title: Transcriptomic analysis of peritoneal macrophages from MED1 fl/fl and macrophage MED1 KO mice

city: Xi'an

first: Liang

last: Bai

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

summary: Purpose: The goal of this study is to obtain the differential gene expression in MED1fl/fl and MED1ΔMac peritoneal macrophages (PMs) stimulated with or without LPS.  Methods: Pooled PMs were collected from 8-week-old MED1fl/fl and MED1ΔMac mice (n=6 mice/group), and then treated without or with lipopolysaccharide (LPS; 50 ng/mL) for 6 hours. PMs mRNA profiles were generated by deep sequencing, in duplicate, using Illumina NextSeq500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: reads were mapped to the mm9 whole genome using tophat and RPKM were calculated using cufflink. qRT–PCR validation was performed using SYBR Green assays.   Results: Using an optimized data analysis workflow, we mapped about 12 million sequence reads per sample to the mouse genome (build mm9) and identified 24,130 transcripts in the PMs of MED1fl/fl and MED1ΔMac mice. Data analysis with TopHat and Cufflinks workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.  Conclusions: Our study represents the detailed analysis of PMs transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that the expression of more than 20 genes involved in innate immune response and M1 polarization was significantly higher in MED1ΔMac than in MED1fl/fl macrophages after LPS treatment. Upregulated genes in MED1ΔMac macrophages are the proinflammatory genes.

overall_design: PMs mRNA profiles of 8-week-old MED1fl/fl and MED1ΔMac mice

first: Yuan

last: Xi

first: Hsien

middle: D

last: Huang

first: John

middle: Y

last: Shyy


title: Next Generation Sequencing to examine common set of transcripts induced in spinal cord neurons by polyPL and mutSOD1-ACM  common set of transcripts

status: Public on Feb 17 2022

city: Worcester

first: Helene

last: Tran

address: 55 Lake Street

country: USA

institute: Umass Medical School

type: Expression profiling by high throughput sequencing

summary: Next Generation Sequencing shows that synthetic polyPL and mutSOD1-ACM alter a large and common set of transcripts in primary ventral spinal cord cultures

overall_design: Rat primary spinal cord cultures were incubated for 90 min with long-chain synthetic polyphosphate (polyPL; 100 μM), astrocyte conditioned media (ACM) from mutSOD1G93A astrocytes (hSOD1G93A) or control astrocytes (hSOD1WT). Untreated cells were used as internal controls (control). Total RNA was isolated from cell lysates (in quadruplicate) and mRNA expression was analyzed by strand-specific RNAseq.

first: Robert

middle: H

last: Brown

first: Sebastían

last: Abarzúa

first: Brigitte

last: van Zundert


title: Variable proportions of Plasmodium falciparum schizonts expressing MSPDBL2 in clinical isolates and genes with correlated expression

city: London

first: Suzanne

last: Hocking

address: Keppel Street

country: United Kingdom

institute: London School of Hygiene and Tropical Medicine

summary: Plasmodium falciparum merozoite surface protein MSPDBL2 is a highly polymorphic target of naturally acquired immune responses encoded by a single copy gene under strong balancing selection in natural populations. The MSPDBL2 protein is expressed in only a minority of mature schizonts of any cultured parasite line, and mspdbl2 gene expression in culture is increased in response to overexpression of the gametocyte development inducer GDV1 in an engineered parasite clone, so there is a need to characterise its natural expression variation. In this study, MSPDBL2 in mature schizonts was analyzed in the first ex vivo culture cycle of 102 clinical isolates from four endemic populations in different West African countries, by immunofluorescence microscopy with antibodies against a conserved region of the protein. In most isolates, less than 1% of mature schizonts were positive for MSPDBL2 (median of 0.6% overall), but the frequency distribution was highly skewed as eleven isolates had more than 3% schizonts positive and one had 73% positive. The expression frequencies were similar across the four endemic populations, and there was no significant difference between the clinical isolates overall and frequencies of positive schizonts previously seen in cultured P. falciparum laboratory lines. To explore whether expression of other gene loci correlated with MSPDBL2 expression, whole transcriptome sequencing was performed on schizont-enriched material from 17 of the clinical isolates with a wide range of proportions of schizonts positive. Transcripts of particular parasite genes were highly significantly positively correlated with MSPDBP2 positivity in schizonts as well as with mspdbl2 gene transcript levels, with overrepresentation of many genes previously implicated as likely to be involved in gametocytogenesis, but not including other genes including the gametocytogenesis master regulator ap2g. Although MSPDBL2 expression occurs in a highly variable proportion of schizonts in clinical isolates, and correlation with expression of some gametocytogenesis-related genes is consistent with regulation by GDV1, it is not apparently a direct marker of sexual commitment and its function in the parasite remains to be determined.

overall_design: Differential gene expression analysis of clinical isolates based on their proportion of MSPDBL2-positive schizonts as measured by IFA

middle: E

first: Lindsay

middle: B

last: Stewart

first: Sarah

last: Tarr

first: Aline

last: Freville

first: Kevin

middle: K

last: Tetteh

first: Ambroise

last: Ahouidi

first: Alfred

last: Amambua-Ngwa

first: Mahamadou

last: Diakite

first: Gordon

middle: A

last: Awandare

first: David

middle: J

last: Conway


title: RNA-binding protein with multiple splicing (Rbpms) contributes to noncompaction cardiomyopathy by regulating cardiomyocyte cytokinesis and binucleation

city: New York

first: Zhaoning

last: Wang

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

summary: Noncompaction cardiomyopathy is a common congenital cardiomyopathy associated with a deficiency of ventricular cardiomyocytes and impaired pump function. The genetic basis and underlying mechanisms of this disorder remain elusive. Polyploidization is an intrinsic feature of mammalian cardiomyocytes, which occurs shortly after birth and is accompanied by cardiomyocyte cell cycle arrest. We show that genetic deletion of the RNA binding protein with multiple splicing (Rbpms) in mice results in premature onset of cardiomyocyte polyploidization (binucleation) and consequent noncompaction cardiomyopathy. A similar blockade to cytokinesis occurs in human iPSC-derived cardiomyocytes with RBPMS gene deletion. Paired-end RNA sequencing analysis revealed that Rbpms plays an essential role in RNA splicing and mediates isoform switching from the short to the long form of Pdlim5, a heart-specific LIM domain protein that connects the sarcomere with various signaling proteins during heart development. The loss of Rbpms leads to abnormal accumulation of short Pdlim5 isoforms that disrupt cardiomyocyte cytokinesis. Our results link premature cardiomyocyte binucleation to noncompaction cardiomyopathy and highlight the central role of Rbpms in this process.

overall_design: RNA was isolated from heart ventricle of 1-day old WT or Rbpms KO mice. Stranded mRNA-seq was performed to profile gene expression changes upon Rbpms KO.

first: Peiheng

last: Gan

first: Eric

middle: N

last: Olson


title: Epithelial LIF signaling limits apoptosis and lung injury during bacterial pneumonia

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: During bacterial pneumonia, alveolar epithelial cells are critical for maintaining gas exchange and providing antimicrobial as well as pro-immune properties. We previously demonstrated that leukemia inhibitory factor (LIF), an IL-6 family cytokine, is produced by type II alveolar epithelial cells (ATII) and is critical for tissue protection during bacterial pneumonia. However, the target cells and mechanisms of LIF-mediated protection remain unknown. Here, we demonstrate that antibody-induced LIF blockade remodels the lung epithelial transcriptome in association with increased apoptosis. Based on these data, we performed pneumonia studies using a novel mouse model in which LIFR (the unique receptor for LIF) is absent in lung epithelium. While LIFR was detected on the surface of epithelial cells, its absence only minimally contributed to tissue protection during pneumonia. Single-cell RNA-sequencing (scRNAseq) was conducted to identify adult murine lung cell types most prominently expressing LIFR, revealing endothelial cells, mesenchymal cells, and ATIIs as major sources of LIFR. Sequencing data indicated that ATII cells were significantly impacted as a result of pneumonia, with additional differences observed in response to LIF neutralization, including but not limited to gene programs related to cell death, injury, and inflammation. Overall, our data suggest that LIF signaling on epithelial cells alters responses in this cell type during pneumonia. However, our results also suggest separate and perhaps more prominent roles of LIFR in other cell types, such as endothelial cells or mesenchymal cells, which provide grounds for future investigation.

overall_design: Refer to individual Series


title: Transcriptomic characterization of locally relapsed brain metastases after neurosurgery

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: Intracranial implantation of H2030-BrM cells in nude mice was performed to obtain established brain metastases. Survival neurosurgery was performed and resected tumors were processed to obtain RNA. Animals were followed for local relapse in the resection area and relapsed tumors were processed at endpoint to obtain RNA. RNA-seq was performed and data was analyzed by matched pairs (resected and relapsed tumors from the same animal).

overall_design: Matched resected and relapsed brain metastases from a novel preclinical model incorporating neurosurgery were compared using RNA-seq

first: Lucía

last: Zhu

last: Graña-Castro

first: Manuel

last: Valiente


title: miR-146a mediated Target Dependent Cooperative Biogenesis of miRNAs in Macrophage Cells

city: Kolkata

first: Ishita

last: Mukherjee

state: West Bengal

address: IICB-Translational Research Unit of Excellence, CN - 6, Sector V, Salt Lake City

country: India

institute: CSIR-Indian Institute of Chemical Biology

summary:
TLR4-activated immune response, elicited by exogenous or endogenous ligands, does give rise to several acute and chronic diseases, and plays a critical role as an amplifier of the inflammatory response. Along with, a cluster of TLR4-responsive miRNAs create a crosstalk during inflammatory escalation. Our data shows miR-146a even not having binding sites for different signalling mediators, alleviates pro-inflammatory response by modulating different stress-induced response (cytokine production, generation of NO, apoptosis etc) to reestablish macrophage homeostasis. We were curious to unravel this phenomenon.

Here, we have reported miR-146a influences the biogenesis of a group of miRNAs after its overexpression. We have adopted a tet-on responsive miR-146a overexpression system in murine macrophages. A group of miRNAs has shown significant differential expression after miR-146a overexpression. Later, our targetome-based study correlated with this observation to establish the link between augmentations of anti-inflammatory response inside the cells with the miR-146a overexpression that probably have a significant role in establishing cellular homeostasis.

overall_design: miR-146a overexpression in RAW264.7 cells regulates expression of other miRNA (Co-ordinate biogenesis)

first: Suvendra

last: Bhattacharrya

first: Saikat

last: Chakrabarti

first: Susanta

last: Chatterjee


title: Expression data from intermediate stage of murine pancreatic ductal adenocarcinoma (PDAC) and control pancreas

city: Marseille

first: Quentin

last: Da Costa

address: 232 boulevard de Sainte Marguerite

country: France

institute: Institut Paoli-Calmettes

summary: We used microarrays to detail the global gene expression signature of PDAC and to identify distinct up- and down-regulated transcripts in these tumors compared to control pancreas. We also established from this dataset the metabolic signature of PDAC in order to define new metabolic therapeutic target for pancreatic cancer.

overall_design: PDAC were removed at an intermediate stage of tumorigenesis in 6-weeks old mice with Mixed genetic background : B6CBAF1 x C57BL/6 x 129/Sv x FVB/n.

first: Sophie

last: Vasseur

first: Fabienne

last: Guillaumond

first: Victoire

last: Gouirand

first: Ghislain

last: Bidaut


title: Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [Pro-seq]

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road, 260 EMRB

department: Biochemistry

institute: University of Iowa

summary: To characterize transcription throughout the HCMV infection, paired-end PRO-Seq was performed on human foreskin fibroblasts (HFF) infected with human cytomegalovirus (HCMV) for 4 h, 12 h, 24 h, 48 h, and 72 h using the TB40/e strain. Cells were treated with 1µM flavopiridol 1 hour prior to isolation. Additionally, PRO-Cap was performed on untreated HFFs after 72 h of infection. Each experiment was performed with adapters containing 8 nt of random sequence flanking both ends (16 total bases of randomness) to enable deduplication.

overall_design: TB40/E Timecourse: PRO-Seq was preformed on HFF infected for 4h, 12h, 24h, 48h, and 72h and treated with 1 µM flavopiridol for 1 hour. TB40/E PRO-Cap was prefromed on HFFs infected for 72 hr.

first: Benjamin

middle: M

last: Spector

first: Mrutyunjaya

last: Parida

first: Chris

last: Ball

first: Ming

last: Li


title: SRC skews cell fate from apoptosis to senescence

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Cells responding to DNA damage implement complex adaptive programs that often culminate in two distinct outcomes: apoptosis or senescence.  Here, to systematically identify factors driving each response, we analyzed human IMR-90 fibroblasts exposed to increasing doses of the genotoxin etoposide.  We identified SRC as a key kinase contributing to this decision fork.  SRC was activated by low (50 μM) etoposide but not by high (200 μM) etoposide levels.  At low DNA damage, SRC-mediated activation of p38 critically promoted cell survival and senescence, and increased pro-survival BCL2L2 levels, while SRC-mediated repression of p53 prevented a rise in pro-apoptotic PUMA levels.  At high DNA damage, SRC was not active, leading to elevation of p53, inhibition of p38, and apoptosis.  In mice exposed to DNA damage, pharmacologic inhibition of SRC prevented the tissue accumulation of senescent cells.  Inhibiting SRC could be exploited for inducing senescent-cell apoptosis in tissues to improve health outcomes.

overall_design: Human IMR-90 fibroblasts were exposed to low (50 μM) or high (200 μM) doses of the genotoxin etoposide for 48 hours, and compared to  control IMR-90 cells.

first: Carlos

last: Anerillas

first: Allison

last: Herman

first: Martina

last: Rossi

first: Rachel

last: Munk

first: Elin

last: Lehrmann

first: Jennifer

middle: L

last: Martindale

first: Chang-Yi

last: Cui

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe


title: Liraglutide + PYY3-36 combination therapy mimics effects of Roux-en-Y bypass on early NAFLD whilst lacking-behind in metabolic improvements.

status: Public on Feb 16 2022

city: Würzburg

first: Tom

last: Gräfenhan

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

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

summary: Background: Non-alcoholic fatty liver disease (NAFLD) is common in the general population. Treatment options for NAFLD are very limited, GLP-1 analogues, however, seem to be effective. Roux-en-Y gastric bypass (RYGB) is highly effective in terms of body weight loss and improves histologic and metabolic markers of NAFLD. We directly compared the effects of RYGB and a treatment with liraglutide and/or peptide tyrosine tyrosine 3-36 (PYY3-36) on early NAFLD. Methods: High-fat diet (HFD)-induced obese male Wistar rats were randomized into 6 treatment groups: RYGB, sham-operation (Sham), liraglutide (0.4mg/kg/day), PYY3-36 (0.1mg/kg/day), li-raglutide+PYY3-36 and saline. Following intervention and after an observation period of 4 weeks liver samples were histologically evaluated, ELISAs and RT-qPCRs +RNA sequencing were per-formed. Results: RYGB and liraglutide+PYY3-36 induced a similar body weight loss and marked histological improvements with significantly less steatosis compared to sham/saline. However, only RYGB induced significant metabolic improvements and mRNA expression changes. Con-clusions: liraglutide+PYY3-36 combination therapy mimics the positive effects of RYGB on weight reduction and on hepatic steatosis, while its effects on insulin resistance and adipose tissue dys-function (adiponectin/leptin ratio) lack behind RYGB.

overall_design: Examination of changes of mRNA in different treatment groupts in livers of male Wistar rats

first: Ulrich

last: Dischinger

first: Julia

last: Hasinger

first: Tobias

last: Heckel

first: Thorsten

last: Bischler

first: Christoph

last: Otto

first: Florian

last: Seyfried

first: Martin

last: Fassnacht

first: Andreas

last: Geier

first: Valentin

last: Metzner

first: Gloria

last: Herzog


title: The impact of physical frailty on the response to inactivated influenza vaccine in older adults

city: PITTSBURGH

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

summary: Physical frailty's impact on hemagglutination inhibition antibody titers (HAI) and peripheral blood mononuclear cell (PBMC) transcriptional responses after influenza vaccination is unclear. Physical frailty was assessed using the 5-item Fried frailty phenotype in 168 community- and assisted-living adults ≥55 years of age during an observational study. Blood was drawn before, 3, 7, and 28 days post-vaccination with the 2017-2018 inactivated influenza vaccine. HAI response to the A/H1N1 strain was measured at Days 0 and 28 using seropositivity, seroconversion, log2 HAI titers, and fold-rise in log2 HAI titers. RNA sequencing of PBMCs from Days 0, 3 and 7 was measured in 28 participants and compared using pathway analyses. Frailty was not significantly associated with any HAI outcome in multivariable models. Compared with non-frail participants, frail participants expressed decreased cell proliferation, metabolism, antibody production, and interferon signaling genes. Conversely, frail participants showed elevated gene expression in IL-8 signaling, T-cell exhaustion, and oxidative stress pathways compared with non-frail participants. These results suggest that reduced effectiveness of influenza vaccine among older, frail individuals may be attributed to immunosenescence-related changes in PBMCs that are not reflected in antibody levels.

overall_design:
Transcriptomic analysis of blood cells from patients before infleunza vaccination and at days 3 and 7 post vaccination.
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Authors state "Due to privacy issues, we will not be uploading raw data because the data consists of human sequences."

first: John

middle: F

last: Alcorn

first: Richard

last: Zimmerman


title: Lung injury in mice exposed to aerosolized staphylococcal enterotoxin B potentiated by lipopolysaccharide: Associated lung transcriptome response

city: Beijing

first: Fuliang

last: Zong

state: China

address: Feitai region Dongda road

country: China

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

summary: The global transcriptome profile of lung tissue in mice after exposure to aerosolized SEB potentiated by LPS or LPS alone

overall_design: Lung mRNA profiles of 6-8 week-old females wild type (WT) mice treated with low dose aerosolized staphylococcal enterotoxin B combined with an intraperitoneal injection of LPS (SEB + LPS group); 2) mice treated with LPS intraperitoneal injection only (LPS group); and 3) control mice (CTRL group).

first: Changjiao

last: Gan

first: Bo

last: Gao

first: Huiying

last: Yang


title: MicroRNA profiling data of fresh lung adenocarcinoma and adjacent normal tissues obtained from ten Korean patients using next-generation sequencing

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

type: Non-coding RNA profiling by high throughput sequencing

summary: Differentially expressed miRNAs and potential miRNA biomarkers for lung adenocarcinoma tissues compared to adjacent normal tissues were identified using DESeq2 and Wx, respectively.

overall_design: MicroRNA transcriptomes from fresh tumor and adjacent normal tissues of ten Korean patients who were diagnosed with lung adenocarcinoma were profiled using a next-generation sequencing (NGS) technique called miRNA-seq.

first: Yoon

last: Ko

first: Young-Ho

last: Ahn


title: Genome wide analysis of circulating miRNAs in growth hormone secreting pituitary neuroendocrine tumor patients' plasma

city: Riga

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

summary: Objective  Circulating plasma miRNAs have been increasingly studied in the field of pituitary neuroendocrine tumor (PitNET) research. Our aim was to discover circulating plasma miRNAs species associated with growth hormone (GH) secreting PitNETs and assess how the plasma levels of discovered miRNA candidates are impacted by SSA therapy and whether there is a difference in their levels between GH secreting PitNETs and other PitNET types.  Methods   miRNA candidates were discovered using the whole miRNA sequencing approach and differential expression analysis. Selected miRNAs were then analyzed using real-time polymerase chain reaction (qPCR).  Results  Whole miRNA sequencing discovered a total of 19 differentially expressed miRNAs (DEMs) in GH secreting PitNET patients' plasma 24 hours after surgery and 19 DEMs between GH secreting PitNET patients’ plasma and non-functioning (NF) PitNET patients’ plasma. Seven miRNAs were selected for further testing of which miR-625-5p, miR-503-5p miR-181a-2-3p and miR-130b-3p showed a significant downregulation in plasma after 1 month of SSA treatment. miR-181a-5p and mir-625-5p were also found to be significantly downregulated in plasma of GH secreting PitNET patients vs. NF PitNET patients.  Conclusions  Our study suggests that expression of plasma miRNAs miR-625-5p, miR-503-5p miR-181a-2-3p and miR-130b-3p in GH secreting PitNETs is affected by SSA treatment. Additionally, miR-625-5p and miR-181a-5p can distinguish GH secreting PitNETs from other PitNET types warranting further research on these miRNAs for treatment efficacy.

overall_design:
We compared plasma miRNA content and levels before (*-x) and after surgery (*-24h) focusing on GH secreting PitNET patients. Selected miRNA candidates from our data and literature were then tested in a longitudinal manner in somatostatin analogues (SSA) treatment group. Additionally, we validated selected targets in an independent GH secreting PitNET group.

Please note that the samples PitNET44-24h and PitNET44-x were determined to be outliers and excluded from the further analysis.

first: Helvijs

last: Niedra

first: Helena

last: Litvina

first: Kaspars

last: Megnis

first: Inga

last: Balcere

first: Mihails

last: Romanovs

first: Liva

last: Steina

first: Janis

last: Stukens

first: Austra

last: Breiksa

first: Jurijs

last: Nazarovs

first: Jelizaveta

last: Sokolovska

first: Rasa

last: Liutkeviciene

first: Alvita

last: Vilkevicute

first: Ilze

last: Konrade

first: Vita

last: Rovite


city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

summary:
Chordoma associated with tuberous sclerosis complex (TSC) are an extremely rare tumor that was described only in 13 cases since 1975. Сhordomas themselves are malignant slow-growing bone tumors thought to arise from vestigial or ectopic notochordal tissue.
In total, with CMA we found 180 regions with CNVs in the chordoma tumor sample. The longest section was 58,014 kbp long (arr[GRCh38] 9q21.31q34.3(79267492_137281464)x1-2), harboring region 9q34 that includes TSC1 gene. Also, 12 oncogenes including KRAS and CBX7 were in amplified regions and 92 tumor suppressor genes were in regions with loss status. Four genes that participate in epigenetic regulation, - ELP3, GTF3C4, MBD2, and  PHF2 were found to be affected. Moreover, members of the APOBEC3 family were amplified.

overall_design: DNA was extracted from FFPE tumor tissues of chordoma from one patient with tuberous sclerosis complex by using GeneRead DNA FFPE kit (Qiagen, cat. № 180134). Copy number variation were analyzed by using OncoScan™ CNV Assay (Thermo Fisher Scientific, USA) on GeneChip Scanner 3000 7G System (Applied Biosystems, USA) according to manufacturer's protocol. No techinal replicates were perfomed.

middle: I

first: Kirill

last: Anoshkin


title: TP53 promotes lineage commitment of human embryonic stem cells through ciliogenesis and sonic hedgehog signaling [ChIP-seq]

city: Dallas

first: Sushama

last: Sivakumar

state: Texas

address: 6001 Forest Park Road

department: Pharmacology

institute: UT Southwestern Medical center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: NGS was used to analyze role of TP53 in differentiation of human embryonic stem cells. TP53, a transcription factor, binds DNA and regulates transcription of specific genes. Chipseq of TP53 was done on WT ESCs and NPCs to identify direct targets of TP53 during differentiation of hESCs into neuronal lineage.

overall_design: TP53 target genes in WT hESCs and in vitro differentiated NPCs were obtained.

first: Ningyan

last: Cheng

first: Mohammed

last: Kanchwala

first: Chao

last: Xing

first: Hongtao

last: Yu


title: TP53 promotes lineage commitment of human embryonic stem cells through ciliogenesis and sonic hedgehog signaling [CRISPR screen]

summary: CRISPR-Cas9 screen was done to identify genes required for NPC differentiation. Sox1 is an established NPC marker. Human ESCs were infected with GecKO v2 library, selected with puromycin and then allowed to differentiate into Neural progenitor cells (NPC) using StemDiff monolayer protocol (Stem cell Technologies). Day 7 NPCs were collected and FACS sorted to obtain bottom 1% of Sox1 expressing cells. NGS was used to identify guide sequences in cell population and determine the genes required for Sox1 expression during NPC differentiation.

overall_design: hESCs were infected with GecKO library v2, selected with puromycin and allowed to differentiate into NPCs by monolayer protocol. Day 7 NPCs were collected and FACS sorted to obtain bottom 1% of Sox1 expressing cells. Thus, genes required for Sox1 expression during NPC differentiation were obtained as screen hits.

first: Shutao

last: Qi

first: Adwait

last: Sathe


title: A 5’ tRNA-Ala derived small RNA regulates anti-fungal defense in plants

city: Beiing

first: Yijun

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

summary: Apart from their primordial role in protein synthesis, tRNAs can be cleaved to produce tRNA-derived small RNAs (tsRNAs). The biological functions of tsRNAs in plants remain largely unknown. In this study, we developed RtcB-based RNA sequencing, a method that captures and distinguishes between 2’,3’-cyclic-phosphate (cP)-terminated RNAs and 3’-OH-terminated RNAs, and profiled 5’ tsRNAs and 5’ tRNA halves in Arabidopsis thaliana. We found that Arabidopsis 5’ tsRNAs and 5’ tRNA halves predominantly contain a cP at the 3’ end and require S-like RNase 1 (RNS1) and RNS3 for their production. One of the most abundant 5’ tsRNA, 5’ tsR-Ala, likely by associating with AGO1, negatively regulates Cytochrome P450 71A13 (CYP71A13) expression and camalexin biosynthesis to repress anti-fungal defense. 5’ tsR-Ala is downregulated upon fungal infection. Our study provides a global view of 5’ tsRNAs and 5’ tRNA halves in Arabidopsis and unravels an important role of a 5’ tsRNA in regulating anti-fungal defense.

overall_design: To profile 5’ tsRNAs and 5’ tRNA halves in Arabidopsis seedlings, we developed a RtcB ligation-based sRNA sequencing (RtcB sRNA-seq) in this study. To understand the functions of 5’ tsRNAs, we perform mRNA-seq of mutants for the biogenesis of 5’ tsRNAs to indentify differentially expressed genes in these mutants

first: Hanqing

last: Gu

first: Bi

last: Lian

first: Yuxiang

last: Yuan

first: Ci

last: Kong

first: Yan

last: Li

first: Chang

last: Liu


title: Molecular Signatures and Cellular Diversity During Mouse Habenula Development

city: Utrecht

first: Lieke

last: van de Haar

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

summary: single-cell RNA sequencing data (plate-based CelSeq2) of developing mouse habenula. DevHb series contains E11, E12, E13, E15, E18, P4, P7 and adult Brn3a-tLacZ mouse habenula and E18 contains C57BL6 mouse habenula.

first: Danai

last: Riga

first: Juliska

last: Boer

first: Youri

last: Adolfs

first: Thomas

last: Sieburgh

first: Roland

last: van Dijk

first: Kyoko

last: Watanabe

first: Nicky

middle: C

last: van Kronenburg

first: Mark

last: Broekhoven

first: Danielle

last: Posthuma

first: Frank

last: Meye

first: Onur

last: Basak

first: R

last: Pasterkamp


title: mRAN expression profiles in bone marrow mesenchymal stem cells (MSC) from Wild Type and Lama4-deficient mice co-cultured with MLL-AF9 AML cells

city: Stockholm

first: Hong

last: Qian

address: Hälsovägen 7C (lastkaj), 14157 Huddinge/Stockholm

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

summary: Bone marrow (BM) niche contributes to hematopoietic regeneration and can be remodeled by leukemic cells. We have found that Lama4 deletion in mouse mesenchymal stem cells (MSCs) could promote the proliferation of MLL-AF9 acute myeloid leukemia (AML) cells and chemoresistance of the cells to chemotherapy cytarabine. However, whether Lama4 deficient MSCs are more susseptible for AML cell remodeling remains to be explored. Here we report that differential molecular alterations in Lama4 deficient MSCs compared to wild type MSCs after being exposed to the AML cells for 48hours, which might be related to the enhanced AML cell proliferation and chemoresistance.

overall_design: Examination of mRNA profiles in mesenchymal stem cells (CD45-TER119-CD31-CD44-CD51+SCA1+) from Wild Type and Lama4-deficient mice co-cultured with MLL-AF9 AML cells

first: Makoto

last: Kondo

first: Huan

last: Cai

first: Lakshmi

last: Sandhow

first: Pingnan

last: Xiao

first: Anne-Sofie

last: Johansson

first: Takako

last: Sasaki

first: Karl

last: Tryggvarson

first: Marja

last: Ekblom


title: TP53 promotes lineage commitment of human embryonic stem cells through ciliogenesis and sonic hedgehog signaling [RNA-Seq]

first: Sushama

last: Sivakumar

summary: H9 WT ESCs or TP53 KO (Clone 1) ESCs were injected subcutaneously into mice for teratoma formation. 6-8 weeks later, teratomas were isolated and total RNA was purified. TruSeq library preparation kit from Illumina was used to make libraries for RNA-Seq. NGS sequencing on Illumina NextSeq 500 was performed and data was analyzed to determine changes in transcriptome between WT and TP53 KO teratoma cells.

overall_design: Transcriptome of WT and TP53 KO teratoma cells.

first: Adwait

last: Sathe

first: Mohammed

last: Kanchwala

first: Chao

last: Xing

first: Hongtao

last: Yu


title: TP53 promotes lineage commitment of human embryonic stem cells through ciliogenesis and sonic hedgehog signaling [RNA-Seq 2]

summary: NGS was used to analyze role of TP53 in differentiation of human embryonic stem cells. RNAseq and was done in WT and p53 KO embryonic stem cells (ESCs) and in in vitro differentiated Neural progenitor cells (NPCs).

overall_design: Transcriptome of WT and TP53 KO ESCs and in vitro differentiated NPCs.


title: Effects on mRNA levels of a Numb and Numb-like conditional knockout in skeletal muscle fibers

city: Bronx

first: christopher

middle: p

last: cardozo

state: NY

address: 130 West Kingsbridge Road

department: CMSCI

institute: Bronx VA Medical Center

summary: We investigated the gene expression changes resulting from loss of Numb from skeletal muscle fibers using a conditional, inducible knockout of Numb and its close homolog Numb-like (NumbL) bulk RNA-sequencing.

overall_design: A 2 X 2 design was used with factors being tamoxifen treatment and presence of a transgene expression an ER2-Cre under the human skeletal actin promoter.

first: Christopher

last: Cardozo

first: Rita

last: De Gasperi

first: Wei

last: Zhao

first: Bin

last: Zhang

first: Lei

last: Guo

first: Marco

last: Brotto


title: RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription

city: Ithaca

first: Charles

middle: G

last: Danko

address: Hungerford Hill Rd

institute: Baker Institute

summary: PRO-seq experiment of Nelfb deg mESC in serum/LIF or during pluripotency transitions, with or without dTAG-13.

overall_design: Triplicates for most conditions. Nuclei were collected at indicated time points after treatment/control. Drosophila S2 nuclei were then added as spike-in and mixture of mouse and S2 cells was frozen together. Run-on reaction and library preparation was performed on the mixture of mouse and S2 cells.

first: Abderhman

last: Abuhashem

first: Alexandra

last: Chivu

first: Anna-Katerina

last: Hadjantonakis


title: Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Developmental origins of dendritic cells (DCs) including conventional DCs (cDCs, comprising cDC1 and cDC2 subsets) and plasmacytoid DCs (pDCs) remain unclear. We studied DC development in unmanipulated adult mice using inducible lineage tracing combined with clonal DNA "barcoding" and single-cell transcriptome and phenotype analysis (CITE-Seq). Inducible tracing of Cx3cr1+ hematopoietic progenitors in the bone marrow showed that they simultaneously produce all DC subsets including pDCs, cDC1s and cDC2s. Clonal tracing of hematopoietic stem cells (HSCs) and of Cx3cr1+ progenitors revealed clone sharing between cDC1s and pDCs, but not between the two cDC subsets or between pDCs and B cells. Accordingly, CITE-Seq analyses of differentiating HSCs and Cx3cr1+ progenitors identified progressive stages of pDC development including Cx3cr1+ Ly-6D+ propDCs that were distinct from lymphoid progenitors. These results reveal the shared origin of pDCs and cDCs, and suggest a revised scheme of DC development whereby pDCs share clonal relationship with cDC1s

overall_design: For transposon integration site cloning, bone marrow cells and splenocytes were isolated from the Pdzk1ip1CreERR26FlipJump mice at weeks 20 post tamoxifen induction. HSC, DC subsets (pDC, cDC1 and cDC2) and Immature B were sorted from isolated bone marrow cells and splenocytes. Splenocytes from Cx3cr1CreERYFP R26FlipJump mice were obtained on days 8 post tamoxifen induction. GFP+ YFPlo/- DC subsets (pDC, cDC1 and cDC2) were sorted. GFP+ DC subsets (pDC, cDC1 and cDC2) from Flt3L cultured Cx3cr1CreERYFPR26FlipJump mouse BM cells were sorted. For CITE-seq experiments, HSC-derived Flt3+ progenitors were isolated from the Pdzk1ip1CreERR26FlipJump mice at weeks 3, 4 or 5 following tamoxifen induction.  Cx3cr1+ progenitors were isolated from Cx3cr1CreERYFP R26FlipJump at days 2 and 5 post tamoxifen induction. For bulk RNA-seq experiments, the pDC with GFP or without GFP was sorted from Cx3cr1CreERYFPR26FlipJump mouse BM cells at 8 days post tamoxifen induction.

first: Jue

last: Feng

first: Joseph

last: Pucella

first: Boris

last: Reizis


title: mRAN expression profiles in mesenchymal progenitor cells freshly-sorted from Wild Type and Lama4-deficient mice

first: Hong

last: Qian

summary: Bone marrow (BM) niche contributes to hematopoietic regeneration under stress like irradiation and leukemia. However, the mechanisms remain poorly defined. We here report that Lama4 deletion in mice results in reduction of mesenchymal progenitors (MPCs) and endothelial cells in BM. Following irradiation, Lama4-/- mice displayed impaired hematopoiesis recovery accompanied with dysregulation of BM niche factors like angiopoietin-1 and Tgfb1 in the MPCs. Post-transplantation of MLL-AF9 acute myeloid leukemia (AML) cells, we observed accelerated AML onset in Lama4-/- mice. Moreover, these Lama4-/- AML mice displayed faster relapse after therapeutic BM transplantation. Mechanistically, Lama4-/- niche promoted AML cell proliferation and chemoresistance to chemotherapy cytarabine by conferring AML greater antioxidant activity. Together, our study demonstrates that Lama4 is required to maintain hematopoietic niche integrity and to suppress AML progression and chemoresistance by restricting metabolic defense support to AML. Therefore, activating Lama4 signaling pathways may offer potential new therapeutic options for AML.

overall_design: Examination of mRNA profiles in mesenchymal progenitor cells (CD45-TER119-CD31-CD44-CD51+SCA1-) freshly-sorted from 3 wild type (WT) and 3 Lama4-/- mice 6 weeks post sublethetal irridation (7Gy)

first: Makoto

last: Kondo

first: Huan

last: Cai

first: Lakshmi

last: Sandhow

first: Pingnan

last: Xiao

first: Anne-Sofie

last: Johansson

first: Takako

last: Sasaki

first: Karl

last: Tryggvarson

first: Marja

last: Ekblom


title: A missense mutation in AIOLOS causes B cell deficiency by interfering with IKAROS

city: Kanagawa

first: Kazuki

last: Okuyama

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

department: IMS

country: Japan

institute: RIKEN Yokohama

summary: A missense mutation (G158R) in Ikzf3 gene resulted in defective generation of B cells in mice. Pre-B cells were profoundly decreased in homozygous mutant mice. Heterozygous mutant mice showed milder B cell developmental defects, and decreased B cells in the secondary lymphoid organs were observed. Ikzf3 encodes Aiolos, which makes heterodimer with Ikaros. Our findings indicate that the loss-of-function mutation in Aiolos hinders B cell development by interfering Ikaros' function via formation of heterodimers.

overall_design:
Sample 1-18: mRNA profiles of pre-pro B cells and pre-B cells in wild-type, heterozygous and homozygous Ikzf3 G158R mutant mice.
Sample 19-30: Genome-wide bindings of Ikaros and Aiolos in pre-B cells and thymocytes of wild-type and homozygous Ikzf3 G158R mutant mice.

first: Motoi

last: Yamashita


title: Small Extracellular Vesicles Secreted by Brown Adipose Tissue Mediate Exercise Cardioprotection via MicroRNA-Dependent Suppression of the MAPK Pathway

status: Public on Feb 15 2022

city: Xi 'an

first: Hang

last: Zhao

address: 127 Changle west road, Xi 'an  China

institute: Air force military medical university

summary: Long-term exercise provides reliable cardioprotection via incompletely understood mechanisms.The sEVs secreted by BAT participate in exercise cardioprotection via delivering the cardioprotective miRNAs into the heart. These results provide novel insights into the mechanisms underlying the BAT-cardiomyocyte interaction and highlight BAT sEVs and their contained miRNAs as alternative candidates for exercise cardioprotection.

overall_design: miRNA-Seq of BAT sEVs and plasma sEVs before and after exercise in mice

first: Ling

last: Tao

first: Fuyang

last: Zhang

first: Xiyao

last: Chen


title: ZmCOI2a and ZmCOI2b redundantly regulate anther dehiscence and gametophytic male fertility in maize

first: Xiaolong

last: Qi

state: Beijing

address: No. 2, Yuanmingyuan west Road

institute: China Agricultural University

summary: We identified two genes, ZmCOI2a and ZmCOI2b, which redundantly regulate male fertility.

overall_design: Examination of 6 different mature anther in maize by RNA-Seq.

first: Shuwei

last: Guo

first: Shaojiang

first: Chenxu

last: Liu


title: Legionella pneumophila cells after sub-lethal heat shock

city: St-Anne-de-Bellevue

first: Sebastien

middle: P

last: Faucher

state: Quebec

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

summary: Legionella pneumophila Philadelphia-1 strain was grown to stationary phase in AYE broth and starved in freshwater for 2 hours and RNA was harvested with or without sublethal heat shock via immersion in a 55 degree C hot water bath for 5 minutes

sample_organism: Legionella pneumophila subsp. pneumophila ATCC 33215

platform_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: Legionella pneumophila Philadelphia-1 strain  with or without sublethal heat shock

first: Jeffrey

last: Liang

last: aucher


title: Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

city: Rochester

first: Fanju

last: Meng

address: 601 Elmwood Avenue

department: Biomedical Genetics

institute: University of Rochester Medical Center

summary: Here we describe successful implementation of CUT&Tag for profiling protein-DNA interactions in zebrafish embryos. We optimized CUT&Tag protocol to generate high resolution maps of enrichment for the histone variant H2A.Z during zebrafish development. We were able to establish dynamics of H2A.Z genomic patterning from shield stage to 24hpf embryos. Our work demonstrates the power of combining CUT&Tag with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

overall_design: Triplicates of CUT&Tag for H2A.Z were performed in 6hpf and 24hpf zebrafish embryos.


title: Marginal Zone B Cells Trogocytose from Dendritic Cells and Present to T cells MHC II–C3 complexes

city: Parkville

first: Nagaraj

middle: Sundara

last: Moily

state: Victoria

address: Bio21 Institute, The University of Melbourne,

department: Biochemistry and Molecular Biology

country: Australia

institute: The University of Melbourne

summary:
Purpose: Production of broad-spectrum antibodies against T cell-dependent antigens requires marginal zone (MZ) B cells to present antigenic peptides complexed to MHC II. Here we describe the trogocytic acquisition of these complexes from dendritic cells (DCs). Complement C3 (C3) binds to MHC II on murine and human DCs. Recognition of C3 by MZ B cell complement receptor 2 triggers trogocytosis of DC plasma membrane and its receptors, which become exposed on the MZ B cells. Excessive trogocytosis is deleterious but prevented by membrane ubiquitin ligase MARCH1, which limits the number of MHC II–C3 complexes displayed on the DC surface. MHC II molecules are thus receptors for constitutively activated and potentially harmful C3, an activity that enables acquisition of DC-like functions by trogocytic MZ B cells.
Methods: mRNA profiles of splenic cDC1s, B cells and CD11cintCD24+CD8int cells of wild type (WT) and March1-/- mice mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. All 100-base-pair single-end reads were mapped to the reference mouse genome (GRCm38/mm10) using STAR aligner, and gene-wise counts were obtained using Subread package. Differential expression analysis of RNA sequencingdata was carried out using the edgeR  and limma-voom packages in Bioconductor.
Results: Using an optimized data analysis workflow, we mapped about 14 million sequence reads per sample to the mouse genome (build mm10) and identified 16,182 genes in the different cell types from WT and March1−/− mice.Transcriptomic profiling revealed over 6500 genes differentially expressed between cDC1s and B cells. Principle component analyses revealed very few differences between WT and March1−/− cDC1s, and between WT and March1−/− B cells. Notably, the transcriptome of CD11cintCD24+CD8int cells was similar to those of WT or March1−/− B cells, indicating they belonged to the B cell lineage.
Conclusions: In our study we have described that MHC II ubiquitination by MARCH1 plays two important roles: first, to enhance the removal of surface MHC II–C3 complexes on all APCs; and second, to limit MZ B cell trogocytosis and elimination of cDCs. It is conceivable these two functions, more than the regulation of MHC II antigen presentation, have been the major drivers for the conservation of MHC II ubiquitination through evolution.

middle: S


title: Rv0500A is a transcription factor that links Mycobacterium tuberculosis environmental response and division

city: Boston

first: Shumin

last: Tan

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

summary: The purpose of this study was to identify genes that are differentially expressed upon rv0500A over-expression, to reveal the impact of Rv0500A on global transcription in different environmental conditions.

sample_organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

overall_design: Mtb strain Erdman harboring a tetracycline inducible N-terminally tagged 6x His-Rv0500A construct was grown to an OD600 of 0.6 in standing, filter-capped  T-75 flasks and treated with either 200 ng/ml anhydrotetracycline (ATC) or ethanol (EtOH) as a carrier control for 2 hours. Bacteria were then subcultured to an OD600 of 0.3 in standing, filter-capped  T-25 flasks in either 7H9, pH 7 media, or 7H9, pH 5.7 media supplemented with 250 mM NaCl, with continued presence of ATC or EtOH as appropriate. Exposure to the different media conditions was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted. RNA was prepared by removing the rRNA and library prepping with a TruSeq Stranded kit (Illumina) before high-throughput sequencing with an Illumina HiSeq 2500 (High Output v4) (100 bp single end reads, one lane). Two biological samples per condition were sequenced.

first: Yuzo

last: Kevorkian

first: Nathan

last: MacGilvary


title: Puerarin attenuates diabetic kidney injury through interaction with Guanidine nucleotide-binding protein Gi subunit alpha-1 (Gnai1) subunit

city: New York

first: Chengguo

last: Wei

address: 1468 Madison Ave, Annenberg 23-16

institute: Icahn School of Medicine at Mount Sinai

summary: Radix puerariae, a traditional Chinese herbal medication, has been used to treat patients with diabetic kidney disease (DKD). Our previous studies demonstrated that puerarin, the active compound of radix puerariae, improves diabetic podocyte injury in type 1 DKD mice through attenuation of oxidative stress. However, the direct molecular target of puerarin and its underlined mechanisms in DKD remains unknown. In this study, we first confirmed that puerarin also improved DKD in type 2 diabetic mice (db/db). Through RNA-sequencing of isolated glomeruli, we found that differentially expressed genes (DEGs) that were altered in the glomeruli of these diabetic mice but reversed by puerarin treatment were involved mostly in oxidative stress, inflammatory, and fibrosis. Further analysis of these reversed DEGs revealed protein kinase A (PKA) was among the top pathways. By utilizing the drug affinity responsive target stability (DARTS) method combined with mass spectrometry analysis we identified guanine nucleotide-binding protein Gi alpha-1 (Gnai1) as the direct binding partner of puerarin. Gnai1 is an inhibitor of cAMP production which is known to have protection against podocyte injury. Searching Nephroseq datasets revealed that Gnai1 expression increased in the glomeruli of human DKD. In vitro, we showed that puerarin not only interacted with Gnai1 but also increased cAMP production in human podocytes and kidney cortex of mice treated with peurarin. Puerarin also enhanced CREB phosphorylation, a downstream transcription factor of cAMP/PKA. Overexpression of CREB reduced high glucose-induced podocyte apoptosis. We conclude that the renal protective effects of puerarin are likely through inhibiting Gnai1 to activate cAMP/PKA/CREB pathway in podocytes.

overall_design: We used unbiased approach to further dissect the molecular mechanisms of puerarin in DKD by focusing on its direct binding partners. We were able to identify Gnai1 as a direct interacting molecule of puerarin in podocytes and our data suggest that puerarin may improve podocyte injury through inhibition of Gnai1 and activation of cAMP/PKA pathway.

first: Qingqing

last: Zhu

last: Yang

first: Yifei

last: Zhong


title: Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures

city: Yokohama

first: Alice

last: Lambolez

state: Kanagawa

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

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Many plants are able to regenerate upon cutting, and this process can be enhanced in vitro by incubating explants on hormone-supplemented media. While such protocols have been used for decades, little is known about the molecular details of how incubation conditions influence their efficiency. In this study, we show that warm temperature promotes both callus formation and shoot regeneration efficiency in Arabidopsis thaliana. Our RNA sequencing analysis unveil that this   accompanied by the enhanced expression of several regeneration-associated genes, such as CUP-SHAPED COTYLEDON 1 (CUC1), encoding a transcription factor involved in shoot meristem formation, and ISOPENTENYLTRANSFERASE (IPT1) and YUCCA1/4 (YUC1/4), encoding key enzymes for cytokinin and auxin biosynthesis, respectively. Consistently, mutations in CUC1 and IPT1 or chemical inhibition of YUCs reduce the enhancement of shoot regeneration at warm temperature. When combined with ChIP sequencing analyses, our RNA sequencing data further reveal that histone variant H2A.Z is enriched on these differentially expressed loci at 17°C and that its occupancy level decreases when the ambient temperature increases to 27°C. This study thus unveil a new epigenetic mechanism that influences hormone-induced regeneration and brings further insights on how incubation temperature is a crucial parameter in optimizing protocols for in vitro tissue culture.

overall_design: RNA sequencing in Arabidopsis thaliana hypocotyl explants exposed to CIM for 4 days then SIM for 4 days, at either 17°C or 27°C

first: Ayako

last: Kawamura

first: Keiko

last: Sugimoto


title: Time-series single-cell RNA sequencing analysis of WT or CCR2-/- murine lungs in silica-induced pulmonary fibrosis model.

city: Noda

first: Tatsuro

last: Ogawa

address: 2641, Yamasaki

institute: Tokyo University of Science

summary: Pulmonary fibrosis (PF) is a progressive fibrotic disease with a poor prognosis and suboptimal therapeutic options. Macrophages have been implicated in PF; however, the roles of macrophage subsets, particularly interstitial macrophages (IM), remain unknown. To address this issue, we performed time-series single-cell RNA sequencing (scRNA-seq) analysis in silica-induced PF model mice and clarify the characteristics of IM. In addition,  to elucidate the origin of IM, we used CCR2-/- mice which supressed classical monocyte infiltration.

overall_design: To clarify transcriptomic landscape of silica-administrated murine lungs, we intratracheally administered with silica (400 mg/kg) to WT or CCR2-/- mice and lungs were harvested at day3, 7, and 21.  scRNA-seq was performed using Illumina Novaseq 6000 sequencer.

first: Shigeyuki

last: Shichino

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima


title: TP53 promotes lineage commitment of human embryonic stem cells through ciliogenesis and sonic hedgehog signaling

first: Sushama

last: Sivakumar

address: 6001 Forest Park Road

institute: UT Southwestern Medical center

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

overall_design: Refer to individual Series


title: Rv0500A is a transcription factor that links Mycobacterium tuberculosis environmental response with division and impacts host colonization

summary: The purpose of this study was to identify genes that are differentially expressed upon rv0500A deletion, to reveal the impact of Rv0500A on global transcription in different environmental conditions.

overall_design: Mtb strain Erdman wild type (WT), ∆rv0500A, and rv0500A* (complemented mutant) were grown to mid-log phase (OD600 ~ 0.6) in standing, filter-capped  T-75 flasks, then subcultured to an OD600 of 0.3 in standing, filter-capped  T-25 flasks in either 7H9, pH 7 media, or 7H9, pH 5.7 media supplemented with 250 mM NaCl. Exposure to the different media conditions was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted. RNA was prepared by removing the rRNA and library prepping with an Illumina Stranded Total RNA with Ribo-Zero Plus kit, before high-throughput sequencing with an Illumina HiSeq 2500 (High Output v4) (100 bp single end reads, one lane). Two biological samples per condition were sequenced.


title: Effects of early life adversity on male reproductive behavior and the medial preoptic area

city: Philadelphia

first: Mathieu

last: Wimmer

address: 1701 N 13th Street

institute: Temple University

summary: Early life adversity has been linked to altered reproductive development in humans, including changes in the timing of pubertal onset and sexual activity. One common form of early life adversity is having limited access to resources. This form of early life adversity can be modeled in rodents using the limited bedding and nesting model (LBN), in which rat dams and pups are placed in a low resource environment from postnatal day (PND) 2 through 9. Our laboratory has previously shown that male rats raised in LBN conditions have elevated levels of plasma estradiol compared to control males. Female rats, on the other hand, show no effect of LBN on plasma hormone levels, pubertal timing, or estrous cycle duration in adulthood. Here, we find that LBN males also show changes in adult reproductive behaviors. LBN males acquired the suite of reproductive behaviors more quickly than their control counterparts over the course of 3 weeks of testing, showing shorter latencies to mount, intromit, and ejaculate compared to controls prior to the final week of testing. We also characterized LBN-induced gene transcription changes across sex in the medial preoptic area (mPOA) which underlies reproductive behaviors. Interestingly, there was no effect of LBN on puberty onset (as measured by preputial separation) or masculinization of the sexually dimorphic nucleus of the preoptic area (SDN/POA; as measured by calbindin immunoreactivity) in males, suggesting LBN may not exert effects on hormone-dependent measures until after puberty.

overall_design: 24 samples were anlayzed, including 6 male controls, 6 male experimental, 6 female controls, and 6 female experimental.

first: Samantha

last: Eck

first: Jamie

last: Palmer

first: Charlotte

last: Bavley

first: Reza

last: Karbalaei

first: Evelyn

middle: O

last: Sanchez

first: James

last: Flowers

first: Amanda

last: Holley

first: Debra

last: Bangasser


title: Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicing

city: New Haven

first: Wendy

last: Gilbert

state: CT

address: 333 Cedar Street – Room C-129

department: MB&B

institute: Yale University

summary: We performed pseudouridine profiling (Pseudo-seq) on 11 biological replicates of chromatin-associated RNA. We performed mRNA-seq of PUS1 knockout, PUS7 knockdown, RPUSD4 knockdown and wildtype HepG2 cells. We used an in vitro pool based strategy to assign pre-mRNA targets to individual human pseudouridine synthases (PUS) .

overall_design: Pseudouridylation was measured using Pseudo-seq, a seqeuncing based technique for identifying Ψs (Carlile et al. Nature 2014).

first: Nicole

last: Martinez

middle: V


title: Single-cell transcriptional and epigenetic dynamics during aortic aging in mice

city: Fuzhou

first: Wenhui

last: Xie

state: Fujian

address: Gulou District, Xinquan Road, No.29

department: Department of Geriatrics, Fujian Key Laboratory of Vascular Aging (Fujian Medical University)

institute: Fujian Medical University Union Hospital

summary: The impact of vascular aging (VA) has been extensively studied, yet little is known regarding the cellular and molecular mechanism underlying age-related VA in aortic cellular subpopulations. Herein, we analyzed transcriptomes and transposase-accessible chromatin profiles from aortas of 4-, 26-, and 86-week-old mice using single-cell RNA sequencing and ATAC sequencing. By integrating the heterogeneous transcriptome and chromatin accessibility data, we identified cell-specific transcription factor (TF) regulatory networks and open chromatin states. Moreover, we found that aortic aging affects cell interactions, inflammation, cell type composition and dysregulation of transcriptional control. Endothelial cell (EC) 1 has higher gene set activity related to senescence, aging, and adipogenesis than EC 2. Construction of senescence trajectories showed that the senescence of EC 1 and fibroblasts is associated with distinct TF open chromatin states and an mRNA expression model. Our data provide a system-wide model for transcriptional and epigenetic regulation during aortic aging at single-cell resolution.

overall_design: Transcriptomes and transposase-accessible chromatin profiles from aortas of two 4-week-old, two 26-week-old, and two 86-week-old mice

first: Wen-Hui

first: Yi-Lang

last: Ke

first: Qin-Yi

last: You

first: Jing

last: Li

first: Lu

last: Chen

first: Dang

first: Jun

last: Fang

first: Xiao-Feng

first: Yuan-Yuan

last: Zhou

first: Liang-Wan

first: Hua-Shan

last: Hong


title: Transcriptional regulation of jaw osteoblasts: development to pathology

status: Public on Feb 14 2022

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Craniofacial and jaw bones have unique physiological specificities when compared to axial and appendicular bones. However, the molecular profile of the jaw osteoblast (OB) remains incomplete. The purpose of this study was to decipher the bone site-specific profile of transcription factors (TF) expressed in jaw osteoblasts in vivo. We accomplished this by performing RNA-seq analysis on flow-sorted osteoblasts isolated from jaw and tibial bones of 9-day-old (P9) transgenic Col1a1*2,3-GFP mice. This study demonstrated the feasibility of a new method to isolate pure OB populations and map their gene expression signature in the context of OB physiological environment, avoiding in vitro culture and its associated biases. Our results provided insights into the site-specific developmental pathways governing OB and identify new major OB regulators of bone physiology.

overall_design: This dataset includes a total of 6 individual samples. This study sought to characterize in vivo the bone site-specific profile of transcription factors (TF) expressed in mandible osteoblasts (Md-OB) and compared this transcriptomic profile with TF expressed in tibia osteoblasts (Tb-OB).

first: J

last: Isaac

first: H

middle: W

first: A

last: Asselin


title: Gene expression profiles from female BasL breast cancer patients

city: Copenhagen Ø

first: Maria

last: Rossing

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Rigshospitalet

summary: Diagnostic samples from routine analysis of female BasL breast cancer patients

overall_design: Tumor specimens from female breast cancer patients were collected as part of routine diagnostics and gene expression patterns were analyzed using the Affymetrix HG-U133 Plus 2.0 platform. CITBCMST molecular subtyping was applied and BasL patients were selected.

first: Christina

middle: B

last: Pedersen


title: Genetic effects on non-CG DNA methylation

city: Fukuoka

first: Eriko

last: Sasaki

state: Fukuoka

address: 744 Nishi-ku, Motooka

institute: Kyushu University

type: Methylation profiling by high throughput sequencing


title: Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation III

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

summary: miRNA expression of HOG and differentiated HOG

overall_design: 3 replicate for HOG and differentiated HOG, respectively

first: Yangping

first: Feng

last: Wang

first: Peng

last: Teng

first: Yue

last: Feng


title: Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation


title: Genetic effects on non-CG DNA methylation [Methyl-C-seq]

summary: The epigenome, in particular variation of DNA methylation profiles across individuals, has long been of interest as a modifier of the genetic code, with “mutations” reflecting past environments, stochastic events, or genetic regulation. To address this issue, we dissected an inherited epigenetics mark, mCHG methylation, using conditional GWAS approaches in Arabidopsis thaliana. Our study revealed the genome-wide mCHG levels largely share the variation with de novo methylation and are under the control of major trans-modifiers, including the key regulators CMT2, CMT3, MIR823A, and a novel regulator JMJ26 that specifically regulated RdDM-targeted TEs.

overall_design: Methyl-C sequencing of mutants in Arabidopsis thaliana

first: Magnus

last: Nordborg


title: Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation II

summary: M17 and HOG cells were induced differentiation and subject to A-tailing RNaseR treatment, circRNA were identified by rRNA depleted RNA-seq data from A-tailing RNaseR and untreated samples

overall_design: M17, HOG, M17dif, HOGdif, each group with 3 replicates. A-tailing RNaseR and untreated library for each sample.


title: Genetic effects on non-CG DNA methylation [RNA-seq]

overall_design: RNA sequencing of mutants in Arabidopsis thaliana


title: Dysregulated microRNAs in uterine fluid from women with recurrent implantation failure are linked to endometrial receptivity and implantation

city: Tartu

first: Vijayachitra

last: Modhukur

address: L. Puusepa 8

country: Estonia

institute: University of Tartu

summary: The objective of the study was to compare the microRNA content in uterine fluid from patients with recurrent implantation failure (RIF) to that of healthy fertile women. It is a descriptive laboratory study including healthy fertile women and patients with RIF, defined as three failed in vitro fertilization cycles with high quality embryos. Study subjects were instructed to monitor their menstrual cycles using a luteinizing hormone test kit. Uterine fluid was collected on day LH+ 7-9 by flushing with saline. Samples were processed for small RNA sequencing and results were analysed using bioinformatics. The main outcome measure was to identify differentially expressed miRNAs between patients with RIF and healthy fertile women.

overall_design: Compare the expression of microRNAs in uterine fluid of women with recurrent implantation failure compared to healthy fertile women

first: Caroline

last: Frisendahl

first: Carolina

last: Von Grothusen

first: Parameswaran

last: Lalitkumar

first: Maire

last: Peters

first: Andres

last: Salumets

first: Nageswara

middle: R

last: Boggavarapu

first: Kristina

last: Gemzell-Danielsson


title: CDK4/6 inhibition enhances the tumor-suppressive activity of high-dose androgens in castration-resistant prostate cancer

first: Changmeng

last: Cai

state: MA

address: 100 William T Morrissey Blvd

country: USA

institute: University of Massachusetts Boston


title: Changes in B10F10 melanoma cells in response to stretch

city: Oviedo

first: Guillermo

last: Albaiceta

address: Avenida de Roma s/n

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: To study the effects induced by mechanical stretch on cancer cells, B16F10 murine melanoma cells were seeded in Flexcell plates and cultured in static or stretch (15% equibiaxial elongation, 15 cycles/min) for 24 hours. Cells were collected, and RNA isolated and sequenced.

overall_design: mRNA profiles of B16F10 melanoma cells cultured in static conditions or under cyclic stretch.

first: Inés

last: López-Alonso

first: Cecilia

last: López-Martínez


title: CDK4/6 inhibition enhances the tumor-suppressive activity of high-dose androgens in castration-resistant prostate cancer [RNA-Seq]

summary: High-dose testosterone (high-T) treatment can effectively suppress the growth of castration-resistant prostate cancer (CRPC) in preclinical studies using patient-derived xenograft (PDX) models and in clinical trials of CRPC. However, the molecular basis for this treatment remains to be determined. In previous studies, we have shown that androgen receptor (AR) can function as a transcription repressor to suppress the expression of genes mediating DNA replication via recruitment of hypophosphorylated retinoblastoma protein (Rb). However, it is unclear how Rb globally mediates this transcriptional repressor activity of AR and contributes to the tumor-suppressive effect of high-dose androgen in CRPC.

overall_design: All xenograft tumor samples for RNA-seq cells were isolated at the end of study. Note: two C4-2-tet-shRB xenograft experiments (with/out doxycycline) were done independently. All RNA-seq samples contain replications.

first: Wanting

last: Han

first: Mingyu

last: Liu

first: Shuai

last: Gao


title: Whole-transcriptome analysis in acute lymphoblastic leukemia: a report from the DFCI ALL Consortium Protocol 16-001

city: Montreal

first: Daniel

last: Sinnett

state: QC

address: 2900 Edouard Montpetit Blvd

institute: University of Montreal

summary: The molecular hallmark of ALL is characterized by recurrent, prognostic genetic alterations, many of which are cryptic by conventional cytogenetics. RNA-seq is a powerful next-generation sequencing technology with the ability to simultaneously identify cryptic gene rearrangements, sequence mutations and gene expression profiles in a single assay. We examined the feasibility and utility of incorporating RNA-seq into a prospective multi-center phase 3 clinical trial for children with newly-diagnosed ALL. Patients enrolled on the DFCI ALL Consortium Protocol 16-001 who consented to optional studies and had available material underwent RNA-seq. RNA-seq was performed in 173 patients with ALL. RNA-seq identified at least one alteration in 157 (91%) patients and fusion detection was 100% concordant with results obtained from conventional cytogenetic analyses. An additional 56 gene fusions were identified by RNA-seq, many of which confer prognostic or therapeutic significance. Gene expression profiling and fusion detection enabled further molecular classification into the following B-ALL subgroups: ETV6-RUNX1/ETV6-RUNX1-like (n=31), high hyperdiploid (n=34), TCF3-PBX1 (n=7), KMT2A-rearranged (n=5), Philadelphia (Ph) chromosome-positive/Ph-like (n=19), DUX4-rearranged (n=11), PAX5-altered (n=7), ZNF384-rearranged (n=4), MEF2D-rearranged (n=1) and NUTM1-rearranged (n=1). RNA-seq identified 141 nonsynonymous mutations in 93 (54%) patients; the most frequent were RAS-MAPK pathway mutations. Among 79 patients with both low-density array and RNA-seq data for the Ph-like gene signature prediction, results were concordant in 74 (94%) patients. In conclusion, RNA-seq is feasible in the context of a multicenter prospective clinical trial. We identified several clinically-relevant genetic alterations not detected by conventional methods, supporting the integration of this technology in frontline pediatric ALL trials.

overall_design: Profiling the transcriptome of pediatric acute lymphoblastic leukemia patients.

first: Thai

middle: H

last: Tran


title: CDK4/6 inhibition enhances the tumor-suppressive activity of high-dose androgens in castration-resistant prostate cancer [ChIP-seq]

overall_design: ChIP-seq of FOXA1, AR and P130 were performed in C42-tet-shRB cells with/out doxycycline. Samples of AR ChIP-seq were also treated with either ethanol (vehicle) or DHT (10nM) for 4 hours. ChIP-seq of RB and MYC were performed in C4-2 cells with/out DHT (10nM, 4hrs). All ChIP-seq samples contain replications.


title: Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation I

first: Bing

last: Yao

summary: HEK293T and SH-SY5Y cells were used to validate A-tailing method

overall_design: HEK293T and SH-SY5Y cells were subjected for A-tailing RNaseR with LiCL, RNaseR with LiCL, RNaseR with KCL with untreated sample as control for rRNA depleted RNA-seq

first: Yangping

last: Li

first: Feng

last: Wang

first: Peng

last: Teng

first: Yue

last: Feng


title: Translation of Circular RNAs in Neural Retina

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

summary: We performed Ribosome-protected mRNA fragment sequencing (Ribo-Seq) to determine if retinal circular RNAs are undergoing translation

overall_design: Lysates from rat retinal tissues were prepared using lysis buffer with or without detergent. Lysates were digested with RNase I, purified and further processed for isolation of ribosome-protected RNA fragments. The recovered RNA fragments were subjected to ribosomal RNA removal using Illumina Ribo-Zero Gold kit and the samples were sequenced using Illumina NextSeq 500.

first: Kalina

last: Andreeva

first: Jae

middle: Y

first: Juw

last: Park

first: Nigel

last: Cooper


title: Identification of a retinoic acid-dependent definitive hematopoietic progenitor from human pluripotent stem cells [HE]

first: Stephanie

last: Luff

address: 1425 Madison Ave

department: Cell, Developmental, & Regenerative Biology

summary: The generation of the hematopoietic stem cells (HSCs) from human pluripotent stem cells (hPSCs) is a major goal for regenerative medicine. HSCs derive from hemogenic endothelium (HE) in a retinoic acid (RA)-dependent manner1. While a WNT-dependent (WNTd) patterning of nascent mesoderm specifies clonally multipotent definitive HE from hPSCs2,3, this HE is functionally unresponsive to RA4. Here we show that WNTd mesoderm, prior to HE specification, is comprised of two distinct KDR+CD34negT+ populations. In a TGFb-independent manner, CXCR4negCYP26A1+ mesoderm is specified, which gives rise to HOXA+ multilineage definitive HE, in an RA-independent manner. In contrast, CXCR4+ALDH1A2+ mesoderm is specified in a TGFb-dependent manner, and gives rise to multilineage definitive HE in a stage-specific, RA-dependent manner. Further, this NOTCH-dependent HE harbored HOXA expression resembling fetal HE. This model of human hematopoietic development defines the mesodermal origins of multiple waves of hematopoiesis, and that RA-dependent hematopoietic development occurs prior to HE development.

overall_design: 6 hPSC-derived hemogenic endothelium samples underwent whole-transcriptome analysis. For 3 samples, the hemogenic endothelium was specified under RA-independent conditions using the ALDH inhibitor DEAB. The other 3 samples were specified with induced RA signaling using retinol.

middle: A

first: John

last: Creamer

first: Carissa

last: Dege

first: Rebecca

last: Scarfo

first: Analisa

last: Dacunto

first: Ivan

last: Merelli

first: Samantha

last: Morris

first: Andrea

last: Ditadi

first: Christopher

middle: M

last: Sturgeon


title: Transcriptomic study of the mechanism by Kai Yu Zhong Yu (KYZY) recipe to improve oocyte quality in the stressed mouse model

city: Tianjin

first: Xiaoli

last: Zhao

address: Changling Road 88, Xiqing District

institute: First Teaching Hospital of Tianjin University of Traditional Chinese Medicine

summary: Female ICR mice were treated with stress or stress plus herbal medicine (KYZY decoction) in chronic unpredictable mild stress (CUMS) model. Fifteen isolated oocytes from each mouse were used for RNA-seq analysis. We used DESeq2 to identify differentially expressed genes (DEGs) between groups. DAVID and GO resources were used to perform gene enrichment analysis on the DEGs.

overall_design: Female ICR mice into experimental groups that were treated with stress or stress plus herbal medicine, and control group that was not treated.

first: Ruihong

last: Ma

first: Tian

last: Xia


title: Identification of a retinoic acid-dependent definitive hematopoietic progenitor from human pluripotent stem cells [CXCR4]

institute: Icahn School of Medicine at Mount Sinai

overall_design: 6 hPSC-derived mesodermal samples underwent whole-transcriptome analysis. 3 of the samples are KDR+CXCR4- and the other 3 are KDR+CXCR4+


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Tartary buckwheat  Transcriptomes

city: Shanghai

first: Moyang

last: Liu

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

summary: We generated 61.9 Gb of high-quality sequencing data (~6.59 Gb per sample) and catalogued the expression profiles of 9,765 annotated Tartary buckwheat genes in each sample. The analysis showed differences of transcriptomes during the development of  buckwheat. We identified numerous differentially expressed genes that exhibited distinct expression patterns. These genes have known or potential roles in development of  buckwheat. Therefore, we are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms.

overall_design: buckwheat mRNA profiles of the development were generated by deep sequencing, in  triplicate, using BGISEQ-500.


title: Intratumor heterogeneity in metastic endometrial carcinoma

city: Madrid

first: Gema

last: Moreno-Bueno

address: Arzobispo Morcillo 4

department: Biochemistry

institute: Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM

type: Genome variation profiling by genome tiling array

summary: Endometrial cancer (EC) is the most common female genital malignancy and the fourth most common cancer in women in the developing world1. EC has been traditionally classified into two main groups with different clinical, pathological and molecular features2,3. Type I or endometrioid endometrial carcinomas (EECs) account for about 75% of the cases and are typically estrogen-related and low-grade tumors with good prognosis that coexist or are preceded by endometrial hyperplasia, mainly diagnosed in perimenopausal women. In contrast, type II or non-endometrioid endometrial carcinomas (NEECs) are high-grade aggressive tumors associated with endometrial atrophy and poor prognosis, unrelated to estrogen and diagnosed in older women. These comprise several histological subtypes, being the most common the serous carcinomas (SEC)4.   In recent years numerous large-scale studies of primary endometrioid and serous tumors have been performed5, revealing new mutated genes and establishing a new molecular subclassification based on the results obtained by The Cancer Genome Atlas (TCGA) consortium6, which implies different clinical outcomes. More recently, the genomic evolution of EC has been analyzed through a comparative study of samples from endometrial atypical hyperplasia, primary tumors and paired metastases7, revealing the presence of intratumor heterogeneity as previously described in primary EC and other tumor types8,9. However an in-depth study considering multiple regions from primary tumor and paired metastases has not been performed up to now to our knowledge.  Here we analyze by whole-exome sequencing (WES), massive parallel targeted sequencing and array comparative genomic hybridization (aCGH) the clonal evolution and intratumor heterogeneity of 7 endometrioid and 3 serous metastatic endometrial carcinomas. Different locations from the primary tumor as well as from their paired metastases were included in the study, allowing the reconstruction of the spatial and temporal phylogenetic evolution of the tumor. Different phylogenetic evolution patterns were identified, independently of the classical histological or molecular classification of the tumor, although similar patterns were found in ovarian metastasis and recurrent disease.

overall_design: At least 5 different tumor regions obtained from primary tumor and metastic disease from the same patient were analyzed

first: Alba

last: Mota

first: Kathleen

last: Burke

first: Pier

last: Selenic

first: Eva

last: Colas

first: Juan

last: Triviño

first: Pablo

last: Garcia-Sanz

first: Sonia

last: Gatius

first: Angel

last: Garcia

first: Alejandro

last: Rojo-Sebastian

first: Sandra

last: Rodriguez-Perales

first: Raul

last: Torres-Ruiz

first: August

last: Vidal

first: Antonio

last: Gil-Moreno

first: Jorge

last: Reis-Filho

first: Britta

middle: X

last: Matias-Guiu


title: Nematode ascarosides attenuate mammalian type 2 inflammatory responses

status: Public on Feb 13 2022

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

summary: Mounting evidence suggests that helminthic infection can protect against disorders of immune dysregulation.  Administration of live parasites or their excretory/secretory products (ES) has shown therapeutic effects across a wide range of animal models for immune disorders including asthma.  Human clinical trials of live parasite ingestion for the treatment of immune disorders have produced promising results, yet concerns persist regarding ingestion of pathogenic organisms and unpredictable immune responses towards their protein components.  Despite extensive efforts toward defining active components of ES, no small molecules with immune regulatory activity have been identified from nematodes.    OBJECTIVE:  Here we have aimed to identify the effect of evolutionarily conserved family of nematode pheromones called ascaroside, which is a small molecule produced by several animal parasitic nematode species, on pulmonary immune response and asthma severity in mice.

overall_design: CD45+ immune cells and   Epithelial cells collected from the lung from mice sensitized with OVA/Alum only or OVA/Alum plus ascr#7 followed by intranasal OVA challenge

first: Kenta

last: Shinoda

first: Andrea

last: Choe

first: Kiyoshi

last: Hirahara

first: Tomomi

last: Ichikawa

first: Jason

last: Hoki

first: Akane

last: Suzuki

first: Judith

last: Appleton

first: Raffi

last: Aroian

first: Frank

last: Schroeder

first: Paul

last: Sternberg

first: Toshinori

last: Nakayama


title: Differentially expressed genes in CMR-treated PANC-1 cells

city: Hangzhou

first: Zhipan

last: Wu

address: College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang

institute: Zhejiang University

summary: To explore the potential mechanism through which CMR regulates PANC-1 cells, a transcriptome sequencing analysis was performed to profile the difference between CMR-treated cells and control cells. Two thousand six hundred seventy-two differentially regulated genes were identified, of which 1678 and 1872 were up- and down-regulated, respectively. Subsequently, we conducted a Gene Ontology (GO) analysis of CMR targets. The results indicated that these targets were broadly distributed in the cytoplasm, nucleus, endoplasmic reticulum, and Golgi apparatus. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis predicted that CMR was involved in various signaling pathways, including mammalian target of rapamycin (mTOR), PI3K-AKT, AMPK, MAPK, FoxO, VEGF, WNT, autophagy, apoptosis and so on.

overall_design: Examination of different expressed genes in PANC-1 cells with or without CMR-treated.


title: Bone Marrow Stroma-induced Transcriptome and Regulome Signatures of Multiple Myeloma

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

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

overall_design: Refer to individual Series


title: messengerRNA-seq of wild type,  GLUT3-deficient and ACLY-deficient T helper 17 (Th17) cells

city: Wuerzburg

first: Sophia

middle: Martina

last: Hochrein

address: Versbacher Str 9

institute: University of Wuerzburg

summary: messengerRNA-sequencing and analysis of in vitro differentiated Th17 cells isolated from WT, Slc2a3-fl/fl Cd4-cre or Acöy-fl/fl Cd4-cre mice in the presence or absence of 20 mM acetate for 24h.

overall_design: Naive T cells were differentiated  in vitro under Th17 polarizing conditions. After 2 days, cells were incubated with ot without 10mM acetate. After 24h, total RNA was harvestred ans subjected to messengerRNA-sequncing analysis.

first: Martin

last: Vaeth


title: Histone H3 K9/14 acetylation of wild type and GLUT3-deficient T helper 17 (Th17) cells

city: Freiburg im Breisgau

first: Josip

middle: Stefan

last: Herman

address: Stuebeweg 51

department: Quantitative Single Cell Biology

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Examination of histone acetlytion in Th17 cells


title: Differential transcriptome analysis of murine embryonic and lung fibroblasts in response to SHH pathway activation

city: DALLAS

first: James

last: Kim

state: TX

address: 5323 HARRY HINES BLVD

department: Internal Medicine

institute: UNIVERSITY OF TEXAS SOUTHWESTERN

summary:
Purpose: To identify differential mRNA expression in response to SHH stimulation in murine embryonic and lung fibroblasts
Methods: NIH-3T3 and MLg cell lines were treated with recombinant SHH or vehicle control and RNA-seq was performed using Illumina Miseq Nano (performed by Admera Health, LLC (South Plainfield, NJ)). The FASTQ files were checked for quality using FastQC (v0.11.2).  FASTQ files were mapped to the mm10 assembly of the mouse genome using TopHat; fragments per kilo base per million mapped reads (FPKM) calculation and differential expression analysis were performed using Cufflinks (v 2.2.1).
Results: Comparison of differentially up-regulated and down-regulated mRNAs of secretory protein genes in NIH-3T3 and MLg cell lines upon SHH activation revealed interesting differences in the production of some ligands.

overall_design: Embryonic (NIH-3T3) and lung fibroblasts (MLg) cell lines were treated with SHH recombinant protein or vehicle control and RNAseq was performed to identify and compare differentially up-regulated and down-regulated genes of

first: Baozhi

last: Chen

first: Rahul

last: Kollipara


title: The alterations of gene expression profiling induced by ts-ARFGEF1 knockdown in MCF-7 cells

status: Public on Feb 12 2022

city: Taipei

first: Trees-Juen

last: Chuang

address: 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academic Sinica

summary: Analysis of high-throughput transcriptome sequencing (RNA-seq) data often observed numerous 'non-co-linear' (NCL) transcripts, which may originate from genetic rearrangements (gene fusion) indicated the importance of fusion events and circRNAs in carcinogenesis; however, the role of ts-RNAs remains largely uninvestigated. Here we developed a hybrid sequencing pipeline ("NCLscan-hybrid"), which integrated different types of short (Illumina-based) and extra-long (PacBio-based) RNA-seq data to eliminate potential false positives from experimental artifacts, fusion events, and circRNAs. We applied NCLscan-hybrid to investigate of ts-RNAs in human breast cancer, the most malignant tumors diagnosed in women worldwide. Through multiple experimental validation steps, we confirmed that the intragenic ts-RNA, ts-ARFGEF1, was highly expressed in breast cancer cells but absent in normal breast cells. Furthermore, we experimentally validated that ts-ARGEF1 can contribute to cell proliferation and apoptosis. Analysis of xenograft in nude mice showed that disruption of ts-ARFGEF1 expression can significantly attenuate tumor growth. Microarray analysis revealed that ts-ARFGEF1 knockdown could trigger PERK/ATF4/CHOP signaling pathway, implying the function of ts-ARFGEF1 in ER homeostasis. Taken together, our findings provide an in-depth view of the true complexity of intragenic NCL events and, for the first time, show further insight into the potential roles of intragenic ts-RNAs in tumor cell development.

overall_design:
We performed knockdown ts-ARFGEF1 in MCF-7 cells.
The microarray results were used to screen gene expression changes by ts-ARFGEF1


title: Translational regulation in response to boron in Arabidopsis thaliana

city: Tokyo

first: Naoyuki

last: Sotta

address: 1-1-1 Yayoi, Bunkyo-ku

department: Department of Applied Biological Chemistry

institute: Graduate School of Agricultural and Life Sciences, The University of Tokyo

summary: We previously reported that ribosome stalling at AUG-stop sequences in the 5'-UTR plays a critical role in regulating the expression of Arabidopsis thaliana NIP5;1, which encodes a boron uptake transporter, in response to boron conditions in media. Here, we conducted ribosome profiling analysis to reveal the genome-wide regulation of translation in response to boron conditions in A. thaliana. We identified 460 translationally regulated genes. Transcripts with reduced translation efficiency were rich in upstream open reading frames (uORFs), highlighting the importance of uORF-mediated translational regulation. We found that 148 uORF instances had greater ribosome density under high boron conditions. Moreover, translationally downregulated transcripts were rich in minimum uORFs (AUG-stops), suggesting that AUG-stops play a global role in the boron response. Boron increased the ribosome occupancy of stop codons, indicating that this element is involved in global translational termination processes.

overall_design: Whole shoot tissues of 14-day-old Arabidopsis thaliana grown under three different boric acid concentrations (–B, 0.3 µM; Ctrl, 30 µM; ++B, 500 µM). 2 biological replicates.

first: Yukako

last: Chiba

first: Kyoko

last: Miwa

first: Seidai

last: Takamatsu

first: Mayuki

last: Tanaka

first: Yui

last: Yamashita

first: Satoshi

last: Naito

first: Toru

last: Fujiwara


title: MiRNA sequencing of Schwann-like cells induced by Schwann cell-derived exosomes

city: Wuhan

last: Zhou

state: Hubei Province

address: 1277 Jiefang Avenue

institute: Wuhan Union Hospital

summary: Background: Adipose-derived stem cells (ADSCs) can differentiate into Schwann cells (SCs) at the site of nerve injury, where Schwann cell-derived exosomes (SC-Exos) are suspected to exert an induction effect. Our study aimed to induce the differentiation of ADSCs in vitro using SC-Exos and to investigate the mechanisms involved through miRNA sequencing.  Methods: Subcutaneous fat was used to extract ADSCs. Exosomes were extracted from Schwann cell lines (RSC96) using ultracentrifugation. After 8 days of induction of ADSCs by SC-Exos, phenotypic characteristics were observed by examining the expression of SC markers (S100, NGFR, MPZ, GFAP) through RT-qPCR, Western blot and immunofluorescence. Additionally, miRNA sequencing was performed on induced ADSCs, followed by bioinformatic analysis and validation of the results.  Results: SC-Exos were taken up by human ADSCs. The RNA and protein expression levels of S100, NGFR, MPZ and GFAP were found to be significantly higher in the SC-Exo induction group than in the uninduced group, despite no significant difference to the Dezawa’s method group, which was also consistent with the immunofluorescence results. According to the sequencing results, there were a total of 72 differentially expressed miRNAs. Bioinformatics analysis indicated that 3506 Gene Ontology terms and 98 Kyoto Encyclopedia of Genes and Genomes pathways were significantly enriched. Ten miRNAs, 6 target mRNAs and elevated expression of the PIK3CD/Akt pathway were validated by RT-qPCR or Western blot, which is consistent with the sequencing results.  Conclusions: Our data suggest that SC-Exos are able to induce the differentiation of ADSCs into SCs in vitro. It is speculated that the differentially expressed miRNAs play a significant role in the differentiation process.

overall_design: MiRNA profiles of Schwann-like cells differentiated human adipose-derived stem cells after 8-days induction of Schwann cell-derived exosomes in vitro

first: Zhao

last: Xu

first: Sen

last: Ren

first: Jing


title: Transcriptomisc Reveals Myometrial Topologically Associated Domains linked to the Onset of Human Term Labor

city: Prahran

first: Sonika

last: Tyagi

state: VIC

address: 99 commercial road

department: Infectious Diseases

institute: Monash University

summary: Changes in cell phenotype are thought to occur through the expression of groups of co-regulated genes within Topologically Associated Domains (TADs). In this paper we locate genes expressed within the myometrium of the human uterus during the onset of term labor into TADs. Transformation of the myometrial cells of the uterus into a contractile phenotype during term human labor is the result of a complex interaction of different epigenomic and genomic layers. Recent work suggests that the transcription factor RelA lies at the top of this regulatory network. Using deep RNAseq analysis of myometrial samples obtained at term from women undergoing caesarean section prior to or after the onset of labor we have identified evidence for how other gene expression regulatory elements interact with transcription factors in the labor phenotype transition. Gene set enrichment analysis of our RNAseq data identified three modules of enriched genes (M1, M2 and M3) which in gene ontology studies are linked to matrix degradation, smooth muscle and immune gene signatures. These genes were predominantly located within chromosomal TADs suggesting co-regulation of expression. Our transcriptomic analysis also identified significant differences in the expression of long-non-coding RNAs (lncRNA), microRNAs (miRNA) and transcription factors that were predicted to target genes within the TADs. Additionally, network analysis revealed 14 new lncRNA (MCM3AP-AS1, TUG1, MIR29B2CHG, HCG18, LINC00963, KCNQ1OT1, NEAT1, HELLPAR, SNHG16, NUTM2B-AS1, MALAT1, PSMA3-AS1, GABPB1-AS1, NORAD, NKILA) and 4 miRNA (mir-145, mir-223, mir-let-7a, mir-132) as top gene hubs with 4 transcription factors (NFKB1, RELA, ESR1) as master regulators. Together, these factors are likely to be involved in co-regulatory networks driving a myometrial transformation to generate an estrogen sensitive phenotype. We conclude that lncRNA and miRNA targeting the ESR1 and NFKB pathways play a key role in the initiation of human labor. For the first time we perform an integrative analysis to present a multi-level genomic signature in the myometrium for spontaneous term labor.

overall_design: The samples were collected under our University of Newcastle John Hunter Hospital, Newcastle, Australia and the Singapore KK Women’s and Children’s Hospital ethics committees (Ethics approval H3820602). Pregnant women gave written informed consent to donate a biopsy of their myometrium at Caesarean section at term according to the institutional guidelines and regulations. All women were between 36 completed weeks and 40 weeks gestational age. Tissues were sampled using a surgical technique standardized such that the bladder is reflected off the lower segment of the uterus (the uterovesical-fold) and the uterine incision is made in the upper part of the lower segment. Candidates for whole transcriptome analysis using RNAseq were chosen from the two distal, ie non-laboring (n=5), and laboring (n=7) groups as well as  women clinically classified as laboring from the middle band to represent mothers in early labor (n=5).

first: Roger

last: Smith


title: murine DP thymocytes transcriptome

city: Frankfurt am Main

first: Adrien

last: Jolly

state: Hessen

address: Theodor Stern Kai 7

institute: University Hospital Frankfurt

summary: single-cell transcriptome of Double Positive Thymocytes from 12 weeks old C57Bl/6 mouse

overall_design: control condition


title: Regulation of HIF1α signaling in ER positive breast cancer by the E3 ubiquitin ligase RBCK1

city: Xinxiang

first: ning

middle: jia

last: fan

state: Henan

address: Xinxiang Medical College

institute: Xinxiang Medical College

summary: RanBP2 type and C3HC4 type zinc finger containing protein 1 (RBCK1,) is a 58 kDa protein containing N-terminal ubiquitin like (UBL) domain, npl4 type zinc finger (NZF) domain and catalytic carbon terminal RBR domain. It is known that it has abnormal expression in tumors, making it a valuable diagnostic marker and drug target. A large number of studies have confirmed that in ER positive breast cancer, about 25%-40% of the tumor showed a visible hypoxia area. Under hypoxia, tumor cells can activate HIF1 pathway and widely activate the expression of downstream genes. Hypoxia inducible factor HIF-1 is composed of HIF-1α and HIF-1β Two subunits, The protein level of HIF-1α is precisely regulated by oxygen concentration. Here, we report RBCK1, a RING family ubiquitin ligase that regulates HIF1α, promoting ER positive breast cancer growth and inhibiting apoptosis. Deletion of RBCK1 inhibits ER positive breast cancer growth and promotes cell death. RNA sequencing analysis showed that in ER positive breast cancer, RBCK1 may be an important modifier of HIF1α signal pathway. Further experiments showed that RBCK1 and HIF1α Interacts and inhibits HIF1α polyubiquitination to inhibit HIF1α degradation in ER positive breast cancer cells. These finding reveals a novel direct HIF1α  regulator and a potential therapeutic target for ER positive breast cancer.

overall_design: ER positive breast cancer cell mRNA samples were summarized in six samples, divided into two groups, siControl and siRBCK1

first: Zhiguo

last: Niu

first: Qingsong

last: Huang

first: Jian

last: Zhu

first: Jianing

last: Fan


title: DUB1 suppresses Hippo signaling via modulating TAZ protein in gastric cancer

first: Zhongbo

last: li

institute: Xinxiang medical university

summary: The Hippo pathway functions as a tumor-suppressor pathway in human cancers, while the dys-function of Hippo pathway is frequently observed in malignancies. Although the YAP/TAZ activity is tightly controlled by the phosphorylation cascade of MST-LATS-YAP/TAZ axis, it is still unclear why YAP/TAZ protein is activated in human cancers, even Hippo pathway is still active. Besides phosphorylation, recent studies implicate that several post-translational modifications also play critical roles in modulating TAZ function, including ubiquitination. Here, by a DUB (Deubiquitinases) siRNA screening library, we discovered DUB1 as a critical modulator to facilitate gastric cancer stemness and progression, which deubiquitinated and activated TAZ protein. We also identified DUB1 was elevated in gastric cancer, which correlated with TAZ activation and poor survival. DUB1 associated with TAZ protein and deubiquitinated TAZ at several lysine sites, which subsequently stabilized and facilitated TAZ function. Our study revealed a novel deubiquitinase of Hippo/TAZ axis and one possible therapeutic target for Hippo-driven gastric cancer.

overall_design: Gastric cancer cell mRNA samples were summarized in six samples, divided into two groups, siControl and siDUB1

first: Dehai

last: Wang

first: Yinlu

last: Ding

first: Peng

last: Su


title: ChIP-Seq revealed c-Jun promotes the transcriptional activities of the p35 and EBI3 promoters in human HepG2 cells.

first: Xuefen

last: Li

state: China

address: 79 Qingchun Road

institute: the First Affiliated Hospital, Zhejiang University School of Medicine

summary: we performed ChIP-Seq to clarify whether c-Jun activated by pCMV-HBx transfection could bind to the promoter of the IL-35 gene.   The results showed that the transcriptional activity of c-Jun was significantly enhanced in the 3-kb region upstream and downstream of the IL-35 transcription start site. This finding suggests that the transcription factor c-Jun binds the promoter sequence of IL-35 and activates its transcription.

overall_design: Examination of target gene transcription, start site binding, and transcriptional activity of c-Jun in HepG2 cells.

first: Yuan

last: Liu


title: RNA-seq of wild type and GLUT3-deficient T helper 17 (Th17) cells

first: Sophia

last: Hochrein

summary: RNA-sequencing and analysis of in vitro differentiated Th1 and Th17 cells isolated from WT and Slc2a3-fl/fl Cd4-cre mice.

overall_design: Naive T cells were differentiated for 3 days in vitro under Th1 and Th17 polarizing conditions. Total RNA was harvestred ans subjected to bulk RNA-sequncing analysis.

first: Martin

last: Vaeth