title: Real-time quantitative PCR analysis of inflammation-related genes of organs and tissues from mice in response to Coxsackievirus A2 (CVA2) infection

status: Public on Nov 26 2021

city: Henan

first: Ruonan

last: Liang

address: No.100 Kexue Avenue

institute: Zhengzhou Univerisity

summary:
For in vivo experiments, mice were inoculated a lethal dose of CVA2 strain (104 TCID50/mouse) or equal volume of culture supernatant of RD cells that were uesd to cultivate virus. Total RNA was extracted from brains, lungs, hearts and skeletal muscle of mice at 3 days post infection (dpi), 5 dpi and corresponding controls using TRIzol reagent to quantitate inflammation-related genes from the CVA2 infected mice and control.
qPCR gene expression profiling. Brains, lungs, hearts and skeletal muscles from four groups were treated separately. Equal amount total RNA from each organ or tissue of mice was harvested to analyze inflammation-related genes.

overall_design: There were 4 duplicate samples per group and 4 different organs or tissues per mouse. Equal amount total RNA was extracted from 64 samples.

first: Yuefei

last: Jin


title: Heterogeneity analysis of astrocytes following spinal cord injury at single-cell resolution

status: Public on Nov 21 2021

city: nanjing

first: Jinxing

last: Hou

state: china

address: Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road

department: Department of Orthopedic Surgery

country: China

type: Expression profiling by high throughput sequencing

summary: Astrocytes play many important functions in response to spinal cord injury (SCI) in an activated manner, including clearance of necrotic tissue, formation of protective barrier, maintenance of microenvironment balance, interaction with immune cells, and formation of the glial scar. More and more studies have shown that the astrocytes are heterogeneous, such as inflammatory astrocyte 1 (A1) and neuroprotective astrocyte 2 (A2) types. However, the subtypes of astrocyte resulting from SCI have not been clearly defined. In this study, using single-cell RNA sequencing, we constructed the transcriptomic profile of astrocytes from uninjured spinal cord tissue and nearby the lesion epicenter at 0.5, 1, 3, 7, 14, 60, and 90 days after mouse hemisection spinal cord tissue. Our analysis uncovered six transcriptionally distinct astrocyte states, including Atp1b2+, S100a4+, Gpr84+, C3+/G0s2+, GFAP+/Tm4sf1+, and Gss+/Cryab+ astrocytes. We used these new signatures combined with canonical astrocyte markers to determine the distribution of morphological and physiologically distinct for each astrocyte population at injured sites by immunofluorescence staining. Then we identified the dynamic evolution process of each astrocyte subtype following SCI. Finally, we also revealed the evolution of highly expressed genes in these astrocyte subtypes at different phases of SCI. Together, we provided six astrocyte subtypes at single-cell resolution following SCI. These data not only contribute to understanding the heterogeneity of astrocytes during SCI but also help to find new astrocyte subtypes as a target for SCI repair.

overall_design: Single cell RNA sequencing of uninjured and injured spinal cord at pSCI0.5d, pSCI1d, pSCI3d, pSCI7d, pSCI14d, pSCI60d and pSCI90d.

first: Huiru

last: Bi

first: Qing

last: Jiang

first: Xiaosong

last: Gu


title: The Birth, Distribution and Evolution of Primate Cerebral Inhibitory Neurons

status: Public on Nov 23 2021

city: San Francisco

first: Alex

middle: A

last: Pollen

state: CA

address: 35 Medical Center Way

department: Neurology

country: USA

institute: UCSF

summary: Neuroanatomists have long speculated that expanded primate brains contain an increased morphological diversity of inhibitory neurons (doi:10.1038/nrn3444, DeFelipe et al.) and recent studies have identified primate-specific neuronal populations at the molecular level(doi:10.1038/s41586-020-2781-z, Krienen et al.). However, we know little about the developmental mechanisms that specify evolutionarily novel cell types in the brain. Here, we reconstructed gene expression trajectories specifying inhibitory neurons spanning the neurogenic period in macaque and mouse by analyzing the transcriptomes of 250,181 cells. We find that the initial classes of inhibitory neurons generated prenatally are largely conserved among mammals. Nonetheless, we identify two contrasting developmental mechanisms for specifying evolutionarily novel cell types during prenatal development. First, we show that recently-identified primate-specific TAC3 striatal interneurons are specified by a unique transcriptional program in progenitors followed by induction of a distinct suite of neuropeptides and neurotransmitter receptors in newborn neurons. Second, we find that multiple classes of transcriptionally-conserved olfactory-bulb bound precursors are redirected to expanded primate white matter and striatum, including a novel peristriatal class, striatum laureatum neurons, that resemble dopaminergic periglomerular cells of the olfactory bulb. We propose an evolutionary model in which conserved initial classes of neurons supplying the smaller primate olfactory bulb are reused in the enlarged striatum and cortex. Together, our results provide a unified developmental taxonomy of initial classes of mammalian inhibitory neurons and reveal multiple developmental mechanisms for neural cell type evolution.

overall_design: 10X Genomics Chromium single cell 3’ capture RNA-sequencing of 9 macaque embryos between embryonic day 40 and 100

first: Matthew

middle: T

last: Schmitz

first: Alexander


title: RNA-seq of Arabidopsis seedlings treated with chemical modifiers of sugar signalling at dawn

status: Public on Nov 20 2021

city: Parkville

first: Michael

middle: James

last: Haydon

state: VIC

address: BioSciences 4, Royal Parade

country: Australia

institute: University of Melbourne

summary: Arabidopsis seedlings were treated with DPI, pentamidine isethionate, tyrphostin AG879, AEG3482 or DMSO (control) at dawn (ZT0). Samples were collected for mRNA-seq for untreated seedlings at ZT0 or treated seedlings at ZT2.

overall_design: 14-day-old Columbia-0 (Col-0) Arabidopsis thaliana seedlings grown on 1/2MS in 12 h light/12 h dark cycles transferred to 1/2MS media at ZT0 (before lights on) containing 0.1% (v/v) DMSO, 10 µM DPI, 25 µM pentamidine isethionate, 2 µM Tyrphostin AG879 or 12.5 µM AEG3482. Untreated samples were collected at ZT0 and treated samples were collected at ZT2 in triplicate.

first: Xiang

last: Li

middle: J


title: Effect of SUFU overexpression and knockdown on gene expression profile in breast cancer epithelial cells

status: Public on Nov 17 2021

city: Dalian

first: dapeng

state: Liaoning

address: lvshun south road no.9

institute: Dalian Medical University

summary: SUFU is a negative regulator of the hedgehog signaling pathway and its abnormal expression has been found in several human cancers, whereas the role of SUFU in the malignant development of breast cancer has not been fully elucidated. We performed RNA-seq to determine the impact of SUFU overexpression and knockdown on global gene expression profile in SKBR3 and HCC1954 cells. Our results show that sufu affects ferroptosis phenotype via modulating yap-dependent ACSL4 in breast cancer cells.

overall_design: SKBR3 and HCC1954 cells tranduced with lentiviruses expressing oeSUFU, shSUFU and control vector were selected for RNA extraction and transcriptomic profiling by RNA-seq.

first: Kun

last: Fang

first: Songshu

last: Meng


title: Impact of secondary TCR engagement on the heterogeneity of pathogen-specific CD8+ T cell response during acute and chronic toxoplasmosis

status: Public on Nov 11 2021

city: Philadelphia

first: Christopher

last: Hunter

state: PA

address: 301 S University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: Initial TCR-dependent engagement of CD8+ T cells results in T cell expansion, and the early events involved in priming influence the generation of diverse effector and memory populations. During infection, some of these activated T cells re-encounter cognate antigen, but whether this influences phenotypic heterogeneity is unclear. To address this issue, OT-I T cells, which are specific for the SIINFEKL peptide from OVA and express the Nur77-GFP reporter of recent TCR activation, were paired with transgenic T. gondii that express OVA to assess the impact of TCR activation on parasite-specific CD8+ T cell responses.

overall_design: Four biological replicates were analyzed for each of Nur77-GFP- and Nur77-GFP+ OT-I from the brains of T. gondii-OVA infected mice 14 days post infection

first: Lindsey

last: Shallberg


title: NextGeneration Sequencing of Pediatric ARDS Nasal and Bronchial Brushings

status: Public on Dec 24 2021

city: Cincinnati

first: Brian

middle: Michael

last: Varisco

state: OH

address: 3333 Burnet Avenue, MLC 7006

department: Critical Care Medicine

institute: Cincinnati Children's Hospital Medical Center

summary: The objective of this study was to determine if nasal transcriptomics could be used to characterize the underlying pathobiology and predict clinical course of patients with pediatric ARDS (PARDS). Subjects meeting consensus PARDS criteria or controls admitted to the Pediatric ICU without lung disease had nasal cytology brushings on days 1, 3, 7 and 14. The gene expression of these brushings was compared to identify subtypes and describe clinical course. Concurrent nasal and bronchial brushings were collected if bronchoscopy was performed. We identified four PARDS subgroups, termed A, B, C, and D. Subgroup B was marked by inflammation and ciliary cell dysfunction. Subgroup D was marked by reduced epithelial stem cell mRNAs without inflammation. Subgroup A had hypo-inflammation and upregulation of pathways important in epithelial cell repair. Subgroup C had increased ciliary cell genes. Control specimens almost entirely clustered with Subgroup C, but one that developed PARDS clustered with Subgroup B and several that developed lung injury clustereced with Subgroups B and A. Over time, Subgroups D and B transitioned to A which transitioned to C. Bronchial and nasal gene expresison were similar.

overall_design: Comparison of PARDS and Control gene expression.

first: James

middle: G

last: Williams


title: Investigating the altered brain metastatic transcriptome in breast cancer

status: Public on Nov 12 2021

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

summary: Brain metastatic disease occurs in 10-30% of metastatic breast cancer cases. The incidence of brain metastases is increasing with median overall survival < 2 years for patients. In order to better characterize oncogenic pathway activity pertinent to breast cancer brain metastasis, exome capture RNA sequencing was carried out on patient matched primary breast with brain metastatic tumor samples for 45 cases of breast cancer brain metastasis (N= 90 samples). Here, exome capture RNA sequencing data is deposited as sequencing batch corrected log2 transformed trimmed M of means (TMM) normalized counts per million (CPM) (log2(TMM-CPM +1) gene expression values (n=16,714 protein coding genes; N=90 tumor samples).

overall_design:
Exome capture RNA sequencing was carried out on patient matched primary breast with brain metastatic tumor samples for 45 cases of breast cancer brain metastasis (N= 90 samples).
>>> Raw RNA sequencing data for the paired primary and metastatic samples are not published openly in order to protect participant identities, but will be made available upon request and under regulatory compliance via a data usage agreement (DUA). Please contact the corresponding author with data access requests that will be granted once the DUA is signed. <<<

first: Adrian

middle: V

last: Lee

first: Steffi

last: Oesttereich

first: Fergus

last: Couch

first: Damir

last: Vareslija

first: Nicola

last: Cosgrove


title: Next generation expression analysis of wild type and Acaca-/- murine small intestinal organoids

status: Public on Nov 10 2021

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary:
Purpose: The goal of this study is to compare NGS-derived transcriptomes of  wild type mouse small interstinal organoids and organoids deficient for the enzyme acetyl-coa-carboxylase (ACC) 1 (Acaca).
Methods: mRNA profiles were generated from organoids at 24h and 96h  upon in vitro deletion of the Acaca gene and the respective non-deleted wild type controls in triplicates. Total RNA was isolated using RNeasy Micro Kit (Qiagen) and libraries were prepared using NEBNext Single Cell/Low Input RNA Library Prep (New England BioLabs). The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S2 Reagent Kit (100 cycles, paired end run). Each FASTQ file gets a quality report generated by FASTQC tool. Before alignment to reference genome each sequence in the raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using Trim Galore! wrapper tool. Reads shorter than 20 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome (GRCm38.) using open source short read aligner STAR (https://code.google.com/p/rna-star/) with settings according to log file.
Results: the sequencing depth of our libraries is > 3 x107 reads per RNA sample. PCA analysis revealed a close relationship between WT and ACC1-deficient organoids at 24h, whereas samples at 96h were distinct from each other.  Lack of ACC1 strongly reduced the expression of genes associated with intestinal epitelial stem cells. Moreover, GSEA revealed downregulation of pathways associated with DNA replication, cell cycle and chromosome segregation in ACC1-deficient organoids.
Conclusions: Our study highlights the importance of ACC1-mediated cellular fatty acid synthesis for the maintenance of intestinal epithelial stem cells in mouse intestinal oganoids.

overall_design: mRNA profiles of wild type and ACC1-deficient murine small intestinal organoids

first: Shu-ting

first: M

last: Lochner

first: R


title: Mapping the molecular signatures in tumors isolated from beta hCG transgenic mice

status: Public on Nov 05 2021

city: New Delhi

first: Rahul

last: Pal

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

summary: We have identified several genes associated with the process of progesterone-mediated decrease in tumor volume in a beta-hCG containing milieu.

overall_design: RNA-seq analysis of LLC1 tumors (subcutaneously implanted) isolated from beta-hCG transgenic mice, ovariectomized beta-hCG transgenic mice (vehicle-supplemented), and ovariectomized beta-hCG transgenic mice (progesterone-supplemented). Supplementation was carried out for 28 days and the respective tumors were isolated post 30 days of implantation.

first: Moumita

last: Sarkar


title: Identification of AIA_H related genes and BHGZD therapeutic effect related genes.

status: Public on Dec 11 2021

city: Beijing

first: Weijie

last: LI

address: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China

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

overall_design: Refer to individual Series


title: MeRIP-seq to explore the targets of METTL3 in pancreatic cancer

status: Public on Dec 13 2021

city: Suita

first: Shotaro

last: Tatekawa

state: Osaka

address: 2-2(D10), Yamadaoka, Suita-city

department: Departments of Radiation Oncology,

country: Japan

institute: The University of Osaka Graduate School of Medicine

type: Methylation profiling by high throughput sequencing

summary: We performed MeRIP-seq of METTL3-knockdown (KD) MIAPaCa-2 and control cells to detect METTL3-methylated genes and extracted genes whose methylation was lost in METTL3-KD cells compared with control cells. Next, we performed mRNA expression analysis using dates of input samples at MeRIP-seq. Genes whose methylation peaks were abolished by METTL3-KD and whose expression changes were observed were analyzed as candidates for METTL3-regulated genes.

overall_design: RIP-sequence data using m6A Ab

first: S

last: Konno

first: H

last: Ihii


title: Single-cell chromatin accessibility of anti-viral CD4  T cells in Bcl6 and Blimp1 deficient conditions

first: Thomas

last: Ciucci

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Single-cell chromatin accessibility of effector CD4+ T cells  WT or Bcl6 Blimp1-deficient was determined by scATACseq  after LCMV Armstrong infection

overall_design: Mixed bone marrow chimera made of  WT,  Bcl6-deficient , Blimp1-deficient or Bcl6 Blimp1-deficient cells were infected with LCMV Armstrong. 7 days post-infection GP66+ CD4+ T cells were sorted and chromarin accessibility was determined by scATACseq

first: Remy

last: Bosselut


title: TGF-β/Nodal signaling boosts glucose uptake during mesendoderm differentiation by inducing a transmembrane micropeptide

status: Public on Nov 03 2021

first: Haipeng

last: Fu

address: Shuangqing Road

institute: Tsinghua University

summary: TGF-β signaling is a central regulator of early development in metazoans, yet our understanding of the scope of TGF-β signaling’s downstream targets and associated physiological mechanisms in specifying developmentally appropriate cell fates is far from complete. Here, we found that a highly conserved, primitive-streak-specific micropeptide is a direct target of TGF-b/Nodal signaling. This transmembrane micropeptide (NEMEP) is essential for mesendoderm differentiation. Depletion of NEMEP impaired mesendoderm differentiation and caused a significant decrease in glucose uptake, while TGF-β signaling enhances glucose uptake in a NEMEP-dependent manner. Biochemically, we show that NEMEP promotes glucose uptake through its interactions with GLUT1/3. Thus, beyond expanding the scope of known TGF-β signaling targets in early development and showing that this target micropeptide augments the glucose uptake function of major glucose transporters during mesendoderm differentiation, our study provides a clear example for the direct functional impact of altered metabolism on cell fate determination in early embryogenesis.

overall_design: Identifiy TGF-β responsive lncRNA/micropeptide, dissect function and molecular mechanism of a micropeptide in mesendoderm differentiation

first: Kun

last: Yan

first: Qiaoran

last: Xi


title: Transcription Level Response of HEK-293T Cells to RfA1 Expression

status: Public on Nov 01 2021

city: Changsha

first: Junyi

last: Song

email: 283693514@qq.com, songjunyi@nudt.edu.cn

address: Deya Road 109

institute: National University of Defense Technology

summary: We transfected HEK-293T cells to express RfA1. The RNA-Seq results indicates that Genes evolved in biological processes such as “regulation of microtubule cytoskeleton organization”, “microtubule polymerization or depolymerization”, “microtubule nucleation” were found to respond to RfA1 expression. Correspondingly, these microtubule relevant genes were also sorted to cellular component items, including “spindle microtubule”, “spindle pole centrosome”, “mitotic spindle”, “spindle” , which indicates the tight relationship between RfA1 and microtubules.

overall_design: Comparison of cells expressing or not expressing RfA1


title: Depletion of oocyte dynamin-related protein 1 shows maternal effect abnormalities in embryonic development

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

address: Wellington Road

institute: Monash Bioinformatics Platform

summary: Eggs contain about 200,000 mitochondria that generate ATP and metabolites essential for oocyte and embryo development. In addition to this energetic role, mitochondria also integrate the cellular metabolic and transcriptional state via metabolites which regulate epigenetic modifiers. The maternal epigenome is established during oogenesis, but there is no direct evidence linking oocyte mitochondrial function to the maternal epigenome and embryo development. The DRP1 protein is required for mitochondrial fission. Here, we demonstrate a dramatic maternal effect in that DRP1-deficient oocytes fertilized by wild-type sperm exhibit a high frequency of failure in peri- and post-implantation development. This failure is associated with altered oocyte mitochondrial function, changes in the oocyte transcriptome and proteome, and a decrease in oocyte DNA methylation and H3K27me3. Transplanting the pronuclei of these fertilized oocytes to normal ooplasm fails to rescue embryonic lethality. We conclude that mitochondrial function plays a role in establishing the maternal epigenome, with serious consequences for embryo development.

overall_design: Single cell sequencing of oocytes from Drp1-KO and WT mice.

first: Deepak

last: Adhikari

first: In-won

last: Lee

first: Jun

last: Liu

first: Usama

last: AL-Zubaidi

first: Qing-Hua

last: Zhang

first: Wai

middle: S

last: Yuen

first: Hiromi

last: Sesaki

first: Jeffrey

middle: R

last: Mann

first: Rebecca

middle: L

last: Robker

first: John

last: Carroll


title: Histone N-terminal acetyltransferase NAA40 links one-carbon metabolism to chemoresistance

status: Public on Nov 15 2021

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

institute: Max Planck Institute

summary: Epigenetic regulation and metabolism are highly interconnected, but it remains unclear if this interplay is harnessed by cancer cells to evade chemotherapy. Here, using transcriptomic and metabolomic analysis in colorectal cancer cells, we demonstrate that N-alpha-acetyltransferase 40 (NAA40), which catalyzes N-terminal acetylation of histones H4 and H2A, controls the expression of key one-carbon metabolic enzymes and the abundance of corresponding metabolites. Specifically, we show that NAA40 deficiency induces the methionine cycle thereby increasing global histone methylation and attenuates transcription of the metabolic gene thymidylate synthase (TYMS) whose product is targeted by 5-fluorouracil (5-FU). Accordingly, we show that NAA40 activates TYMS by preventing deposition of H2A/H4S1ph at the nuclear periphery and confers resistance against the antimetabolite 5-FU in vitro and in xenografts. Consistently, in primary tumours NAA40 expression associates with TYMS levels and poorer 5-FU response. Overall these findings define a novel role for NAA40 in controlling cellular metabolism and chemoresistance.

overall_design: Function of NAA40 in metabolism and chemoresistance

first: Demetriadou

last: Christina

first: Parekh

last: Swati

first: Tessarz

last: Peter

first: Kirmizis

last: Antonis


title: Single cell RNA sequencing of mouse embryonic fibroblasts in autophagy processes

status: Public on Dec 01 2021

city: Dongjak-Gu

first: Junil

last: Kim

state: Seoul

address: 369 Sangdo-Ro

department: Department of Bioinformatics

country: South Korea

institute: SOONGSIL UNIVERSITY

summary: Autophagy, a catabolic process to remove unnecessary or dysfunctional cells, is triggered by various signals including nutrient starvation. Depending on the type of the nutrient deficiency, diverse sensing mechanisms and pathways are used for autophagy, suggesting subsequent nutrient dependent transcriptional regulation. Still, however, our knowledge about nutrient specific transcriptional regulation during autophagy is limited.    To understand nutrient type dependent transcriptional mechanisms during autophagy, we performed single cell RNA sequencing (scRNAseq) for the mouse embryonic fibroblasts (MEFs) before and after applying glucose- (GS) as well as amino acid starvation (AAS). Trajectory analysis using scRNAseq identified sequential induction of potential transcriptional regulators for each deficiency condition. Gene regulatory rules inferred using TENET newly identified CCAAT/enhancer binding protein γ (C/EBPγ) regulates autophagy processes specifically to AAS condition. Strikingly, knockdown of C/EBPγ attenuated the autophagic process only in the AAS condition.  Cell biological and biochemical studies validated that C/EBPγ plays a switching role for ATF4 to activate autophagy genes under AAS, but not under GS. Together, our data identified C/EBPγ as a previously unidentified key regulator under amino acid starvation-induced autophagy.

overall_design: We performed single cell RNA sequencing (scRNAseq) for the mouse embryonic fibroblasts (MEFs) before and after applying glucose (GS) as well as amino acid starvation (AAS).

first: Dongha


title: p21 produces a bioactive secretome that places stressed cells under immuno-surveillance [dataset 12]

status: Public on Oct 29 2021

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: p21 produces a bioactive secretome that places stressed cells under immuno-surveillance.

overall_design: RNA-sequencing analyses on IR-senescent cells with Rela-knockdown or scrambled (Scr) control knockdown.

first: Jan

last: van Deursen


title: Next Generation Sequencing analyses negative control (NC) and TRPC5OS overexpressed MDA-MB-231 Transcriptomes

city: Nanjing

first: hui

middle: jing

last: Peng

state: China

address: Jiangsu Province Hospital

institute: Department of Breast Surgery, The First Hospital Affiliated Hospital with Nanjing Medical University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the differential genes between negative control and TRPC5OS overexpressed MDA-MB-231. Method: RNA was extracted as aforementioned from cells following after TRPC5OS was overexpression.sed. Agarose gel electrophoresis was used for assessing the integrity testingof the extracted RNAs,, and quantification and further quality tests were performed using a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA). Subsequently, an NEB Next ®Poly (A) mRNA Magnetic Isolation Module was used for mRNA enrichment by adding it into the total RNA extract. The library of the processed RNA product RNA was established using the KAPA Stranded RNA-Seq Library Prep Kkit (Illumina, Inc., San Diego, CA, USA). The established library was sequenced using the Illumina HiSeq 4000 platform. Conclusions: The results showed that total 55,256 genes were dysregulateddifferentially expressed, including 3,269 upregulated genes and 1,987 downregulated genes (fold change ≥1.5) .

overall_design: two pairs of NC and TRPC5OS overexpressed MDA-MB-231

first: Jinghui

first: Yangyang

last: Cui

first: Shengbin

last: Pei


title: Identification of AIA_H related genes and BHGZD therapeutic effect related genes. [RNA-Seq]

first: Weijie

last: LI

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

summary: To obtain AIA_H related genes [the significant differentially expressed genes (DEGs) of AIA_H model group vs. Normal control group] and BHGZD therapeutic effect related genes [DEGs of BHGZD treatment group vs. AIA_H model group], the microarray analysis was carried out.

overall_design: 15 rat samples were randomly divided into three groups (5 per group): (1) Normal control group (Con); (2) AIA-H model  group (AIA_H); (3) BHGZD treatment group (AIA_H_BHGZD).

first: Wenjia

last: Chen


title: Biomarker Response of Aerobic Methanotrophs to Methane Oxidation Rates and Short-Term Methane and Oxygen Limitation

city: Ithaca

first: Egidio

middle: F

last: Tentori

state: NY

address: 220 Hollister Hall

department: School of Civil and Environmental Engineering

institute: Cornell University

summary: Methanotrophs, which help regulate atmospheric levels of methane, are active in diverse natural and man-made environments. This range of habitats and the feast-famine cycles seen by many environmental methanotrophs suggest that methanotrophs dynamically mediate rates of methane oxidation. Global methane budgets require ways to account for this variability in time and space. Functional gene biomarker transcripts are increasingly being studied to inform the dynamics of diverse biogeochemical cycles. Previously, per-cell transcript levels of the methane oxidation biomarker, pmoA, were found to vary quantitatively with respect to methane oxidation rates in model aerobic methanotroph, Methylosinus trichosporium OB3b. In the present study, these trends were explored for two additional aerobic methanotroph pure cultures, Methylocystis parvus OBBP and Methylomicrobium album BG8. At steady-state conditions, per cell pmoA mRNA transcript levels strongly correlated with per cell methane oxidation across the three methanotrophs across many orders of magnitude of activity (R2 = 0.91). Additionally, genome-wide expression data (RNA-seq) were used to explore transcriptomic responses of steady state M. album BG8 cultures to short-term CH4 and O2 limitation. These limitations induced regulation of genes involved in central carbon metabolism (including carbon storage), cell motility, and stress response.

overall_design: Comparison of genome-wide expression (RNA-seq) of M. album BG8 grown in bioreactors under steady-state, substrate replete conditions (reference) and corresponding periods of substrate (experimental condtion, methane and oxygen) limited conditions. Samples from substrate limited conditions are two hours after the onset of substrate limitation. Total of eight samples, duplicate for each condition which are from reactor replicates.

first: Shania

last: Fang

first: Ruth

middle: E

last: Richardson


title: p21 produces a bioactive secretome that places stressed cells under immuno-surveillance [dataset 9]

summary: In response to various cellular stresses, the cyclin-dependent kinase inhibitor p21 transiently halts cell cycle progression until the stress is resolved, or indefinitely when permanently damaged cells undergo cellular senescence. p21 does so by repressing the transcription of E2F target genes through hypophosphorylation of Rb, but whether regulation of Rb-mediated gene transcription by p21 controls stress responses beyond cell cycle regulation is unknown. Here we report that in concert with arresting cell growth, a p21-responsive Rb pool interacts with specific Stat and Smad transcription factors at select gene promoters to establish a bioactive secretome, referred to as the p21-activated secretory phenotype (PASP). The PASP consists of several hundred secreted factors that continued to be expressed in a p21-dependent fashion after transiently arrested cells have become senescent. We found that the PASP places stressed cells under immunosurveillance, a property that largely depended on a single factor, the macrophage attractant Cxcl14. In mice, hepatocytes promptly attracted macrophages upon induction of p21 and were eliminated after sequential recruitment of B and T cells several days later. Cells normalizing p21 expression within several days after its induction resumed proliferation and were released from immunosurveillance. Collectively, these findings demonstrate that stressed cells are simultaneously placed under both proliferative arrest and immunosurveillance (to prevent the expansion of stressed, potentially damaged cells), and that p21 coordinates these cell-autonomous and non-autonomous activities at the transcriptional level through regulation of Rb.

overall_design: RNA-sequencing analyses on senescent cells overexpressing p21.


title: p21 produces a bioactive secretome that places stressed cells under immunosurveillance [dataset 3]

overall_design: RNA-sequencing analyses in senescent cells induced by irradiation (IR), serial passaging (REP), KRASG12V-oncogene induciton (OI) and proliferating counterparts (control1).


title: Population gene expression of anti-viral CD4  T cells in Bcl6 and Blimp1 deficient conditions

first: Thomas

last: Ciucci

summary: Population gene expression of effector CD4+ T cells  WT,  Bcl6-deficient , Blimp1-deficient or Bcl6 Blimp1-deficient was determined by RNAseq after LCMV Armstrong infection

overall_design: Mixed bone marrow chimera made of  WT,  Bcl6-deficient , Blimp1-deficient or Bcl6 Blimp1-deficient cells were infected with LCMV Armstrong. 7 days post-infection GP66+ CD4+ T cells were sorted and gene expression was determined by RNAseq

first: Remy

last: Bosselut


title: p21 produces a bioactive secretome that places stressed cells under immunosurveillance [dataset 5]

overall_design: RNA-sequencing analyses in senescent celles induced by irradiation (IR), serial passaging (REP), KRASG12V-oncogene induciton (OI) and proliferating counterparts (control1) as well as proliferating cells that were induced for 2 days (after irradiation or oncogene-induction).


title: p21 produces a bioactive secretome that places stressed cells under immunosurveillance [dataset 6]


title: p21 produces a bioactive secretome that places stressed cells under immuno-surveillance [dataset 7]

overall_design: RNA-sequencing analyses on cells induced by gamma-irradiation after 2 days (D2) or 4 days (D4) as well as proliferating cells (D0). D2 irradiated cells were infected with shRNA-containing lentivirus to produce D4 irradiated cells with p21 knockdown, Rb knockdown or scrambled control knockdown (shScr).


title: p21 produces a bioactive secretome that places stressed cells under immunosurveillance [dataset 4]

overall_design: RNA-sequencing analyses in senescent celles induced by irradiation (IR) and proliferating counterparts (control1).


title: Phage-encoded sigma factors alter bacterial dormancy

city: Bloomington

first: Daniel

last: Schwartz

state: IN

address: 1001 East 3rd Street

department: Biology

institute: Indiana University

summary: By entering a reversible state of reduced metabolic activity, dormant microorganisms are able to contend with suboptimal conditions that would otherwise reduce their fitness. In addition, certain types of dormancy like sporulation, can serve as a refuge from parasitic infections. Phages are unable to attach to spores, but their genomes can be entrapped in the resting structures and are able to resume infection upon host germination. Thus, dormancy has the potential to affect both the reproductive and survival components of phage fitness. Here, we characterized the distribution and diversity of sigma factors in nearly 3,500 phage genomes. Homologs of bacterial sigma factors that are responsible for directing transcription during sporulation were preferentially recovered in phages that infect spore-forming hosts. While non-essential for lytic infection, when expressed in Bacillus subtilis, we demonstrate that phage-encoded sigma factors activated sporulation gene networks and reduced spore yield. Our findings suggest that the acquisition of host-like transcriptional regulators may allow phages to manipulate the expression of complex traits, like the transitions involved in bacterial dormancy.

overall_design: RNAseq of strains with sigma factors cloned under an IPTG-inducible promter in an ectopic locus (amyE). Cultures of each strain (n=3) were grown in LB to mid-exponenial phase, at which time the culture was split into two, and IPTG (1mM) was added to one half. RNAwas extracted two hours after induction. Differential expression was inferred from comparison of a the induced culture to its non-induced paired control.

first: Jay

last: Lennon


title: p21 produces a bioactive secretome that places stressed cells under immunosurveillance [dataset 2]

overall_design: Examination of H3K27ac landscapes in senescent IMR-90 cells induced by irradiation (IR) and proliferating counterparts (control1) as well as proliferating cells that were induced for 2 days (after irradiation or oncogene-induction, control2).


title: p21 produces a bioactive secretome that places stressed cells under immuno-surveillance [dataset 11]

overall_design: RNA-sequencing analyses on non-senescent cells overexpressing p27.


title: Dimethyl Itaconate alleviates the pyroptosis of macrophages through oxidative stress

status: Public on Oct 16 2021

city: Hangzhou

first: shanshan

last: huang

address: No.1229 Gudun Road

institute: Zhejiang Hospital

summary: Macrophages are involved in the pathophysiology of many diseases as critical cells of the innate immune system. Pyroptosis is a form of macrophage death that induces cytokinesis of phagocytic substances in the macrophages, thereby defending against infection. Dimethyl itaconate (DI) is an analog of itaconic acid with anti-inflammatory effects. However, the effect of dimethyl itaconate on macrophage pyroptosis has not been elucidated clearly. Thus, the present study aimed to analyze the effect of DI treatment on a macrophage pyroptosis model (Lipopolysaccharide, LPS+Adenosine Triphosphate, ATP). The results showed that 0.25 mM DI ameliorated macrophage pyroptosis and downregulated interleukin (IL)-1β expression. Then, real-time quantitative polymerase chain reaction (RT-qPCR) was used to confirm the result of RNA-sequencing of the upregulated oxidative stress-related genes (Gclc and Gss) and downregulated inflammation-related genes (IL-12β and IL-1β). In addition, Gene Ontology (GO) enrichment analysis showed that differential genes were associated with transcript levels and DNA replication. Kyoto encyclopedia of genes and genomes (KEGG) enrichment showed that signaling pathways, such as tumor necrosis factor (TNF), Jak, Toll-like receptor and IL-17, were altered after DI treatment. N-acetyl-L-cysteine (NAC) reversed the DI effect on the LPS+ATP-induced macrophage pyroptosis and upregulated the IL-1β expression. Oxidative stress-related protein Nrf2 is involved in the DI regulation of macrophage pyroptosis. Taken together, these findings suggested that DI alleviates the pyroptosis of macrophages through oxidative stress.

overall_design: mRNA profiles of LPS+ATP(control) Groups and DI+LPS+ATP(DI) Groups from BMDMs

first: H

last: Shanshan

first: G

last: Dongyang

first: J

last: Bingbing

first: C

last: Guolong

first: Y

last: Jing

first: L

last: Yan

last: Zhouxin


title: Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome.

status: Public on Oct 21 2021

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute (NKI)

summary: Gene expression is in part controlled by cis-regulatory elements (CREs) such as enhancers and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter need to be biochemically compatible for promoter regulation to occur, but this compatibility has remained poorly characterised in mammalian cells. By systematic reporter assays of thousands of CRE – promoter pairs from three Mb-sized genomic regions in mouse cells, we found that CREs vary substantially in their promoter compatibility, with more than half showing significant selectivity. This selectivity does not correlate with looping interactions, suggesting that chromatin folding and compatibility are two orthogonal mechanisms of gene regulation.

overall_design: 3 Biological replicates of cDNA samples for each library mix, 2 pDNA replicates for each library mix and 1 iPCR sequencing run per separate library. For cDNA samples Library mixes were transfected in mESCs and samples were collected after 24h.

first: Miguel

last: Martinez-Ara

first: Federico

last: Comoglio

first: Joris

last: van Arensbergen


title: Next generation sequencing of isolated R5 ellipsoid body neurons of Drosophila in the morning and evening with and without sleep deprivation

status: Public on Oct 20 2021

city: Evanston

first: Ravi

last: Allada

state: Illinois

address: Department fo neurobiology, Noerthwestern university,, 2205 Tech Drive

department: Department of neurobiology

institute: Northwestern university

summary:
Purpose: After identifying a difference in the response to sleep deprivation between the morning and evening, we assayed gene expression in a key homeostatic circuit in the Drosophila brain: the R5 ellipsoid body neurons. We sought to identify changes in gene expression in this circuit that are critical for the behavioral output.
Methods: Flies expressing GFP via a restrictive R5 driver were entrained to a 12:12 light:dark paradigm at 25C. Mated females were then loaded into individual tubes with sucrose food and placed into behavior boards from Trinkinetics. Control flies were not subjected to any sleep deprivation and were collected in either the morning or evening. Experimental flies were subjected to 2.5 hrs of mechanical sleep deprivation (SD) via vortexing just before either the morning or evening. Following SD (or at the appropriate control timepoint), 40-50 brains were dissected out in dissecting saline with TTX, AP5, and DNQX to inhibit sodium channels, NMDA receptors, and AMPA receptors respectively. The brains were transferred to SM Active medium with channel blockers after dissection, then washed with dissecting saline before being digested with papain. Digestion was stopped after 30 minutes by the addition of SM Active medium with channel blockers. The brains were then triturated by manual pipetting to produce a single cell suspension. GFP+ cells were immediately sorted by fluorescence activated cell sorting into a single tube. 350-500 cells were collected per experiment. In total, we collected 12 samples, three replicates for each timepoint and condition. Cells were lysed in extraction buffer from the Arcturus PicoPure kit and stored at -80C until ready to process. RNA was extracted from each set of cells using the PicoPure kit, and then reverse transcribed into cDNA using a T7/polydT primer. One round of in vitro transcription using the MEGAScript kit was performed to amplify the RNA. Following IVT, library prep was performed using the TruSeq Stranded mRNA Library Prep Kit. We generated 30 million reads per sample on a NovaSeq. Analysis was performed using kallisto and sleuth.

overall_design: mRNA from R5 ellipsoid body neurons of Drosophila in the morning and evening +/- SD

first: Tomas

last: Andreani

first: Clark

last: Rosensweig

first: Shiju

last: Sisobhan

first: Emmanuel

last: Ogunlana

first: William

last: Kath


title: Aberrant ClpP activation disturbs mitochondrial proteome homeostasis to suppress pancreatic ductal adenocarcinoma

city: Shanghai

first: Pengyu

last: Wang

address: 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Pudong

institute: Shanghai Institute of Materia Medica

summary: Targeting the mitochondrial caseinolytic protease P (ClpP) is a potential novel strategy for treating leukemia. However, little is known about the therapeutic effects of ClpP in solid tumors. In this study, we identify a strong activator of the mitochondrial ClpP for subsequent use in targeted pancreatic ductal adenocarcinoma (PDAC) therapy. Analysis of clinical data demonstrated a positive association between ClpP expression and prognosis in PDAC patients. We validated that aberrant ClpP activation can lead to growth arrest in PDAC cells and tumors. We then performed high-throughput screening and synthetic optimization to develop a potent ClpP activator, ZG111, which promoted ClpP to degrade respiratory chain complexes and occurred in a ClpP-dependent manner. This resulted in impaired oxidative phosphorylation in the mitochondria and activation of JNK/c-Jun pathway and endoplasmic reticulum stress response. ZG111 also produced significant antitumor effects on tumors in cell-derived and patient-derived xenografted mice models. Altogether, our identification of ZG111 demonstrated that the aberrant activation of ClpP hydrolysis can be used as a potential therapeutic strategy to treat PDAC cancer.

overall_design: Examination of ZG111 , DMSO treatment, Y118A ClpP activation,or vehicle control on the  transcriptional inluences in BxPC-3 cells.

first: Cai-Guang

last: Yang


title: H3K4me3-marked histone orchestrates neutrophil plasticity from immunity to tissue regeneration

status: Public on Oct 27 2021

city: Lodz

first: Przemyslaw

last: Lewkowicz

address: Pomorska 251/A4

department: Immunogenetics

country: Poland

institute: Medical University of Lodz

summary: In this study, we used chromatin immunoprecipitation sequencing (ChIP-Seq) analysis of histone H3K4me3-marked, to identify various TSSs associated with LPS-, TNF-alfa- and IL-10-stimulated neutrophils from healthy individuals, as well as neutrophils derived from the patients with sepsis (systemic septic inflammation with LPS-stimulated neutrophils), NMOSD (aseptic inflammation with neutrophils pre-activated by TNF-alfa and periodontitis (localized self-limiting septic inflammation with IL-10-positive neutrophils). We provided comprehensive epigenomic analysis within H3K4me3- marked histone that allowed us to identify human neutrophil regulators affecting their plasticity during inflammation as well as suppression.

overall_design: Chromatin immunoprecipitation sequencing (ChIPseq) H3K4me3 histone analysis in circulating neutrophils isolated from helathy voluntires stimulted in vitro by IL-10, TNF-alfa or LPS, as well as neutrophils derived from the patients with sepsis (systemic septic inflammation with LPS-stimulated neutrophils), NMOSD (aseptic inflammation with neutrophils pre-activated by TNF-alfa and periodontitis (localized self-limiting septic inflammation with IL-10-positive neutrophils).


title: DEN-induced rat model reproduces key features of human hepatocellular carcinoma

status: Public on Oct 08 2021

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

summary: Using RNA-seq analysis, we study a DEN-induced HCC rat model during fibrosis progression and HCC development with special focus on liver inflammatory microenvironment. RNA-seq results show that DEN-induced liver tumors in rat model share remarkable molecular characteristics with human HCC, especially with HCC associated with high proliferation. In conclusion, our study provides detailed insight into the hepatocarcinogenesis in a commonly used model of HCC, facilitating the future use of this model for preclinical testing.

overall_design: 7-week-old Fischer 344 male rats  were treated weekly with intra-peritoneal injections of 50 mg/kg DEN. We analysed 3 different time points of DEN treatment: i) after 8 weeks of DEN injections (DEN08), ii) after 14 weeks of DEN injections (DEN14) and iii) after 14 weeks of DEN injection followed by 6 weeks of no DEN injection (DEN20). Animals of the same age, treated with no DEN were used as controls for 8 weeks (NOD08), 14 weeks (NOD14) and 20 weeks time points (NOD20). Non-tumoral (NT) tissues and Tumoral (T) tissues were analysed separately.

first: Florent

last: Chuffart

first: Zuzana

middle: M

last: Jilkova

first: Thomas

last: Decaens


title: p21 produces a bioactive secretome that places stressed cells under immunosurveillance

first: Hu

last: Li

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Neuropilin-1 mediates lung tissue-specific control of ILC2s function in type 2 immunity

status: Public on Oct 22 2021

first: Jingjing

last: Zhang

state: Shanghai

address: No.280 South Chongqing Road

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

summary: ILC2s are highly heterogeneous tissue-resident lymphocytes that regulate inflammation and tissue homeostasis in health and disease. But how they integrate to the respective tissue microenvironment to perform tissue-supportive functions remain poorly defined. Here, we identify neuropilin-1, which is induced postnatally and sustained by lung-derived TGFβ1, as a tissue signature of lung ILC2s. Genetic ablation or pharmacological inhibition of Nrp1 suppresses ILC2s function and protects mice from the development of pulmonary fibrosis. Mechanistically, TGFβ1-Nrp1 signaling enhances ILC2s function and type 2 immunity through upregulation of IL-33 receptor ST2 expression. Our findings identify Nrp1 as a tissue-specific regulator of lung-resident ILC2s activation and highlight Nrp1 as a potential therapeutic target for pulmonary fibrosis

overall_design: lung ILC2s mRNA profiles of bleomycin treated R5/+ (WT) and R5/+Nrp1f/f (KO) mice

first: Lei

last: Shen

first: Jinxin

last: Qiu

first: Ju


title: p21 produces a bioactive secretome that places stressed cells under immuno-surveillance [dataset 10]

first: Jan

last: van Deursen


title: Analysis of miRNA expression through microarray scan in penile carcinoma samples and normal-adjacent tissues

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

type: Non-coding RNA profiling by high throughput sequencing

summary:
Penile cancer is a rare disease that has high morbidity and mortality rates. While a few biomarkers related to prognosis have been previously described to date, none of them was adopted in clinical practice.
We used microarrays to identify miRNA-based molecular signatures to identify penile carcinoma regions from paired normal-adjacent tissues.  We also used microarray information to distinguish patients with a high risk of metastatic penile carcinoma.

overall_design: Fresh frozen tissues of primary tumors were prospectively collected from 11 patients with squamous cell penile carcinoma who underwent surgical treatment between July/2015 and June/2017. Five patients had localized disease (non-metastatic group) and 6 had inguinal lymph node metastases (metastatic group). RNA was purified from tissues and microarray analysis was performed using miRNA 4.0 Genechip (Affymetrix).

first: Claudio

middle: B

last: Murta

first: José

last: Pontes Jr

first: Tatiane

middle: K

last: Furuya

first: Miyuki

last: Uno

first: Alexis

last: Murillo-Carrasco

first: Leonardo

last: Cardili

first: Rafael

last: Coelho

first: Giuliano

last: Guglielmetti

first: Mauricio

middle: D

last: Cordeiro

first: Kátia

last: Leite

first: Laura

middle: C

last: Vettorazzo

first: Luisa

last: Villa

first: Roger

last: Chammas

last: Nahas


title: p21 produces a bioactive secretome that places stressed cells under immuno-surveillance [dataset 8]

first: Hu

last: Li

overall_design: RNA-sequencing analyses on non-senescent cells overexpressing p21 and p16.


title: SureCell - Evaluation of single-Cell RNA Sequencing Platforms

status: Public on Oct 06 2021

first: Jason

last: Myers

address: 601 Elmwood Ave.

institute: University of Rochester

summary: comparison of commercially available scRNA-Seq instrumentation using a well-defined cell line and treatment for evaluation

overall_design:
The SUM149PT cell line was developed from Invasive Ductal Carcinoma from a patient with ER negative, PR negative and Her2 positive (not activated) inflammatory breast cancer. The cell line is immortal and expresses luminal cytokeratins 8, 18, and 19, which is consistent with their origin from luminal breast epithelial cells. SUM149PT has been known to form tumors in nude mice.
Two biological replicates per condition (Mock vs TSA), various number of single cells profiled

first: John

last: Ashton


title: Bulk RNA-Seq - Evaluation of single-Cell RNA Sequencing Platforms


title: Fluidigm96 - Evaluation of single-Cell RNA Sequencing Platforms


title: Transcriptome-wide effects of NusA on RNA polymerase pausing in Bacillus subtilis

city: University Park

first: Oshadhi

last: Jayasinghe

address: 203 Althouse Laboratory

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: In this work we conducted RNET-seq on Wild Type, NusA depletion, nusG deletion, and NusA depletion nusG deletion strains of B. subtilis. Using this data we analysed the transcriptome-wide effects of NusA on RNA polymerase pausing and found that NusA has modest pause stimulating as well as suppressing effects throughout the genome.

overall_design: RNET-seq on Wild Type, NusA depletion, nusG deletion, and NusA depletion nusG deletion strains of B. subtilis followed by in vitro biochemistry follow-up.

middle: T

first: Zachary

last: Mandell

first: Alexander

last: Yakhnin

first: Mikhail

last: Kashlev

first: Paul

last: Babitzke


title: Compatibility logic of human enhancer and promoter sequences

status: Public on Oct 25 2021

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive, Room 3700

department: Department of Genetics

institute: Stanford University School of Medicine

summary: We transfected K562 cells with a STARR-seq plasmid library of paired promoter and enhancer sequences to characterize activation and compatibility between promoters and enhancers.

first: Drew

last: Bergman

first: Thouis

last: Jones

first: Vincen

last: Liu

first: Judhajeet

last: Ray

first: Evelyn

last: Jagoda

first: Layla

last: Siraj

first: Helen

middle: Y

last: Kang

first: Joseph

last: Nassar

first: Michael

last: Kane

first: Antonio

last: Rios

first: Tung

middle: H

last: Nguyen

first: Sharon

last: Grossman

first: Charles

middle: P

last: Fulco

first: Eric

last: Lander


title: Expression profiles of RNA from monocyte-derived small extracellular vesicles in coronary atherosclerosis

city: Chengdu

first: Hongtao

state: Sichuan

address: No.82, qinglong street, qingyang district, chengdu

department: General surgery

institute: Chengdu third people's hospital

summary: Small extracellular vesicles (sEVs)-derived circular RNAs (circRNAs) could regulate gene expression in recipient cells, and dysregulation of sEVs-derived circRNAs has been implicated in several diseases. However, the expression and function of sEVs-derived circRNAs in coronary atherosclerosis (CAD) remain unknown. In this study, we investigated global changes in the expression patterns of circRNAs in sEVs from coronary atherosclerosis-related monocytes.

overall_design: Peripheral blood mononuclear cells (PBMCs) from CAD patients and control individuals were isolated by Ficoll-Paque PLUS density gradient centrifugation (GE Healthcare Bioscience). The PBMCs were cryopreserved for less than 3 months at −80°C in 90% heat-inactivated fetal bovine serum (FBS) (Sigma-Aldrich) and 10% DMSO (Sigma-Aldrich). Monocytes were isolated using the EasySep™ Human Monocytes Isolation Kit (Stemcell Technology) and cultured in RPMI-1640 (Lonza) containing 2 mM glutaMAX (Gibco), 20 µg/mL gentamicin (Gibco), and 2% normal human serum type AB (Invitrogen).

first: T

last: Zhang

first: Xiong

last: Feng


title: Wafergen - Evaluation of single-Cell RNA Sequencing Platforms

first: Jason

last: Myers

first: John

last: Ashton


title: A Novel Mouse Model of Diffuse Midline Glioma Initiated in Neonatal Oligodendrocyte Progenitor Cells Highlights Cell- of-origin Dependent Effects of H3K27M II

status: Public on Oct 05 2021

city: Chicago

first: Yusuke

last: Tomita

address: 225 E Chicago Ave Box 18

department: Pediatrics

institute: Northwestern University

summary: Diffuse midline glioma (DMG) is a type of lethal brain tumor that develops mainly in children. The majority of DMG harbor the K27M mutation in histone H3. Oligodendrocyte progenitor cells (OPCs) in the brainstem are candidate cells-of-origin for DMG, yet there is no genetically engineered mouse model of DMG initiated in OPCs. Here, we used the RCAS/Tv-a avian retroviral system to generate DMG in Olig2-expressing progenitors and Nestin-expressing progenitors in the neonatal mouse brainstem. PDGF-A overexpression, along with p53 deletion, resulted in gliomas. Exogenous overexpression of H3.3K27M had a significant effect on tumor latency and tumor cell proliferation when compared with H3.3WT in Nestin+ cells but not in Olig2+ cells. Further, the fraction of H3.3K27M-positive cells was significantly lower in DMGs initiated in Olig2+ cells relative to Nestin+ cells, suggesting that the requirement for H3.3K27M is reduced when tumorigenesis is initiated in Olig2+ cells.  Interestingly, H3K27 trimethylation was decreased with H3.3K27M induction even in Olig2+ cells. Therefore, we need to find if there is transcriptional changes for the tumorigenesis with H3.3K27M in Olig2+ cells.

overall_design: Five independent tumors with H3.3K27M (PaK) and three independent tumors without H3.3K27M (PaH) were snap frozen, RNA extracted, and RNAseq analysis was performed (PDGF-A; H3.3K27M; p53 loss vs. PDGF-A; H3.3WT; p53 loss)

first: Oren

middle: J

last: Becher


title: Expression data from Staphylococcus aureus planktonic, biofilm, and antibiotic treated biofilm samples

status: Public on Oct 18 2021

city: Bozeman

last: Franklin

state: MT

address: 109 Lewis Hall

department: Microbiology and Cell Biology

institute: Montana State University

summary:
Is there a universal genetically programmed defense providing tolerance to antibiotics when bacteria grow as biofilms?   A comparison between biofilms of three different bacterial species by transcriptomic and metabolomic approaches uncovered no evidence of one. Single-species biofilms of three bacterial species (Pseudomonas aeruginosa, Staphylococcus aureus, and Acinetobacter baumannii) were grown in vitro for three days then challenged with respective antibiotics (ciprofloxacin, daptomycin, tigecycline) for an additional 24 h. All three microorganisms displayed reduced susceptibility in biofilms compared to planktonic cultures. Global transcriptomic profiling of gene expression comparing biofilm to planktonic and antibiotic-treated biofilm to untreated biofilm was performed.  Extracellular metabolites including 18 amino acids, glucose, lactate, acetate, formate, and ethanol were measured to characterize the utilization of carbon sources between biofilms, treated biofilms, and planktonic cells. While all three bacteria exhibited a species-specific signature of stationary phase, no conserved gene, gene set, or common functional pathway could be identified that changed consistently across the three microorganisms. Across the three species, glucose consumption was increased in biofilms compared to planktonic cells and alanine and aspartic acid utilization were decreased in biofilms compared to planktonic cells.  The reasons for these changes were not readily apparent in the transcriptomes. No common shift in the utilization pattern of carbon sources was discerned when comparing untreated to antibiotic-exposed biofilms. Overall, our measurements do not support the existence of a common genetic or biochemical basis for biofilm tolerance against antibiotics. Rather, there are likely myriad genes, proteins, and metabolic pathways that influence the physiological state of microorganisms in biofilms contributing to antibiotic tolerance.
The Staphylococcus aureus microarray data from the study described above is deposited here.

overall_design: 3 independent biological replicates were performed with plankonic, biofilm, and antibiotic treated biofilm samples. Planktonic samples were compared to biofilm samples to identify genes signficantly up- or down-regulated in biofilms. Biofilm samples were compared to antibiotic treated biofilms to indentify genes significantly up- or down-regulated by antibiotic treatment in biofilms.

first: Philip

last: Stewart

first: Kerry

last: Williamson

first: Laura

last: Boegli

first: Timothy

last: Hamerly

first: Ben

last: White

first: Liam

last: Scott

first: Xiao

last: Hu

first: Brendan

last: Mumey

first: Brian

last: Bothner

first: Francisco

middle: G

last: Vital-Lopez

first: Anders

last: Wallqvist

first: Garth

middle: A

last: James


title: p21 produces a bioactive secretome that places stressed cells under immunosurveillance [dataset 1]

first: Hu

last: Li

address: 200 First Street, Gonda Building G19-408

institute: Mayo Clinic

summary: In response to various cellular stresses, the cyclin-dependent kinase inhibitor p21 transiently halts cell cycle progression until the stress is resolved, or indefinitely when permanently damaged cells undergo cellular senescence. p21 does so by repressing the transcription of E2F target genes through hypophosphorylation of Rb, but whether regulation of Rb-mediated gene transcription by p21 controls stress responses beyond cell cycle regulation is unknown. Here we report that in concert with arresting cell growth, a p21-responsive Rb pool interacts with specific Stat and Smad transcription factors at select gene promoters to establish a bioactive secretome, referred to as the p21-activated secretory phenotype (PASP). The PASP consists of several hundred secreted factors that continued to be expressed in a p21-dependent fashion after transiently arrested cells have become senescent. We found that the PASP places stressed cells under immunosurveillance, a property that largely depended on a single factor, the macrophage attractant Cxcl14. In mice, hepatocytes promptly attracted macrophages upon induction of p21 and were eliminated after sequential recruitment of B and T cells several days later. Cells normalizing p21 expression within several days after its induction resumed proliferation and were released from immunosurveillance. Collectively, these findings demonstrate that stressed cells are simultaneously placed under both proliferative arrest and immunosurveillance (to prevent the expansion of stressed, potentially damaged cells), and that p21 coordinates these cell-autonomous and non-autonomous activities at the transcriptional level through regulation of Rb.

overall_design: Examination of H3K27ac landscapes in senescent celles induced by irradiation (IR), serial passaging (REP), KRASG12V-oncogene induciton (OI) and proliferating counterparts (control1) as well as proliferating cells that were induced for 2 days (after irradiation or oncogene-induction).

first: Jan

last: van Deursen


title: Genome-wide differential methylation analysis of ovarian cancer and normal tissue samples

city: Teliyarganj, Prayagraj

first: VIVEK

last: KUMAR

state: Uttar Pradesh

address: Department of Biotechnology, MNNIT Allahabad

department: Biotechnology

institute: Motilal Nehru National Institute of Technology Allahabad

summary:
Purpose: MeDIP based Next-generation sequencing (NGS) has revolutionized differential and funtional mapping of genome-wide methylation signature. The goals of this study are to compare MeDIP-seq derived methylome profiling of miRNA in EOC samples and normal ovary tissue samples, and their downstream expression analysis through quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods.
Methods: Six EOC tissue and two normal  ovary samples were processed and genomic DNA was isolated. MeDIP-seq based library was prepared and for all eight samples and cluster generation and pair end sequencing was performed on Illumina TrueSeq 500 platform. Adptor triming, low quality read and duplicate reads were removed. High qulity read were aligned using BWA-Mem tools. Methylated genome regions and differential methylation analysis was performed using diffReps (v1.55.6). In addition, hypomethylation/hypermethylation of miRNA genes and thier downstream expression analysis was evaluated using qRT–PCR SYBR Green based assays
Results: Using an optimized data analysis workflow, we mapped about ~60-80 million sequence reads per sample to the human. arround 2,24,929 DMR (p<0.05) were identified as differentially methylated regions and out of them 45% were hypermethylated and 55% were hypomethylated compared to normal samples. genomic distribution of DMRs revealed higher enrichment in Gene body, and in other intergenic region. Arround 50 proximal promoter regions of miRNA genes were hypomethylated, while 80 were fall in hypermethylated region. Out of these three miRNA from hypomethylated were screened for further qRT-PCR based expression analysis. qRT-PCR expression analysis revealed upregulation of candidate miRNA in EOC compared to normal samples. Upregulated expression profile of three miRNA obtained from qRT-PCR  confiremed there association with hypomethylation of miRNA genes and their downstream expression.
Conclusions: Our study revealed genome-wide methylome analysis of ovarian cancer tissue samples, using MeDIP NGS based approach. The optimized data analysis workflows reported here should provide a association between gene methylation and their downream expression profiles.  Our results show that MeDIP-seq offers a comprehensive and more accurate genome-wide differential methylation analysis of ovarian cancer tissue. We conclude that MeDIP-seq based  analysis would help in understanding of differential methylation characteristics of cancerous and non-cancerous ovarian tissue samples and could allow us to understand complex biological functions

overall_design: Histologically confirmed six EOC samples (Including three early stage  and three advance stage) and two normal ovary tissue samples, MeDIP-Seq.

first: Vivek

last: Kumar

first: Priyanka

last: Gautam

first: Sameer

last: Gupta

first: Manisha

last: Sachan


title: Single-cell RNA-Seq of premature Rhesus macaques lungs with intra-uterine inflammation and therapuetic blockade

status: Public on Sep 25 2021

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Intrauterine inflammation/infection (IUI), which is present in up to 40% of premature births, leads to elevated levels of pro-inflammatory mediators and microbial products within the amniotic fluid, which come in close contact to fetal mucosae. Yet, knowledge on the fetal mucosal responses to IUI exposure remains limited. To address these questions, we used a non-human primate model of IUI, in which pregnant Rhesus macaques received intra-amniotic (IA) LPS, compared with saline IA.  We found that IA LPS exposure induced a robust and rapid inflammation of the fetal lung.

overall_design: Single-cell RNA-Seq was performed in the premature Rhesus macaques lung in the presence and absence of LPS. Therapuetic intervention was tested in LPS animals with IL-1R, TNF-alpha or combination blockade.

first: Courtney

last: Jackson

first: Shibabrata

last: Mukherjee

first: Paranthaman

last: Senthamaraikannan

first: Pietro

last: Presicce

first: Suhas

last: Kallapur

first: Lisa

last: Miller

first: Ian

last: Lewkowich

first: Martin

last: Demmert

first: Alan

last: Jobe

first: William

last: Zacharias

first: Claire

last: Chougnet


title: JunB regulates the common and lineage-specific transcriptional programs of distinct CD4+ effector T cells

status: Public on Oct 01 2021

city: Onna son

first: Hiroki

last: Ishikawa

state: Okinawa

address: 1919-1 Tancha

institute: Okinawa Institute of Science and Technology Graduate University

summary: IRF4 is critical for differentiation of various CD4+ effector T cells, such as T helper 1 (Th1), Th2, and Th17 subsets, through interaction with BATF-containing AP-1 heterodimers. A major BATF heterodimeric partner, JunB, regulates Th17 differentiation, but the role of JunB in other CD4+ effector T subsets is not fully understood. Here we demonstrate that JunB is essential for accumulation of Th1 and Th2 cells, as well as Th17 cells, both in vitro and in vivo. In mice immunized with lipopolysaccharide (LPS), papain, or complete Freund’s adjuvant (CFA), that induce predominantly Th1, Th2 and Th17 cells, respectively, accumulation of antigen-primed, Junb-deficient CD4+ T cells is significantly impaired. Loss of JunB decreases viability of cells activated under Th1-, Th2-, and Th17-polarizing conditions. RNA-sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) reveal that JunB directly regulates expression of various genes that are commonly induced in priming of naïve CD4+ T cells, including a pro-apoptotic gene Bcl2l11 (encoding Bim), and genes that are specifically induced in Th1, Th2, and Th17 cells. Furthermore, JunB colocalizes with BATF and IRF4 at genomic regions for approximately half of JunB direct target genes. Taken together, JunB, in collaboration with BATF and IRF4, serves a critical function in differentiation of diverse CD4+ T cells by controlling common and lineage-specific gene expression.

overall_design: mRNA profiles of naïve CD4+ T cells collected from Junbfl/fl (WT) and Junbfl/flCd4cre mice (JunB KO) and cultured under Th0, th1 and Th17 polarizing conditions for 48h.

first: Tsunghan

last: Hsieh

first: Daiki

last: Sasaki

first: Hsiaochiao

last: Chien


title: Novel diabetes gene discovery through comprehensive characterization and integrative analysis of longitudinal gene expression changes

status: Public on Sep 16 2021

city: Nashville

first: Hung-Hsin

last: Chen

state: TN

address: 2525 West End Ave., Suite 700

department: Vanderbilt Genetics Institute

institute: Vanderbilt University Medical Center

summary: Type 2 diabetes is a complex, systemic disease affected by both genetic and environmental factors. Previous research has identified genetic variants associated with type 2 diabetes risk, however gene regulatory changes underlying progression to disease are still largely unknown. We investigated RNA expression changes that occur during diabetes progression using a two-stage approach. In our discovery stage, we compared changes in gene expression using two longitudinally collected blood samples from subjects who transitioned to type 2 diabetes between the time points against those who did not with a novel analytical network approach. Our network methodology identified 17 networks, one of which was significantly associated with transition status. This 822-gene network harbors many genes novel to the type 2 diabetes literature, but is also significantly enriched for genes previously associated with type 2 diabetes in GWAS. In the validation stage, we queried associations of genetically determined expression with diabetes-related traits in a large biobank with linked electronic health records. We observed a significant enrichment of genes in our identified network whose genetically determined expression is associated with type 2 diabetes and other metabolic traits and validated 31 gene-level associations that have never been reported by previous type 2 diabetes GWAS. Finally, we performed functional validation, demonstrating that the genes in this network are enriched in enhancers that operate in human pancreatic islet cells. We present an innovative and systematic approach that identified and validated key gene expression changes associated with type 2 diabetes transition status and demonstrated their translational relevance in a large clinical resource.

overall_design: Longitudinal whole blood transcriptome profile of T2D progression

first: Jennifer

last: Below


title: Expression difference of plasma microRNAs between colon adenocarcinoma with or without liver metastasis

status: Public on Sep 30 2021

city: Nanjing

first: Cun-en

last: Wu

address: no.155 Hanzhong Road

institute: Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine

summary: Plasma from a cohort of 6 patients diagnosed with colon adenocarcinoma (3 with hepatic metastasis and 3 without) was selected to identify expression profiles by microRNAs high-throughput RNA-seq analysis. The purpose of this study was to detect the differences in miRNA expression profile of COAD patients with or without liver metastasis, and to explore the potential targets for diagnosis or treatment.

overall_design: Peripheral venous blood was collected from each subject early in the morning on an empty stomach and total cell-free RNA was extracted from the plasma. Then, expression difference of miRNA was evaluated and used for subsequent analysis.

first: Yu-wen

last: Zhuang

first: Jin-yong

last: Zhou


title: RNAseq anaysis of hippocamal parvalbumin-positive interneurons in mice exposed to chronic social defat stress

status: Public on Sep 14 2021

city: New York

first: Marina

last: Schernthanner

state: New York

address: 1230 York Ave.

institute: The Rockefeller University

summary: Purpose: To identify genes differentially expressed in parvalbumin-positive (PV) interneurons of the hippocampus in non-defetaed (CTRL), stress-susceptible and stress-resilient mice.  Method: Translating Ribosome Affinity Purification (TRAP) to isolate RNA from PV+ cells, cDNA synthesis and next generation RNAseq using Illumina Nextseq 500 sequencer. Results: RNA-seq revealed 458 DEGs between non-defeated and resilient mice, 1976 DEGs in non-defeated and susceptible mice, and 3475 DEGs in resilient and susceptible mice.

overall_design:
Cre-dependent EGFP-L10a mice crossed with PV-cre mice (EGFP-L10a+; PV-Cre+) were exposed to chronic social defeat stress. Two hippocampi from one mouse were pooled for one TRAP sample.

CTRL is a TRAP/RNAseq dataset for non-defeat group.
TRL Input is RNAseq dataset for the total RNA sample of non-defeat group before TRAP (translating ribosome affinity purification) procedure.

first: Yong

last: Kim

first: Wei

last: Wang


title: Transcriptomic profiling of plaque psoriasis and cutaneous T cell subsets during treatment with secukinumab

status: Public on Sep 06 2021

city: San Francisco

first: Wilson

last: Liao

address: 2340 Sutter St.

department: Dermatology

institute: University of California, San Francisco

summary: The IL-17A inhibitor secukinumab is efficacious for the treatment of psoriasis. To better understand its mechanism of action, we investigated its impact on psoriatic lesions from 15 moderate-to-severe plaque psoriasis patients undergoing secukinumab treatment. We characterized the longitudinal transcriptomic changes of whole lesional skin tissue as well as cutaneous CD4+ and CD8+ T effector cells and CD4+ T regulatory cells across 12 weeks of treatment. Secukinumab was clinically effective and reduced disease-associated overexpression of IL17A, IL17F, IL23A, IL23R, and IFNG in whole tissue as soon as 2 weeks after initiation of treatment. IL17A overexpression in T cell subsets, primarily CD8+ T cells, was also reduced. While secukinumab treatment resolved 89-97% of psoriasis-associated expression differences in bulk tissue and T cell subsets by week 12 of treatment, we observed expression differences involved in interferon signaling and metallothionein synthesis that remained unresolved at this time point as well as potential treatment-associated expression differences involved in IL-15 signaling. These changes were accompanied by shifts in broader immune cell composition based on deconvolution of RNA-seq data. In conclusion, our study reveals several phenotypic and cellular changes within the lesion that underlie clinical improvement from secukinumab.

overall_design: We biopsied lesional skin from psoriatic patients before secukinumab treatment and at 2, 4, and 12 weeks of treatment for comparison with skin biopsies from 13 healthy subjects. We performed RNA-seq on bulk skin tissue as well as on CD8+ T cells, CD4 T effectors, and CD4+ Tregs sorted from these biopsies

first: Jared

last: Liu

first: Hsin-Wen

last: Chang

first: Robby

last: Grewal

first: Daniel

last: Cummins

first: Audrey

last: Bui

first: Kristen

last: Beck

first: Sahil

last: Sekhon

first: Di

last: Yan

first: Zhi-Ming

last: Huang

first: Tim

last: Schmidt

first: Eric

last: Yang

first: Isabelle

last: Sanchez

first: Mio

last: Nakamura

first: Shrishti

last: Bhattarai

first: Quinn

last: Thibodeaux

first: Richard

last: Ahn

first: Mariela

last: Pauli

first: Tina

last: Bhutani

first: Michael

last: Rosenblum


title: Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing in bovine embryos

status: Public on Aug 18 2021

city: Leuven

first: Joris

middle: R.

last: Vermeesch

address: Herestraat 49 box 606

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

summary: Single-cell whole-genome haplotyping allows simultaneous detection of haplotypes associated with monogenic diseases, chromosome copy-numbering and subsequently, has revealed mosaicism in embryos and embryonic stem cells. Methods, such as karyomapping and haplarithmisis, were deployed as a generic and genome-wide approach for preimplantation genetic testing (PGT) and are replacing traditional PGT methods. While current methods primarily rely on SNP array, we envision sequencing-based methods to become more accessible and cost-efficient. Here, we developed a novel sequencing-based methodology to haplotype and copy-number profile single cells. Following DNA amplification, genomic size and complexity is reduced through restriction enzyme digestion and DNA is genotyped through sequencing. This single-cell genotyping-by-sequencing (scGBS) is the input for haplarithmisis, an algorithm we previously developed for SNP array-based single-cell haplotyping. We established technical parameters and developed an analysis pipeline enabling accurate concurrent haplotyping and copy-number profiling of single cells. We demonstrate its value in human blastomere and trophectoderm samples as application for PGT for monogenic disorders. Furthermore, we demonstrate the method to work in other species through analyzing blastomeres of bovine embryos. Our scGBS method opens up the path for single-cell haplotyping of any species with diploid genomes and could make its way into the clinic as a PGT application.

overall_design: A total of nine samples belonging to two bovine pedigrees were used to compare a sequencing-based with the SNP array-based approach for concurrent haplotyping and copy-number profiling. The semen from the same bull was used for embryo production in both pedigrees. Ovarian tissue samples from the donor cows (mothers) and semen from the bull (father) were used to extract bulk DNA (DNeasy Blood and Tissue kit, Qiagen, Germany). Ovaries were collected separately and retrieval of the oocytes was followed by routine in vitro embryo production.  The embryos were treated with pronase to dissolve zona pellucida and single blastomeres were retrieved from zona free embryos and whole-genome amplified (WGA) using commercial multiple displacement amplification kit (Repli-G Single Cell kit, Qiagen). WGA products and bulk parental and sibling DNA were then SNP genotyped on BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA). Subsequently, the SNP logR and SNP B-allele frequency (BAF) values, as well as the discrete SNP genotype calls were obtained for each single cell and applied in further single-cell analysis to obtain genome-wide haplarithm profiles using a modified version of the siCHILD algorithm (Zamani Esteki et al. 2015).

first: Heleen

last: Masset

first: Jia

last: Ding

first: Eftychia

last: Dimitriadou

first: Sophie

last: Debrock

first: Olga

last: Tšuiko

first: Katrien

last: Smits

first: Karen

last: Peeraer

first: Thierry

last: Voet

first: Masoud

last: Zamani Esteki

middle: R


title: The Tumor Microenvironment Shapes Innate Lymphoid Cells in Patients with Hepatocellular Carcinoma

status: Public on Aug 11 2021

city: Bethesda

first: Tim

last: Greten

state: Maryland

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

summary: Objective: Hepatocellular carcinoma (HCC) represents a typical inflammation-associated cancer. Tissue resident innate lymphoid cells (ILCs) have been suggested to control tumor surveillance. Here we studied how the local cytokine milieu controls ILCs in HCC. Design: We performed bulk RNA sequencing of HCC tissue as well as flow cytometry and single-cell RNA sequencing of enriched ILCs from non-tumor liver, margin and tumor core derived from 48 HCC patients. Simultaneous measurement of protein and RNA expression at the single-cell level (AbSeq) identified precise signatures of ILC subgroups. In-vitro culturing of ILCs was used to validate findings from in-silico analysis. Analysis of RNA-sequencing data from large HCC cohorts allowed stratification and survival analysis based on transcriptomic signatures. Results: RNA sequencing of tumor, non-tumor and margin identified tumor-dependent gradients of which were not only associated with poor survival but also control ILC plasticity. Single-cell RNA sequencing and flow cytometry of ILCs from HCC livers identified NK-like cells in the non-tumor tissue, losing their cytotoxic profile as they transitioned into tumor ILC1 and NK-like-ILC3 cells. Tumor ILC composition was mediated by cytokine gradients that directed ILC plasticity towards activated tumor ILC2s. This was liver-specific and not seen in ILCs from PBMC. Patients with high ILC2/ILC1 ratio expressed IL-33 in the tumor that promoted ILC2 generation which was associated with better survival.  Conclusion: Our results suggest that the tumor cytokine milieu controls ILC composition and HCC outcome. Specific changes of cytokines modify ILC composition in the tumor by inducing plasticity and alter ILC function.

overall_design: Liver tissue and PBMC samples from 6 patients with HCC. 1 additional tissue sample for 10x Genomics WTA analysis.

first: Bernd

last: Heinrich

first: Firouzeh

last: Korangy


title: Evaluation of comprehensive gene expression and NK cell-mediated killing in glioblastoma cell line-derived spheroids [spheroids]

status: Public on Aug 19 2021

city: Kashihara

first: Takayuki

last: Morimoto

state: Nara prefecture

address: 840 Shijo-Cho

department: Department of Neurosurgery

institute: Nara Medical University

summary: GBM is the most common and aggressive primary brain tumor with dismal prognosis. NK cells are large granular lymphocytes with natural cytotoxicity against tumor cells, and they should be established for the novel treatment against patients with GBM. We have previously reported highly activated and ex vivo-expanded NK cells derived from human peripheral blood, which is designated as Genuine-induced natural killer cell (GiNK), induced by our specific culture conditions exerted the cytotoxic effect on GBM cells via apoptosis. First, we comprehensively summarized the molecular characteristics, especially focusing on the expression of stem cell markers, extracellular matrix markers, chemokine, chemokine receptors, and the NK receptors’ ligands, of GBM spheroids compared with 2D adherent GBM cells by using microarray. In the spheroid derived from GBM cell lines, gene expression of stem cell markers, extracellular matrix markers, chemokine, chemokine receptor, NK cell inhibitory receptor’ ligand were up-regulated compared with 2D adherent GBM cells. A preclinical evaluation of the NK cells was performed by ex vivo 3D spheroid model derived from GBM cell lines. In 3D spheroid model, the NK cells accumulated and infiltrated around the spheroids and induced the GBM cell death. Flow cytometry-based apoptosis detection assay clearly showed that the NK cells induced the GBM cell death via apoptosis. Our findings could provide pivotal information for the NK cell based-immunotherapy to patients with GBM.

overall_design: We comprehensively summarized the molecular characteristics, especially focusing on the expression of stem cell markers, extracellular matrix markers, chemokine, chemokine receptors, and the NK receptors’ ligands, of GBM spheroids compared with 2D adherent GBM cells by using microarray. In the spheroid derived from GBM cell lines, gene expression of stem cell markers, extracellular matrix markers, chemokine, chemokine receptor, NK cell inhibitory receptor’ ligand were upregulated compared with 2D adherent GBM cells.

first: Tsutomu

last: Nakazawa

first: Ryosuke

last: Matsuda

first: Fumihiko

last: Nishimura

first: Mitsutoshi

last: Nakamura

first: Shuichi

last: Yamada

first: Ichiro

last: Nakagawa

first: Young

middle: S

last: Park

first: Takahiro

last: Tsujimura

first: Hiroyuki

last: Nakase


title: Differences between the global transcriptomes of Salmonella enterica serovars Dublin and Cerro during infection of bovine epithelial cells

city: Beltsville

first: Serajus

last: Salaheen

address: 10300 Baltimore Ave., Bldg. 173,, BARC-East

department: ARS

institute: USDA

summary: This study compares the global transcriptomes of highly pathogenic bovine-adapted S. enterica serovar Dublin and the less pathogenic bovine-adapted serovar Cerro during interactions with bovine epithelial cells, to identify genes that impact serovar-related outcomes of S. enterica infections in dairy animals

overall_design: Comparing transcriptome profiles of two Salmonella enterica serovars during infection of MAC-T cells.

first: SeonWoo

last: Kim

first: Bradd

last: Haley

first: JoAnn

last: Van Kessel


title: MRG proteins are shared by multiple protein complexes with distinct functions.

status: Public on Aug 17 2021

city: Quebec

first: Maeva

last: Devoucoux

state: Quebec

address: 9 rue MacMahon

country: Canada

institute: Laval University

summary: In this study, we characterized MORF4L1/MRG15 interactome. Using Flag-ChIP-sequencin K562 cells, we first claimed that both MRG15 isoforms (long or short chromodomain) and MORF4L2/MRGX which does not contain any chromodomain, shared mostly the same targets. Then, we described a new factor associated to MRG15, called EP400NL. EP400NL binds to BRD8 also linked to MRGBP and MRG15/X to form a new complex homolog to the yeast TINTIN. Using RNA-sequencing in BRD8 or MRGBP or MRG15/MRGX and KAT5/TIP60-depleted U2OS cells, we observed that human TINTIN plays a role in gene expression regulation independently of NuA4/TIP60 complex.

overall_design: ChIP-sequencing of FLAG versus IgG in K562 cells expressing FLAG tagged MRG15 long CHD, MRG15 short CHD and MRGX protein. RNA-sequencing in U2OS cells after knockdown of MRG15 or MRGX or BRD8 or MRGBP or KAT5/TIP60. siLuciferase was used as control.

first: Samer

last: Hussein

first: Charles

last: Joly-Beauparlant

first: Jacques

last: Cote


title: Gene expression on SARS CoV-2 specific CD8 T cells after SARS CoV-2 vaccination

first: Pablo

last: Penaloza-Macmaster

address: 303 E. Chicago Avenue

department: Microbiology-Immunology

summary:
We studied the impact of a vaccine prime dose on CD8 T cell gene expression
We first immunized mice with an Ad5-SARS CoV-2 spike vaccine and then evaluated gene expression on SARS CoV-2 specific CD8 T cells at week 4.

overall_design: We interrogated whether vaccine prime dose affects gene expression on SARS CoV-2 specific CD8 T cells. To answer this, we immunized C57BL/6 mice intramuscularly with a low dose (LD, 10^6 PFU) or a standard dose (SD, 10^9 PFU) of a SARS CoV-2 vaccine (Ad5-SARS CoV-2 spike). After 4 weeks, we purified splenic CD8 T cells by MACS negative selection, and performed FACS-sorting on live CD8+ CD44+ Kb VNFNFNVL+ (SARS CoV-2 specific CD8 T cells). Purified cells were then delivered to the NUSeq Core for single cell RNA-Seq.

last: Penaloza-MacMaster


title: In vitro expansion of cirrhosis derived liver epithelial cells reveals progenitor-like properties

status: Public on Aug 28 2021

city: Portland

first: Bin

last: Li

state: OR

address: 3181 SW Sam Jackson Pk Rd

department: Oregon Stem Cell Center

institute: Oregon Health and Science University

summary: Our goal is to in vitro expand mouse hepatocytes and human cirrhotic liver hepatocytes. Under the extreme culture condition, mouse hepatocytes proliferated and de-diffrentiated into progenitor cell like cells, moreover, the progenitor like cells could re-differentiate into hepatocytes in vivo. On the other hand, huamn cirrhotic liver cells could also expand and retain the probability of differentiate in vivo.

overall_design: To find the relationship between hepatocytes and hepatocyte derived progenitor cells in vitro. We used TGF-beta, BMP and Hedgehog inhibitors to expand bothe mouse normal hepatocytes and human cirrhotic liver epithelial cells.

first: Carl

last: Pelz

first: Markus

last: Grompe


title: Human AMD

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

summary: Retinal RNA profiles from macula and periphery of each eye were generated by deep sequencing on an Illumina Hi-Seq. 12 biological samples were analyzed.

overall_design: Donor eyes were obtained from non-diabetic Caucasians at a death-to-preservation interval of <6h. Eyes were stored in RNA later before extraction of RNA. For each eye we dissected macula and periphery from retina and RPE/choroid/sclera resulting in 4 samples per eye.


title: FluidigmHT - Evaluation of single-Cell RNA Sequencing Platforms

city: Rochester

first: Jason

last: Myers

state: NY

address: 601 Elmwood Ave.

institute: University of Rochester

summary: comparison of commercially available scRNA-Seq instrumentation using a well-defined cell line and treatment for evaluation

overall_design:
The SUM149PT cell line was developed from Invasive Ductal Carcinoma from a patient with ER negative, PR negative and Her2 positive (not activated) inflammatory breast cancer. The cell line is immortal and expresses luminal cytokeratins 8, 18, and 19, which is consistent with their origin from luminal breast epithelial cells. SUM149PT has been known to form tumors in nude mice.
Two biological replicates per condition (Mock vs TSA), various number of single cells profiled

first: John

last: Ashton


title: Reprogramming of glucocorticoid receptor function by hypoxia: RNA-seq after 6h.

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

summary: Glucocorticoids (GCs) are the most important stress hormones. They act via the GC receptor GR (encoded by the Nr3c1 gene). Their role is to control metabolic pathways, and to limit inflammation. The latter is often compromised, by unknown mechanisms, in severe inflammatory conditions. We here investigated the in vivo impact of hypoxia on GR function in mice, by genome wide analysis in liver and by means of deep hypoxia. Our data reveal that hypoxia leads to profound reductions in transcriptional output of GR, when stimulated with dexamethasone, leading to absent induction of genes with anti-inflammatory functions such as Tsc22d3 and Dusp1 in liver and other organs. Hypoxia also activates the entire HPA axis, by HIF1α and HIF2α activation in hypothalamus, causing long-term corticosterone production by adrenals. The latter leads to lipolysis in adipose tissue, followed by β-oxidation and ketogenesis in liver, but also to the reprogramming of GR, whereby GR limits its anti-inflammatory functions. These genome-wide RNAseq and ChIPSeq data, accompanied with studies using GR inhibitor, GR mutant mice and adrenalectomized animals suggest that hypoxia leads to increased sensitivity for acute inflammation and lack of protection by dexamethasone, due to the chronic HPA axis stimulation. Our data unfold new physiological pathways, that may have consequences for patients suffering from GC resistance or living at high altitudes.

overall_design: A total of 4 condition were subjected to RNA-seq: Normoxia+PBS, Hypoxia+PBS, Normoxia+DEX and Hypoxia+DEX. Each of the 4 condictions has 3 biological replicates.

first: Tineke

last: Vanderhaeghen

first: Deepika

last: Watts

first: Ville

last: Paakinaho

first: Lise

last: Van Wyngene

first: Kelly

last: Van Looveren

first: Jolien

last: Vandewalle

first: Charlotte

last: Wallaeys

first: Louise

last: Nuyttens

first: Melanie

last: Eggermont

first: Sylviane

last: Dewaele

first: Joke

middle: V

last: Berghe

first: Joey

last: De Backer

first: Laura

last: Dirkx

first: Sylvia

last: Dewilde

first: Guy

last: Caljon

first: Bart

last: Ghesquière

first: Ben

last: Wielockx

first: Jorma

last: Palvimo

first: Rudi

last: Beyaert

first: Claude

last: Libert


title: 10X Genomics - Evaluation of single-Cell RNA Sequencing Platforms

first: Jason

last: Myers

first: John

middle: M

last: Ashton


title: Expression data for HMLE-based EMT models

status: Public on Aug 03 2021

city: Detroit

first: Guojun

last: Wu

state: MI

address: 4100 John R

department: Cancer Biology

institute: Wayne State University

summary: EMT was induced using stable overexpression of 1 of 4 EMT transcription factors (FOXQ1, TWIST1, ZEB2, and SNAI1) in the HMLE cell line. HMLE cells with ectopic LACZ expression were used as control cells.

overall_design: RNA was isolated from cells from each condition and hybridized on Affymetrix array. Gene expression changes were compared between models to elucidate the common factors up- and downregulated by EMT-TFs.

first: James

last: Block


title: Systematic functional interrogation of human pseudogenes

status: Public on Aug 01 2021

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

institute: UT MD Anderson Cancer Center

summary: Human genome encodes >14,000 pseudogenes that are evolutionary relics and have long been considered as nonfunctional genomic elements.  Emerging evidence suggests that pseudogene can exert important regulatory function. However, function of most pseudogenes remains unknown. To fill this gap, we developed an integrated computational pipeline and performed to date the first set of pseudogene-focused CRISPRi screens in human cells. Our screens identified >100 pseudogenes that are important for cell fitness, with a more cell-type specific function compared to parent genes. In addition, we discovered a cancer-testis unitary pseudogene MGAT4EP that interacts with FOXA1, a key regulator in luminal A breast cancer.

overall_design: 5703 sgRNAs target pseudogenes and 3727 sgRNAs target their parent genes were included in the library. The CRISPRi screen was conducted in MCF7 cell line. MGAT4EP expression was down-regulated by sgRNA in dcas9 expressed MCF7 cells, and then next generation sequencing was performed to identify MGAT4EP regulated genes.

first: Chen

last: Yiwen

first: Xu

last: Han

first: Sun

last: Ming

first: Wang

last: Yunfei

first: Wei

last: Yanjun


title: ADDICTION OF MERKEL CELL CARCINOMA TO MUC1-C IDENTIFIES A POTENTIAL NEW TARGET FOR TREATMENT OF THIS RECALCITRANT MALIGNANCY [MCC26]

status: Public on Jul 30 2021

city: Boston

first: Yoshihiro

last: Morimoto

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: MCCP and MCCN cells are addicted to the oncogenic MUC1-C protein. MUC1-C is a druggable target that may provide new opportunities for advancing MCC treatment.

overall_design: RNA-seq in MCC cell lines


title: ADDICTION OF MERKEL CELL CARCINOMA TO MUC1-C IDENTIFIES A POTENTIAL NEW TARGET FOR TREATMENT OF THIS RECALCITRANT MALIGNANCY [MKL1]


title: Evaluation of single-Cell RNA Sequencing Platforms

status: Public on Oct 06 2021

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

overall_design: Refer to individual Series


title: ADDICTION OF MERKEL CELL CARCINOMA TO MUC1-C IDENTIFIES   A POTENTIAL NEW TARGET FOR TREATMENT OF THIS RECALCITRANT MALIGNANCY

status: Public on Jul 29 2021

overall_design: RNA-seq in WaGa cells