title: Autophagy facilitates age-related cell apoptosis - a new insight from senile cataract

city: Hangzhou

first: Wei

last: Han

state: Zhejiang

address: 88 Jiefang Road

department: Eye Center

institute: Second Affiliated Hospital, School of Medicine, Zhejiang University

summary: Age-related cell loss underpins many senescence-associated diseases. Senile cataract is a primary blindness-causing age-related ocular disease. Apoptosis of lens epithelial cells (LECs) is the common cellular basis of senile cataract resulted from prolonged exposure to oxidative stress, the mechanism of which remains elusive. Here we reported the concomitance of increased autophagy and apoptosis in the same LEC from senile cataract patients. Oxidative stress triggered autophagy preceded apoptosis, while blocking autophagy by ablation of Atg7 or Atg3 gene remarkably suppressed apoptosis in HLE-B3 cell line. We identified autophagy adaptor SQSTM1/p62 as the critical scaffold protein to sustain a pro-survival signaling PKCι-NF-κB cascades, which antagonized the pro-apoptotic signaling in LECs. Importantly, prolonged autophagy in human senescent LECs responding to oxidative stress induced extensive degradation of p62 protein and therefore facilitated apoptosis. Moreover, pharmacological inhibitor of autophagy, 3-MA, significantly rescued apoptosis of human senescent LECs challenged by oxidative stress. Collectively, our data demonstrated that hyperactivation of autophagy aggravates age-related apoptotic cell death via inhibiting the p62-PKCι-NF-κB pro-survival axis in human senescent LECs. This work expands the understanding of the etiology of senile cataract and provides insight for mechanisms of age-related cell death in senescence-associated diseases.

overall_design: wild type(WT) HLE-B3 or Atg7KO HLE-B3 cells treated with or without 200 μM H2O2 for 12 hrs(three biological replicates per group)


title: Transcriptome-wide expression analysis of pooled brain samples of patients with Alzheimer's disease compared to controls

status: Public on Jan 19 2022

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

type: Expression profiling by genome tiling array

summary:
Brain tissue of 3 patients with Alzheimer's disease (AD) and 3 healthy controls dying without any history of neurological or psychiatric illness was used. The diagnosis of AD was made on the basis of both clinical and neuropathological evidence according to the criteria of the International Working Group (IWG) for New Research Criteria for the diagnosis of AD in the revision of 2014 (IWG-2),16 the NIA-AA diagnostic criteria in the revision of 201117 and the NIA-AA guidelines for the neuropathological assessment of AD. Only cases with typical AD according to IWG-2 criteria were included.
Transcriptome-wide expression of AD and healthy control samples was assessed with Affymetrix Human Whole Genome Tiling Array 1.0 Set.

overall_design: Equal masses of total RNA derived from three patients with Alzheimer's disease and three control samples, respectively, were pooled. For each pool the Affymetrix Human Whole Genome Tiling Array 1.0 Set consisting of 14 arrays was used to assess transcriptome-wide expression.

first: Thomas

last: Arendt

first: Christian

last: Arnold

first: Jörg

last: Hackermüller

first: Friedemann

last: Horn

first: Peter

middle: F

last: Stadler

first: Uwe

last: Ueberham


title: Knocking down CAVIN1 in WPMY-1 normal prostate stromal cells

city: Baltimore

first: Jin-Yih

last: Low

state: MD

address: 1550 Orleans St

department: Radiation Oncology and Molecular Radiation Sciences

country: USA

institute: Johns Hopkins School of Medicine

type: Expression profiling by high throughput sequencing

summary: Lipid uptake occurs through caveolae, plasma membrane invaginations formed by caveolins (CAV) and caveolae-associated protein 1 (CAVIN1). Genetic alterations of CAV1N1 and CAV1 modify lipid metabolism and underpin lipodystrophy syndromes. Lipids contribute to tumorigenesis by providing fuel to cancer metabolism and supporting growth and signaling. Tumor stroma supports tumor proliferation, invasion and metastasis but how stromal lipids influence these processes remain to be defined. Here we show that stromal CAVIN1 regulates lipid abundance in the prostate cancer microenvironment and suppresses metastasis. We show that depletion of CAVIN1 in prostate stromal cells markedly reduces their lipid droplet accumulation and increases inflammation.

overall_design: A total of 6 samples were analyzed, 3 independent biological replicates from each group; shControl and shCAVIN1

first: Marikki

last: Laiho


title: Alzheimer-related genes show accelerated evolution

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

overall_design: Refer to individual Series


title: differential expression analysis in dermal fibroblasts of twins discordant for scleroderma

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary: comparison of the transcriptomic signature in healthy and SSc affected twins, including  by disease subtype (limited or diffuse)

overall_design: dermal fibroblasts were outgrown from skin biopsies of healthy and scleroderma affected twins, total RNA was isolated for RNAseq analysis,

first: Carol

last: Feghali-Bostwick

first: Ludivine

last: Renaud

first: E

middle: S

last: Hazard

first: Willian

middle: A

last: da Silveira

first: Robert

middle: C

last: Wilson


title: Motor Learning Leads to Modifications of Gene Expression Profile in M1 Astrocytes

city: Cambridge

first: Chloe

last: Delepine

state: Massachusetts

address: 43 vassar st

institute: MIT

summary: While motor cortex is crucial for the learning of precise and reliable movements, whether astrocytes contribute to its plasticity and function during motor learning is unknown. Here we report that primary motor cortex (M1) astrocytes in mice show gene expression changes associated with learning a cued lever-push task, including changes in glutamate transport genes

overall_design: Wild-type mice were water restricted and then trained to perform a cued lever push task (Peters et al., 2014) in which a lever press beyond a set threshold following trial start was rewarded with a water drop. We compared transcriptomic profiles of astrocytes isolated from the M1 cortex of mice trained for only three days (novice mice) or fully trained (expert mice) to the transcriptominc profile of untrained, naive mice.

first: Pierre

last: Gaudeaux

first: Mriganka

last: Sur


title: Mutant CHCHD10 causes an extensive metabolic rewiring that precedes OXPHOS dysfunction in a murine model of mitochondiral cardiomyopathy

status: Public on Jan 18 2022

city: New York

first: Nicole

last: Sayles

address: 407 East 61st Street

institute: Weill Cornell

summary: The goal of this study was to analyze the molecular changes that occur over the time course of disease in a mutant CHCHD10-related mouse model of primary mitochondrial cardiomyopathy.

overall_design:
Libraries were sequenced with single-end 86 bps on an Illumina NextSeq500 sequencer

>>>Raw data are unavailble for these samples because the fastq files were not provided by the core facility where the sequencing was performed.<<<

first: Giovanni

last: Manfredi


title: Expression data from cohort of remitted first-episode schizophrenia patients with less than 5 years of evolution

city: Barcelona

first: Sergi

last: Mas

state: BARCELONA

address: Casanova 143, Unidad Farmacologia, Facultad de Medicina, Barcelona

department: Pharmacology Unit

country: Spain

institute: University of Barcelona

summary: To explore the genomic architecture of schizophrenia symptomatology, we analysed blood co-expression modules, i.e. clusters of genes with highly correlated expression, in a cohort of remitted first-episode schizophrenia patients with less than 5 years of evolution, and their association with clinical data, including global functioning, clinical symptomatology and premorbid adjustment.

overall_design: 91 samples of RNA isolated from peripheral blood collected with PAXgene tubes were analyzed using  weighted gene co-expression network analysis

first: Mas

last: Sergi


title: MYCN mediates cysteine addiction and sensitizes to ferroptosis

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

department: Medical Faculty

institute: University Heidelberg

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Overexpression of MYC family members is linked to poor clinical outcome in many human cancers. These oncoproteins drive proliferation, alter metabolism, and mediate an antioxidant response to maintain tumor cell redox balance. However, to date, there are no effective inhibitors that specifically target MYC-amplified tumors. We demonstrate that MYCN-amplified, aggressive childhood neuroblastoma cells undergo ferroptotic cell death in vivo in the absence of intracellular cysteine, thus implicating MYCN as a predictive biomarker for ferroptosis sensitivity in neuroblastoma. Although cysteine is provided by both uptake from the microenvironment and MYCN-induced transsulfuration of methionine, glutathione levels remain low in these highly proliferative cancer cells due to concomitant cysteine utilization for protein and nucleotide synthesis. Consequently, MYCN-amplified neuroblastoma cells are highly susceptible to lipid peroxidation and ferroptosis, which must be counteracted by GPX4 activity. Pharmacological inhibition of both cystine uptake and transsulfuration combined with GPX4 inactivation resulted in tumor remission in an orthotopic MYCN-amplified neuroblastoma model. Our data show that MYCN-amplified neuroblastoma is sensitized to ferroptosis, which can be exploited therapeutically, by depleting the intracellular cysteine pool with concomitant GPX4 inactivation. These findings may help to develop novel clinical strategies to target MYCN-amplified tumors by inducing ferroptotic cell death.

overall_design: H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K36me3, and H3K9me3 histone modifications in 8 neuroblastoma cell-lines

first: Frank

last: Westermann


title: Next Generation Sequencing Facilitates Quantitative Analysis of Hepa1-6 cells treated with 50 μM TMAO  and 50ng/ml TNF-α Transcriptomes

city: Shanghai

first: Xingyu

last: Rong

address: Dongan Road 130

country: China

institute: Fudan university

summary: Liver cancer has a high mortality rate. Chronic inflammation is one of the leading causes of hepatocellular carcinoma. Recent studies suggested high levels of trimethylamine N-oxide (TMAO) may correlate with increased risk of inflammatory-induced liver cancer. However, the mechanisms by which TMAO promotes liver cancer remain elusive. Here, we established a model of inflammatory-induced liver cancer by treating Hepa1-6 cells with TNF-α. TMAO synergistically increased the proliferation, migration and invasion of Hepa1-6 cells in the presence of TNF-α. We conducted bulk RNA-Seq of the TMAO-treated cell model of inflammatory Hepatocellular carcinoma (HCC)

overall_design: mRNA profiles of Hepa1-6 cells treated with 50 μM TMAO  and 50ng/ml TNF-α

first: Chao

last: Zhao

first: Yonglin

last: Wu

first: Miaomiao

last: Pan


title: EZH2 and H3K27ac ChIPseq of SKOV3(AA) and SKOV3(CC)

city: Tianjin

first: Guoli

last: Li

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

summary: A work for studying the effect of rs1192691 on repressing VAV3 enhancer activity via affecting EZH2 enrichment at the SNP location.

first: Zhe

last: Liu


title: H3K27ac, H3K4me3, H3K27me3 and H3K9me3 ChIPseq of SKOV3(AA) and SKOV3(CC)

summary: To study the effect of rs1192691 on histone modifications, we performed H3K27ac, H3K4me3, H3K27me3 and H3K9me3 in SKOV3(AA) and SKOV3(CC).


title: 4Cseq of OVCA432

summary: To examine target genes that interact with different alleles of rs1192691 in a heterozygous cell line OVCA432 (A/C).

overall_design: 4Cseq of OVCA432


title: RNAseq of SKOV3(AA) and SKOV3(CC)

summary: To study the effect of rs1192691 on ovarian cancer cells, we generated SKOV3(CC) from SKOV3(A/A) using CRISPR/Cas9 technology and performed RNA-seq.

overall_design: mRNA profiles of SKOV3(AA) and SKOV3(CC)


title: ATRX loss in glioma results in epigenetic dysregulation of cell cycle phase transition [scRNA-seq]

city: Ann Abor

first: Maureen

last: Sartor

address: 100 Washtenaw Ave.

institute: University of Michigan

summary: ATRX, a chromatin remodeler protein, is recurrently mutated in H3F3A-mutant pediatric glioblastoma (GBM) and IDH-mutant grade 2/3 adult glioma. Previous work has shown that ATRX-deficient GBM cells show enhanced sensitivity to irradiation, but the etiology remains unclear. We found that ATRX binds regulatory elements of cell cycle phase transition genes in GBM cells, and there is a marked reduction in Checkpoint Kinase 1 (CHEK1) expression with ATRX loss, leading to early release of G2/M entry after irradiation. ATRX-deficient cells exhibit enhanced activation of master cell cycle regulator ATM with irradiation. Mice intra-cranially implanted with ATRX-deficient GBM cells demonstrate doubling of median survival compared to the ATRX-Wild Type controls when treated with ATM inhibitor AZD0156 and radiation.  This study demonstrates that ATRX-deficient high-grade gliomas (HGGs) display epigenetic dysregulation of cell cycle phase transitions, which opens a new window for therapies targeting this unique phenotype.

overall_design: scRNA-seq data comparison between one ATRX-KO  U251  sample and one ATRX-WT U251 sample

first: Tingting

last: Qin

first: Brendan

last: Mullan

last: Koschmann


title: Transcriptome profiles of B cells from MS patients and healthy controls

city: San Francisco

first: Qin

last: Ma

state: CA

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

summary: How epigenetic changes contribute to MS pathogenesis is still poorly understood. Therefore, we conducted a comprehensive analysis of genome-wide DNA methylation patterns in four immune cell populations isolated from MS patients at clinical disease onset. We also performed parallel transcriptome analysis in B cells to better understand the functional consequences of the DNA methylation changes in MS.

overall_design: Four immune cell populations, namely CD4+ and CD8+T cells, CD14+ monocytes and CD19+ B cells, were FACS sorted from PBMC samples from a cohort of MS and HC subjects. The total RNA from B cell fractions were used for mRNA-seq.


title: YTHDF1-N6-methyladenosine-ARHGEF2 axis  promoted colorectal tumorigenesis and metastasis

city: Toronto

first: Housheng

middle: Hansen

last: He

state: ON

address: 101 College St

country: Canada

institute: UHN

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) governs the fate of RNAs through m6A readers. Colorectal cancer (CRC) exhibits aberrant m6A modifications and expression of m6A regulators. However, little is known about how m6A readers interpret oncogenic m6A methylome for malignant transformation. m6A reader YTHDF1 was overexpressed by copy number gain/amplification in majority of CRCs. YTHDF1 high expression and CNVs predict increased risk of CRC relapse. Transcriptome profiles of YTHDF1-high tumors exhibit highly metastatic features. YTHDF1 promoted CRC tumor cell and organoid proliferation and enhanced metastasis. Ythdf1 knockout dampened tumor growth in carcinogen-induced CRC model. Through multiomic integration, RhoA activator ARHGEF2 was characterized as the key functional YTHDF1 target based on its m6A and YTHDF1-binding signal, translation efficiency changes, protein correlations with YTHDF1 in clinical samples, and disrupted RhoA features by YTHDF1 knockdown. Moreover, YTHDF1-ARHGEF2 co-regulation was observed in YTHDF1-overexpressing metastatic sites and carcinogen-induced Ythdf1-null CRC tumors. ARHGEF2 overexpression significantly rescued RhoA signaling, tumor cell survival and invasiveness impaired by YTHDF1 knockdown both in vitro and in vivo, further confirming the essential function of ARHGEF2.

overall_design: Multiomic analysis including RNA-seq,  m6A MeRIP-seq, YTHDF1 RIP-seq and quantitative proteomics was performed to key YTHDF1 targets responsible for YTHDF1-mediated transformation.

middle: H

first: Shiyan

last: Wang

first: Yong

last: Zeng


title: ATRX loss in glioma results in epigenetic dysregulation of cell cycle phase transition

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: ATRX loss in glioma results in epigenetic dysregulation of cell cycle phase transition [RNA-seq]

overall_design: 3 biological replicates of ATRX-KO mouse GBM cells were compared to 3 biological replicates of ATRX-WT mouse GBM cell lines


title: Targeting transcription-replication conflicts is an effective therapeutic principle for MYCN-driven neuroblastoma [ChIP-seq_SHEP]

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary:
Targeting the function of MYC proteins for therapy is a major challenge in tumor biology. MYC proteins are transcription factors that can globally release RNA polymerase II (RNAPII) from core promoters. In neuroblastoma, the MYC paralogue, MYCN, and the Aurora-A kinase form a complex during S phase that stabilizes MYCN and enhances Aurora-A kinase activity. Here we show that Aurora-A phosphorylates histone H3 at serine 10 in S phase and suppresses transcription-dependent R-loop formation.
Inhibition of Aurora-A causes global stalling of RNAPII at pause sites and exon/intron boundaries and induces transcription/replication conflicts, activating the Ataxia telangiectasia and Rad3 related (ATR) kinase. Activation of ATR is required to prevent the accumulation of double-strand breaks. In genetically-engineered mice with MYCN-driven neuroblastoma, combined inhibition of Aurora-A and ATR induces rampant tumor-specific apoptosis and tumor regression, leading to permanent eradication of tumors in a subset of mice.
The therapeutic efficacy is not only due to tumor cell-intrinsic mechanisms, but also engages the host immune system for tumor eradication. Since stabilization of MYCN promotes promoter-proximal transcription termination, we propose that MYCN/Aurora-A complex formation enables tumor cells to prevent transcription-replication conflicts and that targeting this mechanism is an effective therapy for MYCN-driven neuroblastoma.

overall_design:
double thymidin block of SH-EP or  SH-EP MYCN wt or SH-EP MYCN T58A cells. Release, Treatment and harvest after 4 h (S)

A combined Input.fastq file was generated by merging the files GB539_INPUT_SHEPMYCNWT_DMSO.fastq, GB539_INPUT_SHEPMYCNWT_MLN.fastq, GB539_INPUT_SHEP_DMSO.fastq, GB539_INPUT_SHEP_MLN.fastq, GB539_INPUT_SHEPMYCNT58A_DMSO.fastq & GB539_INPUT_SHEPMYCNT58A_MLN.fastq.
The file 'Input.fastq' was then randomly subsampled to 15471049, 19654728, and 19657956 reads, resulting in the files Input_sorted15471049.bedgraph, Input_sorted19654728.bedgraph and Input_sorted19657956.bedgraph, which were used as input control for the H3S10P-, H3.3- and H3-ChIPseq samples, respectively.

first: Gabriele

last: Büchel


title: Genome-wide analysis of replication timing in ESC and 2CLC during 2CLC emergence [transitional]

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

summary: The timing of DNA replication is an important developmentally regulated regional property that is correlated with gene expression, chromatin state, GC content, subnuclear structure. These correlations reflect the variable accessibility of origins to a limited pool of initiation factors within different context, and the extent to which changes in replication timing occur during differentiation. Therefore, temporal order of genome replication could be sufficient to identify the cell type. A lot of studies for characterizing DNA replication have been done using many different types of cells, however, the pattern of it in the totipotent cells is still entirely unknown. In this study, we try to understand the molecular basis underlying totipotency by identifying specific DNA replication features found exclusively in totipotent cells.

overall_design: Examination of replication timing in ESC and emerging 2-cell-like cell (2CLC).

first: T

last: Nakatani

first: F

first: V

last: Rechem

first: D

last: Chakraborty

first: R

middle: J

last: Whetstine

last: Sadreyev

first: M

middle: E

last: Torres-Padilla


title: Genome-wide analysis of replication timing in ESC and 2CLC [stable]

summary: The timing of DNA replication is an important developmentally regulated regional property that is correlated with gene expression, chromatin state, GC content, subnuclear structure. These correlations reflect the variable accessibility of origins to a limited pool of initiation factors within different context, and the extent to which changes in replication timing occur during differentiation. Therefore, temporal order of genome replication could be sufficient to identify the cell type. Several studies for characterizing DNA replication have been done using many different types of cells, however, the pattern of it in the totipotent cells is still entirely unknown. In this study, we try to understand the molecular basis underlying totipotency by identifying specific DNA replication features found exclusively in totipotent cells.

overall_design: Examination of replication timing in ESC and 2-cell-like cell (2CLC).


title: DNA methylation profiles of four immune cell types from MS patients and healthy controls

overall_design: Four immune cell populations, namely CD4+ and CD8+T cells, CD14+ monocytes and CD19+ B cells, were FACS sorted from PBMC samples from a cohort of MS and HC subjects. Cell were then used for DNA extraction and DNA methylation profiling by bisulfite sequencing (BS-seq). The total RNA from B cell fractions were used for mRNA-seq.


title: Specific hypomethylation programs underpin B cell activation in early multiple sclerosis

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

overall_design: Refer to individual Series


title: Multi-omic analysis identifies APC/C-mediated degradation of SMN in neurons

first: Amanda

middle: J.

last: Guise

state: MA

address: 3 Blackfan Circle

department: F.M. Kirby Center for Neurobiology

institute: Boston Children's Hospital & Harvard Medical School

summary: Spinal muscular atrophy (SMA) due to loss-of-function of SMN protein is associated with severe loss of voluntary muscle control and is a leading inherited cause of infant mortality. SMA treatments will benefit from in-depth knowledge of functional pathways disrupted in disease and identification of SMN modulators. Here, we present a comprehensive temporal profile of proteogenomic expression patterns in developing mouse spinal cords (Δ7 model), alongside endpoint analyses of human spinal and ventral root tissues in SMA disease, identifying targets for assessing disease progression and treatment response. SMA disease results in development-associated deficiencies in transcription, translation initiation, intracellular transport, and protein folding, and diminished RNA translation efficiency for proteins important in axon development/myelination. The broad impact of SMN deficiency prompted the search for co-regulated proteins that modulate SMN protein levels, resulting in identification of the anaphase promoting complex/cyclosome (APC/C) E3 ubiquitin ligase as a potential modulator of SMN protein stability. Functional studies of APC/C showed that both SMN and HuD are specific interactors of the APC/C in neurons and that selective APC/C inhibition significantly limited SMN and HuD degradation. Finally, we demonstrate that APC/C inhibition rescues motor axon defects characteristic of SMA in a zebrafish model of SMA disease.

overall_design: Total RNA was extracted from whole P2, P6, and P10 homozygote (SMA) or heterozygote (control) murine spinal cords (SMNΔ7 mouse model) for RNAseq comparison.

first: Ruchi

last: Chauhan

first: Hao

last: Le

first: Ivette

last: Zelaya

first: Anaïs

last: Meziani

first: David

last: Valdivia

first: E

last: Brandimarte

first: Bikem

last: Akten

first: Constantin

middle: O

last: d’Ydewalle

first: Hendrik

last: Wesseling

first: Bin

last: Cai

first: Shaojun

last: Tang

first: Thomas

last: Crawford

first: Zhigang

first: Randall

middle: W

last: King

first: Lee

middle: L

last: Rubin

first: Cathleen

middle: M

last: Lutz

first: Giovanni

last: Coppola

last: Hemberg

first: Christine

last: Beattie

first: Charlotte

last: Sumner

first: Hanno

last: Steen

first: Judith


title: Transient transcriptome sequencing (TT-Seq) and 5'P-Seq of ATP-analog sensitive Kin28 budding yeast

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

summary: Inhibition of Kin28/CDK7, the kinase subunit of TFIIH, leads to defects in transcription of protein-coding genes. Despite a severe reduction in nascent RNA synthesis, the majority of mRNAs retain their steady-state level upon inhibition. In this study, we examined the determinants of mRNA stability in cells experiencing transcriptional crisis via irreversible chemical inhibition of Kin28. We discovered that the inhibited Kin28 transcriptome resembles the transcriptome of cells treated with an inhibitor of protein synthesis. Indeed, inhibition of Kin28 induces a coordinated decrease in translation and an increase in P-body formation. Unexpectedly, integrated stress response effectors do not trigger the observed proteostasis and ribostasis. Rather, mRNAs that are buffered from degradation display a preference for Ski2 over Nab2 and are differentially sensitive to the 5′-exonuclease Xrn1. These findings reveal that a nuclear kinase, well-known for its role in early stages of RNA synthesis, orchestrates multiple molecular processes in different cellular compartments.

overall_design: To study the state of transcription and translation in inhibited Kin28 cells, we utilized TT-Seq and 5'P-Seq. Transient transcriptome sequencing (TT-Seq), an optimized RNA-Seq method that combines 4-thiouracil labeling and biotinylation with fragmentation, was utilized because it reduces the 5′ bias in reads during capture of nascent transcripts (Schwalb et al., 2016). We also improved the efficiency of recovering labeled transcripts by utilizing a more reactive biotinylation reagent, MTSEA-biotin (Duffy et al., 2015). 5′P-Seq is an RNA-Seq method that selectively captures RNA with a 5′-monophosphate terminus. Ribosome dynamics can be captured by extracting 5′P-Seq signal that displays a 3-nt periodicity in open reading frames (ORFs) (Pelechano et al., 2015).

middle: Z

first: Sandra

last: Tseng


title: Next-generation sequencing facilitates quantitative analysis of mouse triple negative breast cancer cells treated with glucose-like oxidase and GSH-consuming nanoenzyme systems

status: Public on Jan 17 2022

city: chongqing

first: ke

last: li

address: shazheng street 174

institute: chongqing university

summary: To determine the effects of glucose-like oxidase and GSH-consumed nanoenzymes on regulatory genes and molecular pathways of mouse triple negative breast cancer cells (4T1 cells), we studied the RNA sequences of 4T1 cells treated with medium (control), Cu-TCPP (Fe)-PEG(Cu-TCPP) and Au/Cu-TCPP (Fe)-PEG(Au-TCPP).

overall_design: mRNA profiles of 4T1 cells treated by medium, Cu-TCPP and Au-TCPP(24 h) were generated by deeping sequencing, using Illumina HiSeq2000.

first: Kaiyong

first: Ke

last: Li


title: Characterization of molecular changes associated with complement factor B deficiency in the mouse auditory nerve

first: Jeremy

last: Barth

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Overall goal of the study is to investigate the role of the complement system in auditory nerve development and hearing

overall_design: Three biological replicates of the auditory nerve from young adult (1.5-2.5 months) wildtype and complement factor B knockout mice were compared by RNAseq analysis

first: Hainan

last: Lang


title: Epigenome-wide DNA methylation profiling in colorectal cancer and normal adjacent colon using Infinium Human Methylation 450K

city: Cheras

first: Nurul Syakima

last: Ab Mutalib

state: Kuala Lumpur

address: Jalan Yaacob Latiff

department: UKM Medical Molecular Biology Institute

country: Malaysia

institute: Universiti Kebangsaan Malaysia

type: Methylation profiling by genome tiling array

summary: Genome-wide methylation profilling on 54 paired of CRCs and their adjacent normal tissues using the Infinium Human Methylation 450K beadchip, which covers 485,577 CpG di-nucleotide sites distributed over the whole genome

overall_design: Bisulphite converted DNA from the 108 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Rashidah

last: Baharudin

first: Muhiddin

last: Ishak

first: Azliana

last: Yusof

first: Sazuita

last: Saidin

first: Saiful-Effendi

last: Syafruddin

first: Wan-Fahmi

last: Wan Mohamad Nazarie

first: Learn-Han

last: Lee

first: Nurul-Syakima


title: Characterization of sequence determinants of enhancer function using natural genetic variation [Hi-ChIP]

city: Los Angeles

first: Marty

middle: G

last: Yang

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

summary: Sequence variation in enhancers, a class of cis-regulatory elements that control cell type-specific gene transcription, contributes significantly to phenotypic variation within human populations. Enhancers are short DNA sequences (∼200 bp) composed of multiple binding sites (4-10 bp) for transcription factors (TFs). The transcriptional regulatory activity of an enhancer is encoded by the type, number, and distribution of TF binding sites that it contains. However, the sequence determinants of TF binding to enhancers and the relationship between TF binding and enhancer activity are complex, and thus it remains difficult to predict the effect of any given sequence variant on enhancer function. Here, we generate allele-specific maps of TF binding and enhancer activity in fibroblasts from a panel of F1-hybrid mice that have a high frequency of sequence variants. We identified thousands of enhancers that exhibit differences in TF binding and/or activity between alleles and use these data to define features of sequence variants that are most likely to impact enhancer function. Our data demonstrate a critical role for AP-1 TFs at many fibroblast enhancers, reveal a hierarchical relationship between AP-1 and TEAD TF binding at enhancers, and delineate the nature of sequence variants that contribute to AP-1 TF binding. These data represent one of the most comprehensive assessments to date of the impact of sequence variation on enhancer function in chromatin, with implications for identifying functional cis-regulatory variation in human populations.

overall_design: Genome-wide maps of H3K27ac, H3K4me1/2, H3K4me3, AP-1, CTCF, TEAD, chromatin accessibility, chromatin-associated RNA-seq in starved and serum-stimulated primary mouse embryonic fibroblasts from F1-hybrid mice.

first: Emi

last: Ling

first: Michael

last: Greenberg

first: Thomas

last: Vierbuchen


title: Characterization of sequence determinants of enhancer function using natural genetic variation [ATAC-seq]


title: Characterization of sequence determinants of enhancer function using natural genetic variation [CUT&RUN]


title: HOXA13 Cut & Run of Human Melanoma Cells

first: Joshua

last: Weiss

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: The goal of the experiment was to determine HOXA13 binding loci in human melanoma cells to infer downstream targets of a HOXA13 positional program.

overall_design: We performed Cut&Run for the melanoma cell lines SKME-1088, SKMEL-1176, and SKME-1206. For Cut&Run we used 100’000 cells per condition and it was performed as described in110. We used antibodies against HOXA13 (Invitrogen, #PA5-76440, 1:100), H3K27ac (Active Motiv, #39034, 1:100), IgG (abcam, #ab6709, 1:100) and we added a “no antibody” condition as additional negative control.

first: Arianna

last: Baggiolini

first: Richard

last: Koche

last: White


title: Interrogation of H3.3K27me3 in mESC pluripotency and differentiation through ChIP-seq, RNA-seq, and H3.3K27A RNA-seq analysis

city: Philadelphia

first: Peder

last: Lund

state: PA

address: 3400 Civic Center Blvd, Smilow 9-176

institute: University of Pennsylvania

summary: Histone variant H3.3 is a critical regulator of cell differentiation and development. Likewise, methylation on lysine 27 of the canonical histone H3 (H3K27me3) has been previously characterized in development. However, the effect of methylation on lysine 27 on the variant histone H3.3 remains unclear. By applying proteomics and genomics techniques, we investigate the role of lysine 27 tri-methylation specifically on the histone variant H3.3 (H3.3K27me3) in the context of mouse embryonic stem cell pluripotency and differentiation as a model system for development. Using a custom-made antibody, we identify through ChIP-seq experiments and corresponding RNA-seq experiments that H3.3K27me3 does not show the same strong negative correlation with gene expression as is observed for canonical H3K27me3, nor the same strong positive correlation with gene expression as observed for H3.3. However, a unique enrichment was detected of H3.3K27me3 at lineage-specific genes, such as olfactory receptor genes, and at binding motifs for the transcription factors FOXJ2/3. REST, a predicted FOXJ2/3 target that acts as a transcriptional repressor of terminal neuronal genes, was identified with H3.3K27me3 at its promoter region. H3.3K27A mutant cells confirmed an upregulation of FOXJ2/3 targets upon the loss of methylation at H3.3K27 both at the transcriptomic and proteomic level. Thus, while canonical H3K27me3 has been characterized to regulate the expression of transcription factors that play a general role in differentiation, our work suggests H3.3K27me3 is essential for regulating distinct terminal differentiation genes.

overall_design: Mouse embryonic stem cells (mESC) were grown in pluripotency with leukemia inhibitory factor (LIF), and then differentiated to embryoid bodies upon removal of LIF with the addition of 10 uM of retinoic acid (RA). Cells were collected at day 0 (pluripotency), and day 6 of differentiation. ChIP-seq was performed on sonicated chromatin extracted from the nuclei of previously frozen cell pellets that had been cross-linked with formaldehyde (in biological duplicates for each condition). For ChIP-seq, the pooled sample was sequenced three times to ensure enough total reads for analysis. RNA-seq was performed on polyA-enriched RNA in duplicate for each condition, with an additional day 3 of differentiation time point.  The H3.3K27A and H3.3A knockout cells were generated using the CRISPR/Cas9 system. For the H3.3K27A mutant cells analysis by RNA-seq, cells were grown the same and samples were prepared the same as described above, with the only difference being that only day 0 and day 6 were collected for analysis.

first: Yekaterina

last: Kori

first: Benjamin

last: Garcia


title: DJ-1 depletion prevents immunoaging in T-cell compartments

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Decline in immune function during aging increases susceptibility to different aging related diseases. However, the underlying molecular mechanisms, especially the genetic factors contributing to imbalance of naïve/memory T-cell subpopulations, still remain largely elusive. Here we show that loss of DJ-1 encoded by PARK7/DJ-1, causing early-onset familial Parkinson’s disease (PD), unexpectedly diminished signs of immunoaging in T-cell compartments of both human and mice. Compared with two gender-matched unaffected siblings of similar ages, the index PD patient with DJ-1 deficiency showed a decline in many critical immunoaging features, including almost doubled non-senescent T cells. The observation was further consolidated by the results in 45-week-old DJ-1 knockout mice. Our data demonstrated that DJ-1 regulates several immunoaging features via hematopoietic-intrinsic and naïve-CD8-intrinsic mechanisms. Mechanistically, DJ-1 depletion reduced oxidative phosphorylation (OXPHOS) and impaired TCR sensitivity in naïve CD8 T cells at a young age, accumulatively leading to a reduced aging process in T-cell compartments in older mice. Our finding suggests an unrecognized critical role of DJ-1 in regulating immunoaging, discovering a potent target to interfere with immunoaging- and aging-associated diseases.

overall_design: We analyzed CD4 Tconv cells (CD4+CD25- cells) isolated from the spleen of aged DJ-1 knockout (KO) mice vs. age- and gender-matched WT littermates (3 WT, 3 KO) using the Affymetrix Mouse Gene 2.0 ST Array. RNA samples of CD4+CD25- Tconv cells sorted from ~45-weeks old DJ-1-/- mice and age- and gender-matched DJ-1+/+ littermates using BD FACSAria III, were analysed at EMBL Genomics Core Facility (Heidelberg, Germany). Array data was processed by Affymetrix Expression Console v1.4 using Exon-level analysis. No technical replicates were induced.

first: Ni

last: Zeng

first: Christophe

last: Capelle

first: Rudi

last: Balling

first: Markus

last: Ollert

middle: Q


title: Human CD8 T cell transcriptomic analysis from the three male siblings of similar ages with DJ-1 loss-of-function or heterozygous mutations

overall_design: The family with Parkinson's disease (PD) carrying the c.192G>C mutation in the DJ-1 gene has been already described elsewhere and written informed consent for all participating individuals was obtained. The index patient (56 years) carries the homozygous c.192G>C mutation.  The two unaffected siblings (60 and 63 years) are both heterozygous carriers of the c.192G>C mutation and were devoid of any clinical sign of PD at the recent neurological examination, as expected for this autosomal-recessively inherited condition. The experimental investigators were blind to the genotype of the three siblings until the flow cytometry analysis was complete. Fresh PBMCs of three sibilings were stained with anti-CD4 FITC (BD, 555346, also refer to Supplementary Table 4), anti-CD8 BV605 (BioLegend, 301040) and LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit (ThermoFischer Scientific, L34976) for 30 min at 4 °C. Stained cells were washed with FACS buffer (PBS + 2%FBS) and total CD8 T cells were sorted using the BD Aria III. We analyzed total CD8 T cells using the Affymetrix Human Gene 2.0 ST Array. RNA samples were analysed at EMBL Genomics core facilities (Heidelberg. Germany). Array data was processed by Affymetrix Expression Console v1.4 using Exon-level analysis. No technical replicates were performed.


title: Alpha 4 integrin deficiency in human CD34+ cells engenders a precocious erythroid differentiation ,but inhibits enucleation.

city: Seattle

first: Jennifer

last: Cherone

state: WA

address: 2211 Elliott Ave Ste 600

institute: Altius Institute for Biomedical Sci

summary: The functional impact of integrin expression in erythropoiesis has been previously emphasized through   its decisive influence on erythroid cell-microenvironmental (matrix and cellular) interactions especially under conditions of stress. Beyond that  in several in vitro studies the relationship between the two erythroid integrins, a4 and a5, has been incongruous in terms of a proliferative support, either synergistic or antagonistic, whereas a dominant influence of a4 integrin on terminal erythropoiesis in vitro and in vivo has been consistently emphasized. However, the specific cellular and molecular details  of this effect have not been defined, especially for human cells.  In the present study we have cultured human CD34+ progenitor cells with induced deficiency of a4 integrin (shRNAa4) under erythroid differentiation conditions, in which expanded erythroid progenitor cells are directed to terminal  erythroid maturation stages in the absence of any microenvironmental influence. Our data documented that early proliferative expansion in cells lacking a4 expression is significantly limited, but, although erythroid differentiation can proceed normally to terminal stages, their enucleation is drastically impaired. This novel aspect of a4 integrin participation in the  enucleation process in vitro resonates on the lack of in vivo enucleation of primitive erythroid cells lacking any integrin expression but affecting  adult cells only under stress conditions.

overall_design: CD34+ hematopoietic progenitor cells from three different donors were treated with shRNA specific to either a4 integrin, b1 integrin, a scrambled control, or no virus as an additional control. All samples were harvested at the same day of erythroid culture in biological triplicate. In total, 12 samples were processed: 3 shRNA for a4 + 3 shRNA for b1 + 3 shRNA for scrambled control + 3 WT no transduction.

first: Tatiana

last: Ulyanova

first: Pavel

last: Sova

first: Thalia

last: Papayannopoulou


title: scRNA-seq analysis of cultured bovine satellite cells

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: 3130 Litton Reaves Hall

department: Animal and Poultry Sciences

institute: Virginia Polytechnic Institute and State University

summary: In this study we analyzed the bovine satellite cells with single-cell RNA sequencing (scRNA-seq). We isolated muscle satellite cells from a male calf, cultured them in growth medium for a week, and then constructed two scRNA-seq libraries from them using the 10x Genomics platform. Next generation sequencing yielded 860 million reads. Cell calling analyses revealed that these reads represented 15 cell clusters that differed in gene expression profile from a total of 19,096 individual cells.

overall_design: Two scRNA-seq libraries were constructed and sequenced from the same cells.


title: Genome-wide expression profiling of CRC cells (SW620) upon TIMELESS loss expression and/or ZEB1 down regulation

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary: Colorectal cancer (CRC) is the third most common cancer worldwide. Recent studies pinpointed TIMELESS (TIM) to be crucially involved in replication protection/genomic stability, DNA damage response (DDR) and coordination of mitotic kinase activation with DNA replication termination. Here we present the first direct evidence of a TIM-ZEB1 axis which control key pathological processes in CRC. We found that loss of TIM expression unleashes ZEB1 which triggers epithelial-to-mesenchymal transition program, cell migration/invasion increase and acquirement of stem-like phenotype of CRC cells. Besides, deranged TIM-ZEB1 axis sets off accumulation of DNA damage and delays DNA damage recovery. It is worth noting that the aggressive and genetically unstable ‘CMS4 - colorectal cancer molecular subtype’ matched with low-TIM expressing CRCs and that patients with low-TIM and high-ZEB1 expression have an adverse outcome. Our results support a critical role for TIM-ZEB1 axis derangement and modulation in determining aggressive disease and poor prognosis in CRC patients.

overall_design: We analyzed the transcriptional profile of SW620 colon cancer cell line and of SW620 TIM-KD (p.LKO.1#1 - TRCN0000153760; Sigma-Aldrich, S.Louis, MO, USA), SW620 ZEB1-KD (p.LKO.1#2 - TRCN0000017565;Sigma-Aldrich), and SW620 ZEB1/TIM-KDs cells. A total of 6 different experimental conditions were analyzed in this study. We performed  biological replicates for a total of 12 samples profiled.

first: Gianluigi

last: Mazzoccoli

first: Tommaso

last: Colangelo


title: Loss of SETD1B results in the redistribution of genomic H3K4me3 in the oocyte [PBAT]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Histone 3 lysine 4 trimethylation (H3K4me3) is an epigenetic mark found at active gene promoters and CpG islands. H3K4me3 is essential for mammalian development, yet mechanisms underlying its genomic targeting are poorly understood. H3K4me3 methyltransferases SETD1B and MLL2 are essential for oogenesis. We investigated changes in H3K4me3 in Setd1b conditional knockout (cKO) GV oocytes using ultra-low input ChIP-seq, in complement to DNA methylation and gene expression analysis. Setd1b cKO oocytes showed a redistribution of H3K4me3, with a marked loss at active gene promoters associated with downregulated gene expression. Remarkably, many regions gained H3K4me3 in Setd1b cKOs, in particular those that were DNA hypomethylated, transcriptionally inactive and CpG-rich. All of these are hallmarks of MLL2 targets; thus, loss of SETD1B appears to enable enhanced MLL2 activity. Our work reveals two distinct, complementary mechanisms of genomic targeting of H3K4me3 in oogenesis, with SETD1B linked to transcriptional activity and MLL2 to CpG content.

overall_design: Approximately 100 GV oocytes were collected from females with an oocyte conditional deletion of Setd1b using Gdf9-cre (Setd1b cKO) and females carrying floxed Setd1b (Setd1b WT) for  three biological replicates of each genotype for post-bisulphite adaptor tagging (PBAT).

first: Jiahao

last: Huang

first: Courtney

last: Hanna

first: Gavin

last: Kelsey


title: Loss of SETD1B results in the redistribution of genomic H3K4me3 in the oocyte


title: Loss of SETD1B results in the redistribution of genomic H3K4me3 in the oocyte [ChIP-seq]

overall_design: Approximately 200 GV oocytes were collected from females with an oocyte conditional deletion of Setd1b using Gdf9-cre (Setd1b cKO) and females carrying floxed Setd1b (Setd1b WT) for H3K4me3 ULI-nChIP-seq for three biological replicates of each genotype.


title: Loss of SETD1B results in the redistribution of genomic H3K4me3 in the oocyte [RNA-seq]

overall_design: Single GV oocytes were collected from females with an oocyte conditional deletion of Setd1b using Gdf9-cre (Setd1b cKO) and females carrying floxed Setd1b (Setd1b WT) for single cell RNA-seq for four and three biological replicates, respectively.

first: Susanne

last: Reinhardt

first: Andrea

last: Kranz


title: High-throughput capture of ectopic chromosomal sequence

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

summary: DNA double-strand breaks (DSBs) are a prominent source of genetic instability/variability frequently associating genome rearrangements with the capture of ectopic chromosomal sequences (ECSs) at junctions. Homologous recombination (HR) is considered in textbooks as an error-free DSB repair mechanism that protects against genome instability. Contradicting this dogma, we show that silencing the central HR players RAD51 or BRCA2 suppresses the sequence homology-independent capture of ECS at the junctions of distant DSBs, especially in 53BP1-depleted cells. We confirmed the requirement of RAD51 for ECS capture at a genome-wide level through high-throughput genome translocation sequencing.

overall_design: We performed HTGTS on human fibroblasts CG92 cell line contained the CD4-3200 bp (pSHD-CD4) end-joining reporter and CMV6 primer was used as bait to capture ectopic chromosomal sequences. The captured of ectopic chromosomal sequences (ECSs) at junctions were analyzed and compared among no treatment, si53BP1, siRAD51, si53BP1&siRAD51 cells.

first: Wei

last: Yu

first: Josée

last: Guirouilh-Barbat

first: Chloé

last: Lescale

first: Bernard

last: Lopez


title: The role of  lnc-TMPRSS15 when human lens epithelial cells exposed to dexamethosone

status: Public on Jan 16 2022

city: Harbin

first: lin

last: wang

address: 141 Yiman Street

institute: Eye Hospital, The First Aﬃliated Hospital of Harbin Medical University, Harbin, China

summary: For studying the pathogenesis of glucocorticoid induced cataract, We established stable overexpression of αA- and αB-crystallin in human lens epithelial cells (HLECs). All cells were treated with 0.1 μmol, 1 μmol, 10 μmol and 100 μmol Dex for 12 h, 24 h, 36 h, and 48 h then we detected closely related lncRNAs. Our results showed that αA-crystallin promoted the expression of some anti-apoptotic proteins. Lnc-TMPRSS15 played a very important role which provides a theoretical basis for the mechanism of glucocorticoid-induced cataract.

first: Lin

last: Wang


title: lncRNA expression profile of bovine monocyte derived macrophages infected with Mycobacterium avium subsp. Paratuberculosis

city: Changchun

first: Yanhong

last: Bao

state: jilin

address: jilin changchun

institute: Jilin Agricultural University

summary: In order to gain a better understanding of MAP infection in immature macrophages, high-throughput sequencing technology was used to perform an analysis of lncRNAs profiles of bovine monocyte derived macrophages upon MAP infection.

overall_design: lncRNA-sequencing analysis was performed on an Illumina Hiseq 4000  following the vendor's recommended protocol


title: Investigation of differential microRNAs in the exosomes of alcohol-induced H9c2  myocardial cells

status: Public on Jan 15 2022

city: Jinan

first: Zhenzhen

last: Hu

address: Lixia District

institute: Shandong University

type: Non-coding RNA profiling by high throughput sequencing

summary: We use the illumina high-throughput sequencing technology to identify miRNAs between the exosomes of H9c2 cells with or without alcohol-induced.The H9c2 cells were cultured in serum-free medium and stimulated with ethanol (100 mmol/L) or PBS for 24 h, then collected the exosomes samples from serum-free medium. Exosomes were isolated and extracted by differential centrifugation and detected by electron microscopy, particle size and related marker proteins.In total, 123 differentially expressed miRNAs (12 upregulated and 111 downregulated) were screened by miRNA sequence.

overall_design: Examination of 2 different exosomes in H9c2 myocardial cells.

first: Liyong

last: Chen

first: Yan

last: Meng


title: Investigation of differentially-expressed microRNAs involved in infected nonunion of the human long bones through microRNA expression profiling

city: Nanjing

last: Dai

address: No. 300, Guangzhou Road, Gulou District

department: Department of Infectious Diseases

institute: the First Affiliated Hospital of Nanjing Medical University

summary: 20 miRNAs were identified as differentially expressed in patients with infected nonunion of long bones, which may facilitate the diagnosis of infected nonunion of long bones.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, we analyze the expression of miRNAs from bone tissues of the fractured end of the bone in five patients with infected nonunion of long bones and four patients with freshly-closed fractures in order to provide novel diagnostic tools.

first: Jun


title: Dissecting the Cellular Landscape and Transcriptome Network in Viral Myocarditis by Single-Cell RNA Sequencing

city: Lincoln

first: Jay

last: Reddy

state: Nebraska

address: Room 202, East Campus

department: Veterinary and Biomedical Sciences

institute: University of Nebraska Lincoln

summary: Myocarditis induced with Coxsackievirus B3 (CVB3) is commonly employed to study viral pathogenesis in mice. Although infectious virus is cleared after the acute phase, affected animals chronically develop the features of dilated cardiomyopathy, which may involve the mediation of immune and non-immune cells. To dissect this complexity, we performed single-cell RNA sequencing on heart cells obtained from healthy and myocarditic mice, leading us to note that myocarditic mice had significantly higher proportions of myeloid cells, CD4 and CD8 T cells, and fibroblasts, whereas NK cells, ILCs and B cells were low. While the transcriptome profiles of myeloid cells revealed detection of monocytes and macrophages of M2 phenotype with pathways important in immune metabolism and inflammation, T cells consisted of Th17 cells, CTLs, and Treg cells with transcriptome signatures critical for cytotoxic functions. Although fibroblasts detected in myocarditic mice were phenotypically heterogeneous, their transcriptomes played roles in fibrosis and regulation of inflammation and immune responses. Additionally, analysis of intercellular communication networks revealed unique interactions and signaling pathways in the cardiac cellulome, whereas myeloid cells and T cells in myocarditic mice revealed uniquely upregulated transcription factors modulating cardiac remodeling functions. Taken together, our data suggest that M2 cells, T cells, and fibroblasts may cooperatively or independently participate in the pathogenesis of viral myocarditis.

overall_design: Two replicates, with n=7 mice per treatment group, were used for heart sample processing. Approximately 16,000 cells were loaded onto a single channel of the 10X Genomics chromium controller (10X Genomics, Pleasanton, CA), with a target recovery of ~10,000 cells using the chromium v2 and v3 single-cell reagent kit. Amplified cDNA (50 ng) was used to construct 3’ expression libraries, and the libraries were pooled and run on an Illumina HiSeq 4000. Each lane consisted of 150 base-pair, paired-end reads. The Illumina basecall files were converted to FASTQ format, and these files were aligned to the murine genome (mm10) using the CellRanger v3.0.2 pipeline as described by the manufacturer.

first: Ninaad

last: Lasrado

first: Nicholas

last: Borcherding


title: Emory_U_Mouse_LCA_RCA_Endothelium_Ligation_Ator_Exp1

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

summary: This project is a collaboration between Dr. Jo at Emory U and BMS to identify the mechanosensitive genes that are also statin-sensitive in C57/Bl6 mouse carotid endothelium.

overall_design: At two days before surgery, mice were treated with atorvastatin (10mg/Kg body weight/day) or vehicle by daily oral administration. Subsequently partial ligation surgery of LCA (left common carotid artery) was performed on all the mice. Endothelial RNAs were isolated at 12h, 24h, 48h and 2 weeks from LCA and the control RCA from each mouse. Transcriptional profiling will be carried out with Affymetrix chip to compare the gene expression under various conditions.

first: David

last: Crandall

first: Wen-Pin

last: Yang

first: Ke

last: Xu

first: Sandeep

last: Kumar

first: Jing


title: Comprehensive analysis of circRNA expression profiles in rat cerebral cortex after moderate traumatic brain injury

city: wuhan

first: Gang

last: Li

address: 169 Donghu Road, Wuchang District

institute: Zhongnan Hospital of Wuhan University

summary:
Background: Traumatic brain injury is a medical event of global concern, and a growing body of research suggests that circular RNA can play very important roles in traumatic brain injury. To explore the functions of more novel and valuable circular RNA in traumatic brain injury response, a moderate traumatic brain injury in rat was established and a comprehensive analysis of circular RNA expression profiles in rat cerebral cortex was done.
Results: As a result, 301 up-regulated and 284 down-regulated circular RNAs were obtained in moderate traumatic brain injury rats, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed based on the circular RNA’s host genes, and a circRNA-miRNA interaction network based on differentially expressed circular RNAs was constructed. Also, four circular RNAs were validated by RT-qPCR and sanger sequencing.
Conclusion: This study showed that differentially expressed circular RNAs existed between rat cerebral cortex after moderate traumatic brain injury and control. And this will provide valuable information for circular RNA research in the field of traumatic brain injury.

overall_design: Cerebral cortex circular RNA profiles of sham and mTBI (moderate traumatic brain injury) rat

first: Shaoping

first: Ruining

last: Liu

first: Jiangtao

last: Yu

first: Haoli

last: Ma

last: Zhao


title: Regional heterogeneity of glioblastoma upon single-cell RNA sequencing

city: Daejeon

first: Haemin

last: Chon

address: Daehak-ro 291

department: Graduate school of medical science and engineering

country: South Korea

institute: KAIST

summary: Using spontaneous mouse GBM model, regional dissection of cortical margin, callosal margin, and tumor center was done for single-cell RNA sequencing to investigate molecular characteristics of marginal cancer cells.

overall_design: Cancer cells were sorted from cortex, corpus callosum, and tumor center respectively, then single-cell RNA libraries were made independently.

first: Injune

last: Kim


title: ProSys(1-178) constitutive expression

city: Portici

first: Mariangela

last: Coppola

address: Via Università 100

institute: University of Naples "Federico II"

summary: Transcriptional profiling of tomato plants constitutively expressing the truncate ProSys cDNA compared to tomato untransformed plants.

overall_design: One-condition experiment, Transgenic VS control; Two transgenic genotypes, 3 biological replicates

first: Giandomenico

last: Corrado


title: LiveG4ID-seq identifies the chromatin G-quadruplex landscape in living cells

city: Hefei

first: Xucong

last: Teng

address: No. 96, Jinzhai Road

department: Hefei National Laboratory of Physical Science at Microscale

institute: University of Science and Technology of China

summary: G-quadruplex (G4) structures exist in single-stranded DNA of chromatins and regulate genome function. However, the native chromatin G4 landscape in living cells has yet to be fully characterized. Herein, we fused BG4 antibody and GFP-tag to construct a live-cell G4 identifier (LiveG4ID). We first displayed its function as a high-specificity chromatin G4 probe in living cells by Dox-induced expression LiveG4ID in HEK293T cells and detecting its cellular localization, biocompatibility and G4-binding specificity. By coupling LiveG4ID with CUT&Tag technology, we established LiveG4ID-seq, a method for mapping native chromatin G4 landscape in living cells. LiveG4ID-seq can identify more chromatin G4 motifs than traditional CUT&Tag and ChIP-seq methods. Using LiveG4ID-seq, we profiled the dynamic landscape of chromatin G4 structures during the cell cycle. These data demonstrate the capacity of LiveG4ID-seq to profile a more accurate G4 landscape in living cells and promote future study on chromatin G4 structures.

overall_design: The chromatin G-quadruplex landscape was detected by LiveG4ID-seq and CUT&Tag in HEK293T cells. The binding specificity of LiveG4ID to chromatin G4 was evaluated with CUT&Tag by detecting the competitive binding of G-quadruplex antibody in LiveG4ID expressing cells. Transcriptome of HEK293T cells with different LiveG4ID expression levels were measured by RNA-seq. LiveG4ID-seq was further tested in human HeLa cells and mouse N2a cells. LiveG4ID-seq was also used to profile the dynamic landscape of chromatin G-quadruplexes during the cell cycles.

first: Yicong

last: Dai

first: Yuncong

last: Wu

first: Jinghong


title: Histone citrullination in estrogen receptor signaling and breast cancer

city: Ithaca

first: Scott

last: Coonrod

state: New York

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

institute: Cornell University

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

overall_design: Refer to individual Series


title: Histone citrullination in estrogen receptor signaling and breast cancer [PRO-seq]

summary: PAD2, one of a family of PAD enzymes that convert positively charged arginine residues on target proteins to neutrally charged citrulline, has been shown to play a role in estrogen signaling through interactions with histone H3R26. The objectives of this project are to define the role of PAD2 in estrogen receptor alpha signaling, tumor progression, and tamoxifen resistance.

overall_design: PRO-seq was utilized to investigate the interaction between citrullination and PAD2 upon estrogen treatment in MCF7 cells.

first: Chinatsu

last: Mukai

first: Charles

last: Danko


title: Histone citrullination in estrogen receptor signaling and breast cancer [ChIP-seq]

overall_design: ChIP-seq was utilized to investigate the interaction between citrullination and PAD2 upon estrogen treatment in MCF7 cells.


title: Identification of hyperammonemia-induced changes in the cerebral transcriptome and proteome

city: Düsseldorf

first: Boris

last: Goerg

address: Moorenstrasse 5

department: Clinic for Gastroenterology, Hepatology and Infectiology

institute: Heinrich-Heine Universität Düsseldorf

summary: In this study we applyed transcriptomics and proteomics to brains of mice with systemic hyperammonemia resulting from knockout of hepatic glutamine synthetase to identify new molecular players relevant for ammonia toxicity and hepatic encephalopathy.

overall_design: The dataset comprises 24 samples of mouse brain tissue biopsies obtained from wildtype and liver-specific glutamine synthetase KO mice. Three different brain regions were analyzed.

last: Görg

first: Alina

last: Schrimpf

first: Olivia

last: Knappe

first: Natalia

last: Qvartskhava

first: Gereon

last: Poschmann

first: Kai

last: Stühler

first: Hans

last: Bidmon

first: Dieter

last: Häussinger


title: Identification of cross-species microRNA-based Communication in Brugia malayi with its endosymbiont Wolbachia

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Brugia malayi is a parasitic nematode that causes lymphatic filariasis in humans. A total of 178 novel microRNA were identified from short read transcriptional data, which when combined with known Brugia microRNAs yielded a total of 284 microRNA. Of these, 123 microRNA sequences (43%) are differentially expressed over the mammalian life stages of B. malayi that we examined. Putative targets of these microRNA were identified from inversely expressed target clusters that contain valid seed sequences for the corresponding microRNAs. The largest identified cluster is downregulated in adult females and enriched in zinc finger domains, helicase domains, and DNA binding domains suggesting this microRNA cluster may have regulatory control over a large proportion of adult female specific mRNA genes. MicroRNA-like molecules are identified as produced by the Wolbachia endosymbiont, providing evidence for direct nucleic acid-based interdomain communication between filarial nematodes and their bacterial obligate endosymbiont.

sample_organism:
Brugia malayi
Wolbachia endosymbiont of Brugia malayi

overall_design: Examination of microRNA expression over the life cycle of the filarial nematode Brugia malayi.

first: John

last: Mattick

first: Laura

last: Teigen

first: Matthew

last: Chung

first: Silvia

last: Libro

first: Robin

last: Bromley

first: Dustin

last: Olley

first: Nikhil

last: Kumar

first: Lisa

last: Sadzewicz

first: Luke

last: Tallon

first: Anup

last: Mahurkar

first: Jeremy

last: Foster

first: Michelle

last: Michalski

first: Julie

last: Dunning Hotopp


title: m6A reader CPSF70 controls polyadenylation site choice through m6A-dependent recognition of FUE polyadenylation signal

city: Beijing

first: Peizhe

last: Song

state: Beijing

address: Chengfu Road CCME B234

institute: Peking University

summary: We conduct herein a systematic study of mRNA recognition and consequent polyadenylation processing of the Arabidopsis mRNA by m6A reader protein CPSF70. Transcriptome-wide characterization of CPSF70-binding sites supporting the recognition m6A-methylated mRNA with CPSF70, and the results of which linked polyadenylation signals recognition. We then perform 3’end sequencing with A-seq2 to identify CPSF70-dependent APA process, showing that CPSF70 modulate m6A–dependent polyadenylation with FUE recognition.

overall_design: Examination for m6A-dependent alternative polyadenylation regulation in cpsf70 mutant and wild type.

first: Junbo

last: Yang


title: Compound kushen injection and YFSJ reduce gefitinib resistance in gefitinib resistant lung cancer cell lines

city: Guangzhou

first: Lizhu

last: Lin

address: 12 Jichang Street, Baiyun District

institute: Guangzhou University of Chinese Medicine

summary: Compound Kushen Injection (CKI) has been used in clinics for nearly 20 years to treat different kinds of cancers. In this study, we found that CKI inhibited gefitinib resistant cell line proliferation, reduced drug resistance and improved anti-cancer effects when associated with gefitinib in a dose-dependent fashion. We also identified candidate CKI associated molecular mechanisms that might reduce drug resistance using transcriptome analysis methods, including gene differential expression analysis and pathway over-representation analysis. Multiple pathways were perturbed and the PI3K/AKT/MTOR and autophagy pathways were identified as the potential primary target pathways of CKI in this context. We also investigated the molecular mechanisms of another TCM, Yifei-Sanjie Wan (YFSJ) on reducing gefitinib resistance using transcriptome analysis.

overall_design: High-depth paired-end RNA-seq from H1975 lung cancer cell line. Each sample contains 3 biological replicates.

first: Jue

last: Zhang

first: David

last: Adelson


title: ATAC-seq time course analysis of in vitro differentiated antibody-secreting cells

status: Public on Jan 14 2022

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: We examined the chromatin accessibility changes that occur as antibody-secreting cells (ASC) differentiate and mature using an in vitro culture system. ASC were profiled directly post isolation and at time points weekly out to 14 days in culture. These data reveal how the long-lived ASC accessible chromatin matures over time.

overall_design: Comparison of human blood ASC accessible chromatin landscape over different time points from in vitro cultures.

first: Christopher

middle: D

first: Frances

last: Lee


title: Analysis of the lncRNA-miRNA-mRNA network reveals a potential regulatory mechanism of EGFR-TKIs resistance in NSCLC

first: Jiayuan

last: Zhong

address: 381 Wushan Road, Guangzhou 510640, China

department: School of Mathematics

institute: South China University of technology

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

summary: In this study, to investigate the underlying molecular mechanisms of how EGFR-TKIs resistance occurs in NSCLC, we examined gene expression using microarray technology on gefitinib-resistant NSCLC cells to obtain differentially expressed (DE) lncRNAs and mRNAs. Then we carried out KEGG enrichment analysis for DE-mRNAs and constructed the ceRNA regulatory network of DE-lncRNAs and DE-mRNAs. Our results revealed the downregulated lncRNA LINC01128 acted as ceRNA to decrease PTEN via sponging miR-25-3p, and then the signal reactions caused by the reduction of PTEN would activate PI3K/Akt signaling pathway, which may lead to the development of drug resistance to EGFR-TKIs in NSCLC. Our findings will provide a novel perspective for the underlying molecular mechanisms of EGFR-TKIs resistance in NSCLC. Besides, this research will help to develop new therapeutic targets for EGFR-TKIs resistance in NSCLC.

overall_design: gefitinib resistant PC-9 cells (G); gefitinib-sensitive PC-9 cells (P)

first: D

last: Ding

first: X

last: Xue

first: W

last: Liang

first: J


title: ATAC-seq analysis of human blood and bone marrow naïve B cell subsets

summary: To compare the accessible chromatin landscape of human naïve B cells from the blood or bone marrow, we sorted each population from a diverse healthy cohort and performed ATAC-seq.

overall_design: Comparison of human naïve B cell accessible chromatin from the blood or bone marrow.


title: Exploring the mechanism of Jiangtang Tiaozhi Recipe in the treatment of obese T2DM patients with dyslipidemia based on transcriptomics

first: Tingting

last: Bao

address: No. 5, Bei Xian Ge, Xicheng District, Beijing

institute: Guang'anmen Hospital, China Academy of Chinese Medical Sciences

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

summary: Objective: To explore the mechanism of Jiangtang Tiaozhi Recipe in the treatment of obese T2DM patients with dyslipidemia based on transcriptomics.  Methods: We chose 6 patients with obese type 2 diabetes mellitus and dyslipidemia (syndrome of excess of gastrointestinal heat) who were treated by JTTZR for 24 weeks, while 6 cases included in the healthy control group. We selected 6 cases in each group (disease group before treatment, disease group after treatment and healthy control group) to start the research of lncRNA microarray. According to the differentially expressions of lncRNAs and mRNAs, we secondly performed GO analysis, Pathway analysis, and found out some target lncRNAs as well as their associated mRNAs. The trial register number is NCT04623567.   Results: (1) Disease group before treatment vs. healthy control group: There are 557 upregulated lncRNAs, 273 downregulated lncRNAs, 491 upregulated mRNAs and 1639 downregulated mRNAs. (2) Disease group after treatment vs. Disease group before treatment: There are 128 upregulated lncRNAs, 32 downregulated lncRNAs, 45 upregulated mRNAs and 140 downregulated mRNAs.

overall_design: We chose 12 patients with obese type 2 diabetes mellitus and dyslipidemia (syndrome of excess of gastrointestinal heat) who were treated by JTTZR for 24 weeks, while 12 cases included in the healthy control group. First, we selected 6 cases in each group (disease group before treatment, disease group after treatment and healthy control group) to start the research of lncRNA microarray. According to the differentially expressions of lncRNAs and mRNAs, we secondly performed GO analysis, Pathway analysis, and found out some target lncRNAs as well as their associated mRNAs. Then, the qPCR was utilized to validate these target lncRNAs and mRNAs. Finally, a detailed analysis of the differences on disease group before treatment vs. healthy control group and disease group after treatment vs. disease group before treatment will be managed. In addition, we focused on disease-related pathways, and will analyze the correlation of differentially expressions of target lncRNAs with the clinical indicators. The trial register number is NCT04623567.

first: Song

last: Wang

first: Yingying

first: LiSha

last: He

first: Lin

last: Han

first: Tiangang

last: Zhai

first: Jia

last: Chen

first: Qiang

last: Zhou

first: Xiyan

last: Zhao

first: Fengmei

last: Lian

first: Linhua

first: Xiaolin

last: Tong


title: Genome-wide chromatin state in non-failing and dilated cardiomyaphty human left ventricles [ChIP-Seq]

city: Cleveland

first: Chia-Feng

last: Liu

state: OH

address: 9500 Euclid Avenue,

department: Cardiovascular & Metabolic Sciences

institute: Cleveland Clinic Lerner Research Institute

summary: We conducted chromatin immunoprecipitation followed by sequencing (ChIP-seq) and proximity ligation-assisted ChIP-seq (PLAC-seq) for enhancers and promoters (E-P) using left ventricular tissues from dilated cardiomyopathy (DCM) patients and non-heart failure (NF) donors. Differential active enhancer H3K27ac and promoter H3K4me3 regions were identified between NF and DCM. While the average read density (ARD) for H3K27ac is similar between NF and DCM, the ARD of H3K4me3 is significantly lower in DCM samples than in NF.Super-enhancer (SE) analysis revealed that 929 and 129 genes linked to NF- and DCM-specific SE, respectively, and three unique SE-associated genes between NF and DCM  were identified.Moreover, the differential E-P interactions were observed in the known heart failure gene loci and are correlated with the gene expression levels. Motif analysis identified known cardiac factors and possible novel players for DCM.  We have established cistrome of four histone modifications and long-range chromatin interaction for enhancers and promoters in NF and DCM tissues. The differential histone modifications and E-P interactions were found in DCM, and these differences were associated with the gene expression level of a subset of disease-associated genes in human heart failure.

overall_design: We carried out ChIPseq experiments for four histone modificatoins using the left ventricle (LV) of male patients who underwent cardiac transplantation for dilated cardiomyopathy (DCM) and in matched non-failing donors (NF)

first: Armen

last: Abnousi

first: Peter

last: Bazeley

first: Ying

last: Ni

first: Christine

middle: S

last: Moravec

first: Ming

last: Hu

first: WH Wilson

last: Tang


title: ATAC-seq analysis of human blood and bone marrow antibody-secreting cell subsets

first: Chris

last: Scharer

summary: Antibody-secreting cells (ASC) circulate after vaccination and infection and migrate to the bone marrow (BM) where a subset known as long-lived plasma cells (LLPC) persist and secrete antibodies for a lifetime. The mechanisms of how circulating ASC become LLPC is not well elucidated. Here, we show that human early-minted blood ASCs have distinct morphology, transcriptomes, and epigenetics compared to human BM LLPC. Compared to blood ASC, BM LLPC have decreased nucleus/cytoplasm ratio but increased endoplasmic reticulum and numbers of mitochondria. Additionally, LLPC acquire transcriptional and epigenetic differences in multiple cellular pathways that include apoptosis. Upregulation of the anti-apoptotic genes MCL1, BCL2, BCL-XL while simultaneously downregulation of pro-apoptotic genes HRK1, CASP3, and CASP8 occurs in LLPC. Consistent with the decrease in gene expression, pro-apoptotic gene loci are less accessible in LLPC. In contrast, anti-apoptotic gene expression is increased but is not always accompanied by changes in accessibility. Importantly, we show that early-minted blood ASCs undergo morphological and transcriptional changes that make these cells resemble ex vivo BM ASCs, suggesting that the BM microniche at least in part promotes LLPC maturation. Overall, our study demonstrates that early-minted blood ASC in the BM microniche must undergo morphological, transcriptional, and epigenetic changes to mature into apoptotic-resistant LLPC.

overall_design: Comparison of human blood and BM ASC accessible chromatin landscape.

first: Christopher

first: Frances

last: Lee


title: Enhanced CXCL12/CXCR4 signaling increases tumor progression in radiation-resistant pancreatic cancer

city: Nagoya

first: YOICHI

last: MATSUO

state: Aichi

address: 1 Kawasumi Mizuhocho Mizuhoku

department: Gastroenterological Surgery

country: Japan

institute: Nagoya City University

summary: Pancreatic cancer (PaCa) has one of the poorest prognoses among gastrointestinal cancers because of rapid development of treatment resistance, which renders chemotherapy and radiotherapy no longer effective. As the mechanism by which PaCa becomes resistant to radiotherapy is unknown, we established radiation-resistant PaCa cell lines to investigate the factors involved in radiation resistance. We investigated the role of the C-X-C motif chemokine 12 (CXCL12)/ C-X-C chemokine receptor type 4 (CXCR4) axis in radiation resistance in PaCa and the effect of a CXCR4 antagonist on radiation-resistant PaCa cell lines. As confirmed by immunofluorescence staining, RT-qPCR, and Western blotting, the expression of CXCR4 was higher in the radiation-resistant PaCa cell lines than in normal PaCa cell lines. The invasion ability of radiation-resistant PaCa cell lines was greater than that of normal cell lines and was enhanced by CXCL12 treatment and co-culture with fibroblasts; this enhanced invasion ability was suppressed by the CXCR4 antagonist AMD070. Irradiation after treatment with the CXCR4 antagonist suppressed the colonization of radiation-resistant PaCa cell lines. In conclusion, the CXCL12/CXCR4 axis may be involved in the radiation resistance of PaCa. We believe this result will help develop treatments for PaCa.

overall_design: PaCa cell lines (AsPC-1, BxPC-3, MIA PaCa-2, and SW1990) were seeded in a 100 mm dish and cultured. Upon reaching 50% confluence, the cells were irradiated with 2 Gy radiation and incubated until reaching 90% confluence, after which the cells were passaged. With each passage, the irradiation process was repeated until the total radiation dose reached at least 60 Gy.

first: Tomokatsu

last: Kato

first: Yoichi

last: Matsuo


title: Transcriptomic profiling of M. tuberculosis from human lung tissue

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: Study of the transcriptomic profile of M. tuberculusis in various types of human lung tissues

overall_design: RNA was isolated from various parts of the lungs affected by tuberculosis

first: Tatyana

last: Azhikina


title: Circular RNA Expression Profiles Following Negative Pressure Wound Therapy in Burn Wounds with Experimental Pseudomonas aeruginosa Infection

city: Xi'an

first: Yunshu

last: Yang

state: Shaanxi

address: Changle West Road

institute: Air Force Medical University

summary: Infections of burn wounds, especially those caused by Pseudomonas aeruginosa, could trigger sepsis or septic shock, which is the main cause of death after burn injury. Compared with traditional saline-wet-to-dry dressings, negative pressure wound therapy (NPWT) is more effective for the prevention and treatment of wound infections. However, the mechanism by which NPWT controls infection and accelerates wound healing remains unclear. Accordingly, in this study, the molecular mechanisms underlying the effects of NPWT were explored using a murine model of P. aeruginosa-infected burn wounds. NPWT significantly reduced P. aeruginosa levels in wounds, enhanced blood flow, and promoted wound healing. Additionally, NPWT markedly alleviated wound inflammation and increased the expression of wound healing–related molecules. Recent evidence points to a role of circular RNAs (circRNAs) in wound healing; hence, whole-transcriptome sequencing of wound tissues from NPWT and control groups was performed to evaluate circRNA expression profiles.

overall_design: Whole transcriptome sequencing following negative pressure wound therapy in burn wounds with experimental Pseudomonas aeruginosa infection

first: Yang


title: RNA-sequence data of liver sinusoidal endothelial cells in wild type and endothelial RBPj-conditional knock out (RBPjcKO) mice

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

institute: Fourth Military Medical University

summary: The Notch pathway plays a critical role in regulating the proliferation and differentiation of endothelial cells during liver homeostasis, so we used EC-specific RBPj conditional knock out mice, and compared the gene expression profiles of LSECs isolated from wild type versus RBPjcKO mice.

overall_design: Liver sinusoidal endothelial cells mRNA profiles of 7- to 8-weeks-old wild type (WT) and RBPjcKO mice were generated by RNA sequencing, in triplicate, using Illumina HiSeq 3000.

first: Lin

last: Wang

first: Juanli

last: Duan


title: Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium and age-associated mitochondrial dysfunction [bulk RNA-seq]

city: Philadelphia

first: Kelly

middle: A

last: Whelan

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

summary: We have performed single cell RNA-sequencing to characterize the murine esophageal epithelium in young and aged mice.

overall_design: We used peeled esophageal epithelium from young (≤4 months) and aged (≥18 months) mice to investigate the molecular heterogeneity of the esophageal epithelium at single cell resolution.

first: Adam

last: Karami

first: Mohammad

middle: F

last: Kabir

first: Kelsey

last: Keith

first: Jozef

last: Madzo

first: Jaroslav

last: Jelenik

first: Kumaraswamy

middle: N

last: Chitrala


title: Roux-en-Y gastric bypass and caloric restriction but not gut hormone-based treatments profoundly impact the hypothalamic transcriptome in obese rats

city: Würzburg

first: Tom

last: Gräfenhan

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

department: Core Unit SysMed

institute: University of Wuerzburg

summary: Background: The hypothalamus is an important brain region for the regulation of energy balance. Roux-en-Y gastric bypass (RYGB) surgery and gut hormone-based treatments are known to reduce body weight, but their effects on hypothalamic gene expression and signaling pathways are poorly studied. Methods: Diet-induced obese male Wistar rats were randomized into the following groups: RYGB, sham-operation, sham + body weight-matched (BWM) to the RYGB group, osmotic minipump delivering PYY3-36 (0.1mg/kg/day), liraglutide s.c. (0.4mg/kg/day), PYY3-36+liraglutide and saline. All groups (except BWM) were kept on a free choice of high- and low-fat diets. Four weeks after interventions, hypothalami were collected for RNA-sequencing. Results: While rats in the RYGB, BWM and PYY3-36+liraglutide groups had comparable reductions in body weight, only RYGB and BWM treatment had a major impact on hypothalamic gene expression. In these groups, hypothalamic leptin receptor expression as well as the JAK–STAT, PI3K-Akt and AMPK signaling pathways were upregulated. No significant changes could be detected in PYY3-36+liraglutide, liraglutide and PYY treated groups. Conclusions: Despite causing similar body weight changes compared to RYGB and BWM, PYY3-36+liraglutide treatment does not impact hypothalamic gene expression. Whether this striking difference is favorable or unfavorable to metabolic health in the long term requires further investigation.

overall_design: Examination of hypothalamic changes of mRNA in different treatment groups in male Wistar rats

first: Ulrich

last: Dischinger

first: Julia

last: Hasinger

first: Tobias

last: Heckel

first: Thorsten

last: Bischler

first: Christoph

last: Otto

first: Mohamed

last: Hankir

first: Florian

last: Seyfried

first: Martin

last: Fassnacht

first: Angelika

last: Schmitt-Böhrer


title: RB1 loss promotes a noncanonical activator function of LSD1 and sensitizes castration-resistant prostate cancer to LSD1 inhibition [RNA-seq]

city: Boston

first: Changmeng

last: Cai

state: MA

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

summary: Genomic loss of RB1 is a common alteration in castration-resistant prostate cancer (CRPC) and is associated with poor patient outcomes. RB1-loss is also a driver event that promotes the neuroendocrine transdifferentiation of prostate cancer (PCa). The loss of Rb protein disrupts the Rb-E2F repressor complex and thus hyperactivates E2F transcription activators. While the impact of RB1-loss on PCa progression and linage plasticity has been previously studied, the underline mechanisms remain unclear. Using an integrated cistromic and transcriptomic analysis, we have characterized Rb activities in multiple CRPC models by identifying Rb directly regulated genes and revealed that Rb has distinct binding sites and targets in TP53-mutated CRPC. Significantly, we show that RB1-loss promotes the noncanonical activator function of LSD1/KDM1A, which stabilizes chromatin binding of E2F1, and hence sensitizes CRPC tumor to the LSD1 inhibitor treatment. These results provide new molecular insights of Rb activity in PCa progression and suggest LSD1 as a potential therapeutic target in CRPC with RB1-loss.

overall_design: C4-2-tet-shRB cells were treated with either vehicle or DHT (10nM, 24 hours) under different conditions of doxycycline induction (0, 3, or 30 days). For RNA-seq of GSK study, LNCaP cells were treated with/out 1μM GSK2879552 for 2 days, and C4-2-tet-shRB cells were treated with/out 10μM GSK2879552 for 24 hours under doxycycline condition or not.  VCaP cells were transfected with siNTC or siRB. All RNA-seq samples contain replications.

first: Wanting

last: Han

first: Mingyu

last: Liu

first: Dong

first: Shuai

last: Gao


title: ERK-Mediated Phosphorylation of OLA1 Controls Adaptive Mitochondria to Nucleus Communication Regulating Cellular Homeostasis [ChIP-seq]

city: Milwaukee

first: Adeleye

last: Afolayan

state: Wisconsin

address: 8701 Watertown Plank Rd., PD278, CRI TBRC, Rm C3278

institute: Medical College of Wisconsin

summary: We found that changes in mitochondrial membrane potential or ROS generation trigger the translocation of OLA1 from mitochondria and cytoplasm to the nucleus, regulated by ERK1-mediated phosphorylation of OLA1 on Ser232/Tyr236. Subsequent phosphorylation of nuclear-OLA1 on Thre325 by ERK2 activates its function as a genetic factor regulating cellular homeostasis by modulating HDAC9 expression. Disruption of OLA1 phosphorylation blocks its nuclear translocation, compromised the expression of nuclear-encoded mitochondrial proteins, DNA damage response, and multiple stress-response-related-genes, leading to cellular dysfunction. Our findings reveal that OLA1 is a crucial component of mitonuclear response regulatory hubs essential for regulating cellular adaptation to stress.

overall_design: Examination of the role of OLA1 as a transcription factor.

first: Paul

last: Sidlowski


title: High-throughput single-cell transcriptomes of the brain of the nudibranch Berghia stephanieae

city: Amherst

last: Katz

state: Massachusetts

address: 611 North Pleasant Street, 221 Morrill Science Center III

department: Biology

institute: University of Massachusetts Amherst

summary: Previously, transcriptomics data for mollusc has been obtained by whole-brain bulk RNA-seq and low-throughput scRNA-seq. We want to construct the first molluscan high-throughput single-neuron transcriptomes for Berghia stephanieae. Around 129,000 cells were collected from 20 brains and the libraries were constructed using the 10X Genomics' Chromium platform. The brains were separated into two samples: the main brain (i.e., the cerebropleural, pedal, buccal ganglion) and the rhinophore ganglion sample. After library preparation, around 1,000 cells were receovered and sequenced. After data analysis, the cells formed eight clusters with marker genes for each cluster identified. Various cell populations that express a wide range of both small-molecule neurotransmitters and neuropeptides such as serotonergic, small cardioactive peptide (SCP), APGWamide, and FMRFamide cells were also identified in the dataset. Interestingly, cells from the rhinophore ganglion of Berghia exhibit great cell heterogeneity, with cells splitting into two general categories and four distinct clusters. The project produced a single-cell dissociation protocol that can be adapted for use in other nudibranch molluscs and a custom data analysis pipeline for data of this nature.

overall_design: Single-cell sequencing of whole brain tissue of Berghia stephanieae using 10X Genomics' Chromium Single Cell Gene Expression v3. Two samples (i.e. the main brain and the rhinophore ganglion sample) were fixed in methanol

first: Thi

last: Bui

first: M

last: Ramirez


title: In vivo multiplexed gene activation via improved Cas12a

city: Stanford

first: Augustine

last: Chemparathy

state: CA

address: 290 Jane Stanford Way

department: Bioengineering

institute: Stanford University

summary: To evaluate the specificity of CRISPR activation by vgdCas12a on a genome-wide scale, we carried out whole-transcriptome RNA-seq of HEK293T cells with the TRE3G-GFP reporter transfected with either WT dCas12a or vgdCas12a combined with the TRE3G-targeting crRNA. We also included a non-targeting crRNA as negative control for each case.

overall_design: Total RNA was extracted from cells transfected with Tet or LacZ crRNA, and with dCas12(WT) or vgdCas12, and library preparation and next-generation sequencing were performed by Novogene

first: Lucie

middle: Y

last: Guo

first: Jing

last: Bian

first: Hannah

middle: R

last: Kemptom

first: Alexander

last: Davis

first: Xueqiu

last: Lin

first: Sui

last: Wang

first: Lei

last: Qi


title: Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development

city: Bethesda

first: Kai

last: Yu

state: Maryland

address: 50 South Drive, Bldg 50, Room 5151

institute: NHGRI

summary: Here we used RNA sequencing to characterize the transcriptional profile of the total RNA from c-Kit+ cells of Runx1 KO and control mice.

overall_design: For bulk RNA-sequencing: Total RNA from c-Kit+ cells was extracted with AllPrep DNA/RNA/Protein Mini Kit (QIAGEN). Poly-A selected stranded mRNA libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kits according to manufacturer’s instructions. Unique barcode adapters were applied to each library. All libraries were combined in equimolar proportion into one pool for sequencing with a HiSeq2500 sequencer.

first: Erica

last: Bresciani

first: Erika

last: Kwon

first: Stefania

last: dell'Orso


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

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: Refer to individual Series


title: Lung macrophages mediate helminth resistance through differential activation of recruited monocyte-derived alveolar macrophages and arginine depletion

status: Public on Jan 13 2022

city: Newark

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

overall_design: Cx3cr1CreERT2-EYFP-IRES-YFP/+Rosa26floxed-tdTomato/+ reporter male and female mice aged 8 to 14 weeks were received tamoxfen (75 mg /kg, 100 ul, i.p, day -1, +1) during N. brasiliensis infection. At day 7 mice were sacrificed, lung macrophage subsets were electronically sort purified.

first: Fei

last: Chen

first: Darine

last: El-Naccache

first: Olivia

last: Antao

first: Jason

last: Weinstein


title: STAT3 enhances sensitivity of glioblastoma to drug-induced autophagy-dependent lysosomal cell death

city: Leipzig

first: Knut

last: Krohn

address: Philipp-Rosenthal-Straße 55

department: Medizinische Fakultät

institute: University Leipzig

summary: Glioblastoma (GBM) is a devastating disease and the most common primary brain malignancy of adults with a median survival barely exceeding one year. Recent findings suggest that the antipsychotic drug pimozide triggers an autophagy-dependent, lysosomal type of cell death in GBM cells with possible implications for GBM therapy. One oncoprotein that is often overactivated in these tumors and associated with a particularly dismal prognosis is Signal Transducer and Activator of Transcription 3 (STAT3). Here, we used isogenic human GBM knockout cell lines, advanced fluorescence microscopy, transcriptomic analysis and FACS-based assessment of cell viability to show that STAT3 has an underappreciated, context-dependent role in drug-induced cell death. Specifically, we demonstrate that depletion of STAT3 significantly enhances cell survival after treatment with pimozide, suggesting that STAT3 confers a particular vulnerability to GBM. Furthermore, we show that active STAT3 has no major influence on the early steps of the autophagy pathway, but exacerbates drug-induced lysosomal membrane permeabilisation (LMP) and release of cathepsins into the cytosol. Collectively, our findings support the concept of exploiting the pro-death functions of autophagy and LMP for GBM therapy and to further determine whether STAT3 can be employed as a treatment predictor for highly apoptosis-resistant, but autophagy-proficient cancers.

overall_design: mRNA-profile of human GBM cell line MZ-54 in comparison to two isogenic Crispr/Cas9-mediated STAT3-Knockout lines

first: Donat

last: Kögel

first: Janina

last: Remy

first: Benedikt

last: Linder

first: Ulrike

last: Weirauch

first: Achim

last: Aigner


title: Type I interferon activates MHC class I-dressed CD11b+ conventional dendritic cells to promote protective anti-tumor CD8+ T cell immunity

city: Cambridge

first: Ellen

last: Duong

address: 500 Main Street, 76-401

department: Koch Institute for Integrative Cancer Research; Biology Department

institute: Massachusetts Institute of Technology


title: G3bp1-miR-1 axis regulates cardiomyocyte hypertrophy

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

summary: We examine the role of G3bp1, a RNA binding protein and site specific endoribonuclease in gene expression in isolated neonatal cardiomyocytes. RNAseq data from cardiomyocytes were infected with adenoviruses expressing shRNA against G3bp1 (ad-siG3bp1) or Luciferase (ad-siLUC, control) showed significant decrease in transcript abudnnace of cardiac-enriched genes involved in Calcium handling, contraction, action potential and sacromere function. On the other hand increase was observed in genes that regulate Hippo, TNF and TGFb signaling. Knockdown of G3bp1 inhibited endothelin-1 induced cardiomyocyte hypertrophy.

overall_design: Neonatal Rat Ventricular Mycoytes (NRVM) were isolated and cultured. NRVMs from 3 independent cultures were infected with ad-siG3bp1 or ad-siLUC (control) for 48hrs, the knockdown of endogenous G3bp1 validated and the samples were sent for RNAseq to Active Motif


title: Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA-seq2]

last: Yu

summary: Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type.

overall_design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1-/- siblings  (~2.5 months old, pool of 3 kidneys/replicate).


title: Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem bisulfite and oxidative bisulfite Illumina microarrays

first: Ze

last: Zhang

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

institute: Harvard Medical School

summary: Aim: Tandem bisulfite (BS) and oxidative bisulfite (oxBS) conversion on DNA followed by hybridization to Infinium HumanMethylation BeadChips allows nucleotide resolution of 5-hydroxymethylcytosine genome-wide. Here, the authors compared data quality acquired from BS-treated and oxBS-treated samples. Materials & methods: Raw BeadArray data from 417 pairs of samples across 12 independent datasets were included in the study. Probe call rates were compared between paired BS and oxBS treatments controlling for technical variables. Results: oxBS-treated samples had a significantly lower call-rate. Among technical variables, DNA-specific extraction kits performed better with higher call rates after oxBS conversion. Conclusion: The authors emphasize the importance of quality control during oxBS conversion to minimize information loss and recommend using a DNA-specific extraction kit for DNA extraction and an oxBSQC package for data preprocessing.

overall_design: Bisulphite and oxidative bissulfite converted DNA from 22 pairs of clear cell renal cell carcinoma samples, 18 pairs of human fetal oligodendrocyte replicate samples, and 16 pairs of whole blood samples from glioma patients treated with or without Dexamethasone, were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4

first: Min

middle: K

last: Lee

first: Laurent

last: Perreard

first: Karl

middle: T

last: Kelsey

first: Brock

middle: C

last: Christensen

first: Lucas

last: Salas


first: Kai

summary: We used single cell-RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1-mutant cd41-GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic (2.5 days post fertilization, dpf) and larval stages (6, 10 16 dpf).

overall_design: Single cell RNA-seq with FACS sorted cd41-GFPlow cells from wild type and runx1-/- at 2.5, 6, 10 16 dpf.

first: Erica

last: Bresciani

first: Erika

last: Kwon

first: Stefania

last: dell'Orso


title: Transcriptomic profile of cohesin proficient and deficient cells

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

summary: The goal of this study is to identify the mechanism underlying the notion that loss of cohesin complex could sensitize tumor cells to anti-PD-1 therapy.

overall_design: mRNA profiles of WT, NIPBL Knockout, SMC1A knockdown HCT116 cells and WT, Nipbl knockout, Stag2 knockout CT26 cells were detected by RNA-Sequencing. Duplicate for each knockout or knockdown group.

first: Yumin

last: Han


summary: Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type.

overall_design: Bulk RNA-seq was performed on surgically dissected kidneys from wild type and runx1-/- siblings (~2.5 months old, pool of 3 kidneys/replicate, n= 3 for each genotype).