title: High-throughput mRNA sequencing of CLL cells containing an E571K XPO1 mutations

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

summary:
Purpose: Exportin 1 (XPO1/CRM1) is a key mediator of nuclear export with relevance to multiple cancers, including chronic lymphocytic leukemia (CLL). Whole exome sequencing has identified hot-spot somatic XPO1 point mutations which we found to disrupt highly conserved biophysical interactions in the NES-binding groove, conferring novel cargo-binding abilities and forcing cellular mis-localization of critical regulators. However, the pathogenic role played by change-in-function XPO1 mutations in CLL is not fully understood. Thus, we aimed to identify disrupted cellular pathways in response to the E571K XPO1 mutation, the mutation most frequently cited in CLL patients, via high-throughput RNA-sequencing
Results & Conclusion: Multidimensional scaling (MDS) analysis of the top 1000 most variable genes demonstrated distinctly unique clustering along the first dimension for XPO1-E571K patient and XPO1-wt patient samples. This clustering pattern was driven by a number of genes that were either over- or under-expressed in XPO1-E571K patient cells, contributing to a unique gene expression pattern in patients with this mutation signature.

overall_design: Methods: We performed unbiased RNA-sequencing (RNA-seq) in CLL patient B-CLL cells containing an E571K XPO1 mutation (n=3) and compared this with XPO1-wt IgVH-U patient CLL cells (n=4). Library preparation and RNA-sequencing was performed and analyzed under protocols developed and approved by the Genomic Services Laboratory at Nationwide Children’s Hospital. Downstream pathway analysis of differentially expressed genes was determined via publically available Ingenuity pathway analysis software as previously described. Paired-end 150bp reads were aligned to the human reference genome GRCh38 using HISAT2 and gene counts were generated with featureCounts. Gene expression was quantified as log2 counts per million and differential expression analysis was performed using R limma voom function. Heatmaps were generated using R pheatmap package.

first: Janek

middle: S

last: Walker

first: Zachary

middle: A

last: Hing

first: Hatice

first: Katie

last: Williams

first: Jordan

last: Skinner

first: Casey

middle: B

last: Cempre

first: John

last: Byrd

first: Rosa

last: Lapalombella


title: Global gene expression profiled with RNA-Seq in CYH33-resistant ESCC cells as well as their parental cells

status: Public on Jan 21 2021

city: Shanghai

first: Yuxiang

last: Wang

address: No. 501 Haike Road

country: China

institute: Shanghai Institute of Materia Medica

type: Expression profiling by high throughput sequencing

summary: To investigate the mechanism mediating resistance to CYH33 in ESCC cells, global gene expression was profiled with RNA-Seq in CYH33-resistant cells as well as their parental cells. Gene enrichment analysis revealed that RAS signaling pathway, PI3K-Akt signaling pathway and MAPK signaling pathway were highly activated in most CYH33-resistant cells. To analyze the difference of gene expression profiles between CYH33-resistant cells and their matched parental cells upon CYH33 treatment, cells were treated with CYH33 at 1 μM for 24 hours and RNA-seq was performed. Gene Set Enrichment Analysis was then carried out.

overall_design: Total RNA profiles of 4 established CYH33-resistant ESCC cells and their parental cells treated with 1 μM CYH33 or Vehicle for 24 h

first: Xu

last: Zhang

first: Qingyang

last: Ma

first: Landian

last: Hu

first: Xi

first: Yi

first: Lan

last: Xu

first: Chunhao

last: Yang

first: Cun

last: Tan

first: Xiangyin

last: Kong

first: Jian

last: Ding

first: Linghua

last: Meng


title: Methylation profiling of pediatric choroid plexus tumors

city: Cairo

first: Shahenda

last: El-Naggar

address: 1 Sekket El Emam, El Madbah El Kadeem Yard, Sayeda Zeinab

department: Research Department

country: Egypt

institute: Children’s Cancer Hospital Egypt 57357

summary: Aggresome is a para nuclear inclusion body that functions as a storage compartment for misfolded proteins. Our previous work revealed the presence of aggresomes in pediatric choroid plexus tumors (CPT). CPTs are rare neoplasms comprised of three pathological subgroups; choroid plexus carcinoma (CPC), a grade III tumor, atypical choroid plexus papilloma (ACPP), a grade II tumor, and choroid plexus papilloma (CPP), a grade I tumor. In the current study, we aimed to investigate the prognostic value of aggresomes-positivity and its correlation to the pathological and molecular subtypes. The genome-wide methylation profile of 42 CPT pediatric samples was investigated using Illumina Infinium Methylation EPIC BeadChip array.

overall_design: Primary cohort comprised 42 tumor samples represented by 40 formalin-fixed-paraffin embedded (FFPE), 2 fresh frozen. 17 samples were represented by both FFPE and fresh frozen tissues. In total, we have 59 samples used for the Illumina Infinium 850K EPIC Methylation array.

first: Nada

last: Amer


title: Precise adenine base editors that exhibit minimized cytosine catalysis

city: Seoul

first: You Kyeong

last: Jeong

address: 222, Wangsimni-ro, Seongdong-gu

country: South Korea

institute: Hanyang University

summary: To alleviate the ABE-mediated cytosine editing activity, we engineered the commonly-used version of adenosine deaminase, TadA7.10. We found that the D108Q mutation also reduces cytosine deamination activity in two recently-developed versions of ABE, ABE8e and ABE8s, and has a synergistic effect with V106W, a key mutation that reduces off-target RNA editing.

overall_design: We conducted RNA-seq experiments for one control (nCas9 only) and five ABE variants (ABE8e, ABE8eW, ABE8eWQ, ABE8s, and ABE8sQ).

first: YouKyeong

first: SeokHoon

last: Lee

first: Gue-Ho

last: Hwang

first: Sung-Ah

last: Hong

first: Se-eun

last: Park

first: Jin-Soo

last: Kim

first: Jae-Sung

last: Woo

first: Sangsu

last: Bae


title: Validation of Baboon Pluripotent Cells as a Model for Translational Stem Cell Research [MeDIP]

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

type: Methylation profiling by high throughput sequencing

summary: To investigate the extent of similarity in epigenetic programming among human, baboon and mouse PSCs, we examined genome-wide patterns of four chromatin modifications (H3K4me3, H3K9me3, H3K27me3, H3K27ac) and DNA methylation in baboon iPSC and ESCs. We show that baboon pluripotent cells (PSCs) recapitulate key molecular features of human PSCs with much greater accuracy than that found in PSCs from non-primate species. Specifically, baboon and human PSCs exhibit significantly greater conservation of gene expression patterns, higher sequence and structural homology among pluripotency factors, more equivalent genome-wide patterns of histone and DNA methylation modifications, and similar maintenance of bivalent programming of developmental genes than that found between human and non-primate PSCs.

overall_design: Examination of transcriptome, H3K4me3, H3K27ac, H3K9me3, H3K27me3 and DNA methylation in baboon iPSC and ESC.

first: Keren

last: Cheng

first: Megan

last: Mahlke

first: John

middle: R

last: McCarrey


title: RNA seq of sorted T cell subsets from PBMCs and rectal biopsies from humans and rhesus macaques

city: Davis

first: Smita

last: Iyer

state: CA

address: county rd 98 & hutchison, ccm room 2075

department: Center for Immunology and Infectious Disease

country: USA

institute: University of California-Davis

summary: Memory CD4 T cells facilitate HIV establishment following transmission and contribute to HIV persistence during suppressive antiretroviral therapy (ART). Numerous studies have highlighted the importance of memory CD4 T cells expressing the surface integrin heterodimer, α4β7 in HIV infection. Here, we focused on delineating the molecular characteristics of α4β7+ CD4 T cells and determining how transcriptional profiles of circulating α4β7hi CD4 T cells corresponded to that within the lower GI tract.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Comparision of transciptome profiles across blood and gut compartment


title: Circadian VIPergic neurons of the suprachiasmatic nuclei sculpt the sleep-wake cycle

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

summary: Although the mammalian rest-activity cycle is controlled by a "master clock" in the suprachiasmatic nuclei (SCN) of the hypothalamus, it is unclear how firing of individual SCN neurons gates individual features of daily activity. Here, we demonstrate that a specific transcriptomically identified population of mouse VIP+ SCN neurons is active at the "wrong" time of the day -nighttime- when most SCN neurons are silent. Using chemogenetic and optogenetic strategies, we show that these neurons and their cellular clocks are necessary and sufficient to gate and time nighttime sleep, but have no effect upon daytime sleep. We propose mouse nighttime sleep, analogous to the human siesta, is a "hard-wired" property gated by specific neurons of the master clock to favor subsequent alertness prior to dawn (a circadian "wake maintenance zone"). Thus, the SCN is not simply a 24h metronome: specific populations sculpt critical features of the sleep-wake cycle.

overall_design: SCN neurons were recorded and collected from cFOS-GFP mice at night before and during the siesta. Mice were between 6 and 8 weeks old. We collected 20 SCN neurons.

first: Ben

last: Collins

first: Sara

last: Pierre-Ferrer

first: Christine

last: Muheim

first: David

last: Lukacsovich

first: Yuchen

last: Cai

first: Andrea

last: Spinnler

first: Carolina

middle: G

last: Herrera

first: Shao'Ang

last: Wen

first: Jochen

last: Winterer

first: Mino

middle: D

last: Belle

first: Hugh

last: Piggins

first: Michael

last: Hastings

first: Andrew

last: Loudon

first: Jun

last: Yan

first: Antoine

last: Adamantidis

first: Steven

last: Brown


title: Human Ex Vivo Lung Perfusion: A Model System to study Lung diseases and direct targeted therapies

city: Pittsburgh

first: Nayra

last: Cardenes

state: PA

address: 200 Lothrop st., BST W1230

department: PACCM

institute: University of Pittsburgh

summary: In the present study, we demonstrate the feasibility of the EVLP technique to perfuse lungs from deceased patients with a broad spectrum of chronic lung diseases. We were able to assess gene expression changes over the course of EVLP and between end-stage diseases by RNA sequencing transcriptomics from tissue samples collected at different time points,  revealing fundamental genetic information which has important avenues for modulation in the future. Thus, EVLP can serve as a clinically relevant experimental model to derive mechanistic insights into pulmonary pathophysiology and various human lung diseases.

overall_design: Method: Tissues from chronic lung diseases and normal lungs were collected at time 0 and end of EVLP (6hr), and quality RNA libraries were generated using Illumina TruSeq RNA Access library preparation kit. The coding regions of the transcriptome were then captured from this library using sequence-specific probes to create the final library. The cDNA libraries were validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorometer and quality examined using Agilent Tapestation 2200. Cluster generation and 75 bp Paired-read dual-indexed sequencing was performed on Illumina NextSeq 500’s.

first: John

last: Sembrat

first: Kentaro

last: Noda

first: Tyler

last: Lovelace

first: Diana

last: Alvarez

first: Humberto

middle: E

last: Trejo Bittar

first: Mehdi

last: Nouraie

first: Panayiotis

middle: V

last: Benos

first: Pablo

last: Sanchez

first: Mauricio

last: Rojas


title: mRNA profiling on CD19-directed chimeric antigen receptor T (CART19) cells with and without platelet-poor plasma from untreated chronic lymphocytic leukemia (CLL) patients (CLL-derived extracellular vesicles)

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

summary: Chimeric antigen receptor (CAR) T cell therapy has yielded unprecedented outcomes in some patients with hematological malignancies; however, inhibition by the tumor microenvironment has prevented the broader success of CART cell therapy. We used chronic lymphocytic leukemia (CLL) as a model to investigate the interactions between the tumor microenvironment and CART cells. CLL is characterized by an immunosuppressive microenvironment, an abundance of systemic extracellular vesicles (EVs), and a relatively lower durable response rate to CART cell therapy. In this study, we characterized plasma EVs from untreated CLL patients and identified their leukemic cell origin. CLL-derived EVs were able to induce a state of CART cell dysfunction characterized by phenotypical, functional, and transcriptional changes of exhaustion. We demonstrate that, specifically, PD-L1+ CLL-derived EVs induce CART cell exhaustion. In conclusion, we identify an important mechanism of CART cell exhaustion induced by EVs from CLL patients.

overall_design:
RNA sequencing was performed on antigen-stimulated CART19 co-cultured with three biological replicates of CLL-derived EVs or alone.
CART19 and irradiated JeKo-1 were co-cultured at a 1:1 ratio for 24 hours with CLL-derived EVs at 10:1 and 1:1 EV:CART19 ratios. Three biological replicates of CLL-derived EVs were included as well as antigen-stimulated and unstimulated CART19 controls without EVs. CART19 were isolated using magnetic sorting with CD4 and CD8 microbeads. RNA was isolated from the CART19 cells using QIAGEN miRNeasy Micro Kit.

first: Michelle

last: Cox

first: Fabrice

last: Lucien

first: Neil

last: Kay


title: The beating cluster of adipose tissue-derived stromal cells

city: Kanazawa

first: Shinichiro

last: Takashima

address: 13-1 Takara-machi

department: Cardiovascular Medicine

country: Japan

institute: Kanazawa University

summary:
Adipose tissue-derived stromal vascular fraction (Ad-SVF) contains stem cells and rarely transdifferentiate into spontaneously beating cardiomyocyte-like cells (beating CMs). However, the factors that regulate the differentiation of Ad-SVF into the cardiac lineage is unknown. We developed a simple culture protocol under which the adult murine inguinal Ad-SVF reproducibly transdifferentiates into beating CMs without induction.
We used microarray analyses to evaluate the global gene expressions of the beating CMs and investigated the mechanism underlying the transdifferentiation of SVF cells into CMs.

overall_design: To investigate the phenotype of the beating SVF cells, we performed a global transcriptome analysis. All of the beating SVF colonies in a dish on day 28 were manually picked up and combined, constituting the beating-SVF (beating) group. The other cells were collected as the non-beating SVF (non-beating) group. To test our hypothesis that the round cells were the progenitors of CMs, we performed a single-cell-based global gene expression analysis. At day 14 of primary SVF culture, six round cells were picked up using the ALS CellCelector system and combined for microarray analysis.

first: Masayuki

last: Takamura


title: Genome-wide analysis of normal and high glucose condition

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

institute: Inha university hospital

summary: Transcriptional profiling of Mouse cavernous primary pericytes (MCPs) in comparing normal glucose condition with high glucose condition

overall_design: Total RNA obtained from MCPs, which were treated with Normal glucose (NG) and High glucose (HG) condition. Biological replicates: 1 control replicates, 1 HG replicates.

first: GuoNan

last: Yin

first: Hai-Rong

last: Jin

first: Ji-Kan

last: Ryu

first: Jun-Kyu

last: Suh


title: EBF1 drives hallmark B cell gene expression by enabling the interaction of PAX5 with the MLL H3K4 methyltransferase complex

city: Moncton

first: Rodney

last: Ouellette

address: 35 Providence St.

country: Canada

institute: ATLANTIC CANCER RESEARCH INSTITUTE

summary: We report RNAseq analysis of KIS-1 cells with and without doxycycline-inducible expression of the EBF1 transcription factor. We also compared untreated KIS-1 WT cells to RAJI WT cells.

overall_design: KIS-1 cells stably transduced with either an empty vector or a vector carrying an inducible EBF1 were induced with doxycycline or left untreated.

first: Charles

last: Bullerwell

first: Pierre

middle: M

last: Deprez

first: Andrew

middle: P

last: Joy

first: G

last: Wajnberg

first: Darwin

last: D'Souza

first: Simi

last: Chacko

first: Sébastien

last: Fournier

first: Nicolas

last: Crapoulet

first: David

last: Barnett

first: Stephen

last: Lewis

middle: J


title: Gene expression in honeybees

city: Nottingham

first: Nigel

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

summary: Gene expression in honeybees

overall_design: 15 day old africanized A. mellifera bees were fed a solution containing water and invert sugar (1:1) = control, or a sugar solution with either 2 µg/l Thiamethoxam, or 50 µg/l Thiamethoxam. After 10 days, brains from the bees were dissected and total RNA isolated, using a Trizol method.

first: Reinhard

last: Stöger

first: Thaisa

middle: C

last: Roat

first: Pâmela

last: Decio

first: Ian

middle: W

last: Hardy

first: Kamila

last: Derecka

first: Matthias

last: Soller


title: Validation of Baboon Pluripotent Cells as a Model for Translational Stem Cell Research [RNA-Seq]

first: keren

last: cheng

overall_design: The gene expression profiles of baboon iPSC and ESC.

first: Keren

last: Cheng

first: Megan

last: Mahlke

first: John

last: McCarrey


title: Glycolytic metabolism of pathogenic T cells enables early detection of GvHD by 13C-MRI

city: Bethesda

first: Nataliya

middle: Prokopenko

last: Buxbaum

state: Maryland

address: 10 Center Drive, CRC, 3-3288

department: ETIB

institute: NCI, NIH

summary: Graft-versus-host disease (GvHD) is a prominent barrier to allogeneic hematopoietic stem cell transplantation (HSCT). Definitive diagnosis of GvHD is invasive and biopsies of involved tissues pose a high risk of bleeding and infection. Our previous studies in a chronic GvHD mouse model demonstrated that alloreactive CD4+ T cells are distributed to target organs ahead of overt symptoms, meanwhile CD4+ T cell activation is tied to increased glycolysis. We aimed to compare the gene expression of  allogeneic (mismatched) naive (Tn) and effector memory (Tem) CD4+ T cell subsets early post transplant. Specifically, we hypothesized that allogeneic CD4 effector memory T cells would show upregulated expression of genes related to glycolysis. We found that almost all enzymes of glycolysis were upregulated in effector memory CD4 T cells compared to naive cells, including transporters for glucose. In contrast, enzymes of the tricarboxylic acid cycle were not uniformly elevated.

overall_design: FACS-purified allogeneic Tem and Tn cells from the spleen (> 0.5 million cells per sample) were pooled from multiple study animals on day 14. RNA was extracted from pooled samples of each cell type (n = 1 for Tn, n = 3 for Tem)

first: Christopher

last: Ricketts

first: Thomas

last: Meyer


title: Whole Genome Bisulfite Sequencing of CD4+ T cells from mice developmentally exposed to vehicle or TCDD prior to and during influenza infection

first: B. Paige

last: Lawrence

state: NY

address: 601 Elmwood Ave.

institute: University of Rochester

summary: We used Whole Genome Bisulfite Sequencing (WGBS) to compare DNA methylation patterns across the genome of CD4+ T cells. Specifically, mice were developmentally exposed to vehicle or TCDD. At adulthood, CD4+ T cells were purified from peripheral lymph nodes of naive animals or the mediastinal lymph nodes of influenza A virus (IAV) infected mice (9 days post infection). DNA was isolated from these cells, and WGBS was performed. Differential DNA methylation analyses revealed that both developmental exposure and IAV infection influence the pattern of DNA methylation in CD4+ T cells.

overall_design: Comparing genome wide DNA methylation patters in CD4+  T cells from naïve or IAV infected mice that were developmentally exposed to vehicle or TCDD. 3 biological replicates per sample.

first: Catherine

last: Burke

first: Jason

last: Myers

first: B


title: RNA-sequencing of CD4+ T cells from mice prior to and after infection with influenza virus, and that were exposed developmentally to vehicle or TCDD

summary: We used next generation RNAsequencing to identify how developmental exposure to TCDD alters gene expression in CD4+ T cells. Specifically, mice were developmentally exposed to vehicle or TCDD. At adulthood, CD4+ T cells were purified from peripheral lymph nodes of naive animals or the mediastinal lymph nodes of influenza A virus (IAV) infected mice (9 days post infection). RNA was isolated from these cells, and RNA-seq was performed. Gene expression analysis revealed developmental activation of the aryl hydrocarbon receptor with TCDD changes expression of genes that are involved in important CD4+ T cell functions.

overall_design: Comparing gene expression patters of CD4+ T cells from naïve or IAV infected mice that were developmentally exposed to vehicle or TCDD. 3 biological replicates per sample.


title: RNA-seq profiles of B cells and naive and activated T cells from human peripheral blood

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Mature B cells, CD4+ T cells and CD8+ T cells were isolated from the peripheral blood of two human donors. Naive CD4+ and CD8+ T cells were cultured for three days in the presence of Dynabeads Human T-Activator CD3/CD28 beads (Life Technologies, cat. no. 111.31D) to induce activation. The B cells and naive and activated T cells were profiled by whole transcriptome RNA-seq.

overall_design: Cells were isolated from two human donors, resulting in two biological replicates of each combination of cell type and activation status.

first: Naiara

last: Bediaga

first: Leonard

last: Harrison

first: Alexandra

middle: L

last: Garnham


title: Glycolytic metabolism of pathogenic T cells enables early detection of GvHD by 13C-MRI.

overall_design: FACS-purified CD45+ CD4+ cells were isolated from syngeneic and allogeneic transplanted mice (n= 3 each) in a model of chronic GvHD on day 14 from the liver. After sorting, cells were counted, tested for viability and a target of 6000 cells was loaded onto the 10X system. The cells were processed according to the instructions for the 5' sequencing kit.

first: Michael

last: Kelly

first: Julian

last: Assmann


title: ATAC-seq profiles of B cells and naive and activated T cells from human peripheral blood

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mature B cells, CD4+ T cells and CD8+ T cells were isolated from the peripheral blood of two human donors. Naive CD4+ and CD8+ T cells were cultured for three days in the presence of Dynabeads Human T-Activator CD3/CD28 beads (Life Technologies, cat. no. 111.31D) to induce activation. The B cells and naive and activated T cells were profiled by ATAC-seq to determine chromatin accessibility.


title: Transcription profiles of human dermal sheath cells cultured under 20%-O2 or 6%-O2 condition

city: Ikoma

first: Hitomi

last: Takada

state: Nara

address: 8916-5 Takayama-cho

department: Graduate School of Science and Technology

institute: Nara Institute of Science and Technology

summary: We investigated the effect of low oxygen culture on the proliferation and hair inductive capacity of human dermal papilla cells (DPCs) and dermal sheath cells (DSCs). DPCs and DSCs were cultured in atmospheric/hyperoxia (20% O2), physiological/normoxia (6% O2), or hypoxia (1% O2) conditions, respectively. Proliferation of DPCs and DSCs was highest under normoxia. Hypoxia inhibited proliferation of DPCs but enhanced proliferation of DSCs. In DPCs, hypoxia down-regulated expression of hair inductive capacity-related genes, including BMP4, LEF1, SOX2, and VCAN, and normoxia up-regulated expression of ALP. In DSCs, both normoxia and hypoxia up-regulated SOX2 expression, and hypoxia down-regulated BMP4 expression. Microarray analysis revealed increased expression of pluripotency-related genes, including SPRY, NR0B1, MSX2, IFITM1, and DAZL, under hypoxia. In an in vivo hair follicle reconstitution assay, cultured DPCs and DSCs were transplanted with newborn mouse epidermal keratinocytes into nude mice using a chamber method. In DPCs, normoxia allowed the most efficient induction of hair follicles. In DSCs, hypoxia allowed the most efficient induction and maturation of hair follicles. These results suggest that low oxygen culture enhances the proliferation and maintains functions of human DPCs and DSCs and could be used for skin engineering and clinical applications.

overall_design: Human DSCs were cultured for four weeks under 20%-O2 or 6%-O2 condition. Gene expression profiles were compared between two culture conditions by microarray analysis.

first: Koji

last: Kanayama

first: Kotaro

last: Yoshimura


title: Transcription profiles of human dermal papilla cells cultured under 20%-O2 or 6%-O2 condition

overall_design: Human DPCs were cultured for four weeks under 20%-O2 or 6%-O2 condition. Gene expression profiles were compared between two culture conditions by microarray analysis.


title: Origin of a novel CYP20A1 lncRNA through 23 Alu exaptations in the human lineage creates a potential multi-miRNA sponge

city: pune

first: vineet

last: jha

state: Maharashtra

address: 9 A/12 Pingale Aryabhatta Persistent Tower,

department: LABS

country: India

institute: Persistent systems

type: Non-coding RNA profiling by high throughput sequencing

summary: Alu repeats contribute to lineage specific novelties in conserved transcriptional regulatory networks. We report for the first time the origin of a multi-miRNA human specific sponge through exaptation of 23 Alu repeats that forms a novel principal isoform of CYP20A1 gene with a 9kb 3’UTR. This 3’UTR, confirmed by RACE, is an outlier in terms of its length with expression in multiple cell lines, including brain as evidenced from single nucleus RNA-seq data of 16000 human cortical neurons. It has diverged from its parent gene through exon skipping into a novel lncRNA. Its uniqueness in humans was validated by its presence in rosehip neurons and absence in closely related primate species through RNA-seq datasets. Strikingly, prediction by miRanda revealed ~4700 MREs for ~1000 different miRNAs, majorly in Alu repeats, in this 3’UTR. Permutations on 1000 random sets suggest their creation is non-random and post Alu exaptation. We hypothesise this lncRNA is an miRNA sponge as it has cytosolic localisation and harbours ≥10 MREs for 140 miRNAs (threshold > - 25kcal/mol). Under experimental conditions where CYP20A1 displays differential expression, we probed the expression of the miRNAs that map to this 3’UTR and their cognate targets through small RNA and mRNA-seq, respectively. We observed correlated expression of our lncRNA and a set of 380 genes with downregulation in heat shock and upregulation in HIV1-Tat treatment in primary neurons. GO analyses suggest the involvement of this sponge lncRNA in modulation of processes linked to neuronal development and hemostasis pathways.

overall_design: A total of 18 human primary neuron samples (Control + 5 different treatment conditions; 3 biological replicates for each) were used for stranded paired-end RNA seq and small RNA seq. Since data for RNA as well as small RNA seq have been generated from the same sample, these are paired. Additionally, small RNA seq data have been generated from untreated MCF-7 cells (6 biological replicates).

first: Aniket

last: Bhattacharya

first: Vineet

last: Jha

first: Gaura

last: Chaturvedi

first: Khushboo

last: Singhal

first: Mitali

last: Mukerji

first: Pankaj

last: Seth

first: Mahar

last: Fatima


title: Hi-C profiles of activated CD4+ T cells and CD8+ T cells from human peripheral blood

first: Gordon

last: Smyth

summary: CD4+ T cells and CD8+ T cells were isolated from the peripheral blood of two human donors and were cultured to induce activation. High-throughput chromosome confirmation capture (Hi-C) was used to examine DNA interactions between chromosomes.

overall_design: Cells were isolated from two human donors, resulting in two biological replicates for cell type.

first: Hannah

last: Coughlan


title: Macrophage training to Borrelia burgdorferi governs cardiac inflammation in the mammalian host [RNA-seq]

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

summary: Macrophage exposure to vaccine or vaccine-like formulations results in disparate secondary responses. We have identified the transcriptomic and metabolic changes associated with the memory response of macrophages to Borrelia burgdorferi, an extracellular pathogen able to establish long-term infections in mammals. Memory macrophages show an enhanced ability to bind and internalize the spirochete with decreased inflammatory responses, in part regulated by Irf4. Experienced macrophages also show an augmented glycolytic output. In vivo, glycolysis inhibition results in decreased cardiac inflammation and reduced expression of Irf4. Our data show that B. burgdorferi induces long-term, memory-like responses that are amenable to be manipulated in vivo.

overall_design: Genome-wide changes in gene Expression in mouse bone marrow-derived macrophages stimulated and restimulated with Borrelia burgdorferi at a multiplicity of infection of 25. Groups corresponding to unstimulated (U) or previously stimulated and washed (B) macrophages, either left unstimulated (UU, BU) or restimulated with B. burgdorferi (UB, BB) were generated by RNAseq.

first: Juan

last: Anguita


title: Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19

status: Public on Jan 20 2021

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

summary: SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs),  primary airway cells, or hiPSC-derived alveolar type-II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Infected ALO-monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection, whereas distal alveolar differentiation (AT2→AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Findings validate a human lung model of COVID-19 , which can be immediately utilized to investigate COVID-19 pathogenesis and vet new therapies and vaccines.

overall_design: Human lung organoids were grown in standard culture, ALI and monolayer conditions. Human small airway epithelium and iPSC-derived alveolar epithelial type 2 cells were infected with SARS-CoV2.

first: Soumita

last: Das

first: Pradipta

last: Ghosh


title: Establishment of intestinal organoid cultures modeling injuryassociated epithelial regeneration [bulk RNA-seq]

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

summary: The capacity of 3D organoids to mimic physiological tissue organization and functionality has provided an invaluable tool to model development and disease in vitro. However, conventional organoid cultures primarily represent the homeostasis of self-organizing including VPA, EPZ6438, LDN193189, and R-Spondin 1 conditioned medium, which mimics the gut epithelium regeneration that produces hyperplastic crypts following injury; therefore, these organoids were designated hyperplastic intestinal organoids (Hyperorganoids). Single-cell RNA sequencing identified different regenerative stem cell populations in our Hyper-organoids that shared molecular features with in vivo injury-responsive Lgr5+ stem cells or Clu+ revival stem cells. Further analysis revealed that VPA and EPZ6438 were indispensable for epigenome reprogramming and regeneration in Hyper-organoids, which functioned through  epigenetically regulating YAP signaling. Furthermore, VPA and EPZ6438 synergistically promoted regenerative response in gut upon damage in vivo. In summary, our results demonstrated a new in vitro organoid model to study epithelial regeneration, highlighting the importance of epigenetic reprogramming that pioneers tissue repair.

overall_design: Examination of mRNA expression pattern of intestine organoids with different conditions in vitro and mouse crypts with different treatments in vivo.

first: Molong

last: Qu

first: Liang

last: Xiong

first: Cheng

last: Li

first: Jun

last: Xu

first: Hongkui

last: Deng


title: Establishment of intestinal organoid cultures modeling injuryassociated epithelial regeneration

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

overall_design: Refer to individual Series


title: Establishment of intestinal organoid cultures modeling injuryassociated epithelial regeneration [scRNA-seq]

overall_design: Examination of single cell mRNA expression pattern of intestine organoids with different conditions in vitro and mouse crypts with different treatments in vivo.


title: Transcriptome analysis of WT margina zone B (MZB) cells and CK2⍺-cKO MZB cells.

city: birmingham

first: Etty (Tika)

last: Benveniste

state: Alabama

address: 1918 University Blvd., MCLM 31

department: CDIB

institute: UAB

summary: The goals of this study are to compare the transcriptome profiling of marginal zone B cells from WT and  CK2⍺-cKO mice.

overall_design: RNA was isolated from sorted ex-vivo MZB cells of Wild Type and CK2⍺-cKO mice. Total RAN samples were sent to GENEWIZ,LLC  for RNA library preparatios, sequencing reactions, and initial bioinformatics analysis.

first: Hairong

last: Wei

first: Wei

last: Yang

first: Hongwei

last: Qin

first: Etty


title: Interferon-induced transmembrane protein 1 (IFITM1) inhibits Varicella-Zoster Virus Replication

city: Shreveport

first: Seong

last: Kim

state: Louisiana

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: LSU Health Sciences Center

summary: Hosts have evolved numerous mechanisms to prevent primary viral infections. Interferon signaling is an important host defense mechanism against primary infection. Interferon gamma (IFN-γ) is a potent cytokine produced following primary varicella-zoster virus (VZV) infection. Furthermore, VZV reactivation correlates with a decline in IFN-γ-producing immune cells. Our previous results showed that pretreatment with 20 ng/ml of IFN-γ completely inhibited VZV replication in lung fibroblast MRC-5 and retinal epithelial ARPE-19, suggesting that IFN-γ-stimulated protein(s) inhibit viral replication. Our microarray analysis revealed that a small subset of interferon-stimulated genes (ISGs) was upregulated by greater than 3.5-fold at 8 h post-treatment in both ARPE-19 and MRC-5 cells compared to those of melanoma MeWo cells. The depletion of IFITM1 and IRF1 by siRNA in IFN-γ-treated cells significantly increased (from 0 to ~1x103 pfu/105 cells) VZV yields. In contrast, the depletion of a nontargeting control (siNTC) did not increase virus yield. Ectopic expression of interferon-induced transmembrane protein 1 (IFITM1) reduced the level of IE62 protein as well as intracellular VZV yield in both ARPE-19 and MeWo cells, but did not reduce the expression level of IE62 mRNA, suggesting that IFITM1 expression reduces the expression level of IE62 by post-transcriptional regulation. IFITM1 also reduced the expression levels of VZV IE62, HSV-1 ICP4, and EHV-1 IEP in ARPE-19 cells

overall_design: Human retinal epithelial ARPE-19, human lung fibroblast MRC-5, and human melanoma MeWo cells were treated with 0 or 20 ng/ml of human IFN-γ (Cell Sciences, Canton, MA). The untreated and treated cells were harvested at 8 h post-treatment and used in DNA microarray analyses using the Affymetrix human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA).

first: Akhalesh

last: Shakya

first: Dennis

last: O'Callaghan


title: cinaR: A comprehensive R package for the differential analyses and interpretation of ATAC-seq data

city: Farmington

first: Duygu

last: Ucar

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

summary: ATAC-seq is a frequently used assay to study chromatin accessibility levels. Differential chromatin accessibility level analyses between biological groups and functional interpretation of these differential regions are essential in ATAC-seq data analyses. Although distinct methods and analyses pipelines are developed for this purpose, we are missing a stand-along R package that combines state-of-the art differential analyses and functional enrichment analyses. To fill this gap, we developed cinaR, which is a single wrapper function and provides users with various configurable plots. To show-case this pipeline we provide these bulk ATAC-seq samples from bone-marrow of 3 & 18 months old New Zelland Obese (NZO) mice and show the activation of pro-inflammatory pathways.

overall_design: Bone marrow of NZO mice at 3 and 18 months

first: Onur

last: Karakaslar


title: Protein prenylation drives discrete signaling programs for the differentiation and maintenance of effector Treg cells [Fntb_ATACseq]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: An interplay between immune signals, isoprenoids-mediated protein prenylation, and intracellular signaling for the differentiation and maintenance of eTreg cells.

overall_design: ATAC-seq was performed to compare chromatin accessibility of WT, Fntb-deficient cTreg and eTreg cells from mixed bone marrow chimera

last: Su

first: Hao

last: Shi

first: Yogesh

last: Dhungana


title: Protein prenylation drives discrete signaling programs for the differentiation and maintenance of effector Treg cells [Microarray Dataset 3]

summary:
An interplay between immune signals, isoprenoids-mediated protein prenylation, and intracellular signaling for the differentiation and maintenance of eTreg cells.
We used microarrays to compare the global transcription profiles of in vitro activated CD4+YFP+CD44loCD62Lhi cTreg cells sorted from Foxp3YFP-Cre mice and activated by 10 ug/ml anti-CD3/28 antibodies plus 200 U/ml IL-2 for different time points in the presence of prenylation inhibitors

overall_design: In total 20 samples were analyzed: DMSO at 0 h (n=3), DMSO at 18 h (n=3), FTI at 18 h (n=3), GGTI at 18 h (n=2), DMSO at 48 h (n=3), FTI at 48 h (n=3), GGTI at 48 h (n=3)


title: Antisense ribosomal siRNAs inhibit RNA polymerase I-directed transcription in C. elegans

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

institute: University of Science & Technology of China

summary: Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that function in the nucleus. We previously found that erroneous rRNAs induce the generation of antisense ribosomal siRNAs (risiRNAs) which silence the expression of rRNAs via the nuclear RNAi defective (Nrde) pathway. To further understand the biological roles and mechanisms of this class of small regulatory RNAs, we conducted forward genetic screening to identify factors involved in risiRNA generation in Caenorhabditis elegans. We found that risiRNAs accumulated in the RNA exosome mutants. risiRNAs directed a NRDE-dependent silencing of pre-rRNAs in the nucleolus. In the presence of risiRNAs, NRDE-2 accumulated in the nucleolus and colocalized with RNA polymerase I. risiRNAs inhibited the transcription elongation of RNA polymerase I by decreasing RNAP I occupancy downstream of the RNAi-targeted site. Meanwhile, exosomes mislocalized from the nucleolus to nucleoplasm in suppressor of siRNA (susi) mutants, in which erroneous rRNAs accumulated. These results established a novel model of rRNA surveillance by combining ribonuclease-mediated RNA degradation with small RNA-directed nucleolar RNAi system.

overall_design: In this study, we compared total small RNAs from (1) wild type animal; (2) dis-3(ust56) mutant; (3) exos-1(ust57) mutant. And we compared total small RNAs from (4) eri-1(mg366) animal; (5) eri-1(mg366);dis-3(ust56) mutant; (6) eri-1(mg366);dis-3(ust56);rrf-1(pk1417);rrf-2(ok210) mutant;(7) eri-1(mg366);exos-1(ust57) mutant; (8) eri-1(mg366);exos-10(ok2269) mutant; And we compared the NRDE-3 associated small RNAs in (9) control animals; (10) dis-3(ust56) mutant; and (11) exos-1(ust57) mutant; (12) exos-10(ok2269); (13) dis-3(ust56);rrf-1(pk1417);rrf-2(ok210) mutant. And we also compared total small RNAs from (14) control animals; (15) fib-1 RNAi animals; (16) mtr-4 RNAi animals; (17) nol-56 RNAi animals;


title: Protein prenylation drives discrete signaling programs for the differentiation and maintenance of effector Treg cells [Microarray Dataset 2]

summary:
An interplay between immune signals, isoprenoids-mediated protein prenylation, and intracellular signaling for the differentiation and maintenance of eTreg cells.
We used microarrays to compare the global transcription profiles of CD4+YFP+Treg cells from Foxp3Cre Pggt1bfl/wt and Foxp3Cre Pggt1bfl/fl mixed bone marrow chimeras

overall_design: In total 7 samples were analyzed: Foxp3Cre Pggt1bfl/wt (n=4) compared to Foxp3Cre Pggt1bfl/fl (n=3).


title: Protein prenylation drives discrete signaling programs for the differentiation and maintenance of effector Treg cells [Microarray Dataset 1]

summary:
An interplay between immune signals, isoprenoids-mediated protein prenylation, and intracellular signaling for the differentiation and maintenance of eTreg cells.
We used microarrays to compare the global transcription profiles of CD4+YFP+Treg cells from WT, Foxp3CreFntbfl/fl mixed bone marrow chimeras

overall_design: In total 10 samples were analyzed: WT Treg (n=5) compared to Foxp3CreFntbfl/fl (n=5);


title: Protein prenylation drives discrete signaling programs for the differentiation and maintenance of effector Treg cells [Pggt1b_ATACseq]

overall_design: ATAC-seq was performed to compare chromatin accessibility of WT, Pggt1b-deficient cTreg and eTreg cells from mixed bone marrow chimera


title: RNA binding by Exosc10 in the developing mouse cortex

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: In our RIP-seq experiment, RNAs were purified from the E12.5 WT mouse cortex. By sequencing of the Exosc10-bound RNAs, binding enrichment of Exosc10 on 3159 transcripts was identified (adjusted p-value < 0.05). GO analysis revealed that the Exosc10-bound transcripts participate in various processes of brain development.

overall_design: mRNA binding profile of Exosc10 in the embryonic mouse cortex was generated by RIP-Seq

first: Pauline

last: Ulmke

first: Yuanbin

last: Xie

first: Tran

last: Tuoc


title: The microglial transcriptome of a novel murine model of Alzheimer's Disease: phagocytically active and inactive microglia from homozygous App-SAA mice and WT littermate controls.

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: We created a novel murine model of Alzheimer's Disease using a knock-in strategy to humanize the sequence of the murine App gene and introduced three familial AD (FAD) mutations, Swedish (Swedish  (KM670/671NL), Arctic (E693G)) and Austrian (T712I). To determine whether App-SAA microglia exhibit cellular dysfunctions and whether these dysfunctions relate to fibrillar Ab internalization, mice were intraperitoneally (i.p.) injected with 10 mg/kg methoxy-X04. 24 hours after injection, mice were perfused with PBS, cortical and hippocampal tissues were dissected and processed into single-cell suspension and methoxy-X04-negative and methoxy-X04-positive microglia were isolated using FACS. Mirroring our gene expression studies, we found profound alterations of the AppSAA microglia transcriptome; these changes were exacerbated in methoxy-X04 positive compared to negative cells.

overall_design: This experiments examines FACS-isolated microglia from 20 mice from two backgrounds (N = 10 WT, N = 10 homozygous App-SAA animals) that weren injected with 10 mg/kg methoxy-X04. Microglia were isolated from the brain (cortex & hippocampus) of each animal using FACS. In App-SAA samples, two populations of microglia cells were distinguishabe based on their methoxy-X04 staining. These populations were collected and analyzed separately as methoxy-positive and methoxy-negative fractions. In WT cells, only methoxy-negative cells were observed and processed for analysis.

first: Dan

last: Xia

first: Steve

last: Lianoglou

first: Chia-Ching

last: Lin

first: Elliot

last: Thomsen

first: Connie

last: Ha

first: Pascal

last: Sanchez


title: Microarray data of Atg5 WT and KO hematopoietic stem/progenitor cells

city: Kanazawa

first: Atsushi

last: Hirao

state: Ishikawa

address: Kakuma-machi

department: Cancer Research Institute

institute: Kanazawa University

summary: To comprehensively examine differences of gene expression patterns between  WT and ATG5 KO HSCs/progenitors, we isolated LSK cells and conducted the microarray analysis.

overall_design: WT and ATG5 KO LSK (Lineage marker-/cKit+/Sca1+) cells were sorted by cell sorter. Total RNA was isolated from collected cells and  the microarray analysis was conducted.

first: Yuko

last: Tadokoro

first: Naho

last: Nomura


title: Genome-wide profiling of mutant p53 unveils a subset of lncRNAs correlated with colorectal cancer stemness maintenance

first: Yiran

last: Li

address: 北京市东城区东单三条五号

institute: 北京协和医院基础所


title: Genome-wide profiling of mutant p53 unveils a subset of lncRNAs correlated with colorectal cancer stemness maintenance [ChIP-seq]

address: 北京市东城区东单三条五号

summary: RNA-sequencing and ChIP-sequencing were used to trace the lncRNAs regulated by p53-R273H in HCT116 endogenous p53 point mutant cell lines.

overall_design: We set out to analyze the differentially expressed lncRNAs in p53-R273H colorectal cancer cell lines compared to wildtype control cell lines (wildtype cell lines as reference) by RNA-seq combined with ChIP-seq. RNA-seq profiling contained three replicates including p53-R273H mutant cell lines and wildtype control cell lines respectively. ChIP-seq profiling contained two replicates including input samples and ChIP samples both of p53-R273H mutant cell lines and wildtype control cell lines.


title: Potential role of miRNA in acute hypoxic response of largemouth bass (Micropterus salmoides)

city: Haikou

first: JunLong

last: Sun

state: Hainan

address: No.58 Renmin Avenue, Haikou City, Hainan Province

institute: Hainan University

summary: Intensive aquaculture and environmental changes will inevitably lead to hypoxic stress for largemouth bass (Micropterus salmoides). To better understand the hypoxia responds mechanisms of largemouth bass, we compared the miRNA profile in liver under different environmental DO to determine which miRNAs are most affected during hypoxia. A total of 266 miRNAs were identified, and 84 miRNAs were differentially expressed compared with in control group. GO and KEGG analysis indicated that the miRNAs may play important roles in environment information processing. Specifically, we considered the VEGF signaling pathway, Phosphatidylinositol signaling system and MAPK signaling pathway, the results show that, the 13 miRNAs (miR-15b-5p, miR-30a-3p, miR-133a-3p, miR-19d-5p, miR-1288-3p, miR456, miR-96-5p, miR-23a-3p, miR-23b, miR-214, miR-24, miR-20a-3p and miR-2188-5p) involved in these three pathways are significantly down-regulated during hypoxia stress. And 12 target genes of these miRNAs were showed a higher degree of expression. We found the obvious negative correlation between miRNA and their target mRNAs, providing several miRNA-mRNA interaction networks in largemouth bass in response to hypoxia. Although relatively little information is currently available concerning the biological function of miRNAs identified to date, we strongly suggest that miRNAs play an important role in modulating gene expression involved in the physiological response to hypoxic stress in the fish liver.

overall_design: We used small RNA sequencing to detect miRNA transcriptomes of liver from common carp with low temperature group (LTG) and high temperature group (HTG) compared them with control libraries (CG) (3 vs. 3).

first: Junlong

first: Song

last: Yang


title: Genome-wide profiling of mutant p53 unveils a subset of lncRNAs correlated with colorectal cancer stemness maintenance [RNA-seq]

address: 北京市东城区东单三条五号


title: RNA-seq of HBBP1 suppression during HPCs erythroid differentiation

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

summary: As relics emerged in endless evolution, pseudogenes lost their coding potential compared to their protein homologs and are long believed to be functionless and thus evolve under neutrality. However, evidence supporting their functionality is quickly accumulating in recent two decades. Herein, we uncovered the evolution history and the essential role of hemoglobin subunit beta pseudogene 1 (HBBP1), which situates in the middle of fetal (γ) and adult globin (δ/β) genes, in human erythropoiesis. HBBP1 was born in the common ancestor of eutherian mammals and under functional constraint in human populations. Remove of HBBP1 in human embryonic stem cells completely blocked their differentiation to erythroid cells, while erythroid differentiation of hematopoietic stem/progenitor cells was also dramatically impaired after HBBP1 reduction, evidencing HBBP1 was required for human erythropoiesis. Mechanistically, HBBP1 RNA harbored a binding motif of heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1), competing for the binding of HNRNPA1 and thus stabilizing the key regulator of erythropoiesis, T-cell acute lymphocytic leukemia 1 (TAL1). Moreover, HBBP1 was remarkably increased in β-thalassemia patients and partially required for their fetal hemoglobin elevation.

overall_design: RNA-seq of day8 and day14 cells, respectively differentiated from cord blood derived CD34+ HPCs by EPO. There are three groups: ctrl, HBBP1 shRNA-1 and HBBP1 shRNA-2.

first: Yanni

last: Ma

first: Siqi

last: Liu

first: Jie

last: Gao

first: Jiayue

last: Xu

first: Chenguang

first: Lijun

last: Zhao

first: Lihong

last: Shi

first: Jia

last: Yu


title: Protein prenylation drives discrete signaling programs for the differentiation and maintenance of effector Treg cells

first: Hongbo

last: Chi

overall_design: Refer to individual Series


title: Aberrant RNA expression and splicing in childhood ETV6/RUNX1 acute lymphoblastic leukemia

first: Bao-Fa

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: ETV6/RUNX1 E/R -positive acute lymphoblastic leukemia (ALL), as one of the most common childhood malignancies, its pathogenesis and mechanism remain to be elucidated comprehensively. Global gene expression profiling can provide insight into the underlying pathophysiology of disease processes. In this study we sought to gain further insight into the molecular mechanisms underlying E/R-positive ALL by examining transcriptional profiles of E/R-positive ALL patients. We investigated the Bone marrow transcriptional profiles of E/R-positive ALL patients. Bioinformatic and statistical methods, including differential expression analysis, lncRNA analysis, alternative splicing analysis and metabolic network analysis, were used to characterize the underlying molecular mechanisms for E/R-positive ALL.

overall_design: Examination of gene expression levels, splicing levels in ALL patients.

first: Xiaofan

last: Zhu

first: Baofa

first: Congcong

first: Ting

last: Zhang

first: Lixian

last: Chang


title: Gene expression data from the heart during regeneration in a zebrafish model of heart failure

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary:
Heart Failure (HF) remains the leading cause of mortality and morbidity globally. Novel therapeutic targets to tackle this pandemic are in dire need. Zebrafish, a vertebrate whose heart shares many physiological similarities to the human heart, are able to naturally undergo cardiac regeneration following HF.
We used microarrays to analyse gene expression during cardiac regeneration following heart failure

overall_design: Heart failure was induced in adult zebrafish using phenylhydrazine (PHZ, anaemia inducer) treatment for 5 weeks followed by a regeneration period of 9 days without PHZ. Whole-genome microarray analysis was performed in heart samples at the end of the PHZ treatment and at different time-points thereafter (2, 5 and 9 days after PHZ treatment discontinuation). Gene regulation patterns were characterized using bioinformatics.

first: Andrew

last: Lumley

first: Lu

first: Isabelle

last: Ernens


title: Gene expression in murine Regulatory T cells [PGWAT]

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

institute: King's College London

summary: Ex vivo cells sorted direcly into Trizol

overall_design: Comparison of Tregs isolated from spleen and adipose tissue from FoxP3-YFP-Cre versus Tbx21-flox X Foxp3-YFP-Cre C57BL/6 mice on high fat diet

first: Emilie

last: Stolarczyk


title: Gene expression in murine Regulatory T cells [PGF]

overall_design: Comparison of Tregs isolated from spleen and adipose tissue from FoxP3-YFP-Cre versus Tbx21-flox X Foxp3-YFP-Cre C57BL/6 mice on chow diet


title: Gene expression in murine Regulatory T cells

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


title: VENTX gene expression marks a subset of human primordial germ cells

city: Melbourne

first: Ana Rita

last: Leitoguinho

state: VIC

address: 50 Flemington road

department: Cell Biology

institute: Murdoch Children's Research Institute

summary:
The Ventx genes are a family of non-clustered homeobox transcription factors that confer a ventral phenotype on mesodermal cells in the Xenopus laevis embryo. Ventx genes are conserved in vertebrates, although they have been lost in rodents. We evaluated the expression of VENTX during differentiation of a human pluripotent stem cell (hPSC) line in which a GFP reporter marked the expression of VENTX (VENTXGFP/w), discovering that VENTX was expressed in a subset of early primordial germ cell-like cells (PGCLCs). We generated a dual reporter hPSC line in which mCHERRY marked the pluripotency gene OCT4 (VENTXGFP/wOCT42AmCHERRY/w), and further modified this to also create a VENTX knock out line by deleting the VENTX homeodomain (VENTXGFP/-OCT42AmCHERRY/w).
Transcriptional profiling experiments revealed two populations of PGCLCs, those that co expressed VENTX and OCT4 (GFP+mCHERRY+) and those that were VENTX-OCT4+ (GFP-mCHERRY+). Our analyses showed that VENTX+ and VENTX- PGCLCs clustered together, and also failed to reveal transcriptional consequences of VENTX deletion on commitment to PGCLCs. Evaluation of public databases confirmed expression of VENTX in populations of PGCLCs derived by others and in primary human embryonic germ cell samples. These results identify VENTX as a new PGC-associated gene in humans, however it does not seem to be required for initial human PGC commitment.

overall_design: Undiferentiated hESCs and PGC-like cells derived from hESC. Biological replicates vary from 3 to 5 (refer to number at the end of sample title). Study performed in VENTX^GFP/w OCT4^mCHERRY/w (abreviated to VO) and VENTX^GFP/- OCT4^mCHERRY/w (abreviated to KO) cell lines.

first: Ana

last: Elefanty


title: Effect of intrauterine MGO administration on bovine endometrium

status: Public on Jan 19 2021

city: Aichi-gun

first: Shuichi

last: Matsuyama

address: 94 Hatajiri, Morowa

institute: Nagoya University

summary: To clarify the effect of intrauterine methylglyoxal (MGO) administration on the endometrium, mRNA expression profiles of bovine endometrium were investigated. Hierarchical cluster analysis with the expression levels of all genes was divided these cows into two clusters. First cluster was composed of control cows, second cluster contained MGO (5 mM) treated cows.

overall_design: The day of standing estrous was defined as day 0. In cows, each uterine horn was injected with 25 mL of methylglyoxal (MGO; 0 and 5 mM) on day 1. Then, endometrial tissue from the uterine horn, ipsilateral to the CL, was biopsied on day 7. Using biopsy samples, the mRNA expression profiles of bovine endometrium were investigated to clarify the effect of intrauterine MGO administration on the endometrium.

first: Shiori

last: Minabe

first: Ryoya

last: Abe

first: Yasuhiro

last: Morita

first: Satoshi

last: Ohkura

first: Koji

last: Kimura


title: Single Cell Analysis of Chromatin Accessibility Reveals Genetic and Regulatory Heterogeneity in Glioblastomas

first: Ramya

last: Raviram

state: CA

address: 9500 Gilman Drive

institute: University of California San Diego

summary: Intra-tumoral heterogeneity is a key contributor to therapeutic failure in glioblastomas, the most common form of primary adult brain cancer.  To better define this heterogeneity, genome-wide chromatin accessibility and transcription profiles of clinical glioblastoma specimens were analyzed at single cell resolution. These profiles afforded resolution of intra-tumoral genetic heterogeneity and delineation of sub-populations characterized by focal DNA amplifications including extrachromosomal circular DNA (ecDNA) that harbor highly transcribed oncogenes. The maps of open chromatin helped define cellular states of distinct tumor cell populations characterized by unique regulatory landscapes. Unexpectedly, the diverse tumor cellular states share a common regulatory program involving the Nuclear Factor 1 transcription factors (NFIA and NFIB). Silencing of these genes suppressed glioblastoma growth in vitro and in vivo. These results demonstrate opportunities for glioblastoma therapeutic discovery through integration of single nuclear profiling platforms.

overall_design:
Characterizing tumor heterogeneity in glioblastoma tumors using single nuclei ATAC-seq and RNA-seq

>>>Submitter states that raw data will be submitted to dbGaP due to patient privacy concerns.<<<

first: Clark

last: Chen

first: Bing

last: Ren


title: MDM2 induces EMT via the B-Raf pathway through 14-3-3

city: Chongqing

first: Liling

last: Tang

address: No 174 Shapinba St

institute: Chongqing University

summary: To Study the role of MDM2 in EMT biogenesis and explore the mechanism by which MDM2 promoted EMT in glioma cells, we used whole geneome RNA-seq of U251 cells and stable U251 cells overexpressing MDM2-GFP to study role MDM2 mediated EMT regulation.

overall_design: U251 cells and U251 cells which overexpressing MDM2-GFP were harvested, and then RNA was prepared using the Qiagen RNeasy Kit according to the manufacturer’s instructions. Strand-specific libraries were generated by using the KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KAPA Biosystem Wilmington, MA). After clustering, the Flow Cell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions.

first: Mengting

last: Ou

first: Xichao

last: Xu

first: Ying

first: Li

last: Li

last: Zhang

first: Yi

last: Liao

first: Weichao

last: Sun

first: Christine

last: Quach

first: Jianguo

last: Feng


title: Inhibition of microbiota-dependent TMAO production attenuates chronic kidney disease in mice

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

address: 10833 Le Conte Avenue

institute: UCLA

summary: Methods: RNA-seq analysis was performed on mouse kidney samples isolated from female apoEKO mice on 4 diets for 14 weeks: (1) Control diet, (2) control + iodomethylcholine (IMC), Control + IMC. IMC is a TMA-lyase inhibitor to prevent TMA production by gut

overall_design: mRNA profiles of apoEKO mouse kidneys fed various diets to determine whether a bacterial TMA lyase inhibitor, iodomethylcholine (IMC), can prevent chronic kidney disease induced by adenine feeding.

first: Diana

last: Shih

first: Karolina

last: Kaczor-Urbanowicz


title: RNA-seq of human endometrial stromal cell lines followng LINC00339 overexpression

city: Parkville

first: Sarah

last: Holdsworth-Carson

address: Level 7, University Department, Royal Women's Hospital, Crn Grattan Street and Flemington Rd

institute: University of Melbourne

summary: We report RNA-seq data from 3 hTERT immortalised human endometrial stromal cell (HESC) lines following induced overexpression of LINC00339 realtive to blank vector controls.  RNA-Seq was employed to identify those genes differentially expressed between controls and cells overexpressing LINC00339.  L-HESC cells demonstrated the largest number of significantly differentially expressed genes; 924 genes (FDR threshold <0.05).  T-HESCs demonstrated 280 significantly differentially expressed genes (FDR <0.05) in response to LINC00339 overexpression.  M-HESC cells had 17 differentially expressed genes at an FDR <0.05 (this number increased to 68 significantly differentially expressed genes when the FDR was increased to a cut-off of <0.075).

overall_design: A human expression vector (pPM-N-D-C-HA) containing LINC00339 (RefSeq NR_109759) and a blank control vector were transfected into 3 HESC cell lines for 48 hours.

first: S

first: P

middle: A

last: Rogers


title: Impaired cell-cell communication in multicellular cyanobacteria affects carbon uptake, photosynthesis and the cell wall

city: Rehovot

first: Bareket

last: Dassa

address: 234 Herzl st.

department: Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

summary: Cell-cell communication is an essential attribute of multicellular organisms. We studied the effects of perturbed communication in multicellular filaments of mutant derivatives of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120, in which septal proteins were deleted. Filaments of sepJ and sepJ/fraC/fraD deleted strains showed marked differences in growth, pigment absorption spectra and spatial patterns of expression of the hetR gene encoding a master regulator of heterocyst differentiation. To understand the global changes in gene expression that take place as a result of impaired cell-cell molecular transfer, we mapped the transcriptional landscape of wild-type and mutant filaments using RNA-seq, both under nitrogen-replete and nitrogen-poor conditions. Our results show that the effects of sepJ and fraC/fraD deletions are not additive, and that far from affecting only passive transport between cells, perturbations to cell-cell communication in this model organism lead to significant changes in gene expression. Most significant effects include increased expression of genes encoding carbon uptake systems and some components of the photosynthetic apparatus, and decreased expression of genes encoding cell wall components related to heterocyst differentiation and to polysaccharide export. Thus, impairment of intercellular communication strongly affects specific aspects, notably related to carbon metabolism, of the biology of Anabaena.

overall_design: Anabaena PCC 7120 mRNA profiles of 18 hrs. nitrogen-replete and nitrogen-poor conditions, of Wild type (WT), sepJ deleted strain (CSVM34) and sepJ/fraC/fraD deleted strain(TM, CSVM141)

first: Sergio

last: Camargo

first: Dena

last: Leshkowitz

first: Vicente

last: Mariscal

first: Enrique

last: Flores

first: Joel

last: Stavans

first: Rinat

last: Arbel-Goren


title: SNP array of 121 AML patients at diagnosis

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

summary: Acute myeloid leukemia (AML) patients carrying complex karyotype or aneuploidies have a very poor prognosis, with a 5-year overall survival lower than 20%. We and others have shown that complex karyotype and aneuploid patients are characterized by high genomic instability, along with defects of DNA damage response genes and, occasionally, by chromothripsis. Chromothripsis frequently occurs in AML (6.6%) and influences patient prognosis and disease biology. Moreover, the homology recombination pathway is frequently deregulated at expression level in AML. We showed that PALB2 is affect by copy-number deletions in AML (5.2%) and it may be a potential biomarker for very-poor prognosis AML.

overall_design: DNA obtained from bone marrow mononuclear cells of 121 AML patients was used for Affymetrix genome-wide SNP 6.0 or CytoScan HD array-based genomic profiling.

first: Maria

last: Fontana

first: Antonella

last: Padella

first: Eugenio

last: Fonzi

first: Giovanni

last: Marconi

first: Cristina

last: Papayannidis

last: Martinelli


title: Roles of PKLR in NAFLD

first: Calvin

last: Pan

address: 675 Charles Young Dr South


title: Sex-specific roles of PKLR in NAFLD using gain-of-function mouse models

summary: The etiology of non-alcoholic fatty liver disease (NAFLD) is poorly understood, with males and Mexican population exhibiting markedly increased susceptibility. Using a systems genetics approach, involving multi-omic analysis of ~100 inbred strains, we recently identified several candidate genes driving NAFLD. We investigated the role of one of these candidates, liver pyruvate kinase (L-PK or Pklr) in NAFLD using patient samples and mouse models. We examined L-PK expression in mice of both sexes and in a cohort of bariatric surgery patients. We used liver-specific loss- and gain-of-function strategies in independent animal models of diet-induced steatosis and fibrosis, involving both sexes. Following treatment, we measured several metabolic phenotypes associated with obesity, insulin resistance, dyslipidemia, liver steatosis and fibrosis. Furthermore, liver tissues were used for gene expression and Western blots, and liver mitochondria for bioenergetics. Our results demonstrate that L-PK acts in a male-specific manner in the development of liver steatosis and fibrosis. Given that NAFLD/NASH exhibit sexual dimorphism, our results have important implications for the development of personalized therapeutics.

overall_design: Eight-week-old male and female C57BL/6J mice were randomly injected intravenously with adeno-associated viral 8 (AAV8) vectors containing the cDNA sequences of Pyruvate kinase, liver isoform (PKLR) under a thyroxine binding globulin promoter (10^12 titer). Control mice were injected with AAV8 expressing GFP gene. The animals were then maintained on a HF/HS diet (Research Diets D12266B) until 16 weeks of age. Liver samples (n = 4 per group) were taken for RNASeq expression profiling.

first: A

last: Lusis

first: K

last: Chella Krishnan


title: RNA-seq of a Princess Margaret Cancer Centre human acute myeloid leukemia patient cohort

city: Toronto

first: Stephanie

middle: Zhi-Juan

last: Xie

state: ON

address: 101 College St. TMDT 8-401

institute: University Health Network

summary: The PMCC AML RNAseq dataset consists of 81 AML patient samples (clinical data in Supplemental Table 11),  processed in two batches. These patient samples are able to engraft in the NSG (NOD.Cg PrkdcscidIl2rgtm1Wjl /SzJ) mouse model. Five patients (90543, 598, 90240, 110484, 100500) were included in both batches.

overall_design: 86 Samples total

middle: Z


title: Alarmin S100A8/A9 mediates activation of aberrant neutrophils in the pathogenesis of COVID-19

city: Beijing

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

summary: To characterize the early immune responses against coronavirus infection, we infected rhesus macaques and hACE2 transgenic mice with SARS-CoV-2 and analyzed the transcriptome of infected and non-infected animals. We infected WT mice with IAV as a normal respiratory virus group. During analysis, we found that S100A8 was dramatically upregulated by SARS-CoV-2 and a mouse coronavirus (mouse hepatitis virus, MHV), but not by other tested viruses. A group of non-canonical neutrophils were also activated during SARS-CoV-2 infection.

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design:
WT Rhesus macaques were infected with SARS-CoV-2 intranasally. Lungs were harvested at 0 dpi, 3 dpi, and 5 dpi. RNA extracted from lungs and RNASeq was performed to identify differentially expressed genes.
WT C57BL/6J mice and hACE2 transgenic mice were infected with  IAV and MHV intranasally. Lungs were harvested at 0 hour, 6 hour,  24 hour, 48hour, 3day, 5day, 7 day post-infection. RNA extracted from lungs and RNASeq was performed to identify differentially expressed genes.
Differentially expressed genes in Lungs of WT Rhesus macaques infected with SARS-CoV-2 and WT mice infected with IAV.

first: Linlin

last: Bao

first: Qirui


title: Omics Analysis of Pancreatic Cancer Platelets Reveals Active “Education”, including Dysregulation of Splicing Signature and Inhibition of SPARC by Modified Forms of miRNAs

city: Amsterdam

first: Giulia

last: Mantini

address: De Boelelaan

country: Netherlands

institute: Amsterdam UMC

summary: PDAC cells can activate platelets and change their RNA and protein content, thus, we performed an integrative study investigating the biological processes of differentially spliced mRNAs and expressed miRNAs, as well as proteins. To focus on these “dangerous liaisons”, we used benign disease as a background noise correction for putative inflammatory signals. Gene set enrichment analysis on differential miRNAs, RNA transcripts and proteins revealed an enrichment of RNA splicing, mRNA processing and translation initiation on miRNAs and proteins and depletion on RNA transcripts, as previously described. Furthermore, we provide a new repertoire of PDAC and benign platelet-ome, visualized by the R shiny application, to be exploited for future studies. In conclusion, our data show that platelets change their biological repertoire in the presence of PDAC, through dysregulation of miRNAs and splicing factors, supporting the presence of de novo protein machinery that can “educate” the platelet. This has major clinical implications since the emerging molecules could provide important innovative PDAC biomarkers in the context of liquid biopsies.

overall_design: examination of molecular mechanisms in PDAC and Benign blood platelets

first: Mantini

last: Giulia

first: Connie

last: Jimenez

first: Tom

last: Wurdinger

first: Elisa

last: Giovannetti


title: Emx2 defines bidirectional polarity of neuromasts by changing hair-bundle orientation and not hair-cell positions

city: Bethesda

first: Doris

last: Wu

state: MD

address: 35A Convent Dr., Rm 1D-824

institute: NIDCD

summary: The bidirectional sensitivity of neuromasts to water flow in the zebrafish lateral line system is attributed to the opposite orientation of the hair bundles on top of sensory hair cells (HC) within a neuromast. After each HC precursor divides to form two nascent HCs, HCs of the same bundle orientation are positioned on one side of the neuromast, across from HCs with opposite bundle orientation. The transcription factor emx2 is expressed in only one of the sibling HCs. Loss or gain of function of emx2 in HCs causes unidirectional hair bundle orientation in neuromasts. It is not clear whether Emx2 is required specifically in establishing hair bundle orientation after HC formation or Emx2 has an earlier role in HC fate and/or positioning, which indirectly changes hair bundle orientation. A phenomenon, in which nascent sibling HCs exchange positions with each other, has been postulated to be the mechanism for HCs to acquire their designated positions within the neuromast. We asked whether Emx2 is involved in positional acquisition of HCs within the neuromast. Using live-imaging and our emx2 reporter we find that the HC rearrangement, redefined as two processes named Rock & Roll are required for HCs to acquire their positions. Although Emx2 regulates the duration of the Rock and the frequency of Roll of nascent HCs, it is not required for their positional acquisition. Instead, Emx2 regulates the morphology of nascent HCs, which facilitates the rearrangement process.

overall_design: Single-cell RNA sequencing on FACS sorted Hair-Cells from zebrafish neuromast in 4dpf wild type larvae.

first: Sho

last: Ohta

first: Young

middle: R

last: Ji

first: Daniel

last: Martin


title: Host transcriptional response to TB preventive therapy differentiates two sub-groups of IGRA-positive individuals

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

institute: London School of Hygiene & Tropical Medicine

overall_design: Refer to individual Series


title: Spatially resolved gene expression of human protate tissue slices treated with steroid hormones for 8 hours

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

summary: Spatially resolved gene expression was prepard by dissociated hman prostate tissue to single cells, and collected & prepped for RNA-seq using the Visium Spatial Gene Expression kit. 5000 cells were collected and sequenced at a depth of  50k cells/gene on a 2X150nt lane in a NovaSeq 6000. SpaceRanger alignment was performed to produce the RAW files

overall_design: Two samples:ETOH, 25D

first: Jason

last: Garcia

first: Candice

last: Loitz


title: Uncovering the Gene Regulatory Networks Underlying Macrophage Polarization Through Comparative Analysis of Bulk and Single-Cell Data

city: Irvine

first: Ali

last: Mortazavi

address: 2300E Biological Sciences III

institute: UC Irvine

summary: Gene regulatory networks (GRNs) provide a powerful framework for studying cellular differentiation. However, it is less clear how GRNs encode cellular responses to everyday microenvironmental cues. Macrophages can be polarized and potentially repolarized based on environmental signaling. In order to identify the GRNs that drive macrophage polarization and the heterogeneous single-cell subpopulations that are present in the process, we used a high-resolution time course of bulk and single-cell RNA-seq and ATAC-seq assays of HL-60-derived macrophages polarized towards M1 or M2 over 24 hours. We identified transient M1 and M2 markers, including the main transcription factors that underlie polarization, and subpopulations of naive, transitional, and terminally polarized macrophages. We built bulk and single-cell polarization GRNs to compare the recovered interactions and found that each technology recovered only a subset of known interactions. Our data provide a resource to study the GRN of cellular maturation in response to microenvironmental stimuli in a variety of contexts in homeostasis and disease.

overall_design: We used a high-resolution time course of bulk and single-cell RNA-seq and ATAC-seq assays of HL-60-derived macrophages polarized towards M1 or M2 over 24 hours.

first: Klebea

last: Carvalho

first: S


title: Roles of PKLR in NAFLD using loss- and gain-of-function mouse models

first: Calvin

last: Pan

summary: The etiology of non-alcoholic fatty liver disease (NAFLD) is poorly understood, with males and Mexican population exhibiting markedly increased susceptibility. Using a systems genetics approach, involving multi-omic analysis of ~100 inbred strains, we recently identified several candidate genes driving NAFLD. We investigated the role of one of these candidates, liver pyruvate kinase (L-PK or Pklr) in NAFLD using patient samples and mouse models. We examined L-PK expression in mice of both sexes and in a cohort of bariatric surgery patients. We used liver-specific loss- and gain-of-function strategies in independent animal models of diet-induced steatosis and fibrosis, involving both sexes. Following treatment, we measured several metabolic phenotypes associated with obesity, insulin resistance, dyslipidemia, liver steatosis and fibrosis. Furthermore, liver tissues were used for gene expression and western blots, and liver mitochondria for bioenergetics. Our results demonstrate that L-PK acts in a male-specific manner in the development of liver steatosis and fibrosis. Given that NAFLD/NASH exhibit sexual dimorphism, our results have important implications for the development of personalized therapeutics.

overall_design: Eight-weeks old male C57BL/6J mice were randomly injected intravenously with adeno-associated viral 8 (AAV8) vectors containing either the cDNA or the shRNA sequences against Pyruvate kinase, liver isoform (PKLR) under a thyroxine binding globulin promoter (1012 titer). Control mice were injected with either AAV8 expressing GFP gene (for overexpression models) or AAV8 expressing shRNA against firefly luciferase gene (for knockdown models). The animals were then maintained on a HF/HS diet (Research Diets D12266B) until 25 weeks of age. Liver samples (n = 5 per group) were taken for RNASeq expression profiling.

first: A

last: Lusis

first: K

last: Chella Krishnan


title: circRNA expression pattern in the pathogenesis of aseptic lossening

city: Shenyang

first: Lei

last: Guo

state: Liaoning

address: Nanjing North Street

institute: First Affiliated Hospital, China Medical University

summary: Increasing evidence has demonstrated that circular RNA exerts important function in the pathogenesis of some diseases. While, the contributions of circRNAs to aseptic lossening after total hip arthroplasty remain largely unknown. Our research is to explore the differently expressed circRNAs and elucidate complex regulated mechanism of circRNAs in aseptic lossening. The differently expressed circRNAs were identified by RNA sequencing analysis. Reverse transcription-quantitative polymerase chain reaction was adopted to corroborate these differently expressed circRNAs. The potential function of circRNAs in aseptic lossening tissue was identified by competing endogenous RNA analysis. Enrichment analysis were performed for target mRNAs and host genes of the differently expressed circRNAs by Gene Oncology and Kyoto Encyclopedia of Genes and Genomes. 257 differently expressed circRNAs were obtained from RNA-seq results. Then, circRNA–miRNA–mRNA network was established based on the validated circRNAs. The result of Gene Oncology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis suggested that the circRNAs were related with some biological functions and pathways of aseptic lossening. A novel pathogenesis and treatment strategy about aseptic lossening after total hip arthroplasty was revealed from our study of circRNA–miRNA–mRNA network.

overall_design: RNA profiles of three test and three control samples were generated by deep sequencing, using Illumina HiSeq 4000.

first: Shenghui

last: Ni


title: Xylella fastidiosa causes transcriptional shifts that precede tylose formation and starch depletion in xylem

city: Davis

first: Mélanie

last: Massonnet

state: California

address: 2105 Robert Mondavi Institute-North Building

department: Viticulture and Enology

institute: University of California, Davis

summary: Pierce's disease (PD) in grapevine (Vitis vinifera) is caused by the bacterial pathogen Xylella fastidiosa. X. fastidiosa is limited to the xylem tissue and following infection induces extensive plant‐derived xylem blockages, primarily in the form of tyloses. Tylose‐mediated vessel occlusions are a hallmark of PD, particularly in susceptible V. vinifera. We temporally monitored tylose development over the course of the disease to link symptom severity to the level of tylose occlusion and the presence/absence of the bacterial pathogen at fine‐scale resolution. The majority of vessels containing tyloses were devoid of bacterial cells, indicating that direct, localized perception of X. fastidiosa was not a primary cause of tylose formation. In addition, we used X‐ray computed microtomography and machine‐learning to determine that X. fastidiosa induces significant starch depletion in xylem ray parenchyma cells. This suggests that a signalling mechanism emanating from the vessels colonized by bacteria enables a systemic response to X. fastidiosa infection. To understand the transcriptional changes underlying these phenotypes, we integrated global transcriptomics into the phenotypes we tracked over the disease spectrum. Differential gene expression analysis revealed that considerable transcriptomic reprogramming occurred during early PD before symptom appearance. Specifically, we determined that many genes associated with tylose formation (ethylene signalling and cell wall biogenesis) and drought stress were up‐regulated during both Phase I and Phase II of PD. On the contrary, several genes related to photosynthesis and carbon fixation were down‐regulated during both phases. These responses correlate with significant starch depletion observed in ray cells and tylose synthesis in vessels.

overall_design: Potted V. vinifera cv. Cabernet Sauvignon were mechanically inoculated with Xylella fastidiosa subsp. fastidiosa or 1X PBS (negative controls) on the sixth internode of the stem. Stems were collected at two time points: Phase I (symptom score = 1-2) and Phase II (symptom score = 2-3) of Pierce’s Disease symptom development. Symptom scores were based on the published Pierce's Disease Rating Index (Guilhabert and Kirkpatrick, MPMI, 2005). Three biological replicates, corresponding to individual stems (internode directly above the point of inoculation) were used for RNA extraction.

first: Brian

last: Ingel

first: Clarissa

last: Reyes

first: Bailey

last: Boudreau

first: Yuling

last: Sun

first: Qiang

first: Andrew

last: McElrone

first: Dario

last: Cantu

first: M

last: Roper


title: Deferoxamine mesylate improves splicing and GAA activity of the common c.-32-13T>G allele in late-onset Pompe disease patient fibroblasts

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

institute: University of Trieste

summary: human Pompe Disease (c.-32-13T>G) fibroblasts were exposed to 10 µM Deferoxamine (DFX) or 0.1% DMSO (control condition), for three days.

overall_design: Three DMSO (CTR01Fib, CTR02Fib, CTR03Fib) and Deferoxamine (DFX04, DFX05, DFX06) independent treatments.

first: Emanuele

last: Buratti


title: Host transcriptional response to TB preventive therapy differentiates two sub-groups of IGRA-positive individuals: PAXgene ex vivo samples

city: London

first: Jackie

last: Cliff

summary:
We hypothesized that individuals with immunological sensitization to Mycobacterium tuberculosis (Mtb), conventionally regarded as evidence of latent tuberculosis infection (LTBI), would demonstrate binary responses to preventive therapy. This would reflect the differential immunological consequences of the sterilization of viable infection in those with an active Mtb infection versus no Mtb killing in those who, despite T cell recognition of Mtb antigens, did not harbor viable Mtb bacilli.
We investigated the  blood transcriptional profiles of 18 individuals with a positive IGRA result and known recent exposure to an index person with isoniazid and rifampicin susceptible pulmonary tuberculosis, at baseline, 2  weeks after initiating combined rifampicin/isoniazid (RH) preventive therapy and at treatment completion. Healthy control volunteers with no history of TB exposure and negative IGRA results were also included. RNA from unstimulated and M. tuberculosis peptide stimulated whole blood (from QuantiFERON TB1 and TB2 tubes) was measured using Agilent microarrays.
A set of 474 genes showed the greatest interpersonal and temporal expression variability in antigen-stimulated blood. By performing longitudinal unsupervised clustering analysis with the subset of most variable genes, the IGRA+ participants were separated into two distinct groups. The IGRA-negative controls clustered within one of these groups suggesting that, in contrast to the other subgroup of IGRA+ individuals, RH had no discernible effect in this subgroup. 117 genes were significantly differentially expressed over time between these two groups, with the majority of them associated with immunological pathways known to be important in mycobacterial control. We contend that the different host RNA response reflects lack of Mtb viability in the group that clustered with the IGRA- unexposed healthy controls, and Mtb viability in the one that clustered away.
Gene expression patterns in the blood of IGRA+ individuals emerging during the course of RH treatment which reflect Mtb viability could have major implications in the identification of risk of progression/reactivation, treatment stratification and clinical trials for LTBI therapy.

overall_design: Ex vivo blood. 22 donors (18 IGRA+; 4 IGRA- (healthy controls). All received LTBI preventive treatment. Blood collected at baseline and two weeks for all donors, and after 12-18 weeks for IGRA+ donors.

first: Claire

last: Broderick

first: Jacqueline

first: Ji-Sook

last: Lee

first: Myrsini

last: Kaforou

first: David

last: Moore


title: RNA-seq of  human long-term and short-term hematopoietic stem cells from umblical cord blood with lentiviral overexpression of S1PR3

first: Stephanie

last: Xie

summary: To investigate the molecular and biological pathways altered by S1PR3OE in human hematopoietic stem cells (HSC), we performed RNA-sequencing (RNA-seq) of LT- and ST-HSC 3 days after transduction with control or S1PR3 overexpression (OE) lentiviral vectors

overall_design:
LT-HSC and ST-HSC from 3 pool of CB lin- were FACS-purified, cells were prestimulated for 4 hours and transduced with lentiviral vectors. At day 3, 2000-5300 BFP+ cells were FACS-purified for RNA isolation.  we We were able to isolate only 1600-1800 BFP+ cells from LT-HSC control samples as opposed to 4000-5400 BFP+ cells from S1PR3OE samples. Thus, we pooled all control BFP+ LT-HSC cells into one sample for RNA-seq analysis. BFP- LT-HSC from control vector transduction were purified from CB1 as an additional LT-HSC control.
Submitter states that raw data will be submitted separately to the EGA for controlled access


title: ZFP36L2 post-transcriptionally controls acute myeloid leukemia differentiation (ZFP36L2 eCLIP)

city: New York

first: Hua

last: Zhou

state: NY

address: 550 First Avenue, Smilow 1307

department: PATHOLOGY

institute: NYU SCHOOL OF MEDICINE

summary: Genome-wide ZFP36L2 binding on RNA in AML cells

overall_design: eCLIP analysis of ZFP36L2 in 2 AML cell lines.

first: Eric

last: Wang

first: Iannis

last: Aifantis


title: Fragmentation of Small-cell Lung Cancer Regulatory States in Heterotypic Microenvironments

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

summary: Small-cell lung cancers derive from pulmonary neuroendocrine cells, which have stem-like properties to reprogram into other cell types upon lung injury.  It is difficult to uncouple the plasticity of these transformed cells from heritable changes that evolve in primary tumors or select in metastases to distant organs.  Approaches to single-cell profiling are also problematic if the required sample dissociation activates injury-like signaling and reprogramming.   Here, we defined cell-state heterogeneities in situ through laser capture microdissection-based 10-cell transcriptomics coupled with stochastic-profiling fluctuation analysis.  Using a labeled murine isolate from small-cell lung cancer initiated by neuroendocrine deletion of p53 and Rb, we profiled cell-to-cell transcriptional-regulatory heterogeneity in spheroid cultures and liver colonies seeded intravenously.  Fluctuating transcripts in vitro were partly shared with other epithelial-spheroid models, and candidate heterogeneities increased considerably when cells were delivered to the liver.  Colonization of immunocompromised animals drove the fractional appearance of alveolar type II-like markers and poised cells for paracrine stimulation from immune cells and hepatocytes.  Immunocompetency further exaggerated the fragmentation of tumor states in the liver, yielding mixed stromal signatures evident in bulk sequencing from autochthonous tumors and metastases.  We identified dozens of transcript heterogeneities that recur irrespective of biological context; their orthologs merged observations of murine and human small-cell lung cancer.  Candidate heterogeneities recurrent in the liver also stratified primary human tumors into discrete groups not readily explained by molecular subtype.  We conclude that heterotypic interactions in the liver and lung are an accelerant for intratumor heterogeneity in small-cell lung cancer.

overall_design: 10-cell samples from murine small-cell lung cancer spheroids and liver colonies from both immunocompromised and immuncompetent mice were captured by laser. mRNA was extracted and PCR amplified for RNA-sequencing. capture microdissection

first: Dylan

last: Schaff

first: Shambhavi

last: Singh


title: ZFP36L2 post-transcriptionally controls acute myeloid leukemia differentiation (MOLM13 ATAC)

summary: Genome-wide chromatin accessibility in AML cells

overall_design: Chromatin accessibility in AML cells.


title: ZFP36L2 post-transcriptionally controls acute myeloid leukemia differentiation (ZFP36L2 KO RNA-seq)

summary: Differential gene expression upon ZFP36L2 loss in AML

overall_design: Differential gene expression upon ZFP36L2 knockout in AML


title: Pan-cancer drivers are recurrent transcriptional regulatory heterogeneities in early-stage luminal breast cancer

summary: The heterogeneous composition of solid tumors is known to impact disease progression and response to therapy.  Malignant cells coexist in different regulatory states that can be accessed transcriptomically by RNA sequencing, but single-cell methods have many caveats related to sensitivity, noise, and sample handling.  We revised a statistical fluctuation analysis called stochastic profiling to combine with 10-cell RNA sequencing, which was designed for laser-capture microdissection (LCM) and extended here for immuno-LCM.  When applied to a cohort of late-onset, early-stage luminal breast cancers, the integrated approach identified thousands of candidate regulatory heterogeneities.  Intersecting the candidates from different tumors yielded a relatively stable set of 710 recurrent heterogeneously expressed genes (RHEGs) that were significantly variable in >50% of patients.  RHEGs were not confounded by dissociation artifacts, cell cycle oscillations, or driving mutations for breast cancer.  Rather, we detected RHEG enrichments for epithelial-to-mesenchymal transition genes and, unexpectedly, the latest pan-cancer assembly of driver genes across all cancer types.  Heterogeneous transcriptional regulation conceivably provides a faster, reversible mechanism for malignant cells to sample the effects of potential oncogenes or tumor suppressors on cancer hallmarks.

overall_design: 10-cell samples from human breast cancer biopsies were captured by laser capture microdissection. mRNA was extracted and PCR amplified for RNA-sequencing


title: Ascending dorsal column sensory neurons respond to spinal cord injury and downregulate genes related to lipid metabolism

city: St Louis

last: Ewan

state: MO

address: 660 S Euclid Ave

department: Neuroscience

institute: Washington University in St Louis

summary: The goal of this study was to compare the transcriptional effects of sciatic nerve injury and spinal cord injury on lumbar dorsal root ganglion (DRG) and FACS-sorted dorsal column (DC) sensory neurons. We performed RNA-seq of whole DRG from naïve and spinal cord-injured (SCI) mice (1dpi) and compared this with previously published data for sciatic nerve transection. In order to assess changes specifically in DC neurons, we performed RNA-seq from FACS-sorted DC neurons from Thy1-YFP16 transgenic mice in naïve, sciatic nerve injured (SNI), and SCI (1 and 3dpi). We found that DC neurons alter their transcriptome after SCI, but that gene changes after SCI mostly differ from SNI. These transcriptional differences may reflect both growth promoting and growth inhibitory effects on axon regeneration after SCI.

overall_design:
Examination of 2 injury models (SNI and SCI) versus uninjured in two different samples (whole DRG, FACS-sorted DC sensory neurons).

This study includes the re-analysis of the following SRR:
SRR7691131
SRR7691133
SRR7691134
SRR7691121
SRR7691123
SRR7691124
SRR7691132
SRR7691137
SRR7691138
SRR7691122
SRR7691127
SRR7691128

middle: E

first: Dan

last: Carlin

first: Tassia

last: Mangetti Goncalves

first: Guoyan

last: Zhao

first: Valeria

last: Cavalli


title: miRNA expression profiling in a murine model of KrasG12D induced CMML-like MPD

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary: Mx1-Cre/KrasG12D mice were injected with pIpC to induce a myeloproliferative disease resembling human chronic myelomonocytic leukemia (CMML-like MPD). When the disease was fully developed, CD11b-/Ly6G-/c-Kit+ hematopoietic stem and progenitor cells (HSPCs) were isolated and subjected to miR-microarray expression profiling. pIpC-injected CD11b-/Ly6G-/c-Kit+ HSPCs of age matched wildytpe control mice were used as controls.

overall_design: n=4 (KrasG12D vs. Wt)

first: J

last: Berg

first: Armin

last: Zebisch


title: Genome wide expression change by RNF181 knockdown in MCF-7 cells

city: Shenzhen

first: Juntao

last: Xu

state: Guangdong

address: Yuehai Subdistrict, Nanshan District

country: China

institute: Philrivers

summary: We aim to the investigate the role of RNF181 in breast cancer progression. MCF-7 cells were used as the model , RNF181 was silenced by siRNA.

overall_design: The MCF-7 cells were treated with 50nM stramble siRNA and siRNF181. After 48 hours, cells were harvested and the total RNA was extacted by Qiagen kit. The RNA sample was sent to BGI for RNA expression anaylsis.

first: Jian

last: Zhu

first: Hui


title: ZFP36L2 post-transcriptionally controls acute myeloid leukemia differentiation

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

overall_design: Refer to individual Series


title: Transcription factor Zfp281 sustains CD4+ T lymphocyte activation by directly repressing Ctla-4 transcription

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

institute: zhejiang universiry

summary: Expression of co-inhibitory receptors, such as CTLA-4, on effector T cells is a key mechanism for the negative regulation of T cell activation. However, how CTLA-4 is transcriptionally regulated is not well understood. Zfp281, a C2H2 zinc finger protein, is a negative regulator of maintaining pluripotency for embryonic stem cells. Nevertheless, its function in differentiated cells has not been studied. We generated Zfp281 conditional knockout mice in which the function of Zfp281 gene was conditionally disrupted by Cd4Cre transgene to study its impact on T cell function. Zfp281 was dispensable for T cell development, but CD4+ T cell activation and cytokine production were impaired due to diminished T cell receptor signaling. Furthermore, Zfp281 deficiency inhibited in vivo T cell responses to Listeria monocytogenes infection. Using genome-wide expression profiling assays, we determined that Zfp281 repressed Ctla-4 expression by directly binding GC-rich sites of its promoter, which inhibited the negative feedback of T cell activation. In line with this, CTLA-4 blockade and shRNA knock down can partly rescue the reduced cytokine production caused by Zfp281 deficiency. These findings identify that Zfp281 sustains CD4+ T lymphocyte activation by directly repressing Ctla-4 transcription.

overall_design: CD4+ T cell RNA-SEQ

first: Wang

last: Lie

first: Guo

last: Jing