title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Ahi1-/- mouse embryonic fibroblasts cells Transcriptomes

city: Suzhou

first: Hongguang

address: Renai load 199

institute: Soochow University

summary: We report the application of RNA sequencing technology for high-throughput profiling of gene expression in mammalian cells. By  sequencing from mouse embryonic fibroblasts RNA, we generated genome-wide gene expression maps of mouse embryonic fibroblasts cells. We found a significant difference of relatived gene in Ahi1+/+and Ahi1-/- cells in the basal state. These findings help to understand more functions and roles of the Ahi1 gene.

overall_design: Mouse embryonic fibroblasts cell mRNA profiles of  wild type (WT) and Ahi1-/- mice

first: Zheng

last: Hui

first: Xun

last: Xingshun

first: Zhang

last: Hongguang

first: Wang

last: Bin


title: Differentially expressed genes of C2C12 cells influenced  by murine pancreatic cancer derived exosomes

status: Public on Jan 01 2022

city: Hangzhou

last: Lantian

state: Zhejiang

address: 88 Jiefang Road

department: Department of Surgery

country: China

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

summary: Mice pancreatic cancer derived exosomes(KPC-exosomes) could induce skeletal muscle cells(C2C12) insulin resistance and exosomal microRNAs (miRNAs) may exert an important effect (Sci Rep. 2017;7(1):5384). The data set GSE95741 provided the  differentially expressed micro RNAs. In this work, we aim to detect the differentially expressed genes and  explore the intrinsic link.

overall_design: C2C12 cells cultured in 25cm2 culture-flasks were treated by KPC-exo (4ug) for 24h. The C2C12 cells treated by MPDC-exo (exosomes secreted by murine pancreatic ductal epithelial cells) were used as control.

first: Lantina

last: Wang


title: SMARTseq data of zebrafish sox10+ cells

first: Zhidan

last: Xia

address: NO. 866 Yuhangtang Road

institute: Zhejiang University School of Medicine

type: Expression profiling by high throughput sequencing

summary: The goals of this study are to compare  transcriptome profiling (mRNA level) and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups, and the stem markers of nueral crest progenitors were upregulated in mutants.

overall_design: sox10+ cells from slc30a1 mutant zebrafish and their siblings at 2 dpf and 2.5 dpf were sorting out by FACS machine, whole RNA were extraced and performed SMARTseq analysis.

first: Xinying

last: Bi

first: Fudi

first: Junxia

last: Min


title: SC35 (SRSF2) ChIP-Seq analysis of liver samples from wild type (WT) mice and XBP1 liver-specific knockout (LKO) mice over a 48 hour time series

city: Pittsburgh

first: Bokai

last: Zhu

state: PA

address: 100 Technology Dr, Bridgeside point

country: USA

institute: University of Pittsburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here, we show the in vivo genome-wide interactions of SC35 in the livers of wild type mice and mice with liver-specific knockouts of XBP1

overall_design:
Livers samples from mice kept under constant darkness were collected every 4 hours (for a total of 48 hours) from wild type mice and mice with liver-specific knockouts of XBP1

Grant ID: 1-18-JDF-025
Funding source: American Diabetes Association

first: William

last: Dion


title: Treatment of HCT116 cells with a small molecule inhibitor of ß-catenin/BCL9 interaction

city: Boston

first: Tomasz

last: Sewastianik

state: MA

address: 450 Brookline Ave

department: Oncologic Pathology

institute: Dana-Farber Cancer Institute

summary: HCT116 colorectal cancer cells were treated with a novel inhibitor of ß-catenin/BCL9 interaction and evaluated for transcriptional changes using RNA-seq.

overall_design: Comparison of vehicle and inhibitor treated HCT116 cells.

first: Helen

middle: E

last: Tanton

first: Ruben

middle: D

last: Carrasco


title: Lysophosphatidylcholine acyltransferase 1 controls the mitochondrial reactive oxygen species generation and survival of the retinal photoreceptor cells [P8 photoreceptor]

city: Shinjuku-ku

first: Katsuyuki

last: Nagata

address: 1-21-1 Toyama

country: Japan

institute: National Center for Global Health and Medicine

summary: Due to the high energy demands and characteristic morphology, retinal photoreceptor cells require a specialized lipid metabolism for survival and function. This study focused on the roles of saturated fatty acids and their metabolism. A frameshift mutation of lysophosphatidylcholine acyltransferase 1 (Lpcat1), introducing saturated fatty acids into lysophosphatidylcholine to produce disaturated phosphatidylcholine (PC), has been reported to cause spontaneous retinal degeneration in mice (rd11 mice).　In this study, we performed a detailed characterization of Lpcat1 in the retina and found that Lpcat1 deficiency induces light-independent and photoreceptor-specific apoptosis in mice. Lipidomic analyses of the retina and isolated photoreceptor outer segment (OS) suggested that loss of Lpcat1 affects disaturated PC production and the proper cellular fatty acid flux, presumably by altering saturated fatty acyl-CoA availabilities. Furthermore, we demonstrated that Lpcat1 deletion increased mitochondrial reactive oxygen species (ROS) levels in photoreceptor cells, but not in other retinal cells without affecting the OS structure and trafficking of OS-localized proteins. These results suggest that the LPCAT1-dependent production of disaturated PC is critical for metabolic adaptation during photoreceptor maturation. Our findings highlight the therapeutic potential of saturated fatty acid metabolism in photoreceptor cell degeneration-related retinal diseases.

overall_design: Gene expression in photoreceptor cells was measured in postnatal day 8 Lpcat1 HZ and KO mice.

first: Daisuke

last: Hishikawa


title: Anti-IgE Effect of Naturally Occurring Arctigenin on Food Allergy Association with a Distinct Transcriptome Profile

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

summary: Purpose: To identify IgE inhibitory bioactive compound from A.Lappa for targeted therapy on peanut specific IgE production and hypersensitivity reactions, and to investigate its underlying mechanisms. The goals of this study were to compare the transcriptome map (RNA-seq) and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) before and after PMBC in patients with food allergy, and to evaluate the most critical genes and signaling pathways which  inhibit IgE production by arctigenin.

overall_design: IgE inhibitory effects on human B cells (U266 human myeloma cells) and peripheral blood mononuclear cells (PBMCs) from food allergic patients, and in peanut sensitized and challenged murine model were assessed. And genes involved in IgE inhibition were studied with transcriptome sequencing. Examination of 3 set of  transcriptome profiles  of PBMCs (control, IL-4/anti-CD40 stimulation,  IL-4/anti-CD40 stimulation+arctigenin).

first: Xiumin

last: Li

first: Mingzhuo

last: Cao

first: Changda

last: Liu


title: Gene and miRNA expression data from human platelets infected by EBV in vitro

city: Kunming

first: Jing

last: Sun

state: Yunnan

address: NO. 935,JIAO LIN ROAD

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

type: Non-coding RNA profiling by high throughput sequencing

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: ATAC-seq analysis of radioresistant/sensitive cells in oral cancer

city: Chiba City

first: Takafumi

last: Nobuchi

state: Chiba Prefecture

address: 1-8-1 Inohana, Chuo-ku, Chiba,, Japan

department: Department of Oral Science

institute: Graduate School of Medicine, Chiba University

summary:
ATAC-seq identified a total 80,764 peaks in radioresistant cells (HSC-3;0Gy, 8Gy) and radiosensitive cells (KOSC-2;0Gy, 8Gy) (n=2).
1273 peaks were shown as chromatin opened regions and 839 peaks were shown as chromatin closed regions in HSC-3 8Gy compared to HSC-3 0Gy. 285 peaks were shown as chromatin opened regions and 1760 peaks were shown as chromatin closed regions in KOSC-2 8Gy compared to KOSC-2 0Gy. 3804 peaks were shown as chromatin opened regions and 1929 peaks were shown as chromatin closed regions in KOSC-2 0Gy compared to HSC-3 0Gy. By hierarchical clustering analysis and heatmap, the difference of chromatin accessibility in KOSC-2 was lower than HSC-3.

overall_design: In order to compare the differences in radiosensitivity at the genome level, we prepared irradiated and non-irradiated cells of radioresistant and sensitive cells, respectively.

first: T

last: Saito

first: K

last: Uzawa


title: RNA sequencing of whole sciatic Dorsal Root Ganglia (DRG) from young and aged mice

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

summary:
Purpose: compare the gene expression in whole sciatic DRG of aged mice preceding and after sciatic nerve injury (SNI) compared to the young
Results: we found ageing-dependent gene expression changes repressing axonal regeneration following sciatic nerve injury

overall_design: Method: RNA-seq from sciatic DRG extracted from the young or aged mice  24 hours after sciatic nerve injury or sham. For whole DRG, sciatic DRGs from 2 mice were used for each sample. DRG were collected in RNAlater reagent, and crushed with RNase free micropestle for RNA extraction.

first: Luming

last: Zhou

first: Guiping

last: Kong

first: Ilaria

last: Palmisano

first: Simone

last: Di Giovanni


title: Expression profile of exosomal LncRNA in plasma of pancreatic ductal adenocarcinoma

city: fuzhou

first: weixuan

last: hong

address: fuzhougulou

institute: 900TH Hospital of Joint Logistics Support Force

summary:
Background:Exosomes are extracellular vesicles secreted by a variety of cells and are widely distributed in human body fluids. Exosomal long non-coding RNA (lncRNA) is a by-product of gene transcription and is involved in the regulation of cancer cell growth and migration. Numerous studies have identified aberrant lncRNA levels in pancreatic cancer (PC), but studies on exosomal lncRNA expression in pancreatic ductal adenocarcinoma (PDAC) plasma are relatively few and remain largely unknown.
Methods:We studied the expression of exosomal lncRNAs and mRNAs in the plasma of 5 PDAC patients and 5 healthy human subjects using high-throughput sequencing.
Results:A total of 43715 exosomal lncRNAs were found to be expressed in PDAC and healthy human plasma, of which 5851 were up-regulated, and 1055 were down-regulated in all 5 PDAC plasma (≥2.0-fold change, P<0.05). The expression of eight significantly expressed genes (ABCD4, RP11-77P6.2, FLVCR1-AS1, HMBOX1, TUBA1C, RP11-115C21.2, PRKG1-AS1, and MTATP6P1) were selected to be measured in 5 patients using database and real-time quantitative reverse transcription PCR (qRT-PCR), and the data were consistent with those obtained from high-throughput sequencing. Analysis of their nearby coding genes (mRNAs) showed that the principal functions of most genes were to regulate cell metabolism process, apoptosis, protein binding and receptor binding. The main regulatory pathways included the ErbB signaling pathway, which regulates cell proliferation and differentiation, and the tumour pathway. Analysis of the co-expressed gene regulatory network identified key lncRNA-mRNA pairs that may play an important role in the pathogenesis of PDAC.
Conclusions: Expression differences in exosomal lncRNAs exist between PDAC and healthy human plasma, so the expression profile of exosomal lncRNAs could explain the onset and development of PDAC and could also serve as a candidate biomarker for the diagnosis of PDAC and a potential therapeutic target.

overall_design: Expression profile of exosomal LncRNA of pancreatic ductal adenocarcinoma (PDAC) patients and healthy human

first: C

last: Xiao

first: Lihan

first: Weixuan

last: Hong


title: Expression profiling of THP-1 cells treated with 1a by high thorughput sequencing

city: Münster

first: Luca

last: Abdel Ghani

address: Corrensstrasse 36

country: Germany

institute: Westfälische Wilhelms-Universität

summary: Revealing changes in gene expression in THP-1 cells induced by 1a

overall_design: THP-1 cells were grown in presence or absence of 1 µM 1a for 16 hours. RNA Profiling was obtained in triplicate using Illumina NextSeq

first: Maria

middle: V

last: Yusenko

middle: A

last: Ghani

first: Karl-Heinz

last: Klempnauer


title: Intergenerational metabolic priming by sperm piRNAs

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: Preconception parental environment can reproducibly program offspring phenotype without altering the DNA sequence, yet the mechanisms underpinning this ‘epigenetic inheritance’ remains elusive. Here, we demonstrate the existence of an intact piRNA-pathway in mature Drosophila sperm and show that pathway modulation alters offspring gene transcription in a sequence-specific manner. We map a dynamic small RNA content in developing sperm and find that the mature sperm carry a highly distinct small RNA cargo. By biochemical pulldown, we identify a small RNA subset bound directly to piwi protein. And, we show that piRNA-pathway controlled sperm small RNAs are linked to target gene repression in offspring. Critically, we find that full piRNA-pathway dosage is necessary for the intergenerational metabolic and transcriptional reprogramming events triggered by high paternal dietary sugar. These data provide a direct link between regulation of endogenous mature sperm small RNAs and transcriptional programming of complementary sequences in offspring. Thus, we identify a novel mediator of paternal intergenerational epigenetic inheritance.

overall_design: Drosophila melanogaster small RNA and mRNA samples with differing library preparations, tissue, and genotypes.

first: Heidi

last: Lempradl


title: Estrogen receptor beta promotes endometriosis progression by up-regulating CD47 expression in ectopic endometrial stromal cells

city: Hefei

first: Jinghe

last: Zhang

state: Anhui

address: Huangshan Road 443

institute: University of Science and Technology of China

summary: In this dataset contains 3 cases of transcriptome information from 3 normal endometrial tissue of patients with uterine leiomyoma (NE-1,NE-2,NE-3), 3 cases from ectopic endometrial tissue samples of  patients with endometriosis (EE-1,EE-2,EE-3).

overall_design: Endometrial stromal cells mRNA profiles of 3 patients with endometriosis and 3 patients with uterine leiomyoma

first: Laihua

last: Hu

first: Meiling

last: Zhu


title: NFATc1/αA and Blimp-1 support the follicular and effector phenotype of Tregs

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: CD4+CXCR5+Foxp3+ T follicular regulatory (TFR) cells control the germinal center responses. Like follicular helper T-cells, they express high levels of Nuclear Factor of Activated T-cells c1, predominantly its short isoform NFATc1/αA. Ablation of NFATc1 in Tregs prevents upregulation of CXCR5 and migration of TFR cells into B-cell follicles. By contrast, constitutive active NFATc1/αA defines the surface density of CXCR5, whose level determines how deep a TFR migrates into the GC and how effectively it controls antibody production. NFATc1/αA is necessary to overcome TFR-expressed B lymphocyte-induced maturation protein (Blimp-1), which can directly repress Cxcr5. Blimp-1 then reinforces the recruitment of NFATc1 to Cxcr5 by protein-protein interaction and by those means cooperates with NFATc1 for Cxcr5 transactivation. On the contrary, Blimp-1 is necessary to counterbalance NFATc1/αA, which strengthens the follicular development of Tregs, but bears the inherent risk of causing an ex-Treg phenotype.

overall_design: Prdm1gfp mice were crossed to Nfatc1fl/fl.FIC, Nfatc1caaA.FIC and Nfatc1caaA.Prdm1fl/fl.FIC mouse lines and TFR cells sorted as CD4+B220―GFP+CXCR5+GITRhi cells 10 days post NP-KLH immunization.

first: Stefan

last: Klein-Hessling

first: Anika

last: Koenig

first: Friederike

last: Berberich-Siebelt


title: Gene expression data for BET inhibitors

city: Daejeon

first: Byungho

last: Lim

address: 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea

country: South Korea

institute: KRICT

summary:
The BET (bromodomain and extra-terminal) family of acetyl-lysine reader proteins acts as transcriptional activators. BET inhibitors showed anti-cancer efficacies.
We performed microarray analysis to characterize BET inhibitor-induced gene expression alterations.

overall_design: MV4-11 leukimia cells were cultured using the RPMI1640 medium. Cells were plated on 6-well plates at the day before drug treatment, and DMSO, DW-71374 (300 nM), DW-71177 (300 nM), OTX-015 (300 nM), and RVX-208 (5 uM) were treated during 24 h. After extracting Total RNA and assessing RNA purity and integrity by ND-1000 Spectrophotometer, the RNA samples were applied to the Affymetrix Whole transcript Expression microarray according to the manufacturer's protocol (Affymetrix GeneChip Human 2.0 ST Array).


title: A hexasome is the preferred substrate for the INO80 chromatin remodeling complex allowing versatility of function

city: San Francisco

first: Vijay

last: Ramani

state: California

department: Biochemistry & Biophysics

institute: UCSF

summary: The INO80 chromatin remodeling complex plays critical roles in transcription that are commonly attributed to INO80’s nucleosome sliding activity. Here we find that removal of INO80 in yeast cells disrupts the positions of hexasome-sized particles within genes. We show that in vitro INO80 remodels hexasomes ~60-fold faster than nucleosomes. INO80’s preference for hexasomes is highest when the linker lengths approach the ~18 bp linker lengths found in gene bodies. Our data further suggest that the module formed by the Arp5 and Ies6 subunits promotes nucleosome sliding by dislodging an H2A/H2B dimer, thereby making a nucleosome transiently resemble a hexasome. We propose a model in which the action of the Arp5/Ies6 module allows INO80 to act rapidly on both nucleosome substrates at promoters and hexasome substrates in gene bodies. Rapid repositioning of hexasomes that are generated in the wake of transcription may mitigate spurious transcription. More generally, such versatility could explain how INO80 regulates chromatin architecture during diverse processes ranging from transcription to DNA repair.

overall_design:
MNase mapping of subnucleosomal and nucleosomal fragments in S. cerevisiae WT and ∆ino80 strains with replicates
Please note that these libraries are non-traditional in the sense that the library prep is very different from standard Illumina protocols, and so the raw fastqs have been subjected to non-standard adaptor trimming + read filtration (in addition to read deduplication), generating BAM files as only processed data.

first: Laura

middle: J

last: Hsieh

first: Muryam

last: Gourdet

first: Camille

last: Moore

first: Elise

middle: N

last: Munoz

first: Nathan

last: Gamarra

first: Geeta

last: Narlikar


title: Hoxd12 is indispensable for somatic cells reprogramming and proliferation of embryonic stem cells

city: Guangzhou

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

summary: Somatic cells reprogramming and by exogenous factors requires transcription factors coordinate with each other, but its precise mechanisms still poorly understood. Here, we report that knockdown of Hoxd12 by short-hair RNA interference (shRNA) specifically suppress 7F (Sall4-Jdp2-Esrrb-Kdm2b-Mkk6-Nanog-Glis1) induced reprogramming, nevertheless overexpression of Hoxd12 result in no significant difference of induced pluripotent stem cells (iPSCs) generation. Furthermore, knockout of Hoxd12 hinder embryonic stem cells (ESCs) proliferation, while does not affect differentiation and pluripotent. RNA sequencing (RNA-seq) reveal that Hoxd12 may affect ESCs proliferation by regulated biosynthesis-related genes. Altogether, these results suggest that Hoxd12 is necessary for efficient reprogramming of 7F and ESCs proliferate normally, this may be useful for understanding transcription factors regulatory mechanisms.

overall_design: Compare the transcriptome differences between wild type ESCs and Hoxd12-/- ESCs. There are three repetitions for each group

first: Guoqing

last: Zhao


title: RNA-seq of 4 Crohn's disease and 4 control

city: Shenyang

first: Yue

last: Tan

state: Liao Ning

address: 39 Huaxiang Road, Tiexi District

institute: Shengjing Hospital of China Medical University

summary: mRNA-seq raw data of 4 Crohn's disease and 4 control from colon tissue

overall_design: Colon tissues from 4 Crohn's disease and 4 control individuals were extracted. Pair-ended RNA-seq libraries for this study were prepared using the NEBNext Ultra RNA with Poly-A selection kit and was sequenced on an Illumina Hi-Seq 4000 (Genergy, Shanghai).

first: Daowei

last: Li


title: Transcriptome changes after knocking out MYEOV in two human pancreatic cancer cell lines

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: Pancreatic cancer (PC) remains a highly lethal malignancy worldwide. As metastasis and malignant proliferation are primarily responsible for poor clinical outcomes of PC, it is imminent to dig out the pivotal gene involved in the process as well as its underlying molecular mechanism. In this study, through analysis of TCGA and GTEx data, we found that the expression level of MYEOV was obviously increased in carcinoma tissues relative to healthy ones and associated with poor survival in PC patients. The elevated abundance of MYEOV was positively correlated with enhanced cell proliferation, invasion and migration in vivo and in vitro. The global transcriptome analysis of MYEOV-depleted PC cells revealed the downregulation of various genes involved in active cell proliferation, which indicated that MYEOV overexpression was critical for PC progression. MiRNA-seq analysis showed that MYEOV had a regulatory effect on the expression levels of miR-17-5p and miR-93-5p, depletion of which resulted in reduced cell proliferation, invasion and migration as observed in MYEOV-knockdown PC cells. Such effect was imposed by MYEOV through affecting enrichment of the transcription factor c-myc at the gene promoter regions of the two miRNAs. Furthermore, a complex containing MYEOV and MYC was confirmed to exist in cell nucleus, providing convictive evidence for the association of MYEOV with MYC. Together, these results suggested that the axis of MYEOV-MYC-miR-17/93-5p could be vital for PC progression and could act as a potential therapeutic target to interrupt cell proliferation which will benefit treatment and management of PC patients.

overall_design: Total RNA after knocking out MYEOV in two human pancreatic cancer cell lines were isolated and sequenced by deep sequencing using Illumina HiSeq 4000

first: Juanjuan

last: Zhu


title: Next Generation Sequencing of piRNAs in 3 prostate cancer tissues and 3 paired prostate tissues

city: Nanjing

first: Ling

last: Zhang

address: Hankou road

institute: Nanjing University

summary: iRNAs have been demonstrated to play crucial roles in cancer development by directing the post-transcriptional regulation of target gene expression. We analyzed the expression profile of piRNAs in 3 of the prostate cancer tissues and matched normal adjacent tissues by piRNA sequencing. The aim of this analyse was to find the different expressed piRNAs in prostate cancer.

overall_design: Examination of 3 prostate cancer tissues and 3 paired prostate tissues

first: Xiannan

last: Meng

first: Dongmei

first: Xiaodong

last: Han


title: HSP90 specific nIR probe identifies aggressive prostate cancers: a translational study from preclinical models to a human pilot study

city: Durham

first: Erika

last: Crosby

state: NC

address: 203 Research Dr. MSRBI Room 407

institute: DUKE UNIVERSITY MEDICAL CENTER

summary: Current screening modalities for prostate cancer rely on serologic testing for PSA and transrectal biopsy; however, many prostate cancers behave indolently.Because aggressively growing tumors depend on oncogenic drivers, we hypothesized that we could identify early, but aggressive prostate cancer,by an imaging modality targeting Hsp90, a chaperone for many molecules involved in oncogenic signaling. Previously we observedgreater avidity ofa probe,consisting of a near infrared dye tethered to an Hsp90 inhibitor,for cancers with greatermetastatic potential. We now report that an Hsp90 inhibitor-linked near infrared dye with greater tissue penetration could detect prostate cancers in preclinical models and in a phase I human clinical trial. These data, demonstrating specific uptake into aggressive tumors, in conjunction with our prior observations on photodynamic therapy guided by Hsp90 expression support a theranostic approach todetect and treatearly aggressive prostatecancers.

overall_design: The uptake of anear infrared (nIR)probe-linked to an HSP90 binding drug (designated HS196)was assessed in preclinical models of prostate cancerwith various biologic behaviors. A human phase I study assessed the safety and uptake of HS196 in prostate cancers of patients undergoing prostatectomy. Tumors were removed following treatment with probe and HS196+/neg cells from the tumor were sorted and analyzed by single cell RNAseq to identify the cell types taking up the probe.

first: Takuya

last: Osada

first: H

middle: K

last: Lyerly


title: Injured kidney organoids gene expression profile at single cell

city: BOSTON

last: Matsumoto

state: Massachusetts

address: 1335 BOYLSTON ST

institute: Massachusetts General Hospital

summary: Exploring single cell gene expression profile in kidney organoids modeling fibrosis

overall_design: Examination of 2 different times cisplatin treatments in kidney organoids

first: Navin

last: Gpta

first: Ken

last: Hiratsuka

first: Ryuji

last: Morizane


city: Tianjin

first: Shuo

address: 94 Weijin Road

institute: Nankai University

summary:
Purpose: Analysis of exosomal miRNA in plasma of patients with metastatic and non-metastatic pancreatic cancer. To identify exosomes cargo specific miRNAs promoting cancer metastasis.
Methods: We divide the plasma samples into five groups according to whether they have metastasis and undergo surgery.The five groups are Health(20),Metastasis Pre-operation and Post-operation (14),Non-metastasis Pre-operation and Post-operation(9).Then we collected the exosomes by ultracentrifugation and extracted the small RNA in each sample.Then, we analyzed the expression changes of miRNA by small RNA sequencing.
Result: Different groups have different expression of small RNA. Compared with the non-metastatic group, the expression of miR-92a-3p , miR-148-3p and miR-25-3p increased in the metastatic group.
Conclusion:Exosomal miRNA in pancreatic cancer patient derived plasma were analyze using Hiseq2500 sequencing technique. We identified that miR-92a-3p, miR-148-3p and miR-25-3p enriched in metastatic pancreatic cancer patient plasma derived exosomes.

overall_design: Based on the analysis of exosomal miRNA in plasma samples from 5 different groups to identify the specific exosomal miRNA promoting metastasis.

first: ShiJing

last: yue

last: liu

first: LuHan

last: li


title: Kidney organoids gene expression profile

summary: Exploring gene expression profile in kidney organoids cultured by static and suspension culture system in different time point

overall_design: Examination of gene expression profile in kidney organoids cultured by static and suspension culture system in different time point (day0, day 8, day 21, day 35, day 49)


title: RNA-seq of gastrocnemius (GA) muscle tissue from mice treated with extracellular vesicles (EV) from MCF-10A /miR122 cells

city: SANDIEGO

first: XIANHUI

last: RUAN

address: 9500 Gilman Dr (#0612), La Jolla

department: PATHOLOGY

institute: UCSD

summary: To detect gene expression changes in skeletal muscle caused by EVs from mMCF-10A/miR-122 cells, we analyzed RNA isolated from the GA muscle of EV-treated female NOD scid gamma (NSG) mice. Mice had received tail-vein injections of EVs twice a week for 5 weeks (~10 ug EV per injection). Gene expression in muscle from mice treated with  MCF-10A/miR-122-derived EVs.

overall_design: RNA-seq was used for transcriptomic profiling of GA muscle following a total of 10 times of intravenous MCF-10A/miR122 EV injections in NSG mice. RNA-seq and data processing were performed by Novogene Co., Ltd.

first: Xianhui

last: Ruan

first: Shizhen

last: Wang


title: Whole transcriptome analysis identifies differentially regulated networks during the proliferation inhibition and megakaryocytic differentiation of AML cell induced by 3,8-Di-O-methylellagic acid 2-O-glucoside (DMAG) derived from Sanguisorba offcinalis L.

city: Luzhou

first: Long

state: Sichuan

address: No.1 Section 1, Xiang Lin Road, Longmatan District, Luzhou 646000, China.

institute: Southwest Medical University

summary: We identified the expression profiles of lncRNA, mRNA, miRNA and circRNA by whole-transcriptome sequencing and constructed co-expression network to elucidate the potential mechanisms of 3,8-Di-O-methylellagic acid 2-O-glucoside in anti-AML eﬀect

overall_design: A genome-wide analysis of lncRNAs, mRNA, miRNAs and circRNA expression was detected by whole-transcriptome sequencing on HEL cells after treated with 40 μg/ml DMAG for 3 days, in triplicate.

first: Jianming

last: Wu


title: RNA-seq of peritoneal macrophages transfected by si-Tet2 with or without LM or IFN-γ treatment

city: hangzhou

first: xu

state: zhejiang province

address: shilongshan street 18#

institute: westlake university

summary:
Purpose:The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: total mRNA profiles of si-NCand si-Tet2 transfected macrophages were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow,we knocked down Tet2 in mouse PMs and infected them with LM. RNA sequencing data revealed a broad spectrum of changes in the expression of many cytokines and immune-related genes upon LM infection. Downregulation of Tet2 drastically reversed this LM-induced cytokine overexpression at 12 h post-infection
Conclusions:This finding indicates that Tet2 is either required for cytokine production in immune response, or conversely, Tet2 protects bacteria from clearance. Ablation of Tet2 may accelerate the bacterial clearance in host macrophages, in which cytokines are not needed at the late time point.

overall_design: RNA-seq detection of PMs with related treatments

first: Shuai

first: Xiya

last: Deng

first: Tingting

last: Zheng

first: Xu

last: Li


title: Paradoxical drug sensitization of lung cancer cells by stromal fibroblast-secreted IGF-binding proteins

city: Tampa

first: Eric

last: Welsh

address: 12902 Magnolia Dr

department: Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center

summary: Cells were grown to 80-90% confluency before RNA extraction. Microarray-measured basal gene expression was used to differentiate the various cell types, e.g., CAFs vs NAFs.

overall_design: NSCLC cells lines (H3122, PC9 and gefitinib-resistant PC9_GR), CAFs (CAF7 and CAF12), and NAFs (normal lung cancer fibroblasts, WI38, IMR90 and MRC5; normal bone marrow fibroblast, HS5) were used in the study.  Secretomics, transcriptomics, and tyrosine phosphoproteomics were used to identify signaling components differentially expressed in CAFs vs NAFs and their corresponding downstream signaling effects on cancer cells.

first: Lily

middle: L

last: Remsing Rix

first: Natalia

last: Sumi

first: Qianqian

last: Hu

first: Bina

last: Desai

first: Annamarie

middle: T

last: Bryant

first: Xueli

first: Bin

last: Fang

first: Fumi

last: Kinose

first: Brent

middle: M

last: Kuenzi

first: Y

last: Chen

first: Scott

last: Antonia

first: Christine

last: Lovly

first: John

last: Koomen

middle: B

last: Haura

first: Andriy

last: Marusyk

first: Uwe

last: Rix


title: Single cell RNA sequencing of AATD iPSC-derived hepatocytes following Z mutation correction by base-editing

city: Boston

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: We performed single cell transcriptomic profiling of cells derived from induced human pluripotent stem cells (iPSCs) using hepatocyte directed differentiation protocol which derived iHeps. We used the alpha-1 antitrypsin deficiency (AATD) iPSC line, PiZZ1. On day 15 of differentiation, we transfected cells with base editors to correct the AATD Z mutation.  On day 21 of differentiation, we captured cells for 10x Genomics Single cell capture (V3 protocol). Control cells (MZ and MM stably corrected iHeps) were included in 1 lane, mixed at a ratio of 1:1 and then genotype was identified using the Vartrix Single-Cell Genotyping tool (10X Genomics). Louvain clustering identified 4 major clusters of cells, including a cluster of cells undergoing ER stress.  Base editing decreased the number of cells undergoing ER stress.

overall_design: Single-cell transcriptomic analysis of day 21 iPSC-derived hepatocytes comparing ZZ parental cells with base-edited cells and control (MZ and MM)

first: Rhiannon

last: Werder

first: Andrew

last: Wilson


title: Temporal transcriptome changes in Drosophila eye development

city: Bronx

first: Zhe Jun

last: Ji

state: NY

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: we have performed mRNA-Seq studies of the larval eye and antennal primordial at multiple timepoints within the third larval instar and white prepupal stages

overall_design: mRNA samples were isolated and sequenced from eye-antennal imaginal discs at 72h, 96h, 120h after egg laying (AEL) and at the white prepupal stage.  mRNA was also isolated and sequenced from eye-antennal discs attached to cuticular mouthparts 72h AEL, and from separated eye and antennal portions of the eye-antennal imaginal disc 96h and 120h AEL, as well as from whole larvae 72h, 96h, and 120h AEL.

first: Manon

last: Quiquand

first: Gerard

last: Rimesso

last: Qiao

first: Shengbao

last: Suo

first: Chunyun

last: Zhou

first: Matthew

last: Slattery

first: Kevin

middle: P

last: White

first: Jackie

last: Han

first: Nicholas

last: Baker


title: Dynamic microglial gene expression profiles after ischemic stroke

city: Beijing

first: Yanbing

last: Zhu

address: No. 95, Yong ‘an Road, Xicheng District

department: Experimental and Translational Research Center

institute: Beijing Friendship Hospital, Affiliated to the Capital University of Medical Sciences

summary: Analysis of  microglial gene expression profiles after ischemic stroke. Stroke is a complicated disease caused by the interaction of multiple celltypes. Results provide new insights into the molecular mechanisms underlying microglial activation after ischemic stroke.

overall_design: Microglial gene expression profiles of sham, day1, day3, day7, day21, day60 and day90 focal ischemic stroke mice model

first: Song

last: Wang

first: Jing

last: Guo

first: Yan


title: Stress-driven feedback regulation of multiple tolerant genes improves xylose fermentation of Saccharomyces cerevisiae

first: Lei

last: Qin

address: ZhongGuanCunNan Street 5

institute: Beijing Institute of Technology

summary:
The modification of the  The modification of the tolerance of xylose-fermenting yeast is an urgent issue for improving ethanol production. In this study, multiple genes involving in superoxide dismutase, glutathione biosynthesis, NADPH regeneration and acetic acid degradation were overexpressed using stress-induced promoters, which is selected from the transcriptome data. Stress-induced promoters were used to realize the feedback control of the tolerant genes, which can ultimately improve the tolerance and ethanol production.
We reported the stress-induced promoters for overexpressing tolerant genes and increasing yeast tolerance in a feedback manner

overall_design: Examine the transcriptome under non-stress condition (30°C, 2% glucose) and stress condition (36°C, 10% glucose) of an industrial Saccharomyces cerevisiae CY

first: Chun

last: Li


title: Long-lasting Analgesia via Targeted in situ Repression of NaV1.7

city: La Jolla

first: Prashant

last: Mali

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: University of California San Diego

summary: Current treatments for chronic pain rely largely on opioids despite their significant side effects and risk of addiction. Genetic studies have identified in humans key targets pivotal to nociceptive processing. In particular, a hereditary loss-of-function mutation in NaV1.7, a sodium channel protein associated with signaling in nociceptive sensory afferents, leads to insensitivity to pain without other neurodevelopmental alterations. However, the high sequence and structural similarity between NaV subtypes has frustrated efforts to develop selective inhibitors. Here, we investigated targeted epigenetic repression of NaV1.7 in primary afferents via epigenome engineering approaches based on clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9 and zinc finger proteins at the spinal level as a potential treatment for chronic pain. Towards this end, we first optimized the efficiency of NaV1.7 repression in vitro in Neuro2A cells, and then by the lumbar intrathecal route delivered both epigenome-engineering platforms via adeno-associated viruses (AAVs) to assess their effects in three mouse models of pain: carrageenan-induced inflammatory pain, paclitaxel-induced neuropathic pain and BzATP-induced pain. Our results demonstrate: i) effective repression of NaV1.7 in lumbar dorsal root ganglia; ii) reduced thermal hyperalgesia in the inflammatory state; iii) decreased tactile allodynia in the neuropathic state; and iv) no changes in normal motor function. We anticipate this genomically scarless and non-addictive pain prevention and amelioration approach enabling Long-lasting Analgesia via Targeted in vivo Epigenetic Repression of NaV1.7, a methodology we dub pain LATER, will have significant therapeutic potential in management of persistent pain states.

overall_design: We assess gene expression changes in Neuro2a cells due to zinc-finger and CRISPR/dCas9 knockdown of SCN9A, encoding the soduim channel Nav1.7

first: Ana

last: Moreno

first: Nathan

last: Palmer


title: m6A-seq assays and analysis of breast cancer MDA-MB-231 cells with or without PRMT5 overexpression and Doxrubicin treatment

city: xi'an

first: Wu

last: Ying

state: Shaan'xi

address: Changle west road

institute: Fourth Military Medical University

summary: We report the application of immunoprecipitation of m6A methylated RNA followed by sequencing (MeRIP-Seq) in breast cancer MDA-MB-231 cells to identify PRMT5-mediated transcriptome-wide methylation patterns for doxorubicin response. Total RNAs from breast cancer cells were extracted with TRIzol. Then, mRNA sequencing and m6A sequencing were simultaneously performed. We find that doxorubicin induced the increasing m6A peaks compared to the control group, whereas inhibited by PRMT5. The transcripts exhibiting m6A methylation alteration by doxorubicin and PRMT5 were enriched for gene ontology (GO) terms related to DNA damage response and repair. The GO terms and KEGG annotations analysis identified BRCA1 signaling as being significantly altered through m6A methylation which induced by doxorubicin but inhibited by PRMT5. This study provides that PRMT5 promotes DNA damage repair through regulating m6A methylation of BRCA1 mRNA.

overall_design: Examination of PRMT5-mediated transcriptome-wide methylation patterns for doxorubicin response in breast cancer MDA-MB-231 cells

first: Jian

last: Zhang

first: Rui

last: Ling


title: Inflammatory pathways in peripheral blood expression profile of recent-onset type 1 diabetes

city: marseille

first: christophe

last: chevillard

address: campus de luminy

country: France

institute: INSERM 1090

summary: Changes in innate and adaptive immunity occurring in and around pancreatic islets can also be observed in peripheral  blood mononuclear cells (PBMC) of T1D patients  in Caucasians. The aim of our study was to investigate whether gene expression patterns of PBMC could complement islet autoantibodies for T1D pathogenic mechanisms in the higlty admixed Brazilian population. Methods: We assessed global gene expression in PBMC from  two groups mached for age, sex and BMI: The T1D group with 20 patients with recent-onset T1D (≤ 6 months from diagnosis, in a time  when the autoimmune process is still highly active), testing positive for one or more  islet autoantibodies and 20 islet autoantibody-negative healthy controls (Control group). Results: we identified 474 differentially expressed genes between groups. The most expressed genes in T1D group were mainly related to host defense, with  inflammatory and anti-bacterial/antiviral effects ( LFT, DEFA4, DEFA1, CTSG, KCNMA1) as well as  to cell cycle progression. Several of the downregulated genes in T1D influenced cellular repair, control of inflammation and immune tolerance. They were related to T helper 2 pathway, induction of FOXP3 expression (AREG) and immune tolerance (SMAD6). Conclusion: Our analysis suggested the activation of cell cycle/proliferation, anti-infectious and inflammatory pathways, indicating  immune activation, whereas immunoregulatory pathways were downregulated in PBMC from recent-onset T1D patients. These alterations were elicited by a new genetic profile

overall_design: RNA Extraction was done fresh blood samples of 20 T1 diabetes patients and 20 healthy controls

first: Aritania

middle: S

last: Santos

first: Edecio

last: Cunha-Neto

first: Nelson

last: Gonfinetti

first: Fernanda

last: Bertonha

first: Aurelie

last: Bergon

first: Carlos

last: Moreira-Filho

first: Christophe

last: Chevillard

first: Maria

last: Rossi Silva


title: Modeling melanoma resistance in a genetically engineered mouse model

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: Melanoma is the deadliest type of skin cancer and its incidence is steadily increasing. Targeting melanoma cells posseses significant challenges due to primary or acquired therapy resistance in the majority of patients. Here, we describe the generation of an in vivo mouse model mimicking the key steps in melanoma initiation, progression and resistance acquisition. The well-characterized Tyr::CreERT2 BrafV600E Ptenfl/fl mouse model was used to induce melanoma initiation and subsequently therapy resistance to a combination of BRAF (PLX4720) and MEK (PD0325901) inhibitors. Our data reveal that all of the Tyr::CreERT2 BrafV600E Ptenfl/fl mice subjected to PLX4720+PD0325901 treatment ultimately developed resistance to these inhibitors. Introduction of genetic labelling by crossing Tyr::CreERT2 BrafV600E Ptenfl/fl mice with the TdTomato reporter allele allowed us not only to observe brain metastasis, which are rarely seen in this mouse model, but also to isolate metastatic melanoma cells using flow cytometry. The comparison of the expression profile of metastatic cells before and after resistance acquisition revealed a number of pathways significantly altered in resistant cells. Here, we describe and characterize a suitable mouse model to explore the molecular and cellular mechanisms of multiple stages of drug resistance in melanoma development. Finally, this experimental model might provide further understanding of the interplay between the immune system and melanoma cells.

overall_design: RNA Seq of metastatic melanoma cells from mouse inguinal lymph nodes (FACS sorted by TdTomato marked) treated vs not treated with BRAF+MEK inhibitor combination therapy

first: Anja

last: Krättli

first: Olga

last: Shakhova


title: WM164 BRAF mutant Melanoma cells were treated with 500nM PLX4032 for 60 days and their gene expression was compared to parent cells exposed to a corresponding concentration of DMSO.

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary: Accumulating evidence indicates adaptive cellular reprogramming is a major contributor to disease recurrence and acquired drug resistance in cancer. Here we show that chronic drug exposure results in a multi-state metabolic and epigenetic adaption that allows cancer cells to regain proliferative capacity and eventually develop permanent drug resistance. Specifically, the escape from the previously described slow cycling induced drug tolerant cell state is driven by transiently increased expression of O-GlcNAc transferase (OGT) linking metabolic to epigenetic changes by facilitating global H3K4me3 remodeling. This adaptive process can be blocked by genetic or pharmacological inhibition of OGT or concurrent activation of AMPK to prevent metabolic adaption, subsequent epigenetic remodeling and permanent acquired drug resistance. This novel metabolic and epigenetic remodeling process is also observed following oncogene induced stress and the OGT dependence of this adaptive process uncovered promising targets for combination therapy with current standard of care drugs that could significantly increase response duration and patient outcomes.

overall_design: WM164 treated and untreated cells were kept in triplicate and the mRNA from individual samples were isolated independently for analysis.

first: Dinoop

last: Ravindran Menon

first: Helmut

last: Schaider


title: Transcriptomic profiling of murine aneurysm formation after porcine pancreatic elastase infusion

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

institute: Ludwig-Maximilians-University Munich

summary: In the present work, we aimed to investigate the changes in total RNA expression after porcine pancreatic elastase (PPE) instillation in C57BL/6 mice.

overall_design: RNAseq of murine aortic samples harvested 7 days after saline infusion (n = 4), aortic samples harvested 1 week after PPE infusion (n = 4) and aortic samples harvested 2 weeks after PPE infusion (n = 4) was performed.

middle: H


title: Analysis of global transcriptional changes in H. neptunium cells lacking the cell cycle regulatory genes pleC, divJ or divK

city: Marburg

first: Muriel

last: van Teeseling

address: Hans-Meerwein-Strasse 4

department: Biology

institute: Philipps-Universität Marburg

summary: Within the bacterial phylum of the Alphaproteobacteria many species show complex life cycles. Proper regulation of these life cycles requires cell cycle regulation pathways, one of which is the so-called CtrA pathway. Key factors in the CtrA pathway are the histidine kinases PleC and DivJ (located at opposite poles in the cell) and the response regulator DivK. Within the Alphaproteobacteria, stalked budding bacteria are even more asymmetric than most other representatives. How they regulate their cell cycle has not been studied before. Here, we investigated the transcriptional profiles of Hyphomonas neptunium cells lacking either PleC, DivJ or DivK and compared their profiles to that of wildtype cells. We found that the changes upon deletion of DivJ, PleC and especially DivK were smaller than expected from related organisms.

overall_design: mRNA profiles for the H. neptunium wild-type strain or mutants with in-frame deletion in the pleC, divJ or divK gene were generated in duplicate by next-generation sequencing, using an Illumina NextSeq 500 system with 75 bp read length and a "High 75" sequencing kit

first: Oliver

last: Leicht

first: Martin

last: Thanbichler


title: RNA sequencing data of differentially treated  cancer associated fibroblast, myeloid-derived supression cells, and ICC tumor cells in ICC patient

city: Shanghai

first: Qian

last: Cai

address: No.130 Dongan road

department: Immunology

institute: Fudan University

summary: An interactive tumor microenvironment with different stromal cell types is necessary for supporting cancer stemness. Cancers with dense fibrotic stroma such as intrahepatic cholangiocarcinoma (ICC) are often highly aggressive and chemotherapy resistance. Here, we show that cancer associated fibroblasts (CAF) greatly enhances the capacity of blood CD33+ myeloid-derived suppressor cells (MDSCs) to promote stem-like properties in ICC cells and tumor growth via paracrine signaling. Mechanistically, CAF mediates hyperactivated 5-LO pathway in CD33+ MDSCs via secretion of IL-6 and IL-33, resulting in overproduction of LTB4, which acts on BLT2 to promote cancer stemness via Akt-mTOR signaling. hyperactivated 5-LO pathway are observed in tumor-infiltrating CD33+ MDSCs compared with blood counterparts from the same ICC patients. Moreover, BLT2 blockade augments chemotherapeutic efficacy in ICC PDX models. Thus, our study reveals a previously unrecognized stromal cell network in which CAF educate myeloid cells to shape the optimal supportive microenvironment for the aggressive nature of ICC.

overall_design: Transcription files of blood CD33+MDSCs, tumor CD33+MDSCs, ICC tumor cells, cancer associated fibroblasts (CAFs), FAPkdCAFs, and blood CD33+MDSCs treated with conditional media of FAPkdCAFs or CAFs.

first: Yuli

last: Lin

first: Yu

last: Chen

first: Weiren

last: Liu

first: Li

last: Mao

first: Yinghong

last: Shi

first: Rui

last: He


title: Transcriptome Analysis of TubA Effects on Oocytes Development in Mice

city: Changchun

first: Liyan

last: Sui

address: Xinzhu street 1977

institute: Jilin University

summary: TubA is a specific inhibitor of HDAC6, it could regulate oocytes maturation by regulating acetylation of α-tubulin. However, weather it effects maternal mRNA expression remains unkown. Therefore, in this study,we got in vitro maturated MII oocytes in control and 0.1μg/mL treated .Our study suggests that TubA mainly downregulated cell cycle and DNA methylation related genes.

overall_design: single cell mRNA profiles of control and TubA treated MII oocytes were generated by deep sequencing, 5 samples for each group, using Illumina HiSeq 2000

first: Hao

last: Yu


title: Single-cell RNA sequencing of post-traumatic brain injury day 4 ipsilateral brain leukocytes in C57BL/6 adult male mice

city: San Francisco

first: Walter

last: Eckalbar

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

summary: To determine immune response differences to TBI that correlate with improved function post-TBI in Ccr2-/- mice, single-cell RNA sequencing was performed on brain leukocytes from Ccr2-/- mice and wild type mice isolated during the acute TBI time point of 4 days post-TBI.

overall_design: Brain leukocytes were isolated, CD45+ leukocytes were sorted by flow cytometry and cells were given to UCSF Institute for Human Genomics Core Facility for single-cell RNA sequencing using the 10X Genomics platform.

first: Christine

last: Hsieh


title: Analysis of global transcriptional changes in H. neptunium cells depleted of the cell cycle regulators CckA or ChpT

summary: Within the bacterial phylum of the Alphaproteobacteria many species show complex life cycles. Proper regulation of these life cycles requires cell cycle regulation pathways, one of which is the so-called CtrA pathway. Key factors in the CtrA pathway are the histidine kinase CckA and the phosphotransferase ChpT, which are directly involved in cell cycle specific activation of the response regulator CtrA. Within the Alphaproteobacteria, stalked budding bacteria are even more asymmetric than most other representatives. How they regulate their cell cycle has not been studied before. Here, we investigated the transcriptional profiles of Hyphomonas neptunium cells depleted of CckA or ChpT and compared their profiles to that of wildtype cells. We identified that the essential proteins CckA and ChpT influence the transcription levels of multiple essential processes, such as cell division, as well as specific cell cycle regulated functions such as motility.

overall_design: mRNA profiles for H. neptunium wild-type cells or cells depleted of CckA or ChpT were generated in duplicate by next-generation sequencing, using an Illumina NextSeq 500 system with 75 bp read length and a "High 75" sequencing kit


title: miRNA-based TAPAS II experimental study: respiratory and inflammatory health effects of air pollution and physical activity

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

summary: The study comprises of 24 subjects that have been exposed to high and low Traffic-related air pollution.

overall_design: Serum samples from 24 subjects have been obtained from the TAPAS II cohort (TAPAS II experimental study: respiratory and inflammatory health effects of air pollution and physical activity). The cohort is a controlled crossover study where each participant executed four different scenarios. Each participant was either resting (rest) or cycling (pa) at low (1) and high (4) traffic-related air pollution sites (in a pedestrian square in la Barceloneta neighborhood and on a bridge 5m above Ronda Litoral, the city’s ring road, respectively) in the city of Barcelona.   Plasma samples were recovered from plasma separator tubes following centrifugation of whole blood at 1,600g for 10 min at 4°C. To avoid contamination of the plasma cmiRNAs with blood cell-derived miRNAs, the plasma was subjected to a second centrifugation step at 16,000g before being stored at -80°C (Kroh et al., 2010). Plasma miRNAs were isolated using the miRNeasy Serum/Plasma kit (Qiagen) and the quality was evaluated on a Bioanalyzer using the small RNA Kit (Agilent). Samples were included in the analysis when showing a minimum of 1 ng RNA yield and a peak around 21 nucleotides. The sequencing libraries were prepared using the TruSeq Small RNA-Seq Preparation Kit (Illumina), and sequenced by a HiSeq 2500 (Illumina) according to the manufacture’s protocol

first: Jos

last: Kleinjans


title: Lmo2 is dispensable for maintenance of most Lmo2-induced murine T-cell leukemias

city: Clayton

first: Wei

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

summary: Lmo2 is an oncogenic transcription factor that is a frequent target of chromosomal abnormalities in this T-cell acute lymphoblastic leukemia (T-ALL). In transgenic mouse models, overexpression of Lmo2 causes thymocyte self-renewal leading to T-cell leukemia with long latency. However, the requirement of Lmo2 for maintenance of overt leukemia is poorly understood. We found that Lyl1, a critical cofactor for Lmo2-induced leukemia, is frequently lost in cell lines derived from Lmo2-transgenic mice, raising the possibility that Lmo2 function is dispensable at this stage. To study this, we developed a Tetracycline-repressible knock-in mouse model (Vav-TRE-Lmo2), which expresses Lmo2 throughout the haematopoietic system. This led to specific effects on T-cell development and the development of T-cell leukemia with long latency, preceded by the presence of self-renewing T-cells in the thymus. Repression of Lmo2 overcame the Lmo2-induced thymocyte developmental block at the preleukemic stage and led to elimination of Lmo2-induced thymocyte self-renewal in vivo. In contrast, Lmo2 function was dispensable for the majority of overt Lmo2-induced T-cell leukemias as well as leukemia-derived cell lines, implying an evolution of oncogene addiction in the majority of T-cell leukemias. Lmo2-dependence in T-ALL was associated with an immature gene expression profile, but could not be predicted by immunophenotype or assessment of Notch pathway activation. Thus, Lmo2 can give rise to both Lmo2-depenent and –independent T-cell leukemias. The Vav-TRE-Lmo2 model should be useful to determine the molecular features associated with Lmo2-dependence, as well as the critical components of the Lmo2-induced self-renewal pathways in T-ALL.

overall_design: Transcriptome profiling of cell lines from T-cell leukemias arising in CD2-Lmo2 transgenic mice.

first: Hesham

last: Abdulla

first: Tenae

last: Davies

first: Benjamin

last: Shields

first: Matthew

last: McCormack


title: TGF-β promotes the conversion of human CD5low cDC2s to tolerogenic CD5high cDC2s

first: Xiaoyang

last: Jin

state: -- Please, Select --

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, CAS

summary: Human blood CD1c+ cDC2s can be divided into two functionally distinct subpopulations according to their CD5 expression. CD5high and CD5low cDC2s differ significantly in their gene expression, cytokine production, antigen presentation, and T cell polarization. However, the plasticity of CD5high and CD5low cDC2s was unknown. We found that about 40% CD5low cDC2s upregulated their CD5 expression when cultured in the presence of TGF-β. Transcriptome analysis revealed that the converted CD5high cDC2s are closer to cultured CD5high cDC2s, separating form unconverted CD5low cDC2s. Converted CD5high cDC2s with higher IRF4 upregulated some steady-state DC mature molecules, such CCR7, CD86, PD-L1 and CCL22. Unconverted CD5low cDC2s with higher MAFB upregulated some monocyte signature genes, such CCR2, CSF1R and CCL2. Moreover, Converted CD5high and unconverted CD5low cDC2s were significantly different in inducing CD4+ T cell polarization. Specifically, converted CD5high cDC2s recruited and induced more Treg cells than unconverted CD5low cDC2s. We also found that the ratio of CD5high cDC2s are significantly higher in colorectal tumor tissue comparing with paired paratumor tissue. In summary, TGF-β can effectively promote the conversion from CD5low cDC2s to CD5high cDC2s accompanied by phenotype and function change. This may be another mechanism which contributes to TGF-β induced immune suppression.

overall_design: mRNA profiles of CD5high and CD5low cDC2s after they are cultured in the presence of TGF-β and then sorted according to CD5 expression level

first: Xiangyun

last: Yin


title: Caliban regulates mitochondrial morphology and redox state in enterocytes to maintain intestinal homeostasis in Drosophila

city: Dalian

first: Ying

last: Ge

address: 9 Western Section, Lvshun South Street

institute: Dalian Medical University

summary: Precise regulation of stem cell activity is crucial for tissue homeostasis. In Drosophila, intestinal stem cells (ISCs) maintain the midgut epithelium and respond to oxidative challenges by increasing proliferation rates. However, the connection between intestinal homeostasis and redox signaling remains obscure. Here we identify Caliban (Clbn) as a novel mitochondrial protein involved in regulating the cellular redox state in enterocytes (ECs) and the proliferative activity of ISCs. We find that clbn knock-out flies lose the intestinal homeostasis characterized by increased ISCs proliferation, disrupted intestinal epithelial integrity, reduced viability in response to harmful stress and shortened lifespan. Mechanistically, Clbn is highly expressed and localized to mitochondria in ECs, and loss of clbn impairs mitochondrial morphology and functions, result in accumulation of reactive oxygen species, ECs damage and activation of JNK and JAK-STAT signaling pathways. Furthermore, loss of clbn promotes tumor growth in gut generated by activating Ras in intestinal progenitor cells. Our findings reveal the essential role of Clbn in maintaining intestinal homeostasis and may provide new insight into the functional link among mitochondrial redox modulation, tissue homeostasis and cancer.

overall_design: Gene expression was profiled in 6 samples [embryos of w1118 and clbn knock-out flies, 3 replicates].

first: Xiaolin

last: Bi


title: Skewed macrophage polarization in aging skeletal muscle

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary: Skeletal muscle aging is a major causative factor for disability and frailty in the elderly.  Recent theories about the origins of the progressive impairment of skeletal muscle with aging emphasize a disequilibrium between damage and repair.  Macrophages participate in muscle tissue repair first as pro-inflammatory M1 subtype and then as M2 anti-inflammatory subtype.  However, information on macrophage presence in skeletal muscle is still sporadic and the effect of aging on different phenotypes remains unknown.  In this study, we sought to characterize the polarization status of macrophages human skeletal muscle at different ages.  We found that most macrophages in human skeletal muscle are M2, and that this number increased with advancing age.  On the contrary, M1 macrophages decline with aging, making the total number of macrophages invariant with older age.  Notably, M2 macrophages co-localized with increasing intermuscular adipose tissue (IMAT) in aging skeletal muscle.  The mouse strain BALB/c, intrinsically M2-prone, showed increased IMAT and regenerating myofibers in skeletal muscle, accompanied by elevated expression of adipocyte markers and M2 cytokines.  Collectively, we report that polarization of macrophages to the major M2 subtype is associated with IMAT, and propose that increased M2 in aged skeletal muscle may reflect active repair of aging-associated muscle damage.

overall_design: Total RNAs isolated from 2 months old and 24 months old vastus intermedius muscle of BALB/c mice were profiled with Agilent 44K NIA mouse microarrays.

first: Chang-Yi

last: Cui


title: RNA-seq helps to analyze the regulation mechanism of maize roots under nutrient-deficiency conditions

city: Taian

first: Nana

last: Ma

address: No 61 Daizong Street No 61

institute: Shandong Agricultural University

summary:
To increase crop yield without polluting the environment, improving crop nutrient efficiency is of great importance. The RSA of plants is centrally involved in nutrient use efficiency. Therefore, to uncover the molecular mechanisms that regulate RSA of maize under nutrient-deficiency conditions and to improve maize nutrient use efficiency based on this knowledge, we investigated the morphological changes and ribonucleic acid sequencing (RNA-seq) profiles of maize roots during growth under normal and N-, P-, and K-deficiency conditions. We analyzed the data in different aspects and verified the reliability of the RNA-seq data by real-time quantitative polymerase chain reaction (RT-qPCR). These results will provide theoretical support for improving plant nutrient use efficiency.
The maize (Z. mays) inbred line DengHai 605 was used in this study.  Provided for four treatment conditions: normal N, P, and K level (CK); potassium deficiency (K-DEF); nitrogen deficiency (N-DEF); and phosphorus deficiency (P-DEF). The experiments were carried out by combining sand culture with water culture.
The standard for evaluating differential gene expression is fold change (FC) > 2 or FC < -2 and p value < 0.05.The numbers of DEGs under N-, P-, and K-deficiency conditions were 3494 (1801 up-regulated and 1693 down-regulated), 3424 (1761 up-regulated and 1663 down-regulated), and 1830 (827 up-regulated and 1003 down-regulated), respectively. A total of 1483, 1470, and 519 genes were specifically expressed under the N-, P-, and K-deficiency conditions, respectively.

overall_design: Zea Mays mRNA profiles of 40-day-old normal N, P, and K level (CK); potassium deficiency (K-DEF); nitrogen deficiency (N-DEF); and phosphorus deficiency (P-DEF)were generated by deep sequencing, in triplicate, using illumina Hiseq X Ten.

first: Jinlian

last: Lv


title: Forkhead Box B1 regulates the differentiation timing and neurogenic potential of human neural crest cells [ChIP-Seq]

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Human neural crest cell development progresses via a pre-neural border (pNB) cell state that precedes the induction of the neurectoderm and the neural border. Here, we identify a set of pNB gene candidates, including forkhead box B1 (FOXB1), and their associated enhancers, that are rapidly activated by β-catenin-mediated signaling during human embryonic stem (ES) cell differentiation towards neural crest cells. FOXB1 simultaneously maintains neuroectoderm competency and controls the timing of differentiating ES cells to acquire neural crest fate by directly targeting key neural crest and neural progenitor loci in a context-dependent manner. Notably, the transient expression of FOXB1 in pre-neural crest cells also establishes autonomic neurogenic potential in mature neural crest cells, likely via its regulation of the expression of ASCL1, a master regulator of autonomic neurons. Altogether, our data implicates pNB cell state as the missing link bridging the exit of pluripotency to the acquisition of neural crest fate and its diverse ecto-mesenchymal differentiation potentials.

overall_design: Examination of genomic binding pattern of FOXB1 in human pre-neural crest cells

first: Alan

middle: W

last: Leung

last: López-Giráldez


title: Spleen response following malaria infection in  WT and miR-155 KO mice.

city: Freiburg

first: Yoko

middle: Fukuda

last: Yuzawa

address: Stübeweg 51

institute: Max-Planck Institute of Immunobiology

summary: Analysis of the transcriptome pattern of spleen after maralia infection in WT and miR-155 KO mice.

overall_design: Spleens were extracted from WT and miR-155 KO mice on the 0 and 6th day of malaria infection and samples were sent for deep RNA-seq analysis.

first: Taro

last: Fukao


title: Forkhead Box B1 regulates the differentiation timing and neurogenic potential of human neural crest cells [RNA-Seq 3]

overall_design: Examining the effect of removing FOXB1 protein on gene expression dynamics during neural crest induction


title: B-cell response following malaria infection in WT and miR-155 KO mice

summary: Analysis of the transcriptome pattern of splenic B lymphocytes after malaria infection in WT and miR-155 KO mice.

overall_design: B lymphocytes were purified from the spleens of WT and miR-155 KO mice on the 0, 3rd and 6th day of malaria infection and samples were sent for microarray analysis.


title: Forkhead Box B1 regulates the differentiation timing and neurogenic potential of human neural crest cells [RNA-Seq 1]

overall_design: Examination of the transcriptomic changes during human neural crest induction from ES cells


title: Excitation transcription coupling during acute stretch and tachycardia in non-failing human myocardium

first: Karin

last: Wagner

summary:
Stretch increases wall stress and so far the molecular mechanisms behind increased afterload had been thouroughly studied in vitro and in vivo. Tachycardia when accutelly triggered has the potential to induce cardiac remodeling as stretch does. However the degree of response, similarities and differencess have not been adressed so far.
We aimed to perform whole genome screening for genes that are affected by accute application of stretch and tachycardia in human non-failing tissue.

overall_design: Atrial muscle strips (trabeculae) were subjected to 6h of either condition followed by RNA isolation and hybridisation on the Affymetrix microarrays (5 patients per group - tretament and coresponding control, replicates from the same patients were pooled together were applicable).

first: Natasa

last: Djalinac

first: Ewald

last: Kolesnik

first: Simon

last: Sedej

first: Peter

last: Rainer

first: Daniel

last: Scher

first: Heinrich

last: Maechler

first: Akos

last: Heinemann

first: Dirk

last: van Lewinski

first: Egbert

last: Bisping


title: Kinetics of M-CSF cultured and LPS stimulated WT and miR-155 KO Macrophages.

summary: Analysis of the transcriptome pattern of miR-155 deficient Bone marrow-derived macrophages (BMMΦ) in both steady-state and inflammatory conditions after 6-, 12- and 24 h, in comparison to their WT counterparts.

overall_design: Total bone marrow was cultured in 10 ng/mL M-CSF enriched RPMI-media for 9 days. Adherent cells (Macrophages) were either harvested or stimulated with 100 ng/mL LPS. Samples were taken at 0-, 6-, 12- and 24 h, and samples were sent for microarray analysis.

first: Sebastian

last: Hedlund


title: GM-CSF cultured and LPS stimulated WT and miR-155 KO DC

summary: Analyze the transcriptome pattern of miR-155 deficient BMDC in both steady-state and inflammatory conditions, in comparison to WT counterparts.

overall_design: Total bone marrow was cultured in 40 ng/mL GM-CSF enriched RPMI-media for 7 days. A fraction of the floating cells were stimulated with 100 ng/mL LPS for 16 h, after with both unstimulated and stimulate DC were sorted by FACS for DC markers and activation markers (CD86). Unactivated DC from unstimulated samples (CD86-) were isolated together with activated (adherent) DC from LPS stimulated samples (CD86+), and total RNA was isolated.


title: miR-233 and bone marrow cells

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

overall_design: Refer to individual Series


title: Transcriptomics of water-deficit Stress Responses in TAM Wheat Cultivars

city: Amarillo

first: Shuyu

last: Liu

state: Texas

address: 6500 Amarillo Blvd West

department: Texas A&M AgriLife Research

institute: Texas A&M University System

summary: Water deficit stress between the booting and grain filling stages significantly affect grain yield and quality of hard red winter wheat.  Several stress tolerant cultivars with different adaptation mechanisms have been released and are widely cultivated on the Southern Great Plains of the US.  However, the physiological, molecular, and genetic basis of adaptation to drought stress for these cultivars remains unknown.  Use of transcriptome profiling to identify drought responsive genes in hexaploid wheat is a challenging process given the quantitative nature of drought stress, genome complexity, and the intricacy of interaction effects.  If the information generated from functional genomics studies is to be used in molecular breeding programs for cultivar development, it is highly desirable to use cultivars better adapted for the region.  In the current study we used two well-adapted, drought-tolerant, high-yielding, cultivated varieties, TAM 111 and TAM 112, which appear to have different adaptation mechanisms, to identify drought stress induced transcripts during heading and early dough stages.  A set of 24 Affymetrix GeneChip wheat genome arrays (2 cultivars; 2 water treatments; 2 sampling stages; 3 biological replicates) from plants subjected to water deficit stress under controlled glasshouse conditions.  Differentially expressed genes were identified using a ANOVA (p<0.01) controlling false discovery rate (FDR, q<0.01) using Benjamini Hochberg approach.

overall_design: Total of 24 samples; 2 genotypes * 2 developmental stages * 2 water treatments * 3 replicates

first: Jackie

last: Rudd

first: Qingwu

last: Xue


title: Transcriptomics of induced defense responses to Greenbug aphid feeding in near isogenic wheat lines

summary: The greenbug aphid, Schizaphis graminum (Rondani) is an important cereal pest periodically threatening wheat yields in the United States and around the world.  The wheat breeding program at Texas A&M University has introgressed the greenbug resistance gene Gb3 from synthetic wheat ‘Largo’ into the widely grown cultivars TAM 110 and TAM 112; however, the molecular mechanisms of Gb3-induced defense responses remain unknown. Using Affymetrix GeneChip Wheat Genome Arrays, we investigated the temporal dynamics of Gb3-mediated transcriptional responses upon greenbug feeding on resistant and susceptible bulks (RB and SB respectively) derived from two near-isogenic lines.  Following statistical analysis, the MapMan functional classification on 692 differentially expressed transcripts from the interaction group identified 122 transcripts that were putatively associated with biotic stress responses.  In RB, Gb3 induced transmembrane receptor kinases and downstream early defense signal transduction pathways.  However, non-Gb3 mediated pathways in SB prompted induction of transcripts mediating callose decomposition and transcripts regulating biosynthesis of stress hormones jasmonic acid, ethylene, and abscisic acid.  Additionally, the SB showed elevated levels of transcripts mediating redox homeostasis, peroxidases, glutathione S-transferases, and defense-related secondary metabolites.  Overall, the results indicated that greenbugs inflicted more damage in the SB compared to RB and absence of Gb3-mediated signaling resulted in cell wall remodeling and strong accumulation of toxic compounds warranting production of antioxidant and defense-related compounds.  The study reinforced our knowledge about preferential feeding on S genotypes and plausible antixenosis or tolerance-related defense signaling in Gb3-associated R genotypes and generated several new hypotheses.

overall_design: Total of 18 samples; 2 genotypes * 3 time points * 3 replicates

first: Yiqun

last: Weng


title: Granulocyte and Monocyte

first: Yoko

last: Yuzawa

summary: To analyze gene expression profiles in myeloid differentiation.

overall_design: Granulocytes and Monocytes were sorted from mouse bone marrow cells and analyzed.

first: Manuel

last: Frietsch

last: Fukuda


title: Gene expression profile of calcium oxalate nephrocalcinosis in wild type and NLPR3 knock out mice.

status: Public on Dec 31 2021

city: Wuhan

first: Haoran

state: Hubei

address: Jiefang avenue 1095

department: Urology

institute: Tongji Hospital

summary: Microarray analysis was used to assess the expression levels of mRNAs in kidney tissues of calcium oxalate (CaOx) nephrocalcinosis mouse model and normal mouse kidney tissues.The animals used in the experiment were male 6-8 weeks old  wild type and NLPR3 knock out C57BL/6J mice. To establish a CaOx nephrocalcinosis mouse model, each mouse was intraperitoneally injected with saline or glyoxylate acid (Gly) (75 mg/kg/d, 200 μl) from day 1 to day 7. Animals were euthanized after 7 days, and kidney samples were collected at the time of euthanasia.

overall_design: MRNA expression profile in kidney tissues of of calcium oxalate (CaOx) nephrocalcinosis in wild type and NLPR3 knock out mice.

first: Xiaoqi

last: Yang

first: Chen

last: Duan

first: Tao

last: Ye

first: Xiangyang

last: Yao

first: Peng

last: Lv

first: Bo

last: Li

first: Zhangqun

first: Hua

last: Xu


title: Immature granulocyte in WT and miR-223 KO bone marrow

summary: To analyze the function of miR-223 in steady-state myelopoiesis.

overall_design: Immature granulocytes were sorted from bone marrow cells and analyzed.

first: Taro

last: Fukao

first: Hiroyuki

last: Kayo


title: Leishmania major infected WT and miR-223 KO mice

summary: To analyze the function of miR-223 in chronic infection.

overall_design: Mice were subcutaneously inoculated with Leishmania major promastigotes at right hind foot pad for 4 weeks. Mac1+ cells were sorted from bone marrow cells and analyzed.


title: Transcriptomes analysis of grains of two wheat cultivars with different antioxidant activity

city: Zhengzhou

first: Dongyun

last: Ma

address: No.15 Longzihu College Park,Zhengzhou New District,Zhengzhou

institute: Henan Agricultural University

summary: The goals of this study are to compare transcriptome profiling (RNA-seq) between two wheat cultivars with different antioxidant actvity and to clarify the differences of these two wheat cultivars.

overall_design: Examination of grains sampled from 2 different wheat culitvars at 20 days after anthesis and 30 day after anthesis.

first: Beiming

first: Jianchao

last: Feng

first: Haizhou

last: Hu


title: GM-CSF cultured WT and miR-223 KO bone marrow

first: Yoko

summary: To analyze the function of miR-223 in ex-vivo cultured bone marrow.

overall_design: Bone marrow cells were cultured with 40ng/ml GM-CSF for 4 days. Then expanding immature granulocytes were sorted for analysis.


title: Establishment of mouse primitive endoderm stem cell lines [scRNA-Seq II]

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary: The mammalian blastocyst consists of three distinct cell types: epiblast, trophoblast (TB), and primitive endoderm (PrE). Although embryonic stem cells (ESCs) and trophoblast stem cells (TSCs) retain the functional properties of Epi and TB, the currently available extraembryonic endoderm cells (XENC) do not fully recapitulate the developmental potential of PrE. Here we report derivation of primitive endoderm stem cells (PrESCs) in mice. PrESCs express both PrE and pluripotency marker genes like founder PrE. These cells are efficiently incorporated into PrE upon blastocyst injection, generate functionally competent PrE-derived tissues, and support fetal development of PrE-depleted blastocysts in chimeras. Establishment of PrESCs therefore represents a significant step-forward in elucidating the mechanisms for PrE specification and subsequent pre- and post-implantation development.

overall_design: We investigated the differentiation capability of PrESCs by using a modified blastoid self-organization method, in which PrESCs, ESCs and TSCs were sequentially assembled to form ETP complexes (ETP). In this condition, respective stem cells established uniform contacts in ETPs by day3. We then assessed differentiation status of respective stem cells by scRNA-seq analysis for respective stem cells and day3 and day6 ETPs.

first: Yasuhide

last: Ohinata

first: Haruhiko

last: Koseki


city: wuhan

first: wu

middle: xiao

last: man

address: Donghu South Road

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary:
Purpose:Salinity is an important environmental factor that affects the physiological activities of fish. The goals of this study are investigating  the effect of different saline-alkali stress on grass carp (Ctenopharyngodon idella).
Methods: Grass carp individuals, averaging 12 cm in body length, were obtained from Duofu fish farm (Wuhan, China) and cultured at recirculating aquaculture system for 2 weeks before the experiment began. For the challenge, all grass carp were  randomly divided into three groups, and then cultured at saline-alkali water with the concentration of 0, 3‰ and 6‰. After 30 days, some grass crap cultured at 3‰ and 6‰ saline-alkali water were injured. At the same time, gill samples of grass carp were collected from 0, 3‰ (grass carp was not injured),  3‰ (grass carp was injured), 6‰ (grass carp was not injured) and 6‰ (grass carp was injured)saline-alkali groups. Total RNA of all samples was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's introduction. RNA integrity was assessed using an Agilent 2100 bioanalyzer (Agilent, USA). Samples with RNA integrity numbers (RINs) ≥ 7.5 were subjected to cDNA library construction using TruseqTM RNA sample prep Kit (Illumina).
Results:A total of 15 were processed for transcriptome sequencing, generating 94.99Gb Clean Data. At least 5.76Gb clean data were generated for each sample with minimum 91.87% of clean data achieved quality score of Q30. Clean reads of each sample were mapped to specified reference genome. Mapping ratio ranged from 88.59% to 92.84%. The expression of genes was quantified and differentially expressed genes were identified based on their expression.Criteria for differentially expressed genes was set as Fold Change(FC)≥1.5 and Pvalue<0.05. Fold change(FC) refers to the ratio of gene expression in two samples. These DEGs were further processed for functional annotation and enrichment analysis.
Conclusions: Our study represents Effects and molecular regulation mechanisms of saline-alkali stress on the healthy grass carp by using  RNA-seqtechnology. Our results show that saline-alkali stress will impair the immune system of grass carp.

overall_design: Total RNA was solated from gills of grass carp cultured at saline-alkali water with the concentration of 0, 3‰ and 6‰ for 30 days

first: Hong

last: Fang

first: Xiao

last: Wu

first: Yuan

middle: Y

first: Ming

middle: X

last: Chang


title: Sputum exosomal microRNAs profiling reveals critical pathways modulated by Pseudomonas aeruginosa colonization in bronchiectasis

city: GuangZhou

first: Yan

last: Huang

address: 151 Yanjiang Road, Guangzhou, Guangdong, China

institute: Guangzhou Institute of Respiratory Health

summary: Our findings have clinical implications. Identification of sputum exosomal miRNA helps explore the important biological pathways underlying the pathogenesis of bronchiectasis, thus unraveling candidate targets for future interventions of PA colonization. Apart from canonical inflammatory pathways, we have unraveled the modulation of longevity regulation pathway which opens a new avenue for exploring how PA colonization interacts with the airway epithelium. The significant correlation between sputum inflammatory biomarkers and miR-92b-5p and miR-223-3p provided further evidence on the unresolved inflammation in the PA-colonized microenvironment. However, causality cannot be inferred based on the current study design.

overall_design: Patients collected spontaneous sputum when clinically stable, and were followed-up to determine bacterial colonization status. Pseudomonas aeruginosa colonization is defined as sputum culture positive of Pseudomonas aeruginosa for at least two occasions (at least three months apart) within one year, when clinically stable during the longitudinal follow-up. Bronchiectasis patients were stratified into Pseudomonas aeruginosa and non-Pseudomonas aeruginosa group (unmet the criteria of Pseudomonas aeruginosa colonization). 2 different colonization status in stable bronchiectasis patients were divided. Induced sputum were collected in healthy subjects. All sputum samples were completed by exosomal miRNA sequencing.

first: Wei-jie

last: Guan


title: Overproduction of IFNg by Cbl-b deficient CD8+ T cells provides resistance against regulatory T cells and induce potent anti-tumor immunity

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

summary: Regulatory T cells are one of the integral components of the adaptive immune system that contribute to the regulation of anti-tumor T cell responses. However, studies have suggested that alterations in T cell signaling networks can result in T cells that are resistant to the suppressive effects of Treg cells. Here, we investigated the role of Cbl-b, an E3 ubiquitin ligase and a negative regulator of TCR signaling pathways, in establishing CD8+ T cell resistance to Treg cell-mediated suppression. First, the absence of Cbl-b rendered CD8+ T cells refractory to the suppressive effects of Treg cells in vitro. Transcriptomic analyses suggested that pathways associated with cellular proliferation and cytokine production likely contribute to the observed phenotype. In particular, hyper-secretion of IFN-g by Cbl-b deficient CD8+ T cells served as a novel mechanism which selectively renders CD8+ T cells less sensitive to suppression by Treg cells. To explore our findings in vivo, we utilized tumor-bearing FoxP3DTR-eGFP mice to confirm that the adoptively transferred tumor-specific CD8+ T cells were susceptible to regulation by Treg cells in the tumor. Unlike the wildtype counterpart, Cbl-b deficient CD8+ T cells were resistant to the suppressive effects of Treg cells in the tumor, and the therapeutic benefit of Cbl-b deficiency was abrogated upon IFN-g blockade. Collectively, our data highlight the role of Cbl-b deficiency and subsequent hyper-secretion of IFN-g as a key mechanism which renders CD8+ T cells resistant to Treg cell-mediated suppression.

overall_design: CD8+ T-cells, either CBLB wildtype (WT) or knockout (KO), some stimulated with either anti-CD3 or anti-CD3 + anti-CD28

first: James

last: Han

first: Azin

last: Sayad

first: Pam


title: Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets

city: Seocho-gu

first: June-Young

last: Koh

state: Seoul

address: 2575 Nambusunhwan-ro,

institute: GENOME INSIGHT

summary: While the seroprevalence of SARS-CoV-2 in healthy people does not differ significantly among age groups, those aged 65 years or older exhibit strikingly higher COVID-19 mortality compared to younger individuals. To further understand differing COVID-19 manifestations in patients of different ages, three age groups of ferrets are infected with SARS-CoV-2. Although SARS-CoV-2 is isolated from all ferrets regardless of age, aged ferrets (≥3 years old) shows higher viral loads, longer nasal virus shedding, and more severe lung inflammatory cell infiltration and clinical symptoms compared to juvenile (≤6 months) and young adult (1-2 years) groups. Furthermore, direct contact ferrets co-housed with the virus-infected aged group shed more virus than direct-contact ferrets co-housed with virus-infected juvenile or young adult ferrets. Transcriptome analysis of aged ferret lungs reveals strong enrichment of gene sets related to type I interferon, activated T cells, and M1 macrophage responses, mimicking the gene expression profile of severe COVID-19 patients. Thus, SARS-CoV-2-infected aged ferrets highly recapitulate COVID-19 patients with severe symptoms and are useful for understanding age-associated infection, transmission, and pathogenesis of SARS-CoV-2.

overall_design: RNA sequencing analysis of lung tissues from the juvenile, young adult, and aged ferret groups at pre-infection, 2, and 5 day post infection. (n = 3 per each group)Retinal mRNA profiles of 21-day old wild type (WT) and Nrl-/- mice

first: Young-Il

last: Kim

first: Kwang-Min

last: Yu

first: Jae

middle: U

last: Jung

first: Young

last: Choi


title: Brusatol inhibits proliferation and invasion of glioblastoma by down-regulating the expression of ECM1

city: wenzhou

first: Cai

last: Lin

address: nanbaixiang street

department: Neurosurgery

institute: The First Affiliated Hospital of Wenzhou Medical University

summary: Brusatol (Bru), a Chinese herbal extract, has a variety of anti-tumor effects. However, little is known regarding its role and underlying mechanism in glioblastoma cells. Here, we found that Bru could inhibit the proliferation of glioblastoma cells in vivo and in vitro. Besides, it also had an inhibitory effect on human primary glioblastoma cells. In order to further study the underlying mechanism of Bru’s action on GBM, we performed RNA sequencing array on GBM cells treated by Bru with IC50 for 48 hours. A log2 fold change >1.0 and a P < 0.05 were used as cutoff criteria. The volcano plots results showed that Bru significantly changed the mRNA expression pattern in U251 (819 upregulated genes and 954 downregulated genes) and U87 (485 upregulated genes and 266 downregulated genes) cells. Then, we subjected these differentially expressed genes to the Reactome pathway database (https://reactome.org), which provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations in a single, consistent data model. Reactome enrichment analysis indicated that the collagen and extracellular matrix related pathways (Italic Script with *) were mainly involved in Bru-treated GBM cells. Subsequently, we used the Venn diagram analysis (VDA) to display the shared genes between U251 and U87 cells and finally determined that ESM1, an important factor in extracellular matrix formation, changed obviously by Bru treatment. Down-regulating the expression of ECM1 via transfecting siRNA could weaken the proliferation and invasion of glioblastoma cells and promote the inhibitory effect of Bru treatment. Lentivirus-mediated overexpression of ECM1 could effectively reverse this weakening effect. Our findings indicated that Bru could inhibit the proliferation and invasion of glioblastoma cells by suppressing the expression of ECM1, and Bru might be a novel effective anticancer drug for glioblastoma cells.

overall_design: mRNA profiles of BRU-treated and BRU-untreated GBM cell lines (U251 and U87)

first: Dai

last: Zhang'an

first: Lu

last: Xianghe


title: Evolutionary Origin of Vertebrate Oct4/POUV Functions in Supporting Pluripotency

city: Copenhagen

first: Joshua

last: Brickman

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)

summary: Pluripotency is the capacity of early embryonic cells to make all the future lineages of the organism, and the existence of a pluripotent population of cells is important to both germ cell function and the pool of progenitor cells that enable vertebrate development to proceed over time through the process of gastrulation. Oct4, a class V POU transcription factor, is required for maintenance of pluripotency in embryonic stem cells (ESCs) and induction of pluripotency via transcription factor reprogramming. Homologues of Oct4 have been identified in other gnathostomes and classified into two different paralogues: POU5F1 and POU5F3. Here we provide evidence that these proteins are probably derived from a single POUV gene through ancient whole genome duplication events. To approach this issue, we compared the functional conservation and divergence of different POUV proteins in their capacity to support naïve pluripotency in mouse ESCs. We found a strong correlation between POU5F1 activity in naïve pluripotency and the regulation of germ cell specification programs. In contrast, POU5F3 exhibited reduced capacity to support naïve ESCs and its activity in ESCs correlated with the expression of genes associated with pre-gastrulation stages, or primed pluripotency. We detected evidence of this functional segregation as early as Sarcopterygian ancestors, based on the activities of coelacanth POUV proteins. Furthermore, we were able to identify earlier POUV homologues in lamprey and shark, indicating that the earliest point at which mammalian-level pluripotency of both POUV paralogues emerged is between the osteichthyan-chondrichthyan split and the gnathostome-cyclostome split.Taken together, our work highlights the evolutionary history of POUV activities across jawed vertebrates, suggesting that evolutionary pressure has facilitated maintenance of both paralogues over long periods of evolutionary history. In species with both paralogues, subfunctionalization of these proteins appears conserved.  However, in many branches of vertebrate evolution, one of these paralogues is lost, suggesting a high level of plasticity in function and precarious balance between retaining both proteins and the overall levels of POUV activity in different developmental systems.  While the conserved subfunctionalization of POUV activities evolved at some point just before the appearance of tetrapods, the additional divergent activities of this protein family appear to have evolved independently in each vertebrate lineage after gnathostome radiation.

overall_design: Nanog-eGFP/129 MEF cells were infected with ectopic retrovirus carrying Oct4 or POU5 homologue gene together with other retrovirus carrying Sox2, Klf4 and cMyc. The infection was done at day 0 and day 1 under MEF medium. On day 3, MEF medium was replaced with defined iPSC induction medium. On day 4, induced cells were seeded onto irradiated feeders. Medium was changed daily from day 6 to day 10 and every two-day from day 12 onward. Nanog-eGFP positive iPSC clones were picked and expanded under defined iPSC induction medium. iPSC clones were stained with c-Kit-APC. Nanog-eGFP+c-Kit+ cells were sorted and collected for RNA extraction and DNA microarray.

first: Woranop

last: Sukparangsi


title: The Breast Cancer Single Cell Line Atlas: A blueprint of breast cancer cell lines and their role in disease subtyping, heterogeneity, stemness, and therapeutic testing

city: New York

first: Robert

last: Sebra

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: We investigated the heterogeneous cell populations breast cancer cell lines through single cell RNA sequencing technologies. The assay sequenced over 30,000 cells composing 49 unique subclusters. Following clustering, we identify unqiue gene markers in each population as well as  deeper network functional preditiomns of key populations.

overall_design: 17 scRNAseq samples without replicate. Culture breast cancer cell lines up to P6 and then processsed for scRNAseq through 10X 3' V3 kit.


title: HDAC Inhibitor Titration of Transcription and Axolotl Tail Regeneration

city: Lexington

first: Jeramiah

middle: James

last: Smith

state: KY

address: 101 Morgan Building

institute: University of Kentucky

summary: 10X transcriptome sequencing of control and romidepsin treated embryonic tail regenerates.

overall_design: To map transcripts to axolotl cell types, single-nuclei RNA-Seq was performed. Embryos were administered 2 mm distal tail amputations and either treated in Axololt Rearing Water (N = 100) or 10 uM romidepsin (N=100). At 6 HPA, 1 mm of distal tail tip tissue was collected and pooled for nuclei isolation and 10x single nuclei RNA-Seq. Nuclei isolation, library preparation, and next generation sequencing were performed by Singulomics. The resulting data were mapped to an axolotl transcript assembly as described previously (Rodgers et al., 2020), analyzed using Cell Ranger, and visualized using 10x visualization software (Loupe version 5.0). Default graph-based clustering was used to identify distinct clusters of cells and enriched genes were used to manually identify and differentiate among cell types.

first: S

middle: R

last: Voss

middle: J

first: Nataliya

last: Timoshevskaya

first: Larissa

middle: V

last: Ponomareva

first: Jon

last: Thorson

first: Alan

last: Veliz-Cuba

first: David

last: Murrugarra


title: SHH is downstream of immediate early genes and is targeted by chemotherapy on a specific enhancer [CUT&Tag, ATAC-seq]

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: Sonic Hedgehog (SHH) signaling is a key regulator of embryonic development and tissue homeostasis, and is involved in gastrointestinal (GI) cancer progression. Here we show that SHH gene expression is down-regulated by chemotherapy drugs. The 139Kb upstream enhancer is specifically targeted by the immediate early gene EGR1.

overall_design: Human CRC cell line HT29 was cultured and treated with 5FU for 2h or 4h, and subjected to ATAC-seq or Cut-tag analysis using the corresponding antibodies.

first: Zhicao

last: Yue


title: Leveraging single cell transcriptomics and custom high throughput functional screening assays to resolve cell type, growth kinetic, and stemness heterogeneity within Comma-1D

summary: We investigated the heterogeneous cell populations within the Comma-1D cell line through single cell RNA sequencing technologies. The assay sequenced over 5,000 cells composing 8 unique subclusters. Populations detected included luminal, myoepithelial, and fibroblast like cell types.

overall_design: One scRNAseq sample without replicate. Culture Comma-1D to P5 and then processsed for scRNAseq through 10X 3' V3 kit.


title: Profilling of viral and host transcriptome in SARS-CoV-2 infected A549-ACE2 cells with VIC or B.1.1.7 strains.

city: Oxford

first: Jeffrey

last: Lee

address: Dorothy Hodgkin Road

country: United Kingdom

institute: University of Oxford

summary: Despite an unprecedented global research effort on SARS-CoV-2, early replication events remain poorly understood. Given the clinical importance of emergent viral variants with increased transmission, there is an urgent need to understand the early stages of viral replication and transcription. We used single molecule fluorescence in situ hybridisation (smFISH) to quantify positive sense RNA genomes with 95% detection efficiency, while simultaneously visualising negative sense genomes, sub-genomic RNAs and viral proteins. Our absolute quantification of viral RNAs and replication factories revealed that SARS-CoV-2 genomic RNA is long-lived after entry, suggesting that it avoids degradation by cellular nucleases. Moreover, we observed that SARS-CoV-2 replication is highly variable between cells, with only a small cell population displaying high burden of viral RNA. Unexpectedly, the B.1.1.7 variant, first identified in the UK, exhibits significantly slower replication kinetics than the Victoria strain, suggesting a novel mechanism contributing to its higher transmissibility with important clinical implications.

overall_design: Ribosome-depleted total RNA-seq of A549-ACE2 samples infected with either VIC or B.1.1.7 (Alpha) strain of SARS-CoV-2 at timepoints 2, 8 and 24 hours post infection (hpi). 3 Replicates each.

first: Peter

middle: A

last: Wing

first: Aino

last: Jarvelin

first: Natasha

last: Palmalux