title: Gene expresion analysis among young mouse embryos, aging mouse embryos and aging mouse embryos suppressed their CXCL5-CXCR2 signaling.

city: Narita

first: Yuta

last: Kawagoe

state: Chiba

address: 4-3, Kozunomori

department: Advanced reproductive medicine research center

institute: International University of Health and welfare

summary: CXCL5-CXCR2 signailing is known as senescence-associated secretory phenotype (SASP) factor to promote cellular senescense in diverse cells. We identified CXCL5 as a SASP factor in human and mouse embryos and suppression of CXCL5-CXCR2 signaling during embryo culture improved pregnancy success in aging mice.  Here, we perfomed microarray analysis using mouse blastocysts for comparing gene expression pattarns among young mouse embryos, aging mouse embryos and aging mouse embryos suppressed their CXCL5-CXCR2 signaling. As a results, gene expression pattern of CXCL5-CXCR2 signaling-suppressed aging blastocysts was closer to that of the young blastocysts as compared with aging blastocysts. In addition, cell proliferation-related pathways, such as “PI3K signaling pathway” and “RAS signaling pathway” were significantly enriched in CXCL5-suppressed blastocysts.

overall_design: Two age group of female ICR mice (young; 3-6 weeks of age and aging; 43-53 weeks of age) were purchased from SLC Japan (Shizuoka, Japan) and maintained in a standard laboratory animal facility with controlled environment (temperature; 22 ℃, humidity; 55-65 % and light cycle; 12 hours interval). For embryo collection, super-ovulated mice were mated with male mice immediately after hCG treatment. At 18 hours after hCG injection, zygotes were obtained by flashing the oviducts of mated mice. Collected zygotes were cultured in 30 μl drops of KSOM medium without or with anti-CXCL5 neutralizing antibody (10 μg/ml) and CXCR2 selective antagonist (10nM) for suppressing CXCL5-CXCR2 signal. After 96 hours culture, blastocysts were collected for RNA extraction and microarray analysis.

first: Ikko

last: Kawashima

first: Yorino

last: Sato

first: Naoki

last: Okamoto

first: Kazuei

last: Matsubara

first: Kazuhiro

last: Kawamura


title: Single cell RNA-seq analysis of elastase-induced mouse AAA samples

status: Public on Oct 07 2020

city: Ann Arbor

first: Guizhen

last: Zhao

state: MI

address: 2800 Plymouth Rd

department: Cardiovascular Center

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Single-cell RNA sequencing (scRNA-seq) was performed on the  infrarenal abdominal aortas from C57BL/6J mice at days 7 and 14 post periadventitial elastase-induced AAA or days 14 post periadventitial heat-inactive elastase incubation. This study report the changes of cellular subpopulations, fractions and transcriptomic profiles in response to elastase-induced AAA model.

overall_design: Examination of the transcriptomic profiles of the infrarenal abdominal aortic single cells from five pooled  from C57BL/6J mice at days 7 and 14 post periadventitial elastase-induced AAA or days 14 post periadventitial heat-inactive elastase incubation.

first: Jifeng

last: Zhang

first: Y

middle: E

last: Chen


title: Genome-wide maps of gene expression in mouse Soleus tissue.

city: Albany

first: Sneha

last: Damal Villivalam

state: CA

address: 485 Ohlone Ave, Apt 210

department: NST

institute: UC Berkeley

summary: Using high throughput sequencing we report gene expression changes in mouse Soleus tissue at sedentary and afte exercise in wild-type and MCK-Dnmt3a KO mice.

overall_design: Examination of  gene expression changes in Soleus tissue between WT and Dnmt3a KO mice.   Total RNA was isolated from mouse Soleus kept tissue at sedentary and afte exercise in wild-type and MCK-Dnmt3a KO mice.  3 mice were used in each group per condition.

first: Sona

last: Kang

middle: D

last: Villivalam


title: Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: 5′ methylation of cytosines in DNA molecules is an important epigenetic mark in eukaryotes. Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide scale. However, sodium bisulfite is known to severely degrade DNA, which, in combination with biases introduced during PCR amplification, leads to unbalanced base representation in the final sequencing libraries. Enzymatic conversion of unmethylated cytosines to uracils can achieve the same end product for sequencing as does bisulfite treatment and does not affect the integrity of the DNA; enzymatic methylation sequencing may, thus, provide advantages over bisulfite sequencing.

overall_design: Using an enzymatic methyl-seq (EM-seq) technique to selectively deaminate unmethylated cytosines to uracils, we generated and sequenced libraries based on different amounts of Arabidopsis input DNA and different numbers of PCR cycles, and compared these data to results from traditional whole-genome bisulfite sequencing. We found that EM-seq libraries were more consistent between replicates and had higher mapping and lower duplication rates, lower background noise, higher average coverage, and higher coverage of total cytosines. Differential methylation region (DMR) analysis showed that WGBS tended to over-estimate methylation levels especially in CHG and CHH contexts, whereas EM-seq detected higher CG methylation levels in certain highly methylated areas. These phenomena can be mostly explained by a correlation of WGBS methylation estimation with GC content and methylated cytosine density. We used EM-seq to compare methylation between leaves and flowers, and found that CHG methylation level is greatly elevated in flowers, especially in pericentromeric regions.

first: Zhong

last: Zhenhui

first: Feng

last: Suhua


title: Next-generation sequencing aims to comparative analysis of macrophages infected with EPEC under normal gravity and simulated microgravity

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

country: China

institute: institution of microbology

summary:
Purpose: Microgravity is one of crucial factors which affects astronauts’ health in space. The goals of this study are to compare SMG-pretreated macrophages infected with EPEC by RNA-sequencing to investigate the immunity-related differential expression genes and signaling pathway and to make for prevention and therapy of infectious diseases in space.
Methods: 3-day SMG-pretreatment macrophages were infected with EPEC (a kind of enteropathogen) and macrophages infected with EPEC under normal gravity as control and then we used RNA sequencing on Illumina platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level by Volcano Plot, KEEG database and InnateDB database. qRT–PCR validation was performed using SYBR Green assays.
Results: After RNA sequencing, we got 1272 differential expression genes (DEGs) of which 542 were up-regulated, 720 were down-regulated DEGs. KEGG pathway enrichment scatter plot showed that cytokine-cytokine receptor interaction and MAPK signaling pathway were optimal-related to infection immunity under simulated microgravity. Because of our study involved in infection immunity, we chose a database on immunity called InnateDB to screen the DEGs related to immunity. We found 14 DEGs in cytokine-cytokine receptor interaction, of which 7 were up-regulated, and 7 were down-regulated and 36 DEGs in MAPK signaling pathway, of which 11 were up-regulated, and 25 were down-regulated. In cytokine-cytokine receptor interaction signaling pathway, except for Il 33 (P>0. 05), the results of mRNA expression of DEGs in macrophages infected with EPEC were consistent with the results of RNA sequencing. In MAPK signaling pathway, the mRNA expression of Il 1b, Cd14, Hspa1a, Pdgfrb, Il 1a, Fgf7, Igf1r and Pak1 was not consistent with the RNA sequencing. Compared with normal gravity, simulated microgravity didn’t affect the mRNA expression of Il 1b, Cd14, Hspa1a and Pdgfrb (P>0. 05). The Il 1a and Fgf7 down regulated and Igf1r and Pak1 up regulated under simulated microgravity at the level of mRNA with a comparison to normal gravity, and the results of the rest of DEGs were consistent with the results of RNA sequencing.
Conclusions: This study is the first high-throughput analysis on simulated microgravity of infection immunity. The comparative analysis demonstrates that cytokine-cytokine receptor interaction and MAPK signaling pathway participants in the innate immune response.

overall_design: mRNA profiles of 3-day SMG-pretreated macrophages infected with EPEC were generated by deep sequencing, in triplicate, using Illumina.

first: Jing

last: Wang

first: Zhe

last: Lu

first: Pupu

last: Ge

first: Conghui

last: Han


title: SIX1 and SIX4 homeoproteins regulate PAX7+ progenitor cell properties during fetal epaxial myogenesis

city: PARIS

first: Pascal

last: Maire

address: 24 Rue du Fg St Jacques

department: Développement Reproduction et Cancer

country: France

institute: Institut Cochin. INSERM U1016, CNRS UMR 8104, U.Paris

summary:
Identification of the gene targets of the SIX transcription factors in myogenic stem cells and in whole back muscles during murine fetal development
Pax7 expression marks stem cells in developing skeletal muscles and adult satellite cells during homeostasis and muscle regeneration. The genetic determinants that control the entrance into the myogenic program and the appearance of PAX7+ cells during embryogenesis are poorly understood. SIX homeoproteins are encoded by the Sine oculis homeobox related Six1-Six6 genes in vertebrates. Six1, Six2, Six4 and Six5 are expressed in the muscle lineage. Here we tested the hypothesis that Six1 and Six4 could participate in the genesis of myogenic stem cells. We show that fewer PAX7+ cells occupy a satellite cell position between the myofiber and its associated basal lamina in Six1 and Six4 (s1s4KO) at E18. However, PAX7+ cells are detected in remaining muscle masses present in the epaxial region of the double mutant embryos and are able to divide and contribute to muscle growth. To further characterize the properties of s1s4KO PAX7+ cells, we analyzed their transcriptome and tested their properties after transplantation in adult regenerating tibialis anterior (TA) muscle. Mutant stem cells form hypotrophic myofibers that are not innervated but retain the ability to self-renew.

overall_design: We analyzed three WT, three SIX1/4 mutant myogenic stem cells at E15.5, and the same at E18.5 (PAX7 samples). We analyzed three SIX1/4 mutant and three WT whole back muscle at E15.5 and two WT and two Six1/4 mutant at E18.5 (Muscle samples).

first: Maud

last: Wurmser


title: Next Generation Sequencing based mRNA sequencing of osteogenic differentiation of human mesenchymal stem cells from hair follicle outer root sheath (MSCORS)

city: Leipzig

first: Hanluo

last: Li

address: Liebigstraße 12

department: Clinic and Policlinic for Oral-, Jaw- and Plastic Face Surgery

country: Germany

institute: University Hospital Leipzig

summary: Next Generation Sequencing (NGS)-based mRNA sequencing (RNA-seq) has provided high-throughput measurements OF MRNA COPIES? to analyze the transcriptome of cells. We are reporting  comprehensive transcriptome profiling of primarily isolated human adipose-derived mesenchymal stem cells (ADMSC) throughout consecutive culture passages using NGS-based RNA-seq method.  Human adipose tissue was obtained from operative remains and and digested in collagenase X. ADMSC were isolated, cultivated and characterized as mesenchymal stem cells (MSC) according to the minimum criteria for defining multipotent MSC from the International Society for Cellular Therapy (ISCT).The cells were subjected to osteogenic differentiation for 1, 2 and 3 weeks. mRNA profiles of differentiated MSCORS afer 1, 2, and 3 weeks were quality controlled, and generated by deep sequencing, in triplicate, using Illumina PE150 kits. Paired-end raw data were pre-processed using a published protocol. HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) was used to align reference genome. HTSeq was used to calculate Reads Count, and gene abundence was determined by analyzing FPKM (fragments per kilobase of exon model per million reads mapped).

overall_design: mRNA profiles of differentiated human mesenchymal stem cells from hair follicle outer root sheath after 1 week, 2 weeks and 3 weeks osteogenic differentiation

first: Ulrich

last: Sack

first: Simin

first: Jan

middle: C

last: Simon

first: Bernd

last: Lethaus

first: Vuk

last: Savkovic


title: Transcriptional landscape of the embryonic chicken Müllerian duct

city: Clayton

first: Kirill

last: Tsyganov

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

summary: We report here high-throughput RNA sequencing (RNA-seq)  to characterise the transcriptional landscape of the embryonic chicken Müllerian duct during development.

overall_design: Identification of genes involvement at three key developmetal stages of Mullerian duct

first: Zahida

middle: Y

last: Roly

first: Rasoul

last: Godini

first: Martin

middle: A

last: Estermann

first: Andrew

middle: T

last: Major

first: Roger

last: Pocock

first: Craig

last: Smith


title: Soluble RARRES1 induces podocyte apoptosis to promote glomerular disease progression

city: New York

first: Chengguo

last: Wei

state: NY

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: We try to explore the effect of RARRES1 on human podocyte, so we performed RARRES1 overexpression and knockdown experiments. cell mRNA profiles of human human podocyte cell lines transfected with RARRES1 overexpression vectors orcontrol vectors; and cells transfected with RARRES1 shRNA lentivirus or scramble shRNA lentivirus and stimulated with TNFa (10ng/ml) or without TNFa for 24 hours  were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript. We found that most differentially expressed genes (DEGs) are enriched with cell migration and apoptosis-related pathways, also  DEGs stimulated by TNFα but suppressed by RARRES1 knockdown, were also enriched with cell cycle-related pathways.These data suggest that RARRES1 plays a key role in the regulation of cell cycle and apoptosis, consistent with its role as a tumor suppressor gene.

overall_design: Examination of the effect of RARRES1 on human podocyte

first: Anqun

last: Chen

first: John

last: He

first: Kyung

last: Lee


title: Key circular RNAs identified in male osteoporosis patients by whole transcriptome sequencing

city: Shanghai

first: Niu

last: Qiao

address: 197 Rui Jin Er Road

department: National Research Center for Translational Medicine (Shanghai)

institute: Shanghai Jiao Tong University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Osteoporosis (OP) is a systemic disease with bone loss and microstructural deterioration. Numerous noncoding RNAs have been proved to participate in various diseases, especially for circular RNAs (circRNAs). However, the expression profile and hidden mechanisms of circRNAs in male osteoporosis have not been explored yet.
Methods: Here we investigated the whole transcriptome expression profile and differences of mRNAs, circRNAs and miRNAs in peripheral blood samples of patients with osteoporosis and healthy controls of male with age larger than 60 years old.
Results: A total of 398 circRNAs, 51 miRNAs and 642 mRNAs were identified that were significant differentially expressed in osteoporosis compared with healthy controls. GO and KEGG enrichment analysis showed the host genes of significantly differentially expressed circRNAs were mainly enriched in regulation of cell cycle process BP, organelle part CC, protein binding MF and Toll-like receptor signaling pathway, TNF signaling pathway and Thyroid hormone signaling pathway. circRNA-miRNA-mRNA regulatory network was constructed using the differentialy expressed RNAs. Moreover, key circRNAs in osteoporosis were discovered further and validated by qPCR, such as hsa_circ_0042409. Those key cicrRNAs may play an important role in the pathogenesis of osteoporosis and could be used as potential biomarkers or targets in the diagnosis and treatment of osteoporosis.

overall_design: A total of 6 peripheral blood samples were collected, including 3 healthy controls (NORM1, NORM2, NORM3) and 3 patients with osteoporosis diagnosed (OP1, OP2, OP3)

first: Haijin

last: Zhang

first: Xue

last: Song

first: Zongyan

last: Teng

first: Sujun

last: Cheng

first: Weigang

last: Yu

first: Xiaoyi

last: Mu

first: Zhiqiang

first: Yina


title: Comparison of gene expression profile of human blastocyst between young and aging infertility patients

first: Yuta

last: Kawagoe

country: Japan

summary: The pregnancy rate of women decreases with age due to declining quality of oocytes and embryos. However, there is no established method to improve pregnancy rate in aging women. Here, we performed microarray analysis for detecting candidate genes affected the quality of aging embryos. Based on microarray analysis using young and aging human embryos at the same morphological grade, 820 genes showed > 5-fold change in aging human blastocysts.  Among these genes, C-X-C motif chemokine 5 (CXCL5), one of SASP factors, showed 7.2-fold increases in aging human blastocysts.  These findings indicate CXCL5, one of senescence-associated secretory phenotype (SASP) factors,  partially responsible for the decline in embryo implantation potentia.

overall_design: Gene expression profile of human blastocysts were compared. Blastocysts were obtained from infertility patients which were separated in two age group (young group; 25-37 years of age and aging group; 38-45 years of age). Five blastocysts were used for samples in each age group.

first: Ikko

last: Kawashima

first: Yorino

last: Sato

first: Naoki

last: Okamoto

first: Kazuei

last: Matsubara

first: Kazuhiro

last: Kawamura


title: Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology

city: Adelaide

first: Cedric

last: Bardy

state: SA

address: North Terrace

institute: South Australian Health and Medical Research Institute (SAHMRI)

summary: Neural progenitors derived from human pluripotent stem cells (hPSCs) develop into electrophysiologically active neurons at heterogeneous rates, which can confound disease-relevant discoveries in neurology and psychiatry. The goal of this study was to resolve the diversity of functional states of hPSC-derived neurons in vitro by combining patch clamping with morphological and RNA-sequencing analysis of single neurons (Patch-seq).

overall_design: Whole-transcriptome, single-cell mRNA-seq profiles of 56 patch-clamped and morphologically characterized cells (50 differentiated neurons and 6 astrocytes) generated using Smart-seq (SMARTer) chemistry.

first: Mark

last: van den Hurk

first: Fred

middle: H

last: Gage


title: Effects of TRIM59 on Raw 264.7 macrophage gene expression

city: Changchun

first: Zheng

last: Jin

address: Xinmin Street 126#

department: College of  Basic Medical Science

institute: Jilin University

summary: Macrophages have many functions, such as acting as phagocytic pathogens, antigen presentation and playing a key role in immune response. Tripartite motif containing 59 (TRIM59) protein is highly expressed in a variety of tumor cells and regulates the proliferation of tumor cells as well as their innate immune response. Recent studies have shown that the expression of TRIM59 was differentially expressed under different stimuli of activated macrophages, however, the effects of TRIM59 on macrophage gene expression profiles are still unknown. In our study, we constructed RAW 264.7 macrophages with high and low expression of TRIM59, and used transcriptome sequencing to identify the effects of TRIM59 on macrophage gene expression profiles. Results showed that TRIM59 affected an abundant number of genes, and may affect phagocytosis and cell cycles.

overall_design: RAW 264.7 macrophages with high and low expression of TRIM59 were constructed by transfection. Total RNA extraction and hybridization on Affymetrix microarrays was made.

first: Dongmei

last: Yan

first: Xun

last: Zhu


title: RNA-seq of 32D clone 3 cells transfected with CXCR2 (pEGFP-N1-CXCR2) or an empty vector (pEGFP-N1) with CXCL1/2 treatment

first: Xianlu

last: Zeng

address: No. 5268, Renmin Avenue

institute: Northeast Normal University

summary: Purpose: To elucidate a potential role of non-coding RNA in myeloid progenitor cells during the differentiation induced by CXCR2 activation, the 32D clone 3 cells transfected with CXCR2 to simulate GMPs and were examined by RNA sequencing

overall_design: To research the function of CXCR2 in the differentiation of myeloid progenitor cells to monocytic myeloid-derived suppressor cells, we used 32D clone 3 cells transfected with CXCR2 to simulate myeloid progenitor cells. Then the cells were incubated with CXCL1 and CXCL2 for 4 h and examined by RNA sequencing. The group that 32D clone 3 cells transfected with an empty vector (pEGFP-N1) was used as the Control group, while the Treated group was transfected with CXCR2 (pEGFP-N1-CXCR2).

first: Xiaoqing

last: Han


title: Estrogen signaling modulates the colon microenvironment during obesity

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

country: Sweden

institute: Karolinska Institute

summary: Epidemiological studies highlight a strong association between obesity and colorectal cancer (CRC). This association appears stronger in men and a role for sex hormones is indicated by epidemiological studies. Especially estrogen is protective against CRC and correlated to several aspects of the metabolic syndrome. Anti-inflammatory and anti-tumorigenic effects of estrogen in colon have been demonstrated to act via estrogen receptor beta (ERβ). This led us to hypothesize that estrogenic signaling, through both systemic and local effects might modulate the colon microenvironment during HFD-induced obesity. In order to test our hypothesis mice were fed a control diet or a high fat diet (HFD) for 3 weeks and treated with different estrogenic ligands. In the present study, we demonstrate that there are sex-differences in the response to HFD-induced obesity and in the colon transcriptome. Both sexes develop obesity with an impaired circadian rhythm but the male metabolic profile is more sensitive to HFD and increased the colon epithelial cell proliferation. Females were resistant to impaired glucose metabolism, but HFD-feeding increased the infiltration of macrophages. Estrogen signaling in males, via ERα, presented anti-obesogenic effects. However, systemic and/or local activation of both ERα and ERβ restored the circadian rhythm in the males. In females, systemic activation of ERα restored the circadian rhythm, however, systemic and/or local activation of ERβ down-regulated the expression of macrophage markers. These results suggest that estrogen signaling through systemic and/or local activation of ERβ can regulate the colon microenvironment during HFD-induced obesity.

overall_design: Colon mRNA profiles of C57BL/6J female and male mice fed a control diet or high fat diet and males on a high fat diet treated with estrogen were generated by deep sequencing. 6 biological replicates were used.

first: Linnea

last: Pettersson

first: Amena

last: Archer


title: Development of an in vivo ligated loop model reveals new insight into the host immune response against Campylobacter jejuni

city: Pullman

first: Michael

last: Konkel

state: WA

institute: Washington State University

summary: The symptoms of infectious diarrheal disease are mediated by the interplay between the host and pathogen. Campylobacter jejuni is the leading bacterial cause of diarrhea worldwide due to its near-ubiquitous zoonotic association with poultry. One of the outstanding questions is what factors drive the intestinal inflammation during the development of C. jejuni-mediated disease. Specifically, it is not known the extent to which the bacteria are responsible for the diarrheal symptoms via cell necrosis, or whether there is immune cell recruitment prior to tissue damage. To determine the stepwise process of inflammation that leads to diarrhea, we used a piglet ligated intestinal loop model to study the intestinal environment in response to C. jejuni. Pigs were chosen due to the anatomical similarity of the porcine intestine to the human intestine, as the basis of disease modeling is to understand the process of human disease. Using immunoassays and proteomic approaches, we found that neutrophils are most likely the predominant cell type recruited to the intestines of C. jejuni infected animals. In the lumen of the intestine, a number of neutrophil related proteins increased during C. jejuni infection, including proteins related to neutrophil migration (elastase and MMP9), actin reorganization and bacterial uptake (Cdc42, WAVE-2, and Arp2/3), and antimicrobial proteins (lipocalin-2, myeloperoxidase, S100A8, and S100A9). The appearance of neutrophils also corresponds with increases of both IL-8 and TNF-a. Compared to infection with the C. jejuni wild-type strain, infection with the noninvasive C. jejuni ∆ciaD mutant resulted in a blunted inflammatory response, with less inflammatory cytokines and neutrophil markers. These findings indicate that intestinal inflammation is driven by C. jejuni virulence, and that resident intestinal cells precipitate the inflammatory response. Using this new disease model, we have developed a platform to study the early immune events during C. jejuni infection.

overall_design: Minnesota mini pigs were used in a ligated intestinal loop model of infection, where the pigs were maintained under general anesthesia and 1 x 10^10 C. jejuni was inoculated into ~10 cm discreet ligated intestinal segments. The pigs were maintained for 3, 6, 12, or 30 hours, and luminal C. jejuni was recovered and sequenced. Three animals each were included in the analysis, with two technical replicates (loops) within each animal. These results were compared to co-culture with cultured IPEC-J2 cells for 2.5 or 4 hours (two samples at each time point). All samples were compared to the respective 'input' sample, which is C. jejuni grown in MH broth for 18 hours.

first: Nicholas

middle: M

last: Negretti

first: Yinyin

last: Ye

first: Lais

last: Malavasi

first: Swechha

last: Pokharel

first: Steven

last: Huynh

first: Susan

last: Noh

first: Christopher

middle: R

last: Gourley

first: Claude

last: Ragle

first: Santanu

last: Bose

first: Torey

last: Looft

first: Craig

last: Parker

first: Geremy

last: Clair

first: Joshua

middle: N

last: Adkins


title: Chd8 haploinsufficiency impairs early brain development and impacts protein homeostasis later in life

city: Chapel Hill

first: Travis

last: Ptacek

state: NC

address: 5109 Neuroscience Research Building

institute: UNC Neuroscience Center Bioinformatics Core

summary: Chromodomain helicase DNA-binding protein 8 (CHD8), now considered a master transcriptional regulator for autism, is mutated in more autism probands (0.45%) than any other gene. We generated mutant mice with a human loss-of-function (LOF) mutation in Chd8 (Val986X, henceforth referred to as V986*). Heterozygous mutant mice (Chd8V986*/+) display features of ASD, including anxiety like behavior and macrocephaly. Perturbation of CHD8 also recapitulates increased sociability found in other CHD8 mutant animal models. Our study expands previously identified knowledge of CHD8 mutant mouse models by examining temporal alterations in the transcriptional profile of mouse cortical tissue resulting from a reduction in CHD8 expression. Dysregulation of major cellular processes uniquely includes a reduction in neuronal signaling, focal adhesion, and synaptic function genes early in development, that increase in expression into adulthood. At 12 months, heterozygous mice display decreased endoplasmic reticulum (ER) stress, decreased unfolded protein response (UPR) and increased MET signaling likely resulting from a combination of reduced CHD8 expression and reflecting an altered network structure formed early in development. These data provide greater insight into the role of CHD8 in brain function and how mutations in the gene can contribute to ASD etiology.

overall_design: Transcriptional profiling of dissected cortex from wild type and Chd8 V986*/+ mice

first: Mark

middle: J

last: Zylka

first: Jessica

last: Jimenez

first: Jeremy

last: Simon


title: RNA Transcriptome of Tregs in Idiopathic Aplastic Anemia

city: london

first: syed

last: mian

address: 123 Coldharbour Lane

country: United Kingdom

institute: King's College London

summary: Our report demonstrates that the dominant Treg population in AA are FasL resistant but do not respond to low concentration of IL-2, leading to immune dysregulation. And In vitro expanded AA Tregs are stable, functional and highly express p-BCL-2 with therapeutic potential in AA patients

overall_design: Examination of the transcriptome of Tregs from healthy donors and Aplastic anaemia patients

first: Syed

last: Mian

first: Shahram

last: Kordasti


title: Transcriptome analysis of normal human lung fibroblasts (NHLFs) following FOXL1 knockdown.

city: Bunkyo-ku

first: NAOYA

last: MIYASHITA

state: Tokyo

department: Respiratory Medicine

institute: The University of Tokyo

summary: FOXL1 is a key transcription factor that characterizes the pulmonary origin of lung fibroblasts.. RNA-sequencing analysis on NHLFs following FOXL1 knockdown revealed a broad array of genes possibly regulated by FOXL1.

overall_design: NHLFs were transfected with siRNAs for FOXL1, and RNA-sequencing was performed ugsing Illumina HiSeq/MiSeq.

first: Naoya

last: Miyashita

first: Masafumi

last: Horie

first: Akira

last: Saito

first: Takahide

last: Nagase


title: RNA Helicase DDX5, a Negative Regulator of Wnt Activation and Hepatocyte Reprogramming in Hepatitis B Virus-associated Hepatocellular Carcinoma

city: West Lafayette

first: Majid

last: Kazemian

state: Indiana

address: 201 S. University Street

institute: Purdue university

summary: We demonstrate that HBV infection induces expression of the proto-oncogenic miR17~92 and miR106b~25 clusters which target the downregulation of DDX5. Increased expression of these miRNAs is also detected in HBV-driven HCCs exhibiting reduced DDX5 mRNA. Stable DDX5 knockdown (DDX5KD) in HBV replicating hepatocytes increased viral replication, and resulted in hepatosphere formation, drug resistance, Wnt activation, and pluripotency gene expression. ATAC-seq of DDX5KD compared to DDX5 wild-type (WT) cells identified accessible chromatin regions enriched in regulation of Wnt signaling genes. RNA-seq analysis comparing WT versus DDX5KD cells identified enhanced expression of multiple genes involved in Wnt pathway. Additionally, expression of Disheveled, DVL1, a key regulator of Wnt pathway activation, was significantly higher in liver cancer cells with low DDX5 expression, from two independent cohorts. Importantly, inhibitors (antagomirs) to miR17~92 and miR106b~25 restored DDX5 levels, reduced DVL1 expression, and suppressed both Wnt activation and viral replication.

overall_design:
HepAD38 cells, wild type (WT) and DDX5 knockdown (DDX5KD) were grown +/- tetracycline for 10 days to induce HBV replication. Sorafenib (2.5 μM) treatment was for three days prior to harvesting. Three independent biological replicates were prepared for RNA isolation and RNA sequencing.
HepAD38 cells, wild type (WT) and DDX5 knockdown (KD5), were grown for 10 days. Two independent biological replicates were prepared for ATAC sequencing.

first: Ourania

last: Andrisani

first: Bingyu

last: Yan

first: Nadia

last: Lanman

first: Sagar

last: Utturka


title: Expression data of wild-type and perforin-knockout CAR-T cell

city: bethesda

first: Jack

last: Shern

state: MD

address: 10 Center drive

institute: NCI

summary:
Murine chimeric antigen receptor transduced T cells (CAR-T cells) deficient in perforin recapitulate hemophagocytic lymphohistiocytosis (HLH)-like toxicities occuring in human CAR-T recipients.
We used microarray to describe gene expression profiles of wild-type and perforin-deficient CAR-T cells.

overall_design: RNA was extracted from murine wild-type and perforin-deficient CD8+ CAR-T cells, before and after CAR-mediated in vitro activation of T cells with cognate-antigen-positive leukemia, followed by hybridization on Affymetrix array.

first: Kazusa

last: Ishii

first: Terry

last: Fry

first: Haiyan

last: Lei

first: Nirali

last: Shah


title: BMP/Taz-Hippo signaling modulates VEGF-mediated angiogenesis

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary: The BMP/TGFβ-Smad, Notch and VEGF signaling guides formation of endothelial tip and stalk cells. However, the crosstalk of bone morphogenetic proteins (BMPs) and vascular endothelial growth factor receptor 2 (VEGFR2) signaling has remained largely unknown. We demonstrate that BMP family members regulate VEGFR2 and Notch signaling, and act via TAZ-Hippo signaling pathway. BMPs were found to be regulated after VEGF gene transfer in C57/Bl6 mice and in a porcine myocardial ischemia model. BMPs 2/4/6 were identified as endothelium-specific targets of VEGF. BMP2 modulated VEGF-mediated endothelial sprouting via Delta like Canonical Notch Ligand 4 (DLL4). BMP6 modulated VEGF signaling by regulating VEGFR2 expression and acted via Hippo signaling effector TAZ, known to regulate cell survival/proliferation, and to be dysregulated in cancer. In a matrigel plug assay in nude mice BMP6 was further demonstrated to induce angiogenesis. BMP6 is the first member of BMP family found to directly regulate both Hippo signaling and neovessel formation. It may thus serve as a target in pro/anti-angiogenic therapies.

overall_design: Gene expression profiling of mouse liver tissue in response to iv. AdVEGF-A treatment via tail vain injections.

first: Johanna

middle: P

last: Laakkonen

first: Minna

middle: U

last: Kaikkonen


title: Transcriptional changes in response to 17β-estradiol, cigarette sidestream smoke particulates, and TNFα treatments in ERα-induced and uninduced CL1-5(TO-ERα) cells

city: Zhunan, Miaoli

first: Lih-Ann

last: Li

state: Taiwan

address: R1-5034, 35 Keyan Road

department: National Institute of Environmental Health Sciences

country: Taiwan

institute: National Health Research Institutes

summary: This microarray analysis was designed to determine (1) the impact of ERα expression on cellular TNFα response and estrogen-TNFα signaling crosstalk and (2) whether cigarette sidestream smoke particulates had estrogen-like action in human lung adenocarcinoma cells. The lung adenocarcinoma cell line CL1-5(TO-ERα)#18  was used as a model. Expression of ERα in this cell line is under Tet-on regulation and can be induced by addition of doxycycline. For the Objective 1, we found three types of TNFα responsive genes: estrogen/ERα-dependent, estrogen/ERα-enhanced, and estrogen/ERα-independent. For the Objective 2, the microarray data revealed that cigarette sidestream smoke particulates regulated given genes via ERα as 17β-estradiol in lung adenocarcinoma cells. Some of these ERα target genes had been identified previously.

overall_design: Expression of ERα in CL1-5(TO-ERα)#18 was induced 24 h before treatment by addition of 1 μg/ml doxycycline (D) to cells. To determine the TNFα response in the presence and absence of ERα (Objective 1-1), ERα-induced and uninduced CL1-5(TO-ERα)#18 cells were treated with and without 45 U/ml TNFα (T) for 24 h. 1 nM 17β-estradiol (E) was also given to ERα-induced cells by itself or together with 45 U/ml TNFα to examine the estrogen-TNFα signaling crosstalk (Objective 1-2). Transcript levels were compared among the following treatments: D-E-T-, D-E-T+, D+E-T-, D+E-T+, D+E+T-, and D+E+T+.  To compare the transcriptional effecs of 17β-estradiol and cigarette sidestream smoke particulates (Objective 2),  ERα-induced and uninduced CL1-5(TO-ERα)#18 cells were treated with 1 nM 17β-estradiol (E), 20 μg/ml cigarette sidestream smoke particulates (C), or neither for 24 h. The treatments for Objective 2 were labeled as D-E-T-, D-E+T-, D-C+T-, D+E-T-, D+E+T-, and D+C+T-.  Each treatment had two independent samples for microarray analysis (n=2).

first: Lun-Cheng

last: Kuo

first: Chia-Huei

last: Lee


title: Single-cell genomics reveals a novel cell state during smooth muscle cell phenotypic switching and potential therapeutic targets for atherosclerosis in mouse and human [mouse]

status: Public on Oct 06 2020

first: Chenyi

last: Xue

institute: Columbia University

summary: Smooth muscle cells (SMC) play significant roles in atherosclerosis via phenotypic switching, a pathological process in which SMC dedifferentiation, migration and transdifferentiation into other cell types. Yet, how SMC contribute to pathophysiology of atherosclerosis remains elusive. To reveal the trajectories of SMC transdifferentiation during atherosclerosis and to identify molecular targets for disease therapy, we combined SMC fate mapping and single-cell RNA sequencing of both mouse and human atherosclerotic plaques.

overall_design: SMC-lineage tracing mice, ROSA26 ZsGreen1/+; Myh11-CreERT2 mice, were crossed onto athero-prone backgrounds (Ldlr-/- or ApoE-/-). Mouse single cells digested from arterial tissues (including ascending aorta, brachiocephalic artery and thoracic aorta) for scRNA-seq were prepared from three ROSA26 ZsGreen1/+; Ldlr-/-; Myh11-CreERT2 mice at the same timepoint of Western diet (WD) feeding (0, 8, 16, 26 weeks) and ROSA26 ZsGreen1/+; ApoE-/-; Myh11-CreERT2 mice at the same timepoint of WD feeding (8, 16, 22 weeks). Alive ZsGreen1+ cells (SMC-lineage cells) and ZsGreen1- cells were sorted separately and were immediately subjected to scRNA-seq using Chromium Single Cell Gene Expression system (10x Genomics) in parallel.

first: Pan

last: Huize

first: Xue

last: Chenyi


title: Single-cell genomics reveals a novel cell state during smooth muscle cell phenotypic switching and potential therapeutic targets for atherosclerosis in mouse and human

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Genetic differences in estrous cycle effects on the rat brain transcriptome

city: Aurora

first: Laura

middle: Maren

last: Saba

state: CO

address: 12850 East Montview Blvd.

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

summary: Males and females often differ on propensity for a substance use disorder (SUD), etiology and clinical manifestation of  SUD, and response to SUD treatment strategies (Riley et al 2018). The fluctuation of sex-related hormones in the brain  and/or circulation may contribute to some of these differences. For example, estradiol activity has been associated with  sensitivity to drugs of abuse (Tonn Eisinger et al 2018) and vulnerability to SUD (Anker and Carroll 2011). In particular,  estrogen can affect the dopamine system in brain and this may contribute to differences in the etiology and the clinical  manifestation of SUD (Bobzean et al 2014). Without direct association with SUD, others have shown that stage of the  estrous cycle influences RNA transcription levels and splicing in particular brain regions (Duclot and Kabbaj 2015;  DiCarlo et al 2017). What has not been thoroughly explored is whether genetic factors can modify the effect of estrous  cycle on RNA transcript and ultimately, whether the interaction of these two factors can influence the sex-related  differences in SUD vulnerability.

overall_design: Examination of the interaction between sex/estrus cycle and genotype using two inbred rat strains (BN-Lx and SHR), female rats across 3 different stages of the estrus cycle and male rats on brain RNA expression.

first: Paula

middle: L

last: Hoffman

first: Melinda

last: Dwinell

first: Boris

last: Tabakoff


title: Single-cell genomics reveals a novel cell state during smooth muscle cell phenotypic switching and potential therapeutic targets for atherosclerosis in mouse and human [human]

overall_design: Human atherosclerotic carotid arteries were obtained from three patients undergoing endarterectomy as part of a clinical research protocol approved by the Institutional Review Board (IRB) of Columbia University Irving Medical Center. All patients were fully informed of the research and signed IRB-approved informed consent forms. Single cells were digested from human atherosclerotic carotid arteries and the live cells were sorted for scRNA-seq using Chromium Single Cell Gene Expression system (10x Genomics).


title: Systemic induction of phospholipid-based signaling in leaves of arbuscular mycorrhizal rice plants

city: Bellaterra

first: Blanca

last: San Segundo

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Plant Responses to Stress

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

summary: Most land plants form beneficial associations with arbuscular mycorrhizal (AM) fungi which improves mineral nutrition, mainly phosphorus and nitrogen in the host plant in exchange for photosynthetically fixed carbon. Most of our knowledge on the AM symbiosis derives from dicotyledonous species. We show that inoculation with the AM fungus Funneliformis mossease stimulates growth and increases Pi content in leaves of the rice cultivar Loto (O. sativa ssp japonica). Although rice is a host for AM fungi, the molecular mechanism underlying the AM symbiosis, in particular the systemic transcriptional responses of shoots to AM inoculation, remain largely elusive. Transcript profiling of the shoots indicated the systemic induction of genes involved in the biosynthesis of phospholipids (phosphoinositides, inositol polyphosphates) and down-regulation of non-phosphorus lipids (galactolipids, sulfolipids) in leaves of mycorrhizal rice. Regulation of phospholipid biosynthesis genes appears to be coordinated with a reduced expression of genes involved in jasmonic acid and ethylene biosynthesis and signaling. Genes involved in phosphate starvation responses and remobilization of Pi were also found to be down-regulated in leaves of mycorrhizal rice. These results demonstrated that the AM symbiosis is accompanied by complex alterations in gene expression in shoots which are potentially important to maintain a stable symbiotic relationship in rice plants.

sample_organism:
Oryza sativa
Funneliformis mosseae

platform_organism:
Oryza sativa
Funneliformis mosseae

overall_design: 6 samples in total: wild-type rice plants (Oryza sativa, subsp japonica cv. Loto) with 2 treatments (inoculated or not with the arbuscular micorrhyzae fungus Funneliformis mosseae), 3 biological replicates each treatment

first: Sonia

last: Campo


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1-/- Zebrafish Embryo Transcriptomes

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level, we performed full genome RNA-Seq between aldh3a1+/+ and aldh3a1-/- larvae at 48 hpf.An overview of RNA-Seq, including quality control, principal component analysis (PCA), volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis (normalized enrichment score, -1.72; p=0.0006). Interestingly, endocrine pancreas but not exocrine pancreas development pathway was significantly down-regulated in aldh3a1 mutants . Taken together, these results further suggest Aldh3a1 as an important regulator in the development, morphology and insulin secretion function of primary pancreas. Furthermore, we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA expression profiles of wildtype and aldh3a1-/- zebrafish embryo at 48 hours after post fertilization

first: Bowen

last: Lou

first: Jens

last: Kroll


title: Development of a novel allograft model of prostate cancer:  a new tool to inform clinical translation

city: Belfast

first: Francesca

last: Amoroso

address: 97 Lisburn Road

institute: Queen's University Belfast

summary: This study presents a novel allograft model of high-risk, localised PCa.  In characterising this model we have focused on its response to radiotherapy (RT).

overall_design: The DVL3 cell line was derived from a transgenic trp53-/-/Pten-/- mouse model and characterised both in vitro and in vivo.  The DVL3 cells were allografted and response to RT was investigated.  Extensive tumour profiling was performed using flow cytometry, immunohistochemistry and RNA-seq.

first: Ian

last: Mills

first: Charles

last: Haughey


title: The lipid handling capacity of subcutaneous fat is programmed by mTORC2 during development

city: Worcester

first: David

last: Guertin

state: MA

address: 373 Plantation St.

institute: University of Massachusetts Medical School

summary: Obesity causes type 2 diabetes, cardiovascular diseases, NAFLD, and cancer, but all fat is not equal as subcutaneous white adipose tissue (SWAT) is more metabolically favorable than visceral fat.  Here, we investigate mTORC2 function in SWAT growth by deleting its essential subunit Rictor in SWAT precursor cells and examining its effect on adipocyte differentiation and tissue development.  We found that Rictor/mTORC2 is not required for SWAT preadipocyte differentiation per se; however, SWAT preadipocytes differentiating without Rictor cannot fully induce the lipid storage transcriptional program.  In vivo, this results in smaller adipocytes, reduced SWAT size, lipid re-distribution to visceral and brown fat, and gender-distinct effects on systemic metabolic fitness.  Mechanistically, mTORC2 promotes PPARg activity towards specific lipid metabolism genes independently of ChREBP, but in coordination, to set the lipid handling capacity of SWAT.  Further exploring this pathway may uncover new strategies to stimulate lipid storage in more metabolically favorable SWAT.

overall_design: We isolated primary preadipocytes from subcutaneous adipose tissue harboring UBC-CreERT2;Rictorfloxed, which we can induce Rictor deletion by supplementing the cells with Tamoxifen, and compare the transcriptome change between Control and Rictor-KO cells at different days of adipocyte differentiation.

first: Wen-Yu

last: Hsiao


title: Enforced Expression of NUP98-HOXA10hd Fusion Gene in Multipotent Progenitors Support Long-term Hematopoiesis in primary mice [MP]

city: Guangzhou

first: Juan

last: Du

state: Guangdong

address: 190 Kaiyuan Avenue

department: South China Institutue of Stem Cell & Regneration Medicine

institute: Guangzhou Institutes od Biomedicine and Health

summary: Allogenic hematopoietic stem cell (HSC) transplantation is widely used for treatment of blood disorders to re-establish long-term multi-lineage hematopoiesis. Enhance self-renewal potential of progenitor population to support hematopoiesis offer an alternative and complementary approach to achieve similar therapeutic effects. Nup98-Hoxa10hd fusion gene (NA) has been shown to confer expansion, anti-stress response and engraftment competitiveness on HSC. However, whether the ectopic expression of NA in multipotent progenitors (MPPs) could enhance their self-renewal potential and confer long-term multi-lineage hematopoiesis remains unknown. In this study, we showed that ectopic expression in MPPs confer long-term multi-lineage hematopoiesis in recipient mice. We further showed that NA upregulated pathways of cell cycle regulation, epigenetic regulation and response to stress in MPPs.  These molecular traits increased the self-renewal potential of NA MPPs, which resulting in production of lineage-maintaining committed progenitor cells. Transcriptome analysis of NA myeloid progenitors identified genes regulating hematopoiesis, homeostasis, phosphorylation. In summary, we show that ectopic expression of Nup98-Hoxa10hd fusion gene enhance self-renwal potential of MPPs thus confer long-term multilineage repopulating capacity on MPPs, offering promising means to involve MPPs to augment cell source in clinical transplantation settings.

overall_design: For MP sequencing, 0.1 million myeloid progenitor cells (Lin-ckit+Sca1-) were sorted as one sample from bone marrow nucleated cells of respective recipient mice. Donor-derived NA MP cells (Tdtomato+) were sorted from NA MPP recipient mice 3 months post transplantation, while WT MP cells(CD45.2+) were obtained from control group received WT MPP transplantation at the same time point. Following RNA extraction with RNeasy micro kit (QIAGEN), total RNA of each sorted myeloid progenitor sample was used for sequencing library preparation with illumina Truseq RNA Sample Preparation Kit (RS-122-2001). All libraries were sequenced by illumina sequencer NextSeq 500 (illumina).

first: Kaitao

last: Wang

first: Yong

last: Dong

first: Jinyong


title: Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Enable Transcription Termination

city: Boston

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Efficient release of promoter-proximally paused Pol II into productive elongation is essential for gene expression. Recently, we reported that the Integrator complex can bind paused Pol II and drive premature transcription termination, potently attenuating the activity of target genes. Premature termination requires RNA cleavage by the endonuclease subunit of Integrator, but the roles of other Integrator subunits in gene regulation have yet to be elucidated. Here, we report that Integrator subunit 8 (IntS8) is critical for transcription repression through its association with Protein Phosphatase 2A (PP2A). We find that Integrator-bound PP2A dephosphorylates the Pol II C-terminal domain and Spt5, and prevents the transition to productive elongation. Blocking PP2A association with Integrator thus stimulates pause release and gene activation. These results reveal a second catalytic function associated with Integrator-mediated transcription termination, and suggest a new model for the control of productive elongation involving active competition between transcriptional kinases and phosphatases.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: PRO-seq: Examination of 8 samples (2 biological replicate sets of Drosophila DL1 cells: control, IntS8-depleted, IntS8-depleted + wildtype IntS8 rescue, IntS8-depleted + IntS8 WFEF/A mutant rescue); RNA-seq: Examination of 6 samples in human cell lines (3 biological replicate sets of 293T cells: control knockdown; IntS8 knockdown) and 6 samples in Drosophila DL1 cells treated with copper (3 biological replicate sets of control, IntS8-depleted, IntS8-depleted + wildtype IntS8 rescue, IntS8-depleted + IntS8 WFEF/A mutant rescue) plus 2 samples not treated with copper (3 biological replicate sets of control and IntS8-depleted). The copper treatment was used to induce transgene expression in the DL1 rescue RNA-seq.

first: Eric

last: Wagner

first: Kai-Lieh

last: Huang

last: Jee

first: Nathan

last: Elrod

first: Chad

last: Stein

first: Telmo

last: Henriques

first: Lauren

last: Mascibroda

first: William

middle: K

last: Russell


title: miRNA expression profiling of prostate cancer (PCa) samples

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: Investigation of miRNA expression profiles of prostate cancer (PCa) and normal prostatic samples

overall_design: 48 samples from prostate cancer were analyzed for miRNA expression profiling

first: Giovanna

last: Chiorino

first: Maurizia

last: Mello-Grand


title: DJ-1 (PARK7) affects the gut microbiome, metabolites, and development of Innate lymphoid cells (ILCs)

city: Tübingen

first: Genomics Core Facility

address: Calwerstraße 7

department: Institute of Medical Genetics and Applied Genomics

institute: University Hospital Tübingen

summary: Purpose of this study is to identify the role of DJ-1 in the brain inflammation at moleculer level. Thus, we isolated the mid-brain region including the substantia nigra and performed the RNA-sequencing to decipher the role of inflammation in neurodegeneration.

overall_design: In total, 9 samples were analyzed with 4 and 5 replicates for both wildtype and knockout condition respectively.

first: Yogesh

last: Singh

first: Nicolas

last: Casadei

first: Olaf

last: Riess


title: Ascorbic acid promotes the reproductive function of porcine immature Sertoli cells through transcriptome reprogramming

city: Jingzhou

first: Liang

last: Hao

state: Hubei

address: JingMi road

institute: Yangtze University

summary:
Background：Vitamin C (ascorbic acid, AA) can regulate antioxidation and play a pivotal role in many cellular processes. However, the function of AA in the reproduction of male animals remains less explored.
Results: Here, by first supplementing exogenous AA to porcine immature Sertoli cells (iSCs), we showed that AA could promote the proliferation, suppress apoptosis, and decrease the global nucleic acid methylation (5mC and m6A) levels of iSCs. After we profiled mRNA and long non-coding RNA (lncRNA) expression by transcriptome sequencing on iSCs (treated by 250μM AA for 36h), 1232 mRNAs and 937 lncRNAs were identified to be differentially expressed (DE). Gene enrichment analysis found these DE mRNA and lncRNAs to be significantly enriched in multiple biological pathways, including oxidoreductase activity, cell proliferation and apoptosis, regulation of hormone level, regulation of catalytic activity, developmental process, ATP metabolic and reproductive process. Specifically, for the reproductive process, 49 up- and 36 down-regulated DE mRNAs (including highly expressed genes, such as Tfcp2l1, Hmgcs1, Mmp7, Fndc3a, and Zfp36l1) are involved. Moreover, AA supplementation could promote the secretion of anti-müllerian hormone, inhibin B and lactate, and enhance the activity of lactate dehydrogenase as well.
Conclusions: Taken together, AA could promote the reproductive function of pig iSCs, potentially through reprogramming the global transcriptome, and elevating hormone secretion and metabolite production.

overall_design: Immature Sertoli cells treated with VC.

first: Cai-Xia

last: Yang


title: Cell cycle checkpoints cooperate to suppress DNA and RNA associated molecular pattern recognition and anti-tumor immune responses

city: PHILADELPHIA

first: Irfan

last: Asangani

state: PA

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

summary: The DNA dependent pattern recognition receptor, cGAS mediates communication between genotoxic stress and the immune system. Mitotic chromosome missegregation is an established stimulator of cGAS activity, however, it is unclear if progression through mitosis is required for cancer cell intrinsic activation of immune mediated anti-tumor responses. Moreover, it is unknown if disruption of cell cycle checkpoints can restore responses in cancer cells that are recalcitrant to DNA damage induced inflammation. Here we demonstrate that prolonged cell cycle arrest at the G2-mitosis boundary from either CDK1 inhibition or excessive DNA damage prevents inflammatory stimulated gene expression and immune mediated destruction of tumors outside the field of irradiation. Remarkably, DNA damage induced inflammatory signaling is restored upon concomitant disruption of p53 and the G2 checkpoint, in a cGAS- and RIG-I- dependent manner. These findings link aberrant cell progression and p53 loss to an expanded spectrum of damage associated molecular pattern recognition and have implications for the design of rational approaches to augment anti-tumor immune responses.

overall_design: Genome wide gene expression levels in MCF10A cell line and hTERT RPE-1 cell line were determined with RNA-Seq. The RNA-Seq experiments were divided into three different parts: (1) Cell cycle arrest or deficiency of cGAS/STING compromises irradiation induced inflammatory signaling in MCF10A cells; (2) Loss of p53 and G2-M checkpoint restores irradiation induced inflammatory signaling in c-NHEJ deficient MCF10A cells; (3) Loss of p53 and G2-M checkpoint activates cGAS independent inflammatory signaling in hTERT RPE-1 cells.

first: Ram

last: Natesan

first: Jie

last: Chen

first: Shane

last: Harding

first: Roger

last: Greenberg


title: RUNX1 and CBFβ-SMMHC transactivate target genes together in abnormal myeloid progenitors for leukemogenesis

city: Bethesda

first: Tao

last: Zhen

state: Maryland

address: 9000 Rockville Pike

institute: NIH

summary: Inversion of chromosome 16 is a consistent finding in patients with acute myeloid leukemia subtype M4 with eosinophilia (AML M4Eo), which generates a CBFB-MYH11 fusion gene. It is generally considered that CBFβ-SMMHC, the fusion protein encoded by CBFB-MYH11, is a dominant negative repressor of RUNX1. However, recent findings challenge the RUNX1-repression model for CBFβ-SMMHC mediated leukemogenesis. To definitively address the role of Runx1 in CBFB-MYH11 induced leukemia, we crossed conditional Runx1 knockout mice (Runx1f/f) with conditional Cbfb-MYH11 knockin mice (Cbfb+/56M). Upon Mx1-Cre activation in hematopoietic cells induced by poly (I:C) injection, all Mx1-CreCbfb+/56M mice developed leukemia in 5 months while no leukemia developed in Runx1f/fMx1-CreCbfb+/56M mice, and this effect was cell autonomous. Importantly, the abnormal myeloid progenitors (AMPs), a leukemia initiating cell population induced by Cbfb-MYH11 in the bone marrow, decreased and disappeared in Runx1f/fMx1-CreCbfb+/56M mice. RNA-seq analysis of AMP cells showed that genes associated with proliferation, differentiation blockage and leukemia initiation, were differentially expressed between Mx1-CreCbfb+/56M and Runx1f/fMx1-CreCbfb+/56M mice. In addition, with chromatin immunocleavage sequencing (ChIC-seq) assay, we observed a significant enrichment of RUNX1/CBFβ-SMMHC target genes in Runx1f/fMx1-CreCbfb+/56M cells, especially among down-regulated genes, suggesting that RUNX1 and CBFβ-SMMHC mainly function together as activators of gene expression through direct target gene binding. These data indicate that Runx1 is indispensable for Cbfb-MYH11 induced leukemogenesis by working together with CBFβ-SMMHC to regulate critical genes associated with the generation of a functional AMP population.

overall_design: For bulk RNA-sequening: Total RNA from AMP cells was extracted with AllPrep DNA/RNA/Protein Mini Kit (QIAGEN). Poly-A selected stranded mRNA libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kits according to manufacturer’s instructions. Unique barcode adapters were applied to each library. All libraries were combined in equimolar proportion into one pool for sequencing with a NovaSeq6000 sequencer; For ChIC-seq: AMP cells were fixed with 1% PFA and subjected to ChIC-seq as described.7 Specifically, antibody+PA-MNase complex with 50,000 cells was used for each sample. RUNX1 (Abcam, AB_2184205), CBFβ (Diagenode, C15310002), MYH11 (Diagenode, C15310254), H3K27Ac (Abcam, AB_2118291) and H3K27me3 (Millipore Sigma, AB_310624) antibodies were used to identify the binding sites of the indicated proteins. All libraries were combined in equimolar proportion into one pool for sequencing with a HiSeq 3000 sequencer; For scRNA-seq: 10X genomics chromium platform was used to capture isolated AMP cells and all steps were performed according to manufacturer’s instructions. The Chromium Single Cell 3’ Library & Gel Bead Kit v2 was used. Libraries were sequenced on an Illumina NextSeq 550 sequencer

first: Yaqiang

last: Cao

first: Gang

last: Ren

first: Ling

last: Zhao

first: R

last: Hyde

first: Guadalupe

last: Lopez

first: Lemlem

last: Alemu

first: Keji

first: P

last: Liu


title: Anti-aging effects of Ribes meyeri anthocyanins on adipose-derived stem cells and aged mice

city: Shanghai

first: Hailiang

address: NO 1239, siping road

institute: Tongji university

summary: We implemented RNA-seq analyses of blood of 10-11M mice; These mice with the treatment of Naringenin for 30 days.


title: Modulation of Syndecan-1/4 reduces the invasive potential of endometrioma through TGF-β signalling

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

institute: Karolinska Institutet

summary: We report that modulation of high SDC -1/-4 within certain endometriomas in women having ovarian endometriosis, reversed its higher invasion potential and downregulated several molecules incolved in cancer development.

overall_design: Endometrioma stromal cells were transiently silenced for SDC-1 andSDC-4, followed by TGF-β stimulation in vitro within 3D-invasion assay. RNA sequnecing were perfomed on harvested spheroids from 3D invasion assay (with/without TGF-β stimulation or SDC-1 or SDC4 silencing) using Smart-seq2 protocol , tagmentation via Nextera kit and sequenced using Nextseq 550. Data were analysed using Partek Flow Genomic analysis software.

first: Sakthivignesh

last: Ponandai-Srinivasan

first: Nageswara

last: Bogavarappu


title: Enforced Expression of NUP98-HOXA10hd Fusion Gene in Multipotent Progenitors Support Long-term Hematopoiesis in primary mice [MPP]

first: Juan

last: Du

summary: Allogenic hematopoietic stem cell (HSC) transplantation is widely used for treatment of blood disorders to re-establish long-term multi-lineage hematopoiesis. Enhance self-renewal potential of progenitor population to support hematopoiesis offer an alternative and complementary approach to achieve similar or enhance therapeutic effects. Nup98-Hoxa10hd fusion gene (NA) has been shown to confer expansion, anti-stress response and engraftment competitiveness on HSC. However, whether the ectopic expression of NA in multipotent progenitors (MPPs) could enhance their self-renewal potential and confer long-term multi-lineage hematopoiesis remains unknown. In this study, we showed that ectopic expression in MPPs confer long-term multi-lineage hematopoiesis in recipient mice. We further showed that NA upregulated pathways of cell cycle regulation, epigenetic regulation and response to stress in MPPs.  These molecular traits increased the self-renewal potential of NA MPPs, which resulting in production of lineage-maintaining committed progenitor cells. Transcriptome analysis of NA myeloid progenitors identified genes regulating hematopoiesis, homeostasis, phosphorylation. In summary, we show that ectopic expression of Nup98-Hoxa10hd fusion gene enhance self-renewal potential of MPPs thus confer long-term multi-lineage repopulating capacity on MPPs, offering promising means to involve MPPs to augment cell source in clinical transplantation settings.

overall_design: We sorted 1000 MPP (Lin-CD48-ckit+Sca1+CD135+CD150-) cells for each NA MPP replicate from bone marrow of NA mice. Equal number of WT MPP cells were sorted to generated WT MPP replicate from bone marrow of age-matched CD45.2 mice. Sequencing libraries of MPP were generated as previously described (Dong et al., 2019; Tang et al., 2010). Briefly, cDNA of sorted 1000 MPP aliquots were generated, amplified and used for sequencing library preparation with illumina Nextera XT DNA Sample Preparation Kit (FC-131-1096). All libraries were sequenced by illumina sequencer NextSeq 500 (illumina).

first: Kaitao

last: Wang

first: Yong

last: Dong

first: Jinyong


title: HnRNP-L regulated circCSPP1/miR-520h/EGR1 axis modulates autophagy and promotes progression in prostate cancer

status: Public on Oct 05 2020

first: Jianming

last: Lu

address: No.253, Industrial Avenue Middle

department: Department of Urology

institute: Zhujiang Hospital of Southern Medical University

summary: To explore the downstream autohphagy-related genes modulated by circCSPP1, we constructed circCSPP1 overexpression stable cell line (DU145-circCSPP1 cells) and accquired mRNA profiles by RNA sequencing.

overall_design: RNA sequencing was performed on 3 paired prostate cancer cell with circCSPP1 overexpression and normal from DU145.

first: Chuanfan

last: Zhong


title: Enforced Expression of NUP98-HOXA10hd Fusion Gene in Multipotent Progenitors Support Long-term Hematopoiesis in primary mice

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

overall_design: Refer to individual Series


title: RRF plays critical roles in ribosome homeostasis in E. coli but has little effect on translational coupling

city: Baltimore

first: Allen

last: Buskirk

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: We used ribosome profiling to characterize the biological role of ribosome recycling factor (RRF) in Escherichia coli. As expected, RRF depletion leads to enrichment of post-termination 70S complexes in 3′-UTRs. We also observe that elongating ribosomes are unable to complete translation because they are blocked by non-recycled ribosomes at stop codons. Previous studies have suggested a role for recycling in translational coupling within operons; if a ribosome remains bound to an mRNA after termination, it may re-initiate downstream. We found, however, that RRF depletion did not significantly affect coupling efficiency in reporter assays or in ribosome density genome-wide. These findings argue that re-initiation is not a major mechanism of translational coupling in E. coli. Finally, RRF depletion has dramatic effects on the activity of ribosome rescue factors tmRNA and ArfA. Our results provide a global view of the effects of the loss of ribosome recycling on protein synthesis in E. coli.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Ribosome profiling of RRF knock-down condition derived from E. coli MG1655


title: Prostate cancer organotypic slice cultures (OSC) treated with E2 or DHT

first: Paola

last: Ostano

summary: Organotypic slice cultures from prostate cancer patients were generated and treated with or without 17b-estradiol or DHT to study estrogen and androgen signalling pathways.

overall_design: Organotypic slice cultures from prostate cancer patients were generated and treated with or without 17b-estradiol (E2 ,10-7M) for 6 hours  or DHT for 3 hours before harvesting. Gene expression profiles were analyzed and compared to controls. One replicate per treatment was performed.

first: Antonella

last: Farsetti

first: Giovanna

last: Chiorino


title: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of IL-10 production on sorted mouse pulmonary ILC2 Transcriptomes.

city: Los Angeles

first: Emily

middle: Diane

last: Howard

state: Ca

address: 1450 Biggy St, NRT 5509

department: MMI

institute: University of Southern California

summary: ILC2s are the dominant innate lymphoid cell population in the lungs at steady state and their release of type-2 cytokines is a central driver in responding eosinophil infiltration and increased airway hyperreactivity (AHR). For the first time, our laboratory has identified a unique subset of ILC2s in the lungs that produces and secretes IL-10, an anti-inflammatory cytokine, upon stimulation with IL-4. Overall this study introduces a novel, IL-4-inducible IL-10-producing population of ILC210s in the lung are naturally present in a high Th2 model of murine asthma. This research introduces a novel, cell-based immunotherapeutic potential of ILC210s that can be modulated by the signlaing transcription factors Blimp-1 and cMAF, as well as by glucose availability, opening new avenues for the treatment of ILC2-dependent airway inflammation.

overall_design: mRNA profiles of sorted mouse pulmonary IL-10-negative and IL-10-producing ILC2s from IL-10GFP mice were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.

first: E

last: HOWARD

first: O

last: AKBARI


title: Transcriptome profiling for hidradenitis suppurativa

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: Hidradenitis Suppurativa (HS) is a debilitating chronic inflammatory disease characterized by chronic abscess formation and development of multiple draining sinus tracts in the groin, axillae, and perineum.  Through the use of transcriptomic approaches, we characterize the inflammatory responses in HS in depth, revealing the cell types and immune responses involved.

overall_design: We conducted RNA-seq on whole blood and skin obtained from HS patients, and comparing them against control individuals

first: Errol

last: Prens

first: Johann

middle: E

last: Gudjonsson


title: Microarray was used to detect the expression of lncRNAs and mRNAs in INS-1 cells treated with GLP-1RA Geniposide for 24 hours.

city: Taiyuan

first: Lijuan

last: Cui

state: Shanxi

address: Xinjian south road

department: School of basic medicine

institute: Shanxi Medical University

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

summary: Studies have shown that long noncoding RNAs (lncRNAs) can be widely involved in various physiological and pathological processes. In recent years, there have been many studies on GLP-1 receptor agonists (GLP-1RA) regulating islet β cells function and mass of type 2 diabetes (T2DM) patients. However, the function of lncRNAs in this process have not been fully elucidated. In this study, lncRNA microarray was used to identify the differently expressed (DE) lncRNAs and mRNAs in β cells exposed to Geniposide, which is a GLP-1RA. 308 lncRNAs and 128 mRNAs were detected with a set filter fold change≥1.5 and P-value<0.05. Gene Ontology and KEGG pathway analysis were performed to assess the underlying functions of DE mRNAs. Co-expression network of DE lncRNAs and mRNAs was constructed based on Pearson coefficient of expression level. And hub mRNAs were selected through String database and Cytoscape plugin Cytohubba. Additionally, a ceRNA network was constructed among the co-expressed lncRNAs and hub mRNAs. This study reveals key mRNAs involved in the regulation of GLP-1RA on β cells function and mass. More importantly, screening out lncRNAs that play an importance regulatory role in this process. This original research could provide valuable information for the further investigation between lncRNAs and GLP-AR in the protection of β cells.

overall_design: The experiment was divided into a control group and an experimental group, in which the experimental group INS-1 cells were incubated with 10 μmol/L Geniposide for 24 hours, and the control group INS-1 cells were untreated. Three samples per group were repeated.

first: Tao

last: Bai

first: Yi

last: Zhang


title: Transcriptome analysis of VapC21 overexpression and deletion in Mycobacterium tuberculosis.

city: Bangalore

first: Munmun

last: Bhasin

state: Karnataka

address: CV Raman Rd

department: Molecular Biophysics Unit

country: India

institute: Indian Institute of Science

summary:
We report the effects of VapC21 overexpression on Mycobacterium tuberculosis H37Rv strain. The total RNA was isolated from M. tuberculosis harboring either pTetR-int or pTetR-Int-vapC21 the expression was induced with 50 ng/ml anhydrotetracycline for 24 hrs.
We report the effect of deletion VapC21 on the transciptional profile of Mycobacterium tuberculosis Erdman strain. For RNA-seq analysis, total RNA was isolated from mid-log phase culture of either parental or △vapC21 mutant strain.

overall_design: Experiments were repeated thrice for each overexpression strain and twice for each deletion strain.

first: Arun

last: Sharma

first: Gopinath

last: Chattopadhyay

first: Pankaj

last: Chopra

first: Chandrani

last: Thakur

first: Sakshi

last: Agarwal

first: Shahbaz

last: Ahmed

first: Nagasuma

last: Chandra

first: Raghavan

last: Varadarajan

first: Ramandeep

last: Singh


title: 5/6 nephrectomy (5/6Nx) effect on the cardiac ventricle in mouse

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

institute: kyushu university

summary: Chronic kidney disease (CKD) is a very important problem in global health treatment. CKD increases the disease risk of apoplexy, cardiac failure and cardiac infarction. Cardiovascular disease is especially the most serious problem. In this study, the expression of mRNA in the cardiac ventricre prepared from 5/6 nephrectomy (5/6Nx) mouse  was investigated.

overall_design: Differential gene expression between 5/6 nephrectomized and sham-operated mouse was measured on the cardiac ventricle

first: Yuya

last: Yoshida

first: Naoya

last: Matsunaga

first: Kaori

last: Yasuda

first: Atsushi

last: Doi


title: Modeling Tumor Development and Metastasis using Paired Organoids Derived from Patients with Colorectal Cancer Liver Metastases

first: He

last: Li

address: 26Qiu yue

institute: The Interdisciplinary Research Center on Biology and Chemistry

summary: Tumor metastasis accounts for the majority of cancer-related deaths; it is therefore important to develop preclinical models that faithfully recapitulate disease progression. Here, we generated paired organoids derived from primary tumors and matched liver metastases in the same colorectal cancer patients (CRC). Despite the fact that paired organoids exhibit comparable gene expression and cell morphology. organoids from metastatic lesions demonstrate more aggressive phenotypes, tumorigenesis, and metastatic capacity than those from primary lesions. Transcriptional analyses of the paired organoids reveal signature genes and pathways altered during the progression of CRC. including SOX2, altered during the progression of CRC. Further study shows that inducible knockdown of SOX2 attenuated invasion, proliferation, and liver metastasis outgrowth. Taken together, we use patient-derived organoids to model cancer metastasis. Our data propose that SOX2 is not only a critical biomarker for the development and metastasis of CRC, but also a potent target for the disease treatment.

overall_design: We generated paired organoids derived from primary tumors and matched liver metastases in the same CRC patients. The organoids were trypsinized, plated in BME and overlaid with medium. The medium was changed every 3 days. After 14 days of plating, Organoids were harvested and processed for RNA isolation and transcriptome analysis using AllPrep DNA/RNA Mini Kit.

first: Jing

last: Zhao


title: RNAi Screening Identifies that TEX10 Promotes the Proliferation of Colorectal Cancer Cells by Increasing NF-κB Activation

first: Ziyang

last: Wang

address: 58 Zhongshan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Colorectal cancer (CRC) has become a predominant cancer worldwide. In order to understand the process of carcinogenesis, an shRNA library screening is employed for searching candidate genes that promote proliferation in the CRC cell line HT29. The candidate genes overlapped with differentially expressed genes in 32 CRC tumor tissues in the GEO dataset GSE8671. The seventh-ranked TEX10 is upregulated in CRC and its knockdown decreased cell proliferation. The TEX10 high-expression group exhibits worse overall survival (P = 0.003) and progression-free survival (P < 0.001) than the TEX10 low-expression group. TEX10 depletion decreases the growth of CRC cells in vitro and in vivo. GSEA indicates that the NF-κB pathway is significantly enriched in the genes downregulated by TEX10 knockdown. Mechanistically, TEX10 interacts with p65 and increases its nuclear localization. TEX10 promotes p65 occupancy at gene promoters and regulates the expression of a subset of p65-targeted genes including TNFAIP8, SAT1 and IL6ST. Taken together, this study identifies that TEX10 promotes the proliferation of CRC cells in a p65-dependent manner. In addition, high TEX10 expression is associated with poor prognosis in CRC patients.

overall_design: TEX10 or p65 were knocked down in HCT116 cells, and the differences in gene expression were compared with shNC, respectively, using RNAseq.

first: Shuai

last: Chen


title: Risk-associated alterations in marrow T cells in pediatric leukemia

city: Atlanta

first: Samuel

middle: Spence

last: McCachren

state: GA

address: 1760 Haygood Dr. NE

institute: Emory University

summary: Current management of childhood leukemia is tailored based on disease risk determined by clinical features at presentation. Whether properties of the host immune response impact disease risk and outcome is not known. Here we combine mass cytometry, single cell genomics and functional studies to characterize the bone marrow immune environment in children with B-cell acute lymphoblastic leukemia, and acute myelogenous leukemia at presentation. T cells in leukemia marrow demonstrate evidence of chronic immune activation and exhaustion/dysfunction, with attrition of naïve T cells and TCF1+ stem-like memory T cells and accumulation of terminally-differentiated effector T cells. Marrow-infiltrating natural killer cells also exhibit evidence of dysfunction, particularly in myeloid leukemia. Properties of immune cells identified distinct immune phenotype-based clusters correlating with disease risk in acute lymphoblastic leukemia. High-risk immune signatures were associated with expression of stem-like genes on tumor cells. These data provide a comprehensive assessment of the immune landscape of childhood leukemias and identify targets potentially amenable to therapeutic intervention. These studies also suggest that properties of the host response with depletion of naïve T cells and accumulation of terminal-effector T cells may contribute to the biologic basis of disease risk. Properties of immune microenvironment identified here may also impact optimal application of immune therapies, including T cell-redirection approaches in childhood leukemia.

overall_design: Examination of bone marrow immune cell transcriptomes in pediatric B-cell acute lymphoblastic leukemia patients (B-ALL: n=7), acute myeloid leukemia patients (AML: n=8), and healthy donors (n=4)

first: Jithendra

last: Bailur

middle: S

first: Katherine

last: Pendleton

first: Juan

last: Vasquez

first: Hong

last: Lim

first: Alyssa

last: Duffy

first: Deon

middle: B

last: Doxie

first: Akhilesh

last: Kaushal

first: Connor

last: Foster

first: Deborah

last: DeRyckere

first: Sharon

last: Castellino

first: Melissa

last: Kemp

first: Peng

last: Qiu

first: Madhav

middle: V

last: Dhodapkar

first: Kavita


title: FUBP1 and FUBP2 enforce distinct epigenetic setpoints for MYC expression in primary single murine cells

first: David

last: Levens

address: 10 Center Drive

institute: NCI

summary: We used ChIP-seq to assess where FUBP1 binds to MYC gene in the mouse genome

overall_design: Examination of FUBP1 binding in MYC gene

first: Ying

last: Zheng

first: Wendy

last: Dubois

first: Craig

last: Benham

first: Eric

last: Batchelor


title: Candida albicans phagocytosed by macrophages: intact vs. ruptured phagosomes

city: Jena

first: Lydia

last: Kasper

address: Adolf-Reichwein-Straße 23

department: Microbial Pathogenicity Mechanisms

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)

summary: Transcriptional profiling of Candida albicans after 3 h phagocytosis by vehicle DMSO-treated macrophages (intact, expanding phagosomes) or calcium chelator BAPTA-AM-treated macrophages (inhibits lysosomal repair of expanding phagosomes, leading to phagosome rupture) to determine the effect of preventing phagosome expansion on C. albicans gene expression after phagocytosis by macrophages. Cultivation of Candida only for 3 h in DMEM-FBS cell culture medium or YPD complex medium as non-phagocytosis control conditions.

overall_design: Four-condition experiment,. 5 Biological replicates

first: Johannes

last: Westman

first: Sascha

last: Brunke


title: 5/6 nephrectomy (5/6Nx) effect on the splenic monocytes in mouse

first: naoya

last: matsunaga

summary: Chronic kidney disease (CKD) is a very important problem in global health treatment. CKD increases the disease risk of apoplexy, cardiac failure and cardiac infarction. Cardiovascular disease is especially the most serious problem. In this study, the expression of mRNA in 5/6 nephrectomy (5/6Nx) mouse  splenic monocytes was investigated.

overall_design: Differential gene expression between 5/6 nephrectomized and sham-operated mouse was measured on the splenic monocytes.

first: Yuya

last: Yoshida

first: Naoya

last: Matsunaga

first: Kaori

last: Yasuda

first: Atsushi

last: Doi


title: Next Generation Sequencing Facilitates Quantitative Analysis of cmtR-deleted mutant and wild-type strains Transcriptomes in Mycobacterium tuberculosis H37Ra

city: Wuhan

first: Li

middle: xiao

last: hui

address: Shizishan Street No. 1, Hongshan District

institute: Huazhong Agricultural University

summary: Compare the gene expression difference between MRA_2010 knockout strains and wild-type strains by RNA sequencing in Mycobacterium tuberculosis H37Ra. The goal of this study is that detection cmtR acts as a transcriptional factor and regulates the target genes expression.

overall_design: Two samples in triplicate are analyzed. The control sample is the wild-type strains in Mycobacterium tuberculosis H37Ra.

first: Zhengguo

last: He

first: XiaoHui

last: Li


title: Transcriptome profiling of wildtype, nonoperated mouse hearts compared to wildtype, sham operated hearts

status: Public on Oct 04 2020

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: The purpose of the present study was to investigate the activation of the cardiac inflammatory response in the hearts of SHAM (surgical opening of the chest) mice in comparison to CONTROL hearts isolated from naïve (not operated) mice.  Male C57BL/6J (10 weeks) were subjected to an open-chest ischemia-reperfusion (I/R) SHAM procedure in order to examine the effects of this surgery alone in producing cardiac inflammation. The procedure consisted of thoracotomy and a suture passed around the left anterior descending artery (LAD). The mouse chest was kept open for approximately 45 min. We chose to study an open-chest I/R SHAM because this is the reference surgery for the most common surgical procedure used to study cardiac inflammation. Mice were sacrificed 5 days after the procedure and the hearts were removed and used in RNAseq experiments.

overall_design: mRNA sequencing profiles were generated from 5 each of SHAM (sham-operated) and CONTROL (naïve, no surgery) hearts on an Illumina HiSeq 3000 instrument.

first: Cibele

last: Rocha-Resende

first: Douglas

last: Mann


title: miRNOME of healthy donor and myelodysplastic bone marrow mesenchymal stromal cells (MSC)

city: Grenoble

first: Mathieu

last: Meunier

address: Boulevard de la Chantourne

department: Hematology

institute: CHU Grenoble Alpes

summary: We have demonstrated that DICER1 (a key enzyme of miRNA biogenesis) was underexpressed in myelodysplastic syndrome MSC. We hypothesize that those MSC harbored a deregulated pattern of miRNA versus healthy donors MSC.

overall_design: MSC were selected from CD34+ negative fraction of total bone marrow.

first: Sophie

last: Park


title: Matrix reverses immortalization-mediated stem cell fate determination

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Primary cell culture in vitro suffers from cellular senescence. We hypothesized that expansion on decellularized extracellular matrix (dECM) deposited by simian virus 40 large T antigen (SV40 LT) transduced autologous infrapatellar fat pad stem cells (IPFSCs) could rejuvenate high-passage IPFSCs in both proliferation and chondrogenic differentiation.  Passage 1 (P1) IPFSCs (CTR group) were transduced with lentivirus carrying either SV40 LT (SV40 group) or GFP (GFP group). P5, P10 and P15 cells from each group were compared in proliferation, chondrogenic and adipogenic capacities. P15 IPFSCs were expanded on tissue culture flasks or dECMs deposited by P5 (“young”) or P15 (“old”) IPFSCs with (SP5 and SP15, respectively) or without transduction of SV40 LT (CP5 and CP15, respectively). Cell proliferation was evaluated using population doubling time, flow cytometry for EdU incorporation, cell cycle and surface markers, and real-time quantitative PCR (qPCR) for stemness and senescence gene expression. Chondrogenic capacity was evaluated using Alcian blue staining for sulfated GAGs, immunostaining for type II collagen and qPCR for chondrogenic markers. Adipogenic capacity was evaluated using Oil Red O staining for lipid droplets, western blot and qPCR for adipogenic markers. Proteomics analysis was used to evaluate matrix components from dECMs, expanded cells and chondrogenically induced pellets. We found that SV40 transduced IPFSCs exhibited increased proliferation and adipogenic potential but decreased chondrogenic potential. Expansion on dECMs deposited by SV40 LT transduced IPFSCs yielded IPFSCs with enhanced proliferation and chondrogenic capacity but decreased adipogenic potential, particularly for the dECM group derived from SV40 LT transduced P15 cells. This study provides a promising model for in-depth investigation of ECM proteins to determine how these matrix proteins affect surrounding stem cells’ differentiation preference.

overall_design: Two experiments were designed as follows: (1) TCP (tissue culture plastic) culture regimen (Experiment 1): passage 5 IPFSCs were expanded on TCPs, including three cell groups (“CTR”, “GFP” and “SV40”) and (2) dECM (decellular extracellular matrix) culture regimen (Experiment 2): passage 15 IPFSCs were grown on dECMs deposited by passage 5 versus passage 15 cells and SV40 LT non-transduced (C) versus transduced (S) cells with TCP culture substrate as a control including five expanded cell groups (“C5C”, “C15C”, “S5C”, “S15C”, and “CC”). RNASeq was performed on these cells.

first: Yiming

last: Wang

first: Ryan

last: Hill

first: Monika

last: Dzieciatkowska

first: Kirk

last: Hansen

first: Xiao-Bing

last: Zhang

first: Zuoqin

last: Yan

first: Ming

last: Pei


title: NEIL1 stimulates neurogenesis and suppresses neuroinflammation after stress

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Adult neurogenesis, found in two neurogenic regions of the brain, has profound roles in neural plasticity and brain function. A hallmark feature of neurodegeneration is neuroinflammation, which can either enhance or inhibit neurogenesis depending on the context of the brain microenvironment. The consequences of deficient DNA repair in adult neurogenesis and neuroinflammation are poorly understood despite their potential relevance for homeostasis. We previously reported that loss of NEIL1, an important DNA glycosylase involved in DNA base excision repair, is associated with deficiencies in spatial memory, olfaction, and protection against ischemic stroke in mice. Here, we show that Neil1-/- mice display an anxiety-mediated behavior in the open field test, a deficient recognitive memory in novel object recognition and increased neuroinflammatory response under basal conditions. Further, mice lacking NEIL1 have decreased neurogenesis and deficient resolution of neuroinflammation following gamma irradiation (IR)-induced stress compared to WT mice. Neil1-/- IR-exposed mice also exhibit increased DNA damage and apoptosis in the hippocampus. Interestingly, behavioral tests two weeks after IR showed impaired stress response in the Neil1-/- mice. Our data indicate that NEIL1 plays an important role in adult neurogenesis and in the resolution of neuroinflammation.

overall_design: NEIL1 knockout (KO) and wildtype (WT) mice were placed  in a stereotaxic cube box in a Nordion Gammacell 40 Exactor Irradiator, and was either subjected to whole body gamma irradiation (6 Gy) delivered at a rate of 0.74 Gy/min (irradiated) or no radiation (sham) on Day 0. After exposure, mice were returned to home cages, and cerebral cortex obtained for RNA extraction from four mice from each of the four experimental groups 20 hours after IR or sham-treatment.

first: Beimeng

last: Yang

first: David

last: Figueroa

first: Yujun

last: Hou

first: Mansi

last: Babbar

first: Stephanie

last: Baringer

first: Deborah

last: Croteau

first: Vilhelm

middle: A

last: Bohr


title: Effects of FZR1 knockout on gene expression of breast tumor cells treated with cisplatin

city: Tianjin

first: Shuo

last: Liu

address: 94 Weijin Road

institute: Nankai University

summary: We knockout FZR1 in T-47D breast cancer cell line, and treated the knockout and WT cells with cisplatin. The mRNA profiles were analyze.

overall_design: mRNA profiles of 2 cisplatin treated breast cancer cell lines

first: Shijing

last: Yue


title: Transcriptome analysis of developing Bacillus subtilis biofilms

city: Zagreb

first: Tomislav

last: Domazet-Loso

state: Grad Zagreb

address: Bijenička cesta 54

department: Division of Molecular Biology

country: Croatia

institute: Institut Rudjer Bošković

summary: The objective of the study was to uncover the developmental dynamics in Bacillus subtilis biofilms on a transcriptome level. The experiment covered a developmental timeline over two months of biofilm growth.

overall_design: Bacterial biofilms were sampled during a development period of two months. The experimental period was covered with 11 sampling points starting from a liquid bacterial culture 24h after inoculation followed by biofilm cultures harvested from a solid MSgg agar plate at 6h, 12h, 1 day, 2 days, 3 days, 5 days, 7 days, 14 days, 1 month and 2 months after inoculation. Each sample was represented in three replicates, except the 2M samples which was represented by a single replicate.

first: Momir

last: Futo

first: Luka

last: Opašić

first: Sara

last: Koska

first: Nina

last: Čorak

first: Tin

last: Široki

first: Vaishnavi

last: Ravikumar

first: Annika

last: Thorsell

first: Maša

last: Lenuzzi

first: Domagoj

last: Kiffer

first: Mirjana

last: Domazet-Lošo

first: Kristian

last: Vlahoviček

first: Ivan

last: Mjakovic


title: The stem cell-associated transcription co-factor, ZNF521, interacts with GLI1 and GLI2 and enhances the activity of the Sonic hedgehog pathway

status: Public on Oct 03 2020

city: San Giovanni rotondo

first: Valentina

last: Melocchi

state: Foggia

address: Viale Padre Pio 7

department: ISBReMIT - Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies

institute: Casa Sollievo della Sofferenza Hospital - IRCCS

summary:
ZNF521 is a transcription co-factor with recognized regulatory functions in haematopoietic, osteo-adipogenic and neural progenitor cells. Among its diverse activities, ZNF521 has been implicated in the regulation of medulloblastoma (MB) cells, where the Hedgehog (HH) pathway, has a key role in the development of normal cerebellum and of a substantial fraction of MBs.
Here a functional cross-talk is shown for ZNF521 with the HH pathway, where it interacts with GLI1 and GLI2, the major HH transcriptional effectors and enhances the activity of HH signalling.
In particular, ZNF521 cooperates with GLI1 and GLI2 in the transcriptional activation of GLI (glioma-associated transcription factor)-responsive promoters. This synergism is dependent on the presence of the N-terminal, NuRD-binding motif in ZNF521, and is sensitive to HDAC (histone deacetylase) and GLI inhibitors.
Taken together, these results highlight the role of ZNF521, and its interaction with the NuRD complex, in determining the HH response at the level of transcription. This may be of particular relevance in HH-driven diseases, especially regarding the MBs belonging to the SHH (sonic HH) subgroup where a high expression of ZNF521 is correlated with that of HH pathway components.

overall_design: mRNA sequencing was performed on DAOY WT as control cells treated either with DMSO or with SAG (CTL_DMSO and CTL_SAG) and DAOY overexpressing ZNF521 treated either with DMSO or SAG (ZNF521_DMSO and ZNF521_SAG)

first: Marco

last: Giordano

first: Stefania

last: Scicchitano


title: Effect  of overexpression on miR-486-5p in Healthy doncor CD34+ cells

first: Mathieu

last: Meunier

summary: We report the effect of overexpression of miR-486-5pin heathy donors hematopoietic stem cells

overall_design: CD34+ cells from healthy donors were transfected with mir-486 or with an irrelevant sequence  and then RNA sequencing was performed

first: Sophie

last: Park


title: Enhanced Myocardial Glucose Delivery Accelerates Development of Mitochondrial Dysfunction in the Diabetic Heart

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

summary: Cardiac glucose delivery and utilization are reduced in diabetes despite hyperglycemia. Mitochondrial dysfunction contributes to heart failure in diabetic patients. The loss of mitochondrial substrate flexibility in regulating cellular and cardiac function is actively under investigation.

overall_design: To determine the direct role of glucose delivery in the maintenance of cardiac contractile and mitochondrial function we generated transgenic mice with inducible cardiomyocyte-specific expression of the glucose transporter 4 (mG4H). We examined mice that were made hyperglycemic with low dose streptozotocin (STZ)-induced diabetes 2 weeks prior to increasing intracellular glucose uptake for and additional 2 weeks by transgene induction.

first: Adam

last: Wende

first: John

middle: C

last: Schell

first: Oleh

last: Khalimonchuk

first: Hansjörg

last: Schwertz

first: Renata

middle: O

last: Pereira

first: Manoja

last: Brahma

first: Joseph

last: Tuinei

first: Ariel

last: Contreras-Ferrat

first: Li

last: Wang

first: Chase

last: Andrizzi

first: Curtis

middle: D

last: Olsen

first: Robert

last: Cooksey

first: Ui

last: Yun

first: Amira

last: Klip

first: E

last: Abel


title: RNA-seq for the tissues of GGPPS knockout mice and wild type mice

city: Nanjing

first: Lisha

last: Wei

email: 278530660@qq.com, weils@nicemice.cn

address: Xuefu Road 12#

institute: Nanjing University

summary: Protein prenylation has multiple important physiological function, but the evidence has been to be explored. Now we found that eicosanoid metabolism homestasis was broken after GGPPS deletion in neonatal vascular smooth muscles through GGPP prenylation.

overall_design: mRNA profiles of the aorta of 3-week old GGPPS knockout and wildtype mice were generated by deep sequencing，in double, using Illumina Hiseq X Ten. The raw data had already submitted to SRA. The BioProject accession is PRJNA597493.

first: Minsheng

last: Zhu


title: Estrogen dependent CD4+ T cell specific transcriptomic pathways identified in premenopausal protection against hypertension

city: Tucson

first: Heddwen

last: Brooks

state: Arizona

address: 1656 E Mabel St, RM 413

department: Physiology

institute: University of Arizona

summary: Background: Premenopausal females are protected against T cell-dependent immune activation and development of angiotensin II (Ang II) hypertension compared to males and postmenopausal females. Therefore, the current study hypothesized that specific CD4+ T cell pathways are regulated by estrogen signlaing and Ang II, and contribute to sex differences in T cell cytokine secretion and renal inflammation.  Methods and Results: Transcriptomic profiles of CD4+ T cells isolated from spleens of untreated (Control) and Ang II infused (Ang II) premenopausal C57BL/6 mice were examined via RNA sequencing. Ang II significantly regulated expression of 34 genes, of which 11 (Upregulated: CD163, PRG2, S100A9, MPO, CTSG, NGP, LCN2, S100A8; Downregulated: MARCO, IL1b, HSPA1B)  were confirmed by real-time PCR. To determine the effect of estrogen on premenopausal expression of RNAseq identifed genes during Ang II infusion we used two models of estrogen signlaing disruption. Both animal wide knockdown of estrogen receptor a and 4-vinylcyclohexene diepoxide (VCD) induction of menopause, significantly altered expression of RNAseq identified genes. To examine the effect of T cell activation on RNAseq gene expression, CD4+ T cells from control and Ang II treated premenopausal and male mice were stimulated in vitro. Sex differences in T cell RNAseq gene expression were associated with sex differences in supernatant concentration of IL10, IL4, and IFNg and renal IL10, IL4, and IL2 content.   Conclusions: These estrogen dependent T cell transcriptomic pathways and sex dependent functional differences in T cell cytokine secretion identify novel pathways that may mediate sex specific inflammatory responses during hypertension development.

overall_design: Splenic CD4+ T cell mRNA from premenopausal control and Ang II treated mice (14 days 800 ng/kg/min) (n = 3 mice/group)

first: Joshua

last: Uhlorn