title: Impaired efferocytosis enables apoptotic osteoblasts to escape osteoimmune surveillance during aging (mRNA)

city: Nanjing

first: Rongyao

last: Xu

address: 140 Hanzhong Road, Nanjing, Jiangsu Province 210029, China.

institute: Nanjing medical university

summary: Macrophages efferocytosis of apoptotic osteoblasts (apoOBs) is a key osteoimmune process for bone homeostasis that is highly regulated in osteoimmune surveillance. However, apoOBs accumulate in aged bone marrow, where they might mount proinflammatory responses and progressive bone loss. Why apoOBs were not cleared during aging remains unknown. Here, we show that apoOBs upregulate immune checkpoint molecule CD47 with age to evade macrophages clearance. Using osteoblast- and myeloid-specific gene knockout mice, we identify histone deacetylase SIRT6 as an essential regulator of the CD47–SIRPα checkpoint. Further, apoOBs that require SIRT6-mediated chemotaxis signals can recruit macrophages by releasing apoptotic extracellular vesicles. Therapeutically, we develop two targeting delivery strategies to enhance SIRT6 activity, showing increased apoOBs clearance and delayed age-related bone loss. Collectively, our data revealed a previously unknown linkage between immune surveillance and bone homeostasis and targeting the mechanism of SIRT6-regulated apoOBs clearance could be a promising therapeutic strategy for age-related bone diseases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for apoptotic osteoblasts (apoOBs)  from young and old mice


title: Distinct serum microRNA profiles in patients with active autoimmune hepatitis

status: Public on Apr 27 2022

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

summary: Serum microRNAs are useful for the early diagnosis and management of autoimmune hepatitis

overall_design: Serum microRNA profiles of patients with autoimmune hepatitis (AIH),  primary biliary cholangitis (PBC), overlap syndrome (OS), or without hepatic diseases.

first: Chisato

last: Saeki

first: Juntaro

last: Matsuzaki

first: Makiko

last: Ichikawa

first: Tsunekazu

last: Oikawa

first: Masanori

last: Nakano

first: Yuichi

last: Torisu

first: Tomokazu

last: Matsuura

first: Yasuni

last: Nakanuma

first: Mikio

last: Zeniya

first: Akihito

last: Tsubota

first: Masayuki

last: Saruta

first: Takahiro

last: Ochiya


title: Single Cell RNA-seq data of C1-sgControl, C1-sgEED and C1-sgKMT2D cells

status: Public on Apr 26 2022

city: Cambridge

first: Yun

last: Zhang

email: zhangyunbio@gmail.com, barc@wi.mit.edu

state: MA

address: 455 Main Street

country: USA

institute: Whitehead Institute for Biomedical Research

type: Expression profiling by high throughput sequencing

summary: Analysis of gene expression patterns at single cell level of C1-sgControl, C1-sgEED and C1-sgKMT2D cells.

overall_design: HMLER-derived C1 cells were gene-edited to generate C1-sgControl, C1-sgEED and C1-sgKMT2D cells. Knock-out of EED or KMT2D enabled the initially stable epithelial C1 cells to gain epithelial-to-mesenchymal plasticity and generated more mesenchymal cell populations.C1-sgControl. C1-sgEED and C1-sgKMT2D cells were stained using anti-human Hashtag antibody associated with three distinct barcodes (BioLegend) before library preparation

first: Robert

last: Weinberg


title: Single-cell RNA-sequencing of mouse colonic monocytes and macrophages (chow vs. high fat diet)

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: We performed a single-cell transcriptome analysis of colon monocytes and macrophages in 2 mice fed with control diet (chow) and 2 mice fed with high-fat diet for 1 week.

overall_design: CD11b+nonDCs colonic macrophages (liveCD45+Lin-CD11b+CD24- and pos for CD64 or Ly6C) were sorted for each replicate mouse, and used for single cell RNA-seq on a 10x genomics Chromium platform.

first: Theresa

last: Rohm

first: Claudia

last: Cavelti

first: Julien

last: Roux


title: EPIC Methylation array profiling of MCF-7 cells

city: Oslo

first: Roza Berhanu

last: Lemma

address: Gaustadalléen 21

department: Center for Molecular Medicine Norway

country: Norway

institute: University of Oslo

summary: To study the effect of FOXA1 knock-down on DNA methylation patterns, we performed DNA methylation profiling of MCF-7 cells in three conditions, (1) control cell line, (2) cell line subjected to siRNA-mediated knockdown of endogenous FOXA1 expression and (3) cell line whose endogenous FOXA1 knockdown is rescued with transient expression of FOXA1-V5.

overall_design: EPIC methylation array profiling of MCF-7 cells was made in three different treatment conditions and three biological replicates. (1) MCF-7 cells treated with siCtrl (cat.no 1027281, Qiagen), (2) MCF-7 subjected to siRNA- mediated KD of endogenous FOXA1 using siFOXA1 (sense 5′-GAGAGAAAAAAUCAACAGC-3′ and antisense 5′-GCUGUUGAUUUUUUCUCUC-3′), (3) Rescue of siRNA-mediated endogenous FOXA1 KD with transient expression of C-terminally V5 tagged FOXA1 (RefSeq accession ID NM_004496).

first: Roza

middle: B

first: Thomas

last: Fleischer

first: Anthony

last: Mathelier


title: Microarray profiling of microRNA in Chlamydia trachomatis-infected recurrent spontaneous aborters

city: New Delhi

first: Ankita

last: Ray

state: Delhi

address: Safdarjung hospital campus

country: India

institute: ICMR-National Institute of Pathology

summary:
The present study aimed to investigate the profile of serum-circulating miRNAs and their target genes and elucidate their role in infected and non-infected C. trachomatis RSA patients by microarray
miRNAs and mRNAs were found to be differentially expressed in C. trachomatis-positive RSA patients
Non-heparinized blood samples were collected from 25 RSA patients with history of three or more consecutive abortions

overall_design: Non-heparanized blood was collected from women with history of RSA. Urine sample was also collected to test for presence of C.trachomatis by conventional PCR assay. Samples positive and negative for C. trachomatis were studied for miRNA microarray analysis

first: Sangita

last: Rastogi


title: Cell environment shapes TDP-43 function: implications in neuronal and muscle disease

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

summary: TDP-43 aggregation and redistribution have been recognised as a hallmark of amyotrophic lateral sclerosis, frontotemporal dementia and other neurological disorders. While TDP-43 has been studied extensively in neuronal tissues, TDP-43 inclusions have also been described in the muscle of inclusion body myositis patients, highlighting the need to understand the role of TDP-43 beyond the central nervous system.  Using RNA-seq we performed the first direct comparison of TDP-43-mediated transcription and alternative splicing in muscle (C2C12) and neuronal (NSC34) mouse cells. Our results clearly show that TDP-43 displays a tissue-characteristic behaviour targeting unique transcripts in each cell type. This is not due to variable transcript abundance but rather due to cell-specific expression of RNA-binding proteins, which influences TDP-43 performance. Among splicing events commonly dysregulated in both cell lines, we identified some that are TDP-43-dependent also in human cells and show that inclusion levels of these alternative sequences appear to be altered in affected tissues of FTLD and IBM patients. We therefore propose that TDP-43 dysfunction, reflected in aberrant splicing, contributes to disease development but it does so in a tissue-specific manner.

overall_design: Direct comparison of TDP-43-mediated transcription and alternative splicing in muscle (C2C12) and neuronal (NSC34) mouse cells.

first: Emanuele

last: Buratti


title: Integrated Metabolic Profiling and Gene Expression Analysis Reveals Therapeutic Modalities in Breast Cancer

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Here, we report two distinctive groups defined by metabolites; a TNBC-HIGH group that shows high levels of pyrimidine pathway metabolites and biosynthetic enzymes, and an ER-HIGH group that shows high levels of fatty acid and arginine biosynthesis intermediates. We identify different metabolic enrichment profiles between cell lines grown in vitro vs. in vivo; cell lines grown in vivo recapitulate patient tumors metabolic profiles. Further, we identify a subset of genes that strongly correlates with the TNBC-HIGH metabolic profile using integrated metabolic and gene expression profiling, which strongly predicts patient prognosis when tested on larger human datasets. As a proof-of-principle, when we target TNBC-HIGH metabolic dysregulation with a pyrimidine biosynthesis inhibitor (Brequinar), and/or a glutaminase inhibitor (CB-839), we observe therapeutic efficacy and decreased tumor growth in representative TNBC cell lines, murine p53-null mammary tumors, and in vivo patient-derived xenografts (PDXs) upon multi-agent drug treatment. This study highlights potential new therapeutic opportunities in breast cancers guided by a genomic biomarker, which could prove impactful for breast cancers that rapidly proliferate.

overall_design:
Examination of metabolomics and genomic data for human and murine tumors (in vitro and in vivo) to determine metabolic signatures unqiue to TNBCs vs. other breast cancers.
RNA-Seq raw data is to be made available through dbGaP (controlled access) due to privacy concerns

first: Chengheng

last: Liao

first: Cherise

middle: R

last: Glodowski

first: Cheng

last: Fan

first: Juan

last: Liu

first: Kevin

last: Mott

first: Jason

middle: W

last: Locasale

first: Samuel

middle: K

last: McBrayer

first: Ralph

middle: J

last: DeBerardinis

middle: M

first: Qing


title: Editing the core region in HPFH deletions alters fetal and adult globin expression for treatment of β-hemoglobinopathies  [4C]

city: Vellore

first: Saravanabhavan

last: Thangavel

state: Tamil Nadu

address: Lab-7, Centre for Stem Cell Research, Christian Medical College campus,Bagayam.

department: Centre for Stem Cell Research (an unit of InStem-Bengaluru)

institute: Christian Medical College

summary:
We have identified putative repressor region (PRR) to exon-1 of β-globin (βE1) in the β-globin cluster as a core region in alll the HPFH deletions that activates fetal hemoglobin and silences adult hemoglobin. To test the impact of PRR-βE1 gene editing in β-globin cluster configuration, we employed  Circular chromosome conformation capture (4C) analysis to assess the LCR interaction to the gamma-globin promoter. Using HBG2 promoter as viewpoint,4C analysis showed an increased interaction of HBG promoter to the hypersensitive (HS) sites of the LCR in HUDEP-2 clones harbouring PRR-βE1 biallelic deletions compared to control HUDEP-2 cells.

Link for 4C output files
Mendeley - Venkatesan, Vigneshwaran (2022), “4C data set ”, Mendeley Data, V1, doi: 10.17632/cz3thnr9kf.1

first: Venkatesan

last: Vigneshwaran

first: Thangavel

last: Saravanabhavan


title: Age-associated changes in the skin transcriptome in Naked mole-rats

city: Boston

first: Vladimir

last: Botchkarev

address: 609 Albany Street

institute: Boston University

summary: Naked mole rats (NMRs, Heterocephalus glaber) are long-lived mammals that possess a natural resistance to cancer and other age-related pathologies, maintaining a healthy life span for >30 years. We report application of RNAseq technology to analyze changes in the skin transcriptome of NMRs during aging. RNAseq analyses reveal that the transcript levels of several longevity-associated (Igfbp3, Igf2bp3, Ing2) and tumor-suppressor genes (Btg2, Cdkn1a, Cdkn2c, Dnmt3a, Hic1, Socs3, Sfrp1, Sfrp5, Thbs1, Tsc1, Zfp36) are increased in aged versus young NMR skin. Overall, these data suggest that specific features in the NMR skin aging transcriptome might contribute to the resistance of NMRs to spontaneous skin carcinogenesis and provide a platform for further investigations of NMRs as a model organism for studying the biology and disease resistance of human skin.

overall_design: Total RNA was extracted from full-thickness dorsal skin samples obtained from young and old NMRs. The RNA samples were analyzed by RNAseq.

first: Chris

last: Faulkes

first: Andrei

last: Mardaryev

first: Andrey

last: Sharov


title: Epigenetic reversal of lineage plasticity enhances responsiveness to anti-GD2 therapy in neuroblastoma [ChIP-Seq]

city: West Lafayette

first: Nathaniel

middle: Wesley

last: Mabe

state: Indiana

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: GD2 is a disialoganglioside that is highly expressed on the surface of neuroblastoma cells. Immunotherapy with anti-GD2 antibodies has revolutionized the treatment of children with high-risk neuroblastoma, but nearly half of patients relapse and little is known about mechanisms of resistance to anti-GD2. Neuroblastomas harbor intrinsic transcriptional plasticity by co-opting divergent lineage-specific developmental programs between adrenergic and mesenchymal cell states. We found that reduced GD2 expression was significantly correlated with the adrenergic cell state in neuroblastoma and that an Adrenergic-to-Mesenchymal Transition (AMT) conferred downregulation of GD2 and resistance to anti-GD2 antibody. Induced reprogramming of adrenergic cells with the master AMT regulator PRRX1 was sufficient to promote transcriptional rewiring in isogenic models and downregulate GD2 expression. Mechanistically, low-GD2 expressing cell lines demonstrate significantly reduced expression of the ganglioside synthesis enzyme ST8SIA1 (GD3 synthase), resulting in a bottlenecking of GD2 synthesis. Primary neuroblastoma tumors enriched for mesenchymal features show demonstrably lower GD3 synthase expression as compared to adrenergic tumors. Pharmacologic inhibition of EZH2 resulted in epigenetic rewiring of mesenchymal neuroblastoma cells and re-expression of ST8SIA1, restoring surface expression of GD2 and sensitivity to an anti-GD2 antibody. These data identify developmental lineage as a key determinant of sensitivity to anti-GD2 based immunotherapies and credential EZH2 inhibitors for clinical testing in combination with anti-GD2 antibody to enhance outcomes for children with neuroblastoma.

overall_design: SK-N-AS cells were treated for 14 days with vehicle (V) or 1 uM tazemetostat (T) in biological quadruplicate


title: GOLGA8 increases bulk antisense oligonucleotide uptake and activity in mammalian cells

city: Carlsbad

first: Sagar

middle: S

last: Damle

state: CA

address: 2855 Gazelle Ct

department: Functional Genomics

institute: Ionis Pharmaceuticals

summary: Antisense oligonucleotides (ASOs) are short synthetic nucleic acids that recognize and bind to complementary RNA to modulate gene expression.  It is well-established that single-stranded, phosphorothioate modified ASOs enter cells independent of carrier molecules, primarily via endocytic pathways, but that only a small portion of internalized ASO is released into the cytosol and/or nucleus rendering the majority of ASO as inaccessible to the targeted RNA.  Identifying pathways that can increase the available ASO pool is valuable as a research tool and therapeutically.  Here, we conducted a functional genomic screen for ASO activity by engineering GFP splice reporter cells and applying genome wide CRISPR gene activation.  The screen can identify factors that enhance ASO splice modulation activity.  Characterization of hit genes uncovered GOLGA8, a largely uncharacterized protein, as a novel positive regulator enhancing ASO activity by ~2-fold.  Bulk ASO uptake is 5-fold higher in GOLGA8 overexpressing cells where GOLGA8 and ASOs are observed in the same intracellular compartments. We find GOLGA8 is highly localized to the trans-Golgi and readily detectable at the plasma membrane.  Interestingly, overexpression of GOLGA8 increased activity for both splice modulation and RNase H1-dependent ASOs.  Taken together, these results support a novel role for GOLGA8 in productive ASO uptake.

overall_design: Comparative gene expression analysis of DGE data for K562 cells and derivatives expressing CRISPR components designed to activate gene expression of indicated genes

first: Moira

middle: A

last: McMahon

first: Meghdad

last: Rahdar

first: Swagatam

last: Mukhopadhyay

first: Hyunh-Hoa

last: Bui

first: Christopher

last: Hart

first: Margo

last: Courtney

first: Michael

last: Baughn

first: Don

last: Cleveland

first: C

middle: F

last: Bennett


title: Gamma-glutamyltransferase 7 suppresses gastric cancer by cooperating with RAB7 to induce mitophagy

city: Beijing

first: Xiaohong

last: Wang

address: Fucheng

country: China

institute: Peking university cancer hospital

summary: We identified gamma-glutamyltransferase 7 (GGT7) to be frequently downregulated in gastric cancer, but its role remains unknown. Here we elucidated the clinical significance, functional roles and molecular mechanism of GGT7 in gastric cancer. GGT7 was downregulated by promoter methylation and restored by demethylation treatment in gastric cancer cells. GGT7 methylation inversely correlated with mRNA expression in gastric tumors (n=221; r=-0.686, P<0.0001). High-expression of GGT7 in adjacent non-tumor tissues was significantly associated with favorable survival in gastric cancer patients (n=138; P=0.009), and was an independent prognostic factor by multivariate Cox regression (HR=0.381, P<0.05). GGT7 significantly inhibited gastric cancer cell growth, G1-S transition, and migration and invasion abilities. GGT7 also significantly attenuated the growth of subcutaneous xenograft tumors and reduced metastasis to the lung in nude mice. The mitophagy regulator RAB7 was identified as a direct downstream co-player of GGT7 by co-immunoprecipitation followed by mass spectrometry. Growth suppression effect of GGT7 was at least partly dependent on RAB7 by rescue experiments. GGT7 induced autophagy as shown by electron microscopy and confirmed by the increased LC3B and decreased p62. GGT7 recruited RAB7 by direct binding and drove RAB7 to translocate from nucleus to cytoplasm, subsequently mediating mitophagy by increasing mitophagy mediators/inducers. GGT7 inhibited intracellular ROS, which was associated with increased mitophagy, and subsequently suppressed MAPK signaling. Collectively, GGT7 plays a pivotal tumor-suppressing role in gastric cancer by directly binding with RAB7 to induce mitophagy and inhibit ROS and MAPK cascades. GGT7 is an independent prognostic factor for gastric cancer patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AGS cells and its ectopic expression derivatives (AGS-GGT7).

first: Lianhai

last: Zhang

first: Francis

last: Chan

first: Jiafu

last: Ji

first: Jun

last: Yu

first: Qiaoyi

last: Liang


title: Pleiotropic Fitness Effects of the lncRNA Uhg4 in Drosophila melanogaster

city: Greenwood

first: Rebecca

last: MacPherson

state: SC

address: 114 Gregor Mendel Circle, Dr. Trudy Mackay

department: Center for Human Genetics

institute: Clemson University

summary: Long noncoding RNAs (lncRNAs) are a diverse class of RNAs that are critical for gene regulation, DNA repair and splicing, and have been implicated in cancer, stress response, and development. However, the function of many lncRNAs remains unknown. In Drosophila melanogaster, U snoRNA host gene 4 (Uhg4) encodes an antisense long noncoding RNA that is host to seven small nucleolar RNAs (snoRNAs). Uhg4 is expressed ubiquitously during development and in all adult fly tissues with maximal expression in ovaries; however, it has no annotated function(s). Here, we used CRISPR-Cas9 germline gene editing to generate multiple deletions spanning the promoter region and first exon of Uhg4. Mutant flies were sterile, showed delayed development and decreased viability, and changes in sleep and responses to stress. Whole genome RNA sequencing of Uhg4 deletion flies and their controls identified coregulated genes and genetic interaction networks. Gene ontology analyses highlighted a broad spectrum of biological processes, including morphogenesis, stress response, and regulation of transcription and translation. Thus, Uhg4 is a lncRNA essential for reproduction with pleiotropic effects on multiple fitness traits.

overall_design: RNAseq (post rRNA depletion) of whole body Drosophila melanogaster, sexes separately, in the genetic background DGRP_208 (control), where mutant samples 208A, 208F, 208G have independent deletions of Uhg4. Two replicates per sex per line.

first: Vijay

last: Shankar

first: Lakshmi

middle: T

last: Sunkara

first: Rachel

middle: C

last: Hannah

first: Marion

last: Campbell III

first: Robert

last: Anholt

first: Trudy

last: Mackay


title: Trappc1 is essential for the maintenance and differentiation of common myeloid progenitors in mice

first: Zhaoqi

state: Beijing

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

institute: University of Chinese Academy of Sciences

summary: Trafficking protein particle complex (Trapp complex) is a highly conserved multi-unit protein machinery, and participates in intracellular vesicle traffic related process. Currently, little is known about Trapp complexes in the development of immune cells. Here，we uncovered the continuously up-regulated protein processing in endoplasmic reticulum during myeloid cell development by bioinformatics data mining, and identified trafficking protein particle complex subunit 1 (Trappc1,one of the core subunits of Trapp complexes) as an indispensable master for myeloid cell development. By using the ER-Trappc1 inducible knockout mice and bone marrow chimeric mouse models and in vitro experiments, we demonstrated that the deficiency of Trappc1 led to a sever defect of myeloid cells, including monocytes and neutrophils, resulting from dramatic loss and retardation of common myeloid progenitors (CMPs) differentiation. Mechanistically, Trappc1-depleted CMPs suffered from an irreparable endoplasmic reticulum stress, and underwent apoptosis via Ca2+ mitochondrial dependent pathway. Meanwhile, the depletion of Trappc1 caused the cell cycle arrest and cellular senescence of CMPs by activation of pancreatic endoplasmic reticulum kinase (PERK) and downstream up-regulation of cyclin-dependent kinase inhibitor p21. The proliferation stagnation and elevated apoptosis of CMPs conspired to cause the defect of myeloid cell development. These findings reveal the essential role of Trappc1 in the maintenance and differentiation of CMPs, and contributes to existing knowledge of the significancy endoplasmic reticulum homeostasis during myeloid cell development.

overall_design: Cells were stained with fluorescein conjugated antibodies  in PBS containing 0.1% BSA and 0.1% NaN3 at 4 ℃ for 30 minutes in dark. The stained samples were then sorted by MoFlo Astrios EQ Cell Sorter (Beckman Coulter)，CMPs (Lin-Sca1-CD117+CD16/32lowCD34+)，GMPsCMPs (Lin-Sca1-CD117+CD16/32highCD34+)

first: Yanan

last: Xu


title: Oncogenesis and organ infiltration specific therapy in a preclinical model of Ph-like B cell acute lymphoblastic leukemia

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

country: Germany

institute: University Medical Center - Mainz

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

overall_design: Refer to individual Series


title: IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells

city: Toronto

first: Boaz

last: Nachmias

state: Ontario

address: 101 College St.

country: Canada

institute: Princess Margaret Cancer Centre


title: IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells [ChIP-seq]

summary: Through a comparison between genes that are significant for growth and viability of AML cells by way of a CRISPR screen, with genes that are differentially expressed in leukemia stem cells, we identified importin 11 (IPO11) as a novel target in AML.  In AML, knockdown of IPO11 decreased growth, reduced engraftment potential of stem cells and induced differentiation. Mechanistically, we identified the transcription factors BZW1 and BZW2 as novel cargoes of IPO11. We further show that BZW1/2 mediate a transcriptional signature that promotes stemness and survival of LSC.

overall_design: ChIP seq analysis for BZW1 and BZW2 in OCI-AML2 cells

first: Aaron

middle: D

last: Schimmer


title: Next Generation Sequencing Facilitates Quantitative Analysis of mouse neural stem cells (NSCs) Transcriptomes

city: beijing

first: hong

last: yao

state: beijing

address: shuangqing road 30

department: school of pharmacy

institute: Tsinghua

summary: The aim of this study was to compare the effects of different drug treatments on neural stem cells

overall_design: Methods: neural stem cells from 2-day-old mice were generated by deep sequencing, in triplicate, using Illumina.

first: Hong

last: Yao

first: Gelin

last: Wang


title: Integrated analysis of hepatic miRNA and mRNA expression profiles in the spontaneous recovery of liver fibrosis

city: Chengdu

first: Yang

last: Tai

state: Sichuan

address: NO. 37, Xiang Xue Guo

institute: West China Hospital, Sichuan University

type: Non-coding RNA profiling by high throughput sequencing


title: Epigenetic reversal of lineage plasticity enhances responsiveness to anti-GD2 therapy in neuroblastoma [ATAC-seq SK-N-AS]

first: Nathaniel

last: Mabe


title: Integrated analysis of hepatic miRNA and mRNA expression profiles in the spontaneous recovery of liver fibrosis [miRNA]

summary: Liver fibrosis, results from the imbalance between extracellular matrix (ECM) production and degradation, is a common pathological consequence of various chronic liver diseases. Although a large number of miRNAs have been reported in liver fibrosis progression, miRNA-mRNA interactions involved in its reversal process remain to be fully elucidated. In the current study, we performed an integrated analysis of miRNA and mRNA expression profiles in a hepatic fibrosis recovery mouse model induced by thioacetamide. A total of 102 miRNA and 2,845 mRNAs showed significant differential expression in recovery mice compared to fibrotic mice. Moreover, 3,769 putative negatively correlated miRNA-mRNA pairs were revealed to be potentially implicated in the biological function regulation of small molecule metabolism and ECM organization. By integrating miRNA-mRNA regulatory networks, mmu-miR-1843a-5p, mmu-miR-193a-5p, mmu-miR-194-2-3p and mmu-miR-30c-2-3p were identified as lysyl oxidase-specific miRNAs that were associated with the pathogenesis of fibrosis recovery. Our results provide potential novel biomarkers and candidate targets for the treatment of liver fibrosis.

overall_design: Liver fibrosis was induced by intraperitoneal injection of thioacetamide (TAA) for 8 weeks. Control mice received the same volume of normal saline (NS).  Liver fibrosis recovery model (Recovery) was established via 8-week TAA injection and then withdrew the repeated liver damages, following by spontaneous recovery for additional 8 weeks. miRNA expression profile was performed in the liver tissues of TAA-fibrotic mice, recovery mice and control mice.

first: Jinhang

last: Gao

first: Chengwei

last: Tang


title: Exosomes secreted by the CCND2OECMs promote proliferation and hypoxia tolerance in cultured CMs

city: Hangzhou

first: meng

last: zhao

state: Zhejiang

address: 501 Buliding 1, 18 Shilongshan Road, Cloud Town, Xihu District, Hangzhou, P.R. China

department: Life Science school

institute: Westlake Universituy

summary: CCND2OEExos (exosomes from CCND2-overexpressing hiPSC-derived cardiomyocytes (CCND2OECMs)) were found to be able to promote proliferation of not only cardiomyocytes, but also human umbilical vein endothelial cells (HUVEC) and human vascular smooth muscle cells (HVSMC) in vitro, as indicated by the large number of ki67+ and PH3+ HUVECs and SMCs in the CCND2OEExos-treated group, relative to those in the vehicle only- or CCND2WTExos-treated groups. A comparative bulk sequence analysis of miRNAs from CCND2WTExos and CCND2OEExos (exosomes from wild type hiPSC-derived cardiomyocytes) was performed to identify some underlying mechanisms about proliferation induction.

overall_design: Examination of 2 different miRNA profiles in CCND2WTExos and CCND2OEExos

first: Meng

last: Zhao

first: Anton

middle: V

last: Borovjagin

first: Jay

last: Zhang


title: IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells [RNA-Seq]

overall_design: OCI-AML2 cells were trransfected with sh against IPO11 or BZW1/2 and compared to non-target scrammbeled sh


title: Epigenetic reversal of lineage plasticity enhances responsiveness to anti-GD2 therapy in neuroblastoma [RNA-seq kelly cells]

overall_design: Parental Kelly cells were stained with GD2-APC antibody, then FACS-sorted into GD2-low (GD2_L) and GD2-high (GD2_H) populations


title: Mesoderm-Derived PDGFRA+ Cells Regulate the Emergence of Hematopoietic Stem Cells in the Dorsal Aorta

city: Sydney

first: Dominik

last: Beck

state: NSW

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

country: Australia

institute: University of Technology Sydney

summary: Mouse hematopoietic stem cells (HSCs) first emerge at embryonic day 10.5 (E10.5) on the ventral surface of the dorsal aorta, by endothelial-to-hematopoietic transition (EHT). We investigated whether cells with mesenchymal stem cell-like cell (MSC-LCs) activity that provide an essential niche for HSCs in the bone marrow reside in the aorta-gonad-mesonephros (AGM) and contribute to the structural development of the dorsal aorta and EHT. Using transgenic mice, we demonstrate a lineage hierarchy for AGM MSC-LCs and trace the aortic endothelium and HSCs to mesoderm-derived (Mesp1) PDGFRA+ cells. Mesp1/PDGFRA+ MSC-LCs dominate the sub-endothelial and ventral stroma in the E10.5–E11.5 AGM but by E13.5 are replaced by neural crest (Wnt1) MSC-LCs. Co-aggregating endothelial cells with Mesp1 but not with Wnt1 MSC-LCs resulted in EHT and generation of LT-HSCs that is interrupted by dose-dependent inhibition of PDGFRA signalling. This partnership between endothelial cells and AGM Mesp1 MSC-LCs could be harnessed to manufacture HSCs from endothelium.

overall_design: Single cell RNA sequencing was used to identify differences and similarities between the tested populations of fresh adult cardiac endothelium and co-aggregated culture with MesP1(der)/PSCs for 24, 48, 72 and 96 hours..

first: Vashe

last: Chandrakanthan

first: John

last: Pimanda

first: Diego

last: Chacon


title: Editing the core region in HPFH deletions alters fetal and adult globin expression for treatment of β-hemoglobinopathies

status: Public on Apr 25 2022

first: Saravanabhavan

last: Thangavel

summary: We have identified putative repressor region (PRR) to exon-1 of β-globin (βE1) in the β-globin cluster as a core region in alll the HPFH deletions that activates fetal hemoglobin and silences adult hemoglobin. Here we charactised the transcriptome of the erythroblasts derived from PRR-βE1 gene edited HSPCs. Transcriptome analysis showed an increased expression of HBG, HBBP1 and decreased expression of HBB transcripts compared to control.

overall_design: RNA-seq

first: Venkatesan

last: Vigneshwaran

first: Thangavel

last: Saravanabhavan


title: Whole transcriptome expression profiling of pancreatic cancers patients with T4 stage but diametrically opposing survival outcomes

city: nanjing

first: Guodong

last: Shi

state: Jiangsu

address: guangzhou road 300

institute: the First Affliated Hospital of Nanjing Medical University

summary: Pancreatic cancer is a highly malignant tumor in the digestive tract, with its incidence increasing year by year. Due to the insidious onset and rapid progression, most patients have already advanced disease at the time of the initial diagnosis, and the overall 5-year survival rate was only 11%. Tumors in T4 stage often have the invasion of key upperabdominal vessels, mainly referring to artery-involved pancreatic cancer with a worse prognosis. Resection of pancreatic ductal adenocarcinoma (PDAC) with T4 stage is more challenging and usually needs advanced surgical techniques including treatment of the involved artery including sub-adventitial divestment technique (SDT) and arterial resection with reconstruction, and periarterial dissection such as the Heidelberg Triangle Operation. SDT means a technique to separate the tumor from the artery by dissecting into the plane between the external elastic lamina (EEL) and the tunic media when the tumor was not invaded to EEL of the involved artery. Our previous study revealed that SDT procedure appears to be relatively safe, without excessive mortality, as compared to arterial resection with reconstruction. However, survival times can vary widely among different patients. So a strategy to select the T4 patients who may benefit from the surgery with SDT procedure is urgently needed.  Our previous RNA-seq dataset has identified a series of differentially expressed circRNAs including circNEIL3 and circRHOBTB3 in PDACs. These results suggested that circRNAs might be prominent prognostic markers for PDAC. So to explore the prognostic value of circRNAs in pancreatic cancer and seek a useful biomarker for distinguishing specified population with a good prognosis from the whole T4 patients, we further performed whole transcriptome sequencing including miRNAs, mRNAs, lncRNAs and circRNAs in ten PDAC cancer samples with T4 stage but diametrically opposing survival outcomes. They all underwent radical surgery and received the assessments of pre- and post-operative contrast-enhanced computed tomography, five of these patients developed newly discovered metastasis soon after surgery and died within 4-9 months. In contrast, the other five patients had no recurrence or metastasis and had long-term survival for more than 39 months. We systematically identified differentially expressed circRNAs in our previous dataset and in patients with T4 stage through combining three popular circRNAs detection algorithms (CIRI2 v2.0.6, CIRCexplorer2 v2.3.8, and find_circ v1.2) and two differential analysis methods (DEGseq and DEseq). Results were validated by using quantitative RT-PCR. circRNA alternative splicing events and highly expressed circRNAs with high circular ratio were also identified by CircSplice and CIRCexplorer3-CLEAR pipeline.

overall_design: RNA was extracted from frozen pancreatic tissues for RNA-seq analysis. Total RNAs were isolated from 10 patients with T4 pathological stage using TRIzol Reagent (Invitrogen, CA, USA). After passing the assessment of RNA purity and RNA integrity (RIN), two different RNA sequencing strategies (ribo- RNA-seq, poly(A)-/ribo- plus RNase R-treated RNA-seq) were applied to profile circRNAs and mRNAs/lncRNAs. Small RNA library was also prepared according to the prescribed procedure and standards of the Illumina Sample Preparation Protocol. Poly(A)-/ribo- plus RNase R-treated RNA-seq dataset was used to detect differentially expressed circRNAs by three popular circRNAs detection algorithms and detect circRNA alternative splicing events by CircSplice algorithm. Ribo- RNA-seq dataset was used to identify highly expressed circRNAs with high circular ratio by CIRCexplorer3-CLEAR pipeline. Ribo- RNA-seq dataset can also be used to detect the expression profile of mRNAs/lncRNAs by Hisat2 (version 2.1.0) and featureCounts function from the Subread package (version 1.6.3).

first: Zipeng

last: Lu

first: Min

last: Tu

first: Kuirong

last: Jiang


title: Variant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2 [bulk VDJ-seq]

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

summary: We generated LNP-mRNAs specifically encoding wildtype (WT), B.1.351 and B.1.617 SARS-CoV-2 spikes, and systematically studied their immune responses. BCR-seq and TCR-seq unveiled repertoire diversity and clonal expansions in vaccinated animals.

overall_design: Splenocytes were isolated and processed from immunized mice and analyzed by bulk VDJ-seq.

first: Paul

last: Renauer


title: Variant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2


title: Variant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2 [scRNA-seq]

summary: We generated LNP-mRNAs specifically encoding wildtype (WT), B.1.351 and B.1.617 SARS-CoV-2 spikes, and systematically studied their immune responses. Single cell transcriptomics of WT- and variant-specific LNP-mRNA vaccinated animals revealed a systematic landscape of immune cell populations and global gene expression.

overall_design: Splenocytes were isolated and processed from immunized mice and analyzed by scRNA-seq.


title: Genome-wide association study finds multiple loci associated with intraocular pressure in HS rats

city: La Jolla

first: Daniel

last: Munro

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

summary: Elevated intraocular pressure (IOP) is influenced by environmental and genetic factors. It is associated with 23 multiple disease processes with primary open angle glaucoma (POAG) being the most prevalent. Due to its 24 complex, multifactorial nature, genetic predisposition is not completely understood thus, there is an urgent 25 need for additional investigations into the genetic regulation of IOP. Heterogenous stock (HS) outbred rats are 26 a multigenerational outbred population derived from eight inbred strains that have been fully sequenced. This 27 population is ideal for genome-wide association studies (GWAS) due to the accumulated recombinations 28 among well-defined haplotypes, the relatively high allele frequencies, access to a large collection of tissue 29 samples, and the large allelic effect size compared to human studies. The purpose of this study was to identify 30 genetic loci underlying elevated IOP using HS rats. Both male and female HS rats (N=1,812) were used in the 31 study. Genotyping-by-sequencing was used to obtain ~3.5M single nucleotide polymorphisms from each 32 individual. We performed a GWAS for the IOP phenotype using a linear mixed model and used permutation to 33 determine a genome-wide significance threshold. We also estimated SNP heritabilities. Our GWAS results 34 identified three genome-wide significant loci for elevated IOP on chromosomes 1, 5, and 16. These loci 35 contained 7 genes in total including Tyr, Grm5, Ctsc, Rab38, MGC94199, Plekhf2, and Csmd1. We also 36 mapped expression quantitative trait loci (eQTLs) in HS rat eye tissue and discovered a cis-eQTL for Ctsc 37 among our significant loci. Tyr is the only gene that has been previously associated with human IOP. This 38 study highlights the efficacy of HS rats for investigating the genetics of elevated IOP and identifying potential 39 candidate genes for future functional testing. In summary, GWAS using HS rats is a powerful method for 40 identifying genome regions that harbor variants responsible for the variation in quantitative traits, such as IOP. 41 Additional studies are ongoing to further narrow the list of candidate genes in these intervals.

overall_design: mRNA profiles from the eye tissue of 53 HS rats

first: Samuel

last: Fowler

first: Tengfei

last: Wang

first: Apurva

last: Chitre

first: T

last: Hollingsworth

first: Angel

last: Garcia Martinez

first: Celine

last: St. Pierre

first: Hannah

last: Bimschleger

first: Jianjun

last: Gao

first: Riyan

last: Cheng

first: Pejman

last: Mohammadi

first: Hao

first: Oksana

last: Polesskaya

first: Abraham

last: Palmer

first: Monica

last: Jablonski


title: Epigenetic reversal of lineage plasticity enhances responsiveness to anti-GD2 therapy in neuroblastoma [RNA-seq SK-N-AS]

first: Nathaniel

last: Mabe

overall_design: SK-N-AS cells were treated for 14 days with vehicle (V) or 1 uM tazemetostat (T) in biological quadruplicate


title: Alkali therapy protects renal function, suppresses inflammation, and modulates cellular metabolism in kidney disease

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

summary:
Purpose: Characterize the renal transcriptome of a chronic kidney disease model in the presence and absence of alkali therapy (bicarbonate supplementation in water)
Methods: Crystal nephropathy mice were fed a calcium-free, 0.67% oxalate diet for 10 days. Control mice were fed a calcium-free diet for the same period. Afterwards, mice were fed a standard diet containing calcium for 28 days (recovery). Therapeutically treated mice ("late") received 0.2M NaHCO3 in water during the whole recovery period. An untreated group  drank tap water instead. Total RNA was extracted from whole kidney samples and used for RNAseq.
Results: Using a PolyA, Truseq strategy with p-value <0.05 and log2(fold change) ≥ 0.5 or ≤ - 0.5, we identified that crystallopathy altered the expression levels of 4923 transcripts. Alkali therapy normalized or attenuated the dysregulation of 795 of those genes. Alkali therapy also altered the expression of 179 transcripts in control kidneys.
Conclusions: Pathway analysis identified that alkali therapy mostly restored pathways associated to inflammation and cell metabolism.

overall_design: Alkali therapy via bicarbonate supplementation in crystal nephropathy mice.

first: Pedro

middle: H

last: Imenez Silva

first: Giancarlo

last: Russo

first: Carsten

last: Wagner


title: Genome-wide transcriptome profiling of Acidithiobacillus ferrooxidans ATCC 23270 in response to the cyc2 knockout

city: Qingdao

first: Xiangmei

last: Liu

state: Shandong Province

address: 72 Binhai Road

department: State Key laboratory of Microbial Technology

institute: Shandong University

summary: The outer-membrane c-type cytochrome Cyc2 is generally considered to be the initial electron acceptor in iron respiratory chain of Acidithiobacillus ferrooxidans ATCC 23270, a model microorganism in acidophilic bioleaching environment. In our work, however, the knockout of cyc2 did not result in impaired Fe(II) consumption or growth capacity. To screen the potential genes for alternative initial electron acceptors other than Cyc2, RNA-Seq was employed to compare global gene expressions in the A. ferrooxidans ATCC 23270 wild type and the Δcyc2 mutant grown on Fe(II) or switched energy source from S0 to Fe(II). The data focused on 29 up-regulated and 19 down-regulated genes in the mutant under both conditions, among which AFE_1428 was the most highest one. in-silico analysis also suggested that the product of AFE_1428 might act as an alternative initial electron acceptor when Cyc2 was absent, which needs to be further validated.

overall_design: Differential mRNA profiles of A. ferrooxidans Δcyc2 mutant were generated by Next-generation sequencing using wild-type strain grown on Fe(II) or switched energy source from S0 to Fe(II) as  control.

first: Xuanji

last: Li

first: Yang

first: Xiaoyan

last: Qin

first: Qing

last: Wen

first: Jianqun

last: Lin

first: Huiyan

last: Wang


title: Variant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2 [scVDJ-seq]

first: Sidi

last: Chen

summary: We generated LNP-mRNAs specifically encoding wildtype (WT), B.1.351 and B.1.617 SARS-CoV-2 spikes, and systematically studied their immune responses. Single cell BCR-seq and TCR-seq unveiled repertoire diversity and clonal expansions in vaccinated animals.

overall_design: Splenocytes were isolated and processed from immunized mice and analyzed by scVDJ-seq.

first: Paul

last: Renauer


title: Identifying Dihydropyrimidine Dehydrogenase as a Novel Regulator of Hepatic Steatosis

city: Newton

first: Ye

last: Zhang

state: MA

address: 39 Cout St, #6

institute: NIBR

summary: Pyrimidine catabolism is implicated in hepatic steatosis. Dihydropyrimidine Dehydrogenase (DPYD) is an enzyme responsible for uracil and thymine catabolism, and DPYD human genetic variability affects clinically observed toxicity following 5-Fluorouracil (5-FU) administration. In an in vitro model of diet-inducedfatty acid-induced steatosis, the pharmacologic inhibition of DPYD resulted in protection from lipid accumulation. Additionally, a gain-of-function mutation of DPYD, created through clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) engineering, led to an increased lipid burden, which was associated with altered mitochondrial functionality in a hepatocarcionma cell line. The studies presented herein describe a novel role for DPYD in hepatocyte metabolic regulation as a modulator of hepatic steatosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Primary Human Hepatocytes treated different doses of DPD inhibitor, Gimeracil with or without exposure to free fatty acid(FFA).

first: Kelly

middle: E

last: Sullivan

first: Sheetal

last: Kumar

first: Fan

last: Fan


title: Improved predictions of immunogenicity reveal SARS-Cov-2 CD8 T-cell epitopes

city: Lausanne

first: David

last: Gfeller

address: Bugnon 25A

department: Department of Oncology

institute: University of Lausanne

summary: CD8 T cells from human donors were sorted with peptide-MHC multimers based on SARS-Cov-2 epitopes. For each donor the alpha and beta chains were sequenced separately

overall_design: TCR-seq of CD8 T cells specific for SARS-Cov-2 epitopes

first: Julien

last: Schmidt

first: Raphael

last: Genolet

first: Alexandre

last: Harari


title: Effects of Exogenous N6-methyladenosine (m6A) Incorporation on the Expression of Cellular mRNA Transcripts

first: Jie

last: Cao

address: Zheda Road 38

department: Department of Polymer Science and Engineering

institute: Zhejiang University

summary: N6-methyladenosine (m6A) is the most prevalent and reversible internal mRNA modification in eukaryotic cells, and plays an essential role in RNA fate determination. In this work, we studied the exogenous incorporation of m6A into cellular mRNA through salvage pathway and evaluated its resultant biological effects. First, we found that feeding of HeLa cells with m6A nucleoside significantly altered cell morphology and viability. We then synthesized isotope-labelled d3-m6A (N6-methyl-d3-adenosine) and examined the d3-m6A incorporation rate in cellular mRNA along with incubation time using mass spectrometry. Next, RNA sequencing (RNA-seq) was used to study the biological effects of exogenous m6A incorporation. Finally, thousands of genes were found to be differentially expressed, and were dramatically enriched in pathways such as ribosome biogenesis, mRNA metabolic process and cell morphogenesis differentiation. All these results suggested that exogenous m6A could be incorporated into mRNAs through a metabolic pathway to influence cellular gene expression.

overall_design: 500 μM d3-m6A was added into HeLa cells and incubated for 24 h and until passage 7 (168 h), total RNAs were extracted and subjected to library construction

first: Qingyi

first: Jianzhao


title: Adaptive evolution of gene promoters driven by primate-specific KRAB zinc finger proteins

city: Amsterdam

first: Frank

last: Jacobs

address: Science Park 904

department: Sammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

summary: RNA analysis of CRISPR/Cas9 ZNF519 knockout (KO), ZNF441 knockout (KO), ZNF468 knockout (KO) and wild type hESC-derived cortical organoids and ChIP-seq analysis of CRISPR/Cas9 ZNF519 knockout (KO) and wild type hESC-derived cortical organoids, and HEK293 cells with ZNF519 overexpression (OE).

overall_design: RNA analysis of CRISPR/Cas9 ZNF519 knockout, ZNF441 knockout, ZNF468 knockout and wild type hESC-derived cortical organoids and ChIP-seq analysis of CRISPR/Cas9 ZNF519 knockout  and wild type hESC-derived cortical organoids, and HEK293 cells with ZNF519 overexpression.

first: Elisabeth

last: van Bree

first: Grace

last: Farmiloe

first: Lara

last: J.M. Janssen

first: Lisa

last: Mol


title: RNA-Seq analysis comparing gene expression in bovine mammary stromal and parenchymal regions

city: Bet Dagan

first: Itamar

last: Barash

state: israel

address: P.O. Box 6

country: Israel

institute: ARO, The Volcani Center

summary: The aim of this analysis was to compare gene expression in bovine mammary parenchyma, adjacent stroma (close stroma) and distant stroma (far stroma). The close stroma appeared genetically more similar to the parenchyma than to the far stroma due to epithelial characteristics, mainly of fibroblasts

overall_design: Mammary samples from the three mammary regions were analyzed.

first: Anna

last: Kosenko

first: Tomer-Meir

last: Salame

first: Gilgi

last: Fridlander


title: Whole blood gene expression profiling at day 1, 3 and 7 after total-body irradiation in Gottingen minipigs

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: Gottingen minipigs mirror the physiological radiation response observed in humans and hence make an ideal candidate model for studying radiation biodosimetry for both limited-sized and mass casualty incidents.  We examined the whole blood gene expression profiles at day 1, 3 and 7 after total-body irradiation with 1.7, 1.9, 2.1 and 2.3 Gy doses of gamma-rays. Blood taken one day prior to radiation served as control. Six animals per dose group were used The minipigs were monitored for up to 45 days or time to euthanasia necessitated by radiation effects. Survival correlative signatures were identified from the data.

overall_design: Six animals per dose group were used. Blood was drawn at day 1, 3 and 7 post-raidtaion. Blood drawn one day prior to radiation was used as control.

first: Sunita

last: Chopra

first: Maria

last: Moroni

first: Jaleal

last: Sanjak

first: Laurel

last: MacMillan

first: Bernadette

last: Hritzo

first: Shannon

last: Martello

first: Michelle

last: Bylicky

first: Jared

last: May

first: C

middle: N

last: Coleman

first: Molykutty

last: Aryankalayil


title: Transcriptional landscape of oncogenic PI3K

city: New York

first: Erik

last: Ladewig

state: New York

address: 435 East 65th Street

institute: MSKCC

summary: RNA-seq performed in triplicates in MCF10A and MEF cells. Wildtype/parental vs PIK3CA H1047R mutant. MEFs were treated with DMSO or GDC0032 (500nM) PI3Ka inhibitor treatment while MCF10A cells were treated with DMSO or  alpelisib (BYL719)  at 1uM.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Eneda

last: Toska

first: Flavia

last: Michelini


title: Zinc increases hormone receptor expression in human ovarian granulosa cells and gene profiling

city: Changchun

first: Xiaodan

last: Lu

address: 1183 Gongnong Road, Chaoyang District, Changchun City, Jilin Province

institute: Jilin Provincial General Hospital

summary:
To investigate the critical role of the trace element zinc in the expression of resistance to oxidative stress and hormonal responses in human ovarian granulosa cells (GCs).
To investigate the critical role of the trace element zinc in the expression of antioxidant stress and hormonal responses in human ovarian granulosa cells (GCs).

overall_design: In this study gradient centrifugation was used to successfully isolate human primary ovarian GCs. After extinction treatment, changes in oxidative stress levels and hormone-receptive expression in glutamatergic cells were sought. Examining the effect of zinc on the viability of ovarian granulosa cells in a zinc-deficlient micro environment.

first: Shizhuo

last: Sun


title: CDK4/6 inhibitors modulate the ubiquitin proteosomal pathway by suppression of the ubiquitin conjugating enzymes UBE2C/S/T

status: Public on Apr 23 2022

city: Taipei City

first: Chih Yi

last: Lin

address: No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City 112304, Taiwan

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Despite significant improvement in therapeutic development in the past decades, breast cancer remains a formidable cause of death for women worldwide. The hormone positive subtype (HR(+)) (also known as luminal type) is the most prevalant category of breast cancer, comprising ~70% of patients. The clinical success of the three CDK4/6 inhibitors palbociclib, ribociclib, and abemaciclib has revolutionzied the treatment of choice for metastatic HR(+) breast cancer. Accumulating evidence demonstrate that the properties of CDK4/6 inhibitors extend beyond inhibition of the cell cycle, including modulation of immune function , sensitizing PI3K inhibitors, metabolism reprogramming , kinome rewiring, modulation of the proteosome, and many others. The ubiquitin–proteasome pathway (UPP) is a crucial cellular proteolytic system that maintains the homeostasis and turnover of proteins. By transcriptional profiling of the HR(+) breast cancer cell lines treated with the three CDK4/6 inhibitors, we have uncovered a novel mechanism that demonstrate the CDK4/6 inhibitors suppress the expression of three ubiquitin conjugating enzymes UBE2C, UBE2S, UBE2T. These three E2 enzymes modulate a number of E3 ubiquitin ligases, including the APC/C complex which plays a role in G1/S progression. Our study provide a novel link between CDK4/6 inhibitor and UPP which could have important implications in cancer biology.

overall_design: The hormone (+) breast cancer cell lines MCF-7, T47D were treated with the CDK4/6 inhibitors palbociclib for 5 days and subject to RNA-sequencing to profile the transcriptomic changes.

first: Jiun-I

last: Lai

first: Ting-I

first: Chung-Jen

last: Yu

first: Yi-Ru

last: Tseng

first: Chih-Yi


title: PGE2-EP3 axis controls brown adipose tissue development through  stabilization of WTAP protein

city: Tianjin

first: Yujun

last: Shen

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

summary: By conducting CUT&TAG, we reported that brown adipogenesis induction markedly increased ZFP410 occupancy on chromatin. GO analysis revealed that genes containing the ZFP410-bound peaks were enriched in fat cell differentiation. Consistently, binding signals of ZFP410 on the promoter regions of CHD4 as well as brown genes such as Pgc-1a, Prdm16 and Cyto C were markedly increased in differentiated pre-adipocytes compared to those in control cells.

overall_design: Examination of ZFP410 binding signaling on chromatin in differentiated brown preadipocytes.

first: Shumin

last: Guo

first: Xiangling

last: Feng


title: Effect of depletion of FABP4 in  mice intestinal epithelial cells on gene expression

city: TianJin

first: xiaomin

last: su

address: WeiJin Road

institute: Nankai University

summary:
To investigate the  function of  FABP4 in the intestinal  in vitro cultured organoids,FABP4, which located in crypt lyszyme+ Paneth cells can regulate the expression of defensins, especially HFD-mediated downregulation of defensin in Paneth cells will provide insights into factor(s) underlying modern diseases.
We then performed gene expression profiling analysis using data obtained from RNA-seq of FABP4fl/flpvillinCreT (FABP4KO) mice and FABP4fl/fl (WT)mice in vitro cultured intestinal organoids.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FABP4fl/flpvillinCreT (FABP4KO) mice and FABP4fl/fl (WT)mice in vitro cultured intestinal organoids.

first: Xiaomin

last: Su

first: Rongcun

last: Yang


title: Complete transcriptome analysis of gene expression in colorectal cancer cells treated with β-elemene

city: Hefei

first: Heng

last: Deng

address: 300 Shouchun Road, Hefei, Anhui, China

institute: Anhui acupuncture hospital

summary: We treated HCT116 cells with β -elememe to find the differential expression of the gene in the treatment of colorectal cancer by transcriptome sequencing.

overall_design: β-- Elememe has a certain therapeutic effect on colorectal cancer, and we used a certain concentration of β-- Elememe to treat colorectal cancer cells for whole-transcriptome sequencing to study the related mechanism.


title: Expression data from MV4-11 cells after treatment with ATRA, NVP-BEZ235 or the combination of both drugs for 3h, 12h and 24h

city: Jena

first: Sven

last: Stengel

address: Am Klinikum 1

department: Clinic for Internal Medicine IV

institute: Jena University Hospital

summary:
Aberrant activity of the PI3K/AKT/mTOR (PAM) pathway as well as suppressed retinoic acid signaling contribute to enhanced proliferation and a block in differentiation of immature myeloid cells in AML Therefore, we sought to target MV4-11 cells by a combined strategy using small molecule inhibitors against members of the PAM signaling pathway in conjunction with all-trans retinoic acid (ATRA).
A detailed analysis of transcriptome changes in MV4-11 cells revealed that NVP-BEZ235 and ATRA regulated the same biologic pathways, but acted on different gene sets within these pathways. Especially, we found a strong repression of MYC-target genes and genes involved in cellular programs such as cell cycle regulation, metabolism or differentiation.

overall_design: MV4-11 cells were treated with either 100 nM ATRA, 100 nM NVP-BEZ235, 100 nM ATRA + 100 nM NVP-BEZ235 or left untreated. Treatment was stopped 3h, 12h or 24h following treatment start and total RNA was isolated.

first: Tino

last: Schenk


title: RESTRICTION checkpoint controls bradyzoite development in Toxoplasma gondii

city: Tampa

first: Elena

last: Suvorova

state: FL

address: IRB 3720 Spectrum Blvd Suite 304

institute: University of South Florida

summary: The Toxoplasma gondii G1 RESTRICTION checkpoint operates the switch between parasite growth and differentiation. The Cdk-related G1 kinase TgCrk2 forms alternative complexes with atypical cyclins (TgCycP1, TgCycP2 and TgCyc5) in the rapidly dividing developmentally incompetent RH and slower dividing developmentally competent ME49 tachyzoites and bradyzoites. The TgCycP1 expression interferes with bradyzoite differentiation. The TgCycP2 regulates G1 in the developmentally competent ME49 but not in the developmentally incompetent RH tachyzoites. Examination of TgCycP2 and TgCyc5 in alkaline induced and spontaneous bradyzoite differentiation (rat embryonic brain cells) models confirmed TgCycP2 role in bradyzoite replication and revealed that stress induced TgCyc5 is critical for efficient tissue cyst maturation.

overall_design: Total RNA was extracted from the purified tachyzoites and bradyzoites of the ME49DKu80Dhxgprt AtTIR1 strain and derivatives. RNA-Seq Library were prepared and sequenced according to manufacturer’s instructions (Illumina).

first: Thomas

last: Keller

first: Kami

last: Kim

first: Li-Min

last: Ting


title: MUC3A promotes the progression of colorectal cancer through the PI3K/Akt/mTOR pathway

city: shanghai

first: wei

state: shanghai

address: 2800 Gongwei Road

institute: fudan university

summary: Mucin 3A(MUC3A) is overexpressed in colorectal cancer (CRC) and associated with poor prognosis, but the related mechanism remains unclear. Our study found that MUC3A promotes the progression of CRC by activating the PI3K/Akt/mTOR signaling pathway. Knockout of MUC3A significantly inhibited the proliferation of CRC cells and induced G1 phase arrest by upregulating p21 protein, an important cell cycle regulator. Moreover, knockout of MUC3A significantly inhibited invasion ability and enhanced the sensitivity to the chemotherapeutic agent 5-FU. Furthermore, we found that knockout of MUC3A repressed the PI3K/Akt/mTOR pathway through RNA-seq. Treatment with the PI3K/Akt/mTOR pathway inhibitor rapamycin successfully eliminated the difference in proliferation, invasion and chemoresistance between MUC3A knockout cells and control cells. Our study suggests that MUC3A is a potential oncogene that promotes the proliferation, invasion, and chemotherapy resistance of CRC. Moreover, CRC patients with high expression of MUC3A may benefit from rapamycin treatment.

overall_design: We used HCT116 cells as experimental samples. Wild-type HCT116 cells (HCT116-WT and HCT-WT) were control group. And two groups of MUC3A knockout HCT116 cells(KO1 and KO2) by different sgRNA were experimental groups. All groups had two replicates.

first: Minghua

first: Wei

first: Baijie

first: Lina

last: Hu

first: Xianzhi


title: Integrated analysis of hepatic miRNA and mRNA expression profiles in the spontaneous recovery of liver fibrosis [mRNA]

city: Chengdu

first: Yang

last: Tai

address: NO. 37, Xiang Xue Guo

institute: West China Hospital, Sichuan University

summary: Liver fibrosis, results from the imbalance between extracellular matrix (ECM) production and degradation, is a common pathological consequence of various chronic liver diseases. Although a large number of miRNAs have been reported in liver fibrosis progression, miRNA-mRNA interactions involved in its reversal process remain to be fully elucidated. In the current study, we performed an integrated analysis of miRNA and mRNA expression profiles in a hepatic fibrosis recovery mouse model induced by thioacetamide. A total of 102 miRNA and 2,845 mRNAs showed significant differential expression in recovery mice compared to fibrotic mice. Moreover, 3,769 putative negatively correlated miRNA-mRNA pairs were revealed to be potentially implicated in the biological function regulation of small molecule metabolism and ECM organization. By integrating miRNA-mRNA regulatory networks, mmu-miR-1843a-5p, mmu-miR-193a-5p, mmu-miR-194-2-3p and mmu-miR-30c-2-3p were identified as lysyl oxidase-specific miRNAs that were associated with the pathogenesis of fibrosis recovery. Our results provide potential novel biomarkers and candidate targets for the treatment of liver fibrosis.

overall_design: Liver fibrosis was induced by intraperitoneal injection of thioacetamide (TAA) for 8 weeks. Control mice received the same volume of normal saline (NS). Liver fibrosis recovery model (Recovery) was established via 8-week TAA injection and then withdrew the repeated liver damages, following by spontaneous recovery for additional 8 weeks. mRNA expression profile was performed in the liver tissues of TAA-fibrotic mice, recovery mice and control mice.

first: Jinhang

last: Gao

first: Chengwei

last: Tang


title: Integrated clinical and genomic evaluation of guadecitabine (SGI-110) in peripheral T-cell lymphoma [CRISPR screen]

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

summary: Investigation of epigenetic regulators that module hypomethylating agent response in T-cell lymphoma.

overall_design: CRISPR/Cas9 screen in T-cell lymphoma cell line (Hut78). Hut78 Cas9 cells were transduced with a library of sgRNAs targeting epigenetic regulators and treated with DMSO, Azacitidine (300nM) or Guadecitabine (150nM) for 24 days. Drop-out and enrichment analysis was performed.


title: Genome-Wide High Resolution Expression Pattern of Crown Root Primordia in Rice

status: Public on Apr 24 2022

city: Roorkee

first: Shri Ram

last: Yadav

state: Uttarakhand

address: Civil Lines

department: Biosciences and Bioengineering

institute: Indian Institute of Technology Roorkee

summary: RNA sequencing data from laser microdissected crown root primordia (CRP) during CRP initiation (stage-I) and CRP outgrowth (stage-II) as compared to competent tissues (control)

overall_design: CRP at the stage of initiation and outgrowth together with control tissues were collected using laser caprute microdissection (LCM). RNA extracted from these tissue were subjected to RNA sequencing.

first: Tushar

last: Garg

first: Anuj

last: Dwivedi

first: Raj

last: Singh

first: Mukesh

last: Jain

first: Shri


title: Adeno-associated virus (AAV) 9-mediated gene delivery of Nurr1 and Foxa2 cures symptoms and pathologies of Alzheimer disease model mice by suppressing neuro-inflammation and glial pathology.

city: Seoul

first: Yunseon

last: Yang

address: 222, Wangsimni-ro

country: South Korea

institute: Hanyang University

summary: In this study, AAV9-Nurr1 and AAV9-Foxa2 (or AAV9-Control as sham-operated control) were injected to hippocampus of 15-18 months old 3xTg Alzheimer's disease mice. And mouse hippocampal glia were primarily cultured at postnatal day 1 and forced expression of Nurr1 and Foxa2 with lentivirus (or lenti-Control).

overall_design: mRNA profile of 3xTg AD mice hippocampus and hippocampal primary cultured glia.

first: Sang-Hun

last: Lee

first: Heh-In

last: Im

first: Seong-Ho

last: Koh

first: Min-Jong

last: Seok


title: Integrated clinical and genomic evaluation of guadecitabine (SGI-110) in peripheral T-cell lymphoma [RNA-seq]

summary: Investigation of the transcriptional profile of T-cell lymphomas in response to 72 hrs of treatment with hypomethylating agents (AZA and GDAC)

overall_design: Gene expression profiles of DMSO, Azacitidine and Guadecitabine treated Hut78 and Smz1 cells


title: Mammalian UPF3A and UPF3B activate NMD independently of their EJC binding

city: Columbus

first: Zhongxia

last: Yi

state: OH

department: Molecular Genetics

institute: The Ohio State University

summary: Nonsense-mediated mRNA decay (NMD) can occur independently of some NMD factors such as UPF3B. We have performed total RNA-Seq in HCT116 cells under NMD factor knockout (with CRISPR-Cas9) and/or knockdown (with siRNA transfection) conditions to identify mRNA substrates regulated by different NMD factors. We have also performed RIPiT-Seq to identify the footprints of three compositionally distinct EJCs that contain the following pairs of proteins: MAGOH-EIF4A3, UPF3B-EIF4A3 or CASC3-EIF4A3 in WT HCT116 cells.

overall_design: Total RNA-Seq were performed in three different batches. Controls from the same batch are used for downstream analysis. For total RNA-Seq, three replicates of each condition are used and for RIPiT-Seq experiments, four replicates of each RIPiT are used.

first: Rene

last: Arvola

first: Sean

last: Myers

first: Corinne

last: Dilsavor

first: Rabab

last: Abu Alhasan

first: Bayley

last: Carter

first: Robert

last: Patton

first: Ralf

last: Bundschuh

first: Guramrit


title: mRNA-sequencing  in drug-resistant acute myeloid leukemia

city: jinan

first: bing

last: zhang

address: 107 Wenhua Xilu

institute: Qilu Hospital of Shandong University

summary: mRNA sequencing for AML cells(HL-60) and drug-resistant AML Cells(HL60/MX2).

overall_design: Compare mRNA expression in AML cells(HL-60) and drug-resistant AML Cells(HL60/MX2).

first: Bing

last: Zhang

first: Dong

last: Li

first: Ran

last: Wang


title: Characterization of Transcriptome Diversity and In Vitro Behavior of Primary Human Breast Cells at Increased Risk for Breast Cancer Development

status: Public on Apr 22 2022

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

institute: Dankook University

summary: Studying properties of non-cancerous high-risk human breast epithelial cells is challenged by limitations in acquiring primary epithelial cells for investigation. Here we used conditional reprogramming cell (CRC) technology to isolate n=27 serial samples of non-cancer derived mammary epithelial cells ipsilateral to breast cancer, considered at risk cells for future breast cancer development. Comparative samples included cancer (n=8) and contralateral (n=3) and prophylactic mastectomy (n=1) non-cancer derived breast epithelial cells. Significant in vitro behavioral differences between samples were connected to baseline transcriptome characteristics. An exploratory analysis identified patterns of aberrantly expressed pregnancy development genes in both at risk and cancer samples. In conclusion, it is possible to approach the investigation of breast cancer risk utilizing human primary breast epithelial cells for targeted in vitro and genetic studies.

overall_design: Primary human breast epithelial cell mRNA profiles from breast epithelial cells isolated using CRC technology from non-cancerous breast tissue ipsilateral and contralateral to breast cancer and from a prophylactic mastectomy performed for breast cancer prevention, and cells isolated from breast cancer tissue.

first: Priscilla

last: Furth

first: Kang

last: Keunsoo


title: mRNA sequencing of SKMEL28 cells

city: Basel

first: Daniel

last: Marbach

address: Grenzacherstrasse 124

department: pRED Pharmaceutical Sciences

institute: F. Hoffmann - La Roche Ltd

summary: A RNA-seq analysis was performed to characterize the molecular intermediates responsible for the deleterious effects upon DUSP4 loss in SKMEL28 cells. Methods:SKMEL28 cells were transfected with siRNA against DUSP4 or non-targeting control with or without Trametinib (Tram) at 0.25nM. After 16 hours, cell were collected and RNAseq experiments were performed. Results: the expression of MITF and some of its target genes were significantly downregulated in the absence of DUSP4 and completely rescued by trametinib treatment. Conclusions: In mutant melanoma cells, the expression of MITF and its related target genes is subject to regulation by the DUSP4-ERK axis.

overall_design: Examination of mRNA profiles of siNT and siDUSP4 SKMEL28 cells treated with or without 0.25nM Trametinib for 16h

first: Nuria

middle: G

last: Prat

first: Zahra

last: Karimaddini

first: Luise

last: Wolf

first: Stefka

last: Tyanova

first: Lisa

last: Wellinger

first: Hedwig

middle: L

last: Huberer

first: Vera

last: Griesser

first: Piergiorgio

last: Pettazzoni

first: James

last: Bischoff

last: Rohle

first: Chiara

last: Palladino

first: Igor

last: Vivanco


title: Isolation and long-term expansion of adult SOX9+ renal epithelial cells with efficient kidney regeneration capacity

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

summary: We show that in an appropriate feeder cell-based culture system, it is feasible to isolate and long-term expand the progenitor-like SOX9+ renal epithelial cells (SOX9+ RECs) from adult mammalians. Single cell-derived SOX9+ REC lines can be established from human needle biopsy or urine samples with molecular homogeneity and genomic stability maintained during culture. Such cells grown in 3D culture system could self-organize into renal organoids composed of proximal tubular, Loop of Henle (LOH) and distal tubular cells as illustrated by single cell transcriptomic analysis.

overall_design: SOX9+ renal epithelial cells grown in 3D culture system self-organized into organoids. These cells were isolated and performed 10X genomics single-cell RNA sequencing.

middle: W

last: Henry


title: Single-cell RNA sequencing of PBMCs sampled from COVID-19 patients

city: Beijing

first: Yingmei

last: Feng

address: No. 8 Xi-Tou-Tiao

institute: Beijing Youan Hospital, Capital Medical University

summary: To explore the underlying mechanism of recurrent SARS-CoV-2 infection in convalescent patients. We performed single-cell RNA sequencing on peripheral blood mononuclear cells isolated from a recurrent patient, taking 14 recovered COVID-19 patients and 4 dead COVID-19 patients as controls.

overall_design:
Single-cell expression profiles of 19 COVID-19 patients with recovery, recurrence and death outcome.

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

first: Bin

last: Su

first: Ruya

last: Sun

first: Lili

last: Zhang

first: Jiaying

first: Xia

first: Zhenhuan

last: Cao

last: Hou

first: Xianghua

last: Guo

first: Qing

last: Ge

first: Qinghua

last: Cui

first: Yuan

last: Zhou

first: Yingmin

last: Ma

first: Ronghua

last: Jin


title: Analyses of miRNA in the ileum of diarrheic piglets caused by Clostridium perfringens type C

city: Lanzhou

first: Pengfei

last: Wang

state: Gansu

address: No. 1 Yingmen village, Anning District

institute: Gansu Agricultural University

summary:
Purpose: RNA-Seq has become a powerful tool for investigating transcriptional profiles in gene expression analysis, which would help to reveal the molecular mechanism of Clostridium perfringens type C infecting the piglets. In this study, we analyzed miRNA profiles of the ileum of piglets caused by Clostridium perfringens type C.
Methods: 30 normal 7-day-old piglets (Y x L), without infecting Clostridium perfringens type C, Escherichia coli and Salmonella, were selected as experimental subjects. 25 piglets were randomly selected as the experimental group, which were disposed once a day for 5 days. Each piglet was dosed with 1 ml of bouillon culture-medium inoculated Clostridium perfringens type C at 37℃ for 16h, which approximate to 1 x10e9 CFU per ml. Then, 5 piglets were randomly selected as the control group (IC), which were taken the equal volume medium for 5 days.Based on total diarrhea scores, 25 piglets were ranked from high to low. The top and last five piglet were considered as sensitive group (IS) and resistant group (IR), respectively. Finally, ileum were collected and sequenced for miRNA.
Result: 53 differentially expressed miRNAs were found. KEGG pathway analysis for target genes revealed that these miRNAs were involved in ErbB signaling pathway, MAPK signaling pathway, Jak-STAT signaling pathway and Wnt signaling pathway. The expression correlation analysis between miRNAs and target genes revealed that the expression of miR-7134-5p had negative correlation with target NFATC4, miR-500 had negative correlation with target ELK1, HSPA2 and IL7R, and miR-92b-3p had negative correlation with target CLCF1 in ileum of IR vs IS group, suggesting that miR-7134-5p targeting to NFATC4, miR-500 targeting to ELK1, HSPA2 and IL7R, and miR-92b-3p targeting to CLCF1 were probably involved in piglet resisting C. perfringens type C.
Conclusions: The results will provide value resources for better understanding of the genetic basis of C. perfringens type C resistance in piglet and lays a new foundation for identifying novel markers of C. perfringens type C resistance

overall_design: miRNA profiles of ileum in piglets were generated by deep sequencing,three group,five sample in each group,using Illumina

first: Xiaoyu

last: Huang

first: Zunqiang

last: Yan

first: Qiaoli

last: Yang

first: Wenyang

first: Xiaoli

last: Gao

first: Ruirui

last: Luo

first: Shuangbao

last: Gun


title: Comparison of expression profiles of fetal and adult BMPR1B+ chondrocytes

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary: This research was designed to determine why fetal chondrocytes evidence regenerative capacity and adult chondrocytes do not. We then also compared adult chondrocytes treated with a newly discovered small molecule agonist of gp130 to those that weren't treated.

overall_design: 7 samples were included in the developmental study:  4 replicates sorted from fetal knee articular cartilage and 3 replicates sorted from adult artilcular cartilage obtained from NDRI. In the experiment to assess the effects of drug treatment, 7 adult chondrocyte samples were sequenced after being cultured with or without the drug in 3D conditions.


title: 5PSeq supporting study Probing 3’UTRs as modular regulators of gene  expression

city: Edinburgh

first: Edward

last: Wallace

address: Waddington 2.18, Max Born Crescent, King’s Buildings

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

summary: The goal of the study is to analyse the function of 3'-UTR motifs in the non-native context. Several 3'-UTR motifs predicted to have stabilizing or destabilizing effects on mRNA were inserted into terminators controlling the expression of reporter mCherry gene in following contexts: pRps3-mCherry-tRps3, pPgk1-mCherry-tRps3, pTsa1-mCherry-tTsa. 5'P sequencing was used to determine whether or not modifications in the 3'-UTR region affect ribosomal dynamics and co-translational degradation of mRNA in the 3' end region of reporter coding sequence.

overall_design: 5'P sequencing of Saccharomyces cerevisiae strains expressing mCherry reporter controlled by modified and non-modified terminators. mCherry reporter constructs are expressed from a low copy number plasmid. All modified constructs have three 9bp insertion sites with different combinations of the following motifs: N, a randomly generated sequence;  A, an ATATTC motif; H, a TTTCATTTC motif; and T, a TGTACAATA motif.

first: Sam

last: Haynes

first: Jamie

last: Auxillos

first: Weronika

last: Danecka

first: Yujie

last: Zhang

first: Vicente

last: Pelechano


title: Microarray of lysyl oxidase-like 2 (LOXL2)-overexpressing human buccal SCC TW2.6 and hypopharyngeal SCC FaDu cells against respective vector controls

city: Taipei

first: YI-JIE

last: LU

address: 1, Chang-Te street

institute: National Taiwan University

summary: To investigated the effects of LOXL2 overexpression in HNSCC TW2.6/FaDu  cells. 8 samples

overall_design: Transfection of HNSCC cells with plasmids [pCMV-LOXL2, pCMV vector (OriGene Technologies, Rockville, MD, USA) Head and neck squamous cell carcinoma Cell line FaDu groups: Vehicle control and LOXL2 overexpressed; oral squamous carcinoma cell line TW2.6 cell group; vehicle control and LOXL2 overexpressed.

first: Yi-Jie

last: Lu

first: Mark

middle: Y

last: Kuo


title: Stochastic activation of a family of TetR type transcriptional regulators controls a virulence switch in Acinetobacter baumannii

city: Decatur

first: María

last: Pérez-Varela

state: Georgia

address: 1670 Clairmont Rd

institute: Emory University

summary: Phenotypic heterogeneity is an important mechanism to regulate bacterial virulence, where a single regulatory switch is typically activated to generate virulent and avirulent subpopulations. The opportunistic pathogen Acinetobacter baumannii can transition at high-frequency between virulent (VIR-O) and avirulent (AV-T) subpopulations, distinguished by cells that form opaque or translucent colonies. We demonstrate that expression of twelve TetR-type transcriptional regulators (TTTRs) can drive cells from the VIR-O subpopulation to the AV-T state. Remarkably, in a subpopulation of VIR-O cells, four of these TTTRs were stochastically activated in different combinations to drive cells to the AV-T state, with each resulting AV-T subvariant exhibiting unique phenotypic differences. Due to their functional redundancy, a quadruple mutant with all four of these TTTRs inactivated was required to see a loss of VIR-O to AV-T switching. Further, we demonstrate a small RNA, SrvS, acts as a “rheostat”, where the levels of SrvS expression influences both the VIR-O to AV-T switching frequency and which TTTR is activated when VIR-O cells switch to AV-T. In summary, this work has revealed a new paradigm for phenotypic switching in bacteria, where an unprecedented number of related transcriptional regulators are activated in different combinations to control virulence and generate unique AV-T subvariants with distinct phenotypic properties.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for VIR-O pWH1266, VIR-O pWH1266_1959 and VIR-O pWH1266_2818. Gene expression was determined via RNA-sequencing. Three biological replicates per sample.

first: Aimee

middle: R

last: Tierney

first: Emma

last: Dawson

first: Anna

last: Hutcheson

first: Kyle

last: Tipton

first: Sarah

last: Anderson

first: Shaina

last: Song

first: Chui-Yoke

last: Chin

first: Brooke

last: Tomlinson

first: Lindsey

last: Shaw

first: David

last: Weiss

first: Minsu

last: Kim

first: Philip

last: Rather


title: Next Generation Sequencing to identify the gene expression profile of cardiosphere-derived cells (CDCs) and c-kitpos cardiac progenitor (c-kitpos CPC) cells derived from adult and young donors

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: In this study we therefore focused on 2 heart-derived progenitor cell populations that have been recently introduced in clinical translation, autologous c-kitpos–selected CPCs and CDCs. For the first time we compared molecular signatures and proliferation and differentiation characteristics of progenitor cells from young donor hearts (c-kitpos yCPC and yCDC) with cells obtained from adult donors with advanced ischemic disease (c-kitpos aCPC and aCDC). Here we report that culture expanded CDCs derived from adult donors have a distinct transcriptional profile with greater cell cycle activity and superior in vitro paracrine growth factor release compared to yCDCs. The molecular signature of aduIt CDCs favours cardiac repair via pro-angiogenic, cytotrophic and immunomodulatory effects while cardiac transdifferentiation potential is modest and comparable in all progenitor cell populations.

overall_design: Comparison of gene expression profile in 2 different cardiac stem cell populations derived from both adult and young donors

first: Ann-Sophie

last: Walravens

first: Stefan

last: Janssens


title: Infection with Listeria monocytogenes alters the placental transcriptome and eicosanome

status: Public on Apr 21 2022

city: Lansing

first: Kayla

last: Conner

state: Michigan

address: 4125 Beaumont Rd

institute: Michigan State University

summary: Introduction: Placental infection and inflammation are risk factors for adverse pregnancy outcomes, including preterm labor. However, the mechanisms underlying these outcomes are poorly understood.  Methods: To study this response, we have employed a pregnant mouse model of placental infection caused by the bacterial pathogen Listeria monocyogenes, which infects the human placenta. Through in vivo bioluminescence imaging, we confirm the presence of placental infection and quantify relative infection levels. Infected and control placentas were collected on embryonic day 18 for RNA sequencing to evaluate gene expression signatures associated with infection by Listeria. Results: We identified an enrichment of genes associated with eicosanoid biosynthesis, suggesting an increase in eicosanoid production in infected tissues. Because of the known importance of eicosanoids in inflammation and timing of labor, we quantified eicosanoid levels in infected and uninfected placentas using semi-targeted mass spectrometry. We found a significant increase in the concentrations of several key eicosanoids: leukotriene B4, lipoxin A4, prostaglandin A2, prostaglandin D2, and eicosatrienoic acid. Discussion: Our study provides a likely explanation for dysregulation of the timing of labor following placental infection. Further, our results suggest potential biomarkers of placental pathology and targets for clinical intervention.

overall_design: Mouse placental samples. 20 infected replicates (infected with L. monocytogenes) and four uninfected controls.

first: Derek

last: Holman

first: Todd

last: Lydic

first: Jonathan

last: Hardy


title: Single Cell RNA sequencing of mouse early periodontitis gingiva

first: Ichiro

last: Nishimura

department: Dentistry

institute: UCLA

summary: Purpose: The goal of this study was to characterize the gingival oral barrier immunity of mouse early periodontitis gingiva. Method: A silk thread (ligature) was tied wround the mouse maxillary molar. Mouse palatal gingiva was harvested at 1 days after the ligature placement. Gingival cells were harvested and subjected to 10X Genomix scRNA-seq. Cell Ranger processed data were analysed.

overall_design: Gingival oral barrier cells were examined in early periodontitis gingiva.

first: Takeru

last: Kondo


title: Integrated clinical and genomic evaluation of guadecitabine (SGI-110) in peripheral T-cell lymphoma

first: Emily

last: Gruber

institute: Peter MacCallum Cancer Centre

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

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Transcriptomic analysis of mouse brain tissue post treatment by 5-ALA-mediated photodynamic therapy at different timepoints

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

institute: Henan University

summary: We report the application of 5-ALA ( 5-Aminolevulinic acid)-mediated photodynamic therapy on mouse brain  tissue, and further explored the impact of PDT on nervous system.

overall_design: Examination of transcriptome levels in mouse brain tissue treated with PDT.

last: Wu

first: Bingyang

last: Shi


title: RNA-seq analysis of various strains of Mycobacterium tuberculosis.

city: CHANDIGARH

first: Dibyendu

last: Sarkar

address: SECTOR 39A

institute: CSIR-IMTECH

summary: We have performred RNA-seq analysis of WT Mtb H37Rv, ∆phoP Mtb and H37Rv-pde (WT Mtb H37Rv overexpressing gene Rv0805 which codes for a phosphodiesterase), to look for the similarity in ∆phoP Mtb and H37Rv-pde transcriptome. RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. Briefly, 25 ml of bacterial culture was grown to mid-log phase (OD600= 0.4 to 0.6) and combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen). RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies). Library construction, RNA-sequencing and data analysis have been carried out by Agrigenome Labs Private Limited (Cochin), India.

overall_design: Investigating Mycobacterium tuberculosis transcriptional regulation by  PhoP.

first: Hina

last: Khan


title: Research on the circular RNA bioinformatics in patients with acute myocardial infarction

city: Nanning

first: Yinghua

last: Tang

state: Guangxi

address: No. 89-9 Dongge Road

department: Department of Clinical Laboratory

institute: The First Affiliated Hospital of Guangxi University of Chinese Medicine

summary: To further development of our gene expression approach to biodosimetry, We through the detection of circular RNA (circRNA) using expression profiling chips, we searched for circRNAs related to acute myocardial infarction (AMI) and explored their relationship and possible mechanisms with AMI. The study subjects included 3 AMI patients and 3 controls, and circRNA expression profiling analysis was performed using a microarray gene chip to identify circRNAs with large differences in expression between groups and to construct a circRNA-microRNA (circRNA-miRNA) network.

overall_design: The total RNA from the each patient's plasma was extracted using TRIzol reagent according to the manufacturer's instructions. The purity and concentration of the RNA were determined from a 260/280 reading by using a spectrophotometer. RNA integrity was determined with a lab-on-a-chip kit using an RNA 6000 nano chip and Bioanalyzer 2100 to assess RNA quality comprehensively. Fluorescent dye Cy3 dCTP-labeled cDNA was prepared using Eberwine linear RNA amplification and enzymatic reaction. Data normalization and difference analysis were performed on the circRNA array data using GeneSpring software V13.0.

first: Lianli

last: Yin


title: RNA-seq and ATAC-seq in pancreatic islets isolated from mice with/without pancreatectomy

city: Dallas

first: Hao

last: Zhu

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center


title: MiRNA sequencing for CSF-derived EVs microRNAs in patients with moyamoya disease and arteriosclerotic cerebral ischemia

city: Showa-ku, Nagoya

first: Kinya

last: Yokoyama

state: Aichi

address: Tsurumai 65

department: Neurosurgery

institute: Nagoya University Hospital

summary: We aimed to clarify what specific changes occur in the expression level of extracellular vesicles (EVs) -derived microRNAs (miRNAs) in intracranial cerebrospinal fluid (CSF) in moyamoya disease. Patients with arteriosclerotic cerebral ischemia were used as controls to eliminate the effects of cerebral ischemia. Comprehensive expression analysis of miRNAs extracted from EVs by the next-generation sequencer was performed.

overall_design: Experiments were conducted on 8 cases of moyamoya disease and 4 cases of atherosclerotic brain ischemia as control.

last: Yokoyayma

first: Fumiaki

last: Kanamori


title: Transcription Factor Acj6 Controls Dendrite Targeting via Combinatorial Cell-Surface Codes

city: Stanford

first: Qijing

last: Xie

state: California

address: Bass Biology Building, Room 334

department: Department of Biology

institute: Howard Hughes Medical Institute

summary: Transcription factors specify the fate and connectivity of developing neurons. We investigate how a lineage-specific transcription factor, Acj6, controls the precise dendrite targeting of Drosophila olfactory projection neurons (PNs) by regulating the expression of cell-surface proteins. Quantitative cell-surface proteomic profiling of wild-type and acj6 mutant PNs in intact developing brains and a proteome-informed genetic screen identified PN surface proteins that execute Acj6-regulated wiring decisions. These include canonical cell adhesion molecules and proteins previously not associated with wiring, such as Piezo, whose mechanosensitive ion channel activity is dispensable for its function in PN dendrite targeting. Comprehensive genetic analyses revealed that Acj6 employs unique sets of cell-surface proteins in different PN types for dendrite targeting. Combinatorial expression of Acj6 wiring executors rescued acj6 mutant phenotypes with higher efficacy and breadth than expression of individual executors. Thus, Acj6 controls wiring specificity of different neuron types by specifying distinct combinatorial expression of cell-surface executors.

overall_design: Bulk RNA-seq of wild-type and acj6 mutant Drosophila olfactory projection neurons of the anterodorsal lineage


title: Expression data from differentiated murine 3T3-L1 pre-adipocytes treated with alpha-linolenic acid (ALA) and delta-6-desaturase (D6D) inhibitor

city: Guelph

first: David

middle: M

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

summary: The goal of this study was to investigate the individual and combined effects of alpha-linolenic acid (the essential omega-3 fatty acid) and an inhibitor of the delta-6 desaturse (SC-26196) during adipocye differentiation.

overall_design: 12 total samples were analyzed. Differential expression analysis was conducted in R with limma, where the following treated samples were compared: control vs ALA, control vs d6d inhibitor, and ALA vs ALA+d6d inhibitor. In each comparison, linear models were fitted with weighted least squares for each transcript cluster. Transcript clusters were ranked through log-odds ratios and un-adjusted p-values with eBayes and topTable with p < 0.01 considered statistically significant.

first: Chenxuan

last: Wang

first: Brittany

last: MacIntyre


title: Transcriptomic and epigenomic profiling of Myotis lucifugus embryonic fibroblast cells

city: Boulder

first: Edward

middle: B

last: Chuong

state: Colorado

address: 3415 Colorado Ave., room E251

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder


title: Modulation of Plant Development and Chilling Stress Responses by An Sm Core Protein Controlled Pre-mRNA Splicing in Arabidopsis

city: Hefei

first: Zhen

state: Anhui

address: 130 Changjiangxilu

institute: Anhui Agricultural University

summary:
Cold stress resulting from chilling and freezing temperatures substantially inhibits plant growth and reduces crop production worldwide. Tremendous research efforts have been focused on elucidating the molecular mechanisms of freezing tolerance in plants. Little is known about the molecular nature of chilling stress responses in plants. Here we found that two allelic mutants in a spliceosome component gene SmEb (smeb-1 and smeb-2) are defective in development and responses to chilling stress. RNA-seq analysis revealed that SmEb controls the splicing of many pre-mRNAs under chilling stress. The intron retentive COP1b splicing variant was dramatically induced by chilling stress in the smeb mutants. This nuclear-depleted COP1b lacks the nuclear speckle-localization capacity, supporting the regulatory role of COP1-HY5 interaction in hypocotyl elongation during chilling stress. Genetic evidence indicates that chilling-sensitive phenotype of the smeb mutants are partially rescued by the hy5 mutation. The transcription factor BES1 shows a dramatic defect in pre-mRNA splicing in the smeb mutants. Ectopic expression of the two BES1 splicing variants enhances the chilling sensitivity of the smeb-1 mutant. Biochemical and genetic analysis showed that CBFs act as negative upstream regulators of SmEb by directly suppressing its transcription. Together, our results demonstrate that proper alternative splicing of pre-mRNAs controlled by the spliceosome component SmEb is critical for plant development and chilling stress responses.
Cold stress resulting from chilling and freezing temperatures substantially inhibits plant growth and reduces crop production worldwide. Tremendous research efforts have been focused on elucidating the molecular mechanisms of freezing tolerance in plants. Little is known about the molecular nature of chilling stress responses in plants. Here we found that two allelic mutants in a spliceosome component gene SmEb (smeb-1 and smeb-2) are defective in development and responses to chilling stress. RNA-seq analysis revealed that SmEb controls the splicing of many pre-mRNAs under chilling stress. The intron retentive COP1b splicing variant was dramatically induced by chilling stress in the smeb mutants. This nuclear-depleted COP1b lacks the nuclear speckle-localization capacity, supporting the regulatory role of COP1-HY5 interaction in hypocotyl elongation during chilling stress. Genetic evidence indicates that chilling-sensitive phenotype of the smeb mutants are partially rescued by the hy5 mutation. The transcription factor BES1 shows a dramatic defect in pre-mRNA splicing in the smeb mutants. Ectopic expression of the two BES1 splicing variants enhances the chilling sensitivity of the smeb-1 mutant. Biochemical and genetic analysis showed that CBFs act as negative upstream regulators of SmEb by directly suppressing its transcription. Together, our results demonstrate that proper alternative splicing of pre-mRNAs controlled by the spliceosome component SmEb is critical for plant development and chilling stress responses.

overall_design: Twelve-day-old smeb-1, smeb-2, and Col-0 seedlings grown on 0.5× MS medium were treated at 4°C for 0 or 24 h.

first: Jia

last: Pang


title: scRNAseq profile of Day 4 Neurloids derived from WT and HD isogenic hESC lines

city: Neew York City

first: Ji-Dung

last: Luo

state: NY

address: 1230 York Avenue

department: Bioinformatics Resource Center

institute: The Rockefeller University

summary: We report the scRNAseq obtained from Wt hESC (RUES2) or isogenic lines carrying monoallelic HD mutation (56CAG) on endogenous HTT locus

overall_design: Comparison between WT and HD neuruloid

first: Francesco

last: Piccolo

first: Riccardo

last: De Santis

first: Ali

last: Brivanlou

first: Thomas

middle: S

last: Carroll