardiac differentiation. The cells were treated with either tetrahydrofuran or with 200nM 4-hydroxytamoxifen in tatrahydrofuran at D2 to have WT and conditional BRG1 KO respectively.


title: 32 Kinase-Inhibitor Perturbed RNA sequencing of 11 cancer cell-lines

city: Athens

first: Eugene

last: Douglass

state: GA

address: 240 West Green Street

institute: University of Georgia

summary: The goal of the CTD2 Pancancer Drug Activity DREAM Challenge is to foster the development and benchmarking of algorithms to predict targets of chemotherapeutic compounds from post-treatment transcriptional data.  The drug perturbational profiles on 11 cell lines for 32 kinase inhibitors with well-established targets were provided to challenge participants, without revealing the identity of the drugs. These profiles were used to predict the drug-targets of the 32 anonymized drugs using publically available datasets for training.

overall_design: 1728 RNAseq profiles of a cell-line perturbed with 32 kinase inhibitors.  Cell-lines were treated at a 48-hour IC20 for each drug and RNA was collected at 24 hours to minimize cell-death.   Samples were prepared and sequences in batches of 96 that included 6 vehicle (DMSO) and 6 water controls.   2 replicates were taken for each drug-cell-line pair.

middle: F


title: Day4_Day6_Day10_normalBMP4_highBMP4_single_cell_RNAseq

summary:
We invetigated the transcriptional consequences of BRM loss at D4, D6 and D10 stages of cardiac differentiation both at normal BMP4 and high level of BMP4 inducing conditions
Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization How robust canalization is established or maintained is unclear. Here we show that deletion of the BRG1/BRM-associated factor (BAF) chromatin remodeling complex ATPase gene Brm (encoding Brahma) results in a radical identity switch during directed cardiogenesis of mouse embryonic stem cells (ESCs). Despite establishment of well-differentiated precardiac mesoderm, Brm-null cells subsequently shifted identities, predominantly becoming neural precursors, violating germ layer assignment. Trajectory inference showed sudden acquisition of non-mesodermal identity in Brm-null cells, consistent with a new transition state inducing a saddle-node bifurcation. Mechanistically, loss of Brm prevented de novo accessibility of cardiac enhancers while increasing expression of the neurogenic factor POU3F1 and preventing expression of the neural suppressor REST.  Brm mutant identity switch was overcome by increasing BMP4 levels during mesoderm induction, repressing Pou3f1 and re-establishing a cardiogenic chromatin landscape. Our results reveal BRM as a compensable safeguard for fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory that must be safeguarded.

overall_design: single cell RNAseq of WT and BRM KO cells during three different  stages (D4, D6, D10) of cardiac differentiation in presence of normal or high BMP4 inducing conditions


title: H3K27ac amd H3K27me3 ChIPseq of WT and BRM KO at D4, D6 and D10 of cardiac differentiation

summary:
Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization How robust canalization is established or maintained is unclear. Here we show that deletion of the BRG1/BRM-associated factor (BAF) chromatin remodeling complex ATPase gene Brm (encoding Brahma) results in a radical identity switch during directed cardiogenesis of mouse embryonic stem cells (ESCs). Despite establishment of well-differentiated precardiac mesoderm, Brm-null cells subsequently shifted identities, predominantly becoming neural precursors, violating germ layer assignment. Trajectory inference showed sudden acquisition of non-mesodermal identity in Brm-null cells, consistent with a new transition state inducing a saddle-node bifurcation. Mechanistically, loss of Brm prevented de novo accessibility of cardiac enhancers while increasing expression of the neurogenic factor POU3F1 and preventing expression of the neural suppressor REST.  Brm mutant identity switch was overcome by increasing BMP4 levels during mesoderm induction, repressing Pou3f1 and re-establishing a cardiogenic chromatin landscape. Our results reveal BRM as a compensable safeguard for fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory that must be safeguarded.
We invetigated H3K27ac and H3K27me3 marks in WT and BRM KO cells  at D4 and D10 stages of cardiac differentiation

overall_design: H3K27ac and H3K27me3 ChIPseq of WT and BRM KO cells during D4, D6 and D10 of cardiac differentiation.


title: Chromatin remodeler Brahma safeguards canalization in cardiac mesoderm differentiation [RNA-seq]

summary: We compared differential gene expression between WT and BRM KO  in mesoderm, cardiac precursors and cardiomyocytes

overall_design: 18 samples


title: Single-cell transcription mapping of neural subtype development in human spinal cord

city: Beijing

first: Xianming

last: Wu

state: Chaoyang District

address: Unit 2, No.1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: The spinal cord possesses precise neural circuitry to transmit messages between the brain and body. Detailed transcriptomic profiling of the developing human spinal cord has not been reported. Here, we performed single cell RNA sequencing of developing human spinal cord cells and compared these data with similar mouse spinal cord RNA sequencing datasets. The differentiation tendency of proliferative neural progenitor cells changed from neuronal to glial cells at gestational week (GW) 8 and we identified a diverse set of excitatory, inhibitory and motor neuron cell types. Human ventral neuronal differentiation occurred earlier than GW7, while DI4/5 interneurons are born between GW7–11. We identified glial cell molecular diversity and revealed that ependymal cell specification occurs before birth. We also demonstrate differences between human and mouse spinal cord, including unique cell subtypes, gene expression, neurotransmitter receptors, and glial differentiation timing. Our results offer insight into human spinal cord development.

overall_design: Here we performed both nucleus single-cell RNA sequencing and cellular single-cell RNA sequencing analyses of more than 880,000 cells isolated from the human spinal cord at gestation week 7 to 25.

first: Qi

first: Yongheng

last: Fan

first: Zhifeng

first: Peipei

last: Jiang

first: Yannan

last: Zhao

first: Yaming

last: Yang

first: Sufang

last: Han

first: Bing

last: Chen

first: Jin

first: Minghan

last: Sun

first: Guangfeng

first: Yali

last: hu

first: Jianwu


title: BRM-3xFLAG ChIPseq  at D4, D6 and D10 of cardiac differentiation

first: Benoit

summary:
We tagged native Brm gene at its c-terminal with 3XFLAG tags and carried FLAG ChIP followed by sequencing at D4, D6 and D10 of cardiac differentiation.
Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization How robust canalization is established or maintained is unclear. Here we show that deletion of the BRG1/BRM-associated factor (BAF) chromatin remodeling complex ATPase gene Brm (encoding Brahma) results in a radical identity switch during directed cardiogenesis of mouse embryonic stem cells (ESCs). Despite establishment of well-differentiated precardiac mesoderm, Brm-null cells subsequently shifted identities, predominantly becoming neural precursors, violating germ layer assignment. Trajectory inference showed sudden acquisition of non-mesodermal identity in Brm-null cells, consistent with a new transition state inducing a saddle-node bifurcation. Mechanistically, loss of Brm prevented de novo accessibility of cardiac enhancers while increasing expression of the neurogenic factor POU3F1 and preventing expression of the neural suppressor REST.  Brm mutant identity switch was overcome by increasing BMP4 levels during mesoderm induction, repressing Pou3f1 and re-establishing a cardiogenic chromatin landscape. Our results reveal BRM as a compensable safeguard for fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory that must be safeguarded.

overall_design: BRM-3xFLAG ChIPseq during D4, D6 and D10 of cardiac differentiation were performed with different condition of elutions (low SDS , highSDS with either elution with FLAG peptides or followed by 65C). We combined the peaks from each of these conditions at a particular stage of differentiation

first: Swetansu


title: ATACseq of WT and BRM KO cells at D4, D6 and D10 of cardiac differentiation

summary:
We performed ATAC-seq  on WT, BAF60c KO, BAF170 KO and BRM KO CPs and CMs in 2-5 biological replicates follwing Corces et al., 2017 paper.
Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization How robust canalization is established or maintained is unclear. Here we show that deletion of the BRG1/BRM-associated factor (BAF) chromatin remodeling complex ATPase gene Brm (encoding Brahma) results in a radical identity switch during directed cardiogenesis of mouse embryonic stem cells (ESCs). Despite establishment of well-differentiated precardiac mesoderm, Brm-null cells subsequently shifted identities, predominantly becoming neural precursors, violating germ layer assignment. Trajectory inference showed sudden acquisition of non-mesodermal identity in Brm-null cells, consistent with a new transition state inducing a saddle-node bifurcation. Mechanistically, loss of Brm prevented de novo accessibility of cardiac enhancers while increasing expression of the neurogenic factor POU3F1 and preventing expression of the neural suppressor REST.  Brm mutant identity switch was overcome by increasing BMP4 levels during mesoderm induction, repressing Pou3f1 and re-establishing a cardiogenic chromatin landscape. Our results reveal BRM as a compensable safeguard for fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory that must be safeguarded.

overall_design:
ATACSeq was performed for each samples with 50, 000 viable cells, libraries were sequenced with NEB nextSeq system using high throuput V2 150 cycle kit.
Please note that Average_*bw ws generated from all replicates and is linked to the corresponding *Rep1 sample records.


title: Integrative transcriptomic profiling of a mouse model of hypertension-accelerated diabetic kidney disease

status: Public on Oct 24 2021

city: Hørsholm

first: Jens Christian

last: Nielsen

address: Hørsholm Kongevej

institute: Gubra

summary:
Aim: To compare transcriptomic profiles of kidney cortex between healthy db/m mice, and mice with early stage diabetic kidney disease (uninephrectomized db/db injected with LacZAAV) and advanced stage diabetic kidney disease (uninephrectomized db/db mice injected with ReninAAV)
Methods: Bulk RNA sequecing using the Illumina NextSeq 500 platform.
Results: We identified 5,500 differentially expressed genes (DEGs) in db/db UNx LacZAVV mice compared to healthy controls, and  4,470 DEGs were identified in db/db UNx ReninAAV mice compared to healthy controls. Also, we showed in supplementery files that 3,039 DEGs were identified between db/db UNx LacZAAV mice and db/db UNx ReninAAV mice.
Conclusion: We identified several gene expression changes in our two animal models of diabetic kidney disease.

overall_design: Transcriptomic profiles of kidney cortex from healthy db/m mice, uninephrectomized db/db mice injected with a LacZ adeno-associated virus (AAV), and uninephrectomized db/db mice injected with AAV encoding renin to induce hypertension in the model.

first: Frederikke

last: Sembach

first: Helene

last: Ægidius

first: Lisbeth

middle: N

last: Fink

first: Thomas

last: Secher

first: Annemarie

last: Aarup

first: Jacob

last: Jelsing

first: Niels

last: Vrang

first: Bo

last: Feldt-Rasmussen

first: Kristoffer

last: Rigbolt

first: Jens

first: Mette

middle: V

last: Østergaard


title: The landscape of accessible chromatin in quiescent cardiac fibroblasts and cardiac fibroblasts activated after myocardial infarction

status: Public on Oct 21 2021

city: Norfolk

first: Sanjeeva

middle: Reddy

last: Dodlapati

state: VA

address: E&CS, odu

department: Computer Science

institute: old dominion university

summary: In this study, the gene expression profiling and genome-wide accessible chromatin mapping of mouse cardiac fibroblasts isolated from the uninjured myocardium and the infarct at multiple time points corresponding to different differentiation states were performed by RNA sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), respectively.

overall_design: The integrated analysis of ATAC-seq and RNA-seq data for the important role of chromatin remodeling in post-MI gene expression regulation in cardiac fibroblasts.

first: Xing

last: Fu

first: Jiangwen


title: Regional spinal cord gene expression profiling of adult astrocytes

status: Public on Oct 25 2021

city: Houston

first: Ekin

middle: Su

last: Akdemir

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: There is emerging evidence that astrocytes exhibit molecular and cellular heterogeneity; however, whether distinct subpopulations perform these diverse roles remains poorly defined. Previous studies used Aldhl1l1 as a bulk astrocyte marker.  Here we show that the Lunatic Fringe-GFP (Lfng-GFP) bacteria artificial chromosome mouse line specifically labels astrocyte populations within lamina III and IV of the dorsal spinal cord. We compared the transcriptional profile of Lfng-GFP+ astrocytes with Aldh1l1-GFP astrocytes to identify what is unique about the astrocyte population.

overall_design: FAC sorted astrocytes from the spinal cord were collected from Lfng-GFP and Aldh1l1-GFP mouse.

first: Brittney

last: Lozzi

first: Harmanci

last: Akdes

first: Benjamin

last: Deneen


title: Muscle biopsy RNA-seq from 5 week bedrest study volunteers

status: Public on Oct 20 2021

city: Richardson

first: Theodore

middle: John

last: Price

address: 800 W Campbell Rd

department: Behavioral and Brain Sciences

institute: The University of Texas at Dallas

summary: Sedentary lifestyle, chronic disease or microgravity can cause muscle deconditioning that then has an impact on other physiological systems. An example is the nervous system, which is adversely affected by decreased physical activity resulting in increased incidence of neurological problems such as chronic pain. We sought to better understand how this might occur by conducting RNA sequencing experiments on muscle biopsies from human volunteers in a 5-week bed-rest study with an exercise intervention arm. We also used a computational method for examining ligand-receptor interactions between muscle and human dorsal root ganglion (DRG) neurons, the latter of which play a key role in nociception and are generators of signals responsible for chronic pain. We identified 1352 differentially expressed genes (DEGs) in bed rest subjects without an exercise intervention but only 132 DEGs in subjects with the intervention. Thirty-six genes were shared between the exercise and no intervention groups. Among 591 upregulated muscle genes in the no intervention arm, 26 of these were ligands that have receptors that are expressed by human DRG neurons.

overall_design: Skeletal muscle biopsies were collected at the Institute for Exercise and Environmental Medicine. Methods and subject characteristics for this study have been previously described (Krainski et al., 2014). Subjects were healthy, nonsmoking, adults aged 20-54 years. Subjects were randomly assigned to one of two groups: bed rest only (BR-CON; n=9, 1 female), or bed rest with exercise countermeasure (BR-EX; n=16, 2 female). All subjects underwent-6-degree head down tilt bed rest for 35 consecutive days. BR-EX subjects received an exercise countermeasure consisting of rowing ergometer training on 6 days/week and biweekly resistance training for the duration of the bed rest period. A needle muscle biopsy of 300 mg tissue on average was obtained from the midbelly of the right (pre) and left (post) vastus lateralis muscle before and after the five week bed rest period (Krainski et al., 2014). Part of each biopsy was used for a previously published study (Krainski et al., 2014); at least 50 mg per sample remained for use in the present study.    Library Generation and Sequencing  Based on available muscle following initial ultrastructural and histochemical analysis (Krainski et al., 2014) biopsy samples from 13 subjects underwent RNA sequencing, consisting of all three female samples (1 BR-CON, 2 BR-EX), and ten male samples (5 BR-CON, 5 BR-EX; matched for age and exercise tolerance at baseline). Researchers performing sequencing and subsequent analyses were informed of subject pair matches and whether samples were from baseline or post-intervention, but were blinded to intervention received by individual subjects (i.e. the researchers did not know whether subjects were sedentary or exercised during bedrest until the first round of analysis was complete). Following RNA extraction (RNeasy Plus Universal Mini Kit, Qiagen), RNA yield was quantified using a Nanodrop system (ThermoFisher Scientific), and RNA quality assessed by fragment analyzer (Advanced Analytical Technologies). Stranded mRNA library preparation and sequencing were completed at the University of Texas at Dallas (UT Dallas), TX, USA. 76-bp, single-end sequencing of RNA-seq libraries was performed on the Illumina Hi-Seq sequencing platform.    Mapping and Quantification of RNA-seq data:   RNA-seq read files (fastq files) were checked for quality by FastQC (Babraham Bioinformatics) and read trimming was done based on Phred score and per-base nucleotide content, with trimmed, 60 bp reads from the 13 – 72 bp positions being used for downstream analysis. Trimmed reads were mapped to the reference transcriptome GENCODE v27 (Frankish et al., 2019), and its underlying reference genome GRCh38.p10 retaining only uniquely mapped reads by using the STAR (v2.7.3a) aligner (Dobin et al., 2013) with the following command line mapping parameters:    STAR --runThreadN 20 --runMode alignReads --genomeLoad NoSharedMemory -- outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMattrIHstart 0 --outSAMprimaryFlag AllBestScore --outBAMcompression-1 -- outBAMsortingThreadN 20 --outFilterType BySJout --outFilterMultimapNmax 10 -- outFilterMismatchNoverReadLmax 0.06 --twopassMode Basic --quantMode GeneCounts -- alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --alignIntronMax 1000000 -- alignMatesGapMax 1000000 --outFilterIntronMotifs RemoveNoncanonical -- outSAMstrandField intronMotif --outFilterScoreMinOverLread 0.3 -- outFilterMatchNminOverLread 0.3 --readFilesCommand zcat --alignSoftClipAtReferenceEnds No --alignEndsType EndToEnd  Relative abundance per sample (in Transcripts per Million or TPM) was calculated from the mapped reads using Stringtie (Pertea et al., 2015). Genes were filtered to only retain protein-coding genes and TPMs were re-normalized per sample to a million based only on the set of coding genes A fold-change ratio (post intervention / baseline) was calculated for each coding gene in every subject.

middle: J

last: Levine

first: Salman

last: Bhai

first: Pradipta

last: Ray

first: Amelia

last: McFarland