title: High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets

city: Worcester

first: Athma

last: Pai

state: MA

address: 368 Plantation Street, ASC5-2057

department: RNA Therapeutics Institute

institute: University of Massachusetts Medical School

summary: The antisense non-coding RNA in the INK locus (ANRIL), which originates from the CDKN2A/B (INK4-ARF) locus, has been identified as a hotspot for genetic variants associated with cardiometabolic disease including coronary artery disease (CAD) and Type 2 diabetes (T2D). We recently found that ANRIL abundance in human pancreatic islets was increased in donors carrying certain T2D risk-SNPs, and that a T2D risk-SNP located within exon2 of ANRIL conferred reduced beta cell proliferation index, pointing to a role for ANRIL in the regulation of T2D pathogenicity via an impact on insulin secretory capacity. Recent studies in other cell types have found that the balance between linear and circular species of ANRIL is linked to the regulation of cardiovascular disease phenotypes. Less is known about circular ANRIL expression in diabetes-relevant cell types and how their abundance might influence the risk of T2D. Herein, we use high-throughput and divergent primer sequencing of circular RNA in human pancreatic islet cells to quantify and characterize circular isoforms of ANRIL. We identified several circular ANRIL isoforms that are more abundant than linear ANRIL and whose expression was correlated across dozens of individuals. Back-splicing did not occur with equal probability at all ANRIL splice sites. Rather, some specific splice sites were found to have a higher propensity to be involved in back-splicing and are weakly enriched for sequence features known to promote back-splicing. Finally, we found that islets from carriers of the T2D risk allele at rs564398 in exon 2 of ANRIL had a higher ratio of circular ANRIL relative to linear ANRIL compared to protective-allele carriers, and that higher circular:linear ANRIL ratio was associated with a decreased beta cell proliferation index. Together, our study points to the combined involvement of both linear and circular ANRIL species in T2D phenotypes and opens the door for future studies to understand the molecular mechanisms by which ANRIL impacts cellular function in human pancreatic islets.

overall_design: PE RNA-seq was carried out on 5 frozen pancreatic islet donor preps. Each donor prep has two RNA-seq libraries: one RNase R digested and one mock digested (control).

first: Hannah

middle: J

last: MacMillan

first: Yahui

last: Kong

first: Ezequiel

last: Calvo-Roitberg

first: Laura

last: Alonso


title: Single cell RNA-seq of mouse lung endothelial cells

status: Public on May 11 2022

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

type: Expression profiling by high throughput sequencing

summary: Single cell RNA sequencing of endothelial cells isolated from adult Prox1-GFP mouse lung

overall_design: Lymphatic endothelial cells (PECAM1+ Prox1-GFP+ CD45- CD11b- Ter119-) and blood endothelial cells (PECAM1+ Prox1-GFP- CD45- CD11b- Ter119-) from adult Prox1-GFP mouse lung were sorted by flow cytometry into 384-well plates and subjected to single cell RNA-seq analysis by Smart-seq2.

first: Simon

last: Stritt

first: Taija

last: Mäkinen


title: Differentially expressed genes between ACh-stimulated KYSE30 cells and the respective control cells

city: Nanjing

first: Bin

last: Wei

state: Jiangsu

address: 101 Longmian Avenue

country: China

institute: Nanjing medical university

summary:
Purpose:RNA sequencing explored the possible altered gene transcriptome and signal pathways between ACh-stimulated KYSE30 cells and the respective control cells.
Methods:RNA sequencing explored the  ACh-stimulated KYSE30 cells and the respective control cells.

overall_design: Conclusions:Comparative gene expression profiling analysis of RNA-seq data for  ACh-stimulated KYSE30 cells and the respective control cells

first: Tao

last: Wang

first: Beibei

last: Ge


title: Improved methods for deamination-based m6A detection

city: Durham

first: Huanyu

last: Zhu

state: NC

address: 307 Research Drive

department: Biochemistry

country: USA

institute: Duke University

summary: We present an improved version of DART-seq which utilizes a variant of the YTH domain engineered to achieve enhanced m6A recognition in APO1-YTH (D422N). In addition, we develop in vitro DART-seq and show that it performs similarly to cellular DART-seq and can map m6A in any sample of interest using nanogram amounts of total RNA.

overall_design: Cellular DART-seq: We performed  RNA-seq on RNA from HEK293T cells expressing various DART constructs (containing APO domain or YTH domain variants) tested in the paper. We also sequenced RNA from cells expressing APO1-YTHmut, ADAR-YTHmut, or ADAR alone which serves as controls. There are at least 3 biological replicates included for each of these samples. In vitro DART-seq: We performed RNA-seq on RNA columned purified after incubation under various in vitro DART-seq conditions (time, protein:RNA, protein variant). We also sequenced RNA column purified after incubation with APO1-YTHmut or treated under YTH blocking conditions as negative control for in vitro DART-seq.

first: Kate

middle: D

last: Meyer


title: Gene expression (mRNA-seq) in the developing chicken retinal pigment epithelium

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins University

summary: The retinal pigment epithelium (RPE) exhibits a diverse range of plasticity across vertebrates and is a potential source of cells for the regeneration of retinal neurons. Embryonic amniotes possess a transitory ability to regenerate neural retina through the reprogramming of RPE cells in an FGF-dependent manner. Chicken RPE can regenerate neural retina at embryonic day 4 (E4) of development, but RPE neural competence is lost by embryonic day 5 (E5). To identify mechanisms that underlie loss of regenerative competence, we performed RNA and ATAC sequencing using E4 and E5 chicken RPE, as well as at both stages following retinectomy and FGF2 treatment. We find that genes associated with neural retina fate remain FGF2-inducible in the non-regenerative E5 RPE. Coinciding with fate restriction, RPE cells stably exit the cell cycle and dampen the expression of cell cycle progression genes normally expressed during regeneration, including E2F1. E5 RPE exhibits progressive activation of gene pathways associated with mature function independently of retinectomy or FGF2 treatment, including retinal metabolism, pigmentation synthesis, and ion transport. Moreover, the E5 RPE fails to efficiently repress OTX2 expression in response to FGF2. Predicted OTX2 binding motifs undergo robust accessibility increases in E5 RPE, many of which coincide with putative regulatory elements for genes known to facilitate RPE differentiation and maturation. Together, these results uncover widespread alterations in gene regulation that culminate in the loss of RPE neural competence and implicate OTX2 as a key determinant in solidifying the RPE fate. These results yield valuable insight to the basis of RPE lineage restriction during early development and will be of importance in understanding the varying capacities for RPE-derived retinal regeneration observed among vertebrates.

overall_design: RNA was extracted from the RPE of embryonic chickens at embryonic day 4 (E4) or embryonic day 5 (E5) and mRNA-seq was performed. In addition, mRNA-seq was performed on both the E4 and E5 RPE 6 hours post-retinectomy (6hPR), as well as 6hPR and treatment with FGF2-containing beads (6hPR+FGF2). Biological replicates were collected in triplicate.

first: Jared

middle: A

last: Tangeman

first: J

middle: R

last: Pérez-Estrada

first: Emily

last: Van Zeeland

first: Lin

last: Liu

first: Alexandra

last: Danciutiu

first: Erika

last: Grajales-Esquivel

first: Chun

last: Liang

first: Katia

last: Del Rio-Tsonis


title: OTX2 regulatory network and maturation-associated gene programs are inherent barriers to RPE neural competency

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Chromatin accessibility (ATAC-seq) in the developing chicken retinal pigment epithelium

overall_design: Nuclei were extracted from the RPE of embryonic chickens at embryonic day 4 (E4) or embryonic day 5 (E5) and ATAC-seq was performed. In addition, ATAC-seq was performed on both the E4 and E5 RPE 6 hours post-retinectomy and treatment with FGF2-containing beads (6hPR+FGF2). Biological replicates were collected in duplicate.


title: Use of Bulk Segregant Analysis for Determining the Genetic Basis of Azole Resistance in the Opportunistic Pathogen Aspergillus fumigatus

city: Nottingham

first: Fei

last: Sang

address: QMC

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

type: Genome variation profiling by high throughput sequencing

summary: Genome sequence data results are reported from experimental and bioinfomatic work using the technique 'Bulk Segregant Analysis' to determine the genetic basis of observed resistance to the azole antifungal compound itraconazole in the opportunistic fungal pathogen Aspergillus fumigatus.

overall_design: Sexual crosses were set up between a sensitive parent (47-51) and an azole resistant parent (47-308). Progeny were collected from both a second and sixth backcross to the sensitive parent and were screened into either azole sensistive or resistant bulk pools of 40-60 isolates. The respective parents and pools were then sequenced in triplicate and a dedicated bioinfiormatic pipeline used to identify a genome region found only in the resistant parent and resistant progeny that contained a causal mutation for azole resistance. The three replicate trimmed genome sequence files for the parents and progeny pools are here deposited,

first: Paul

middle: S

last: Dyer

first: George

last: Ashton

first: Victoria

last: Wright


title: IGF2BP2-regulated alternative splicing of NFIC causes excessive granulosa cell proliferation in PCOS [IRIP-seq]

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: The expression of IGF2BP2 in GCs from PCOS patients was detected using RT-qPCR and western blot. We captured IGF2BP2-interacting transcripts, global transcriptome together with alternative splicing by RNA immunoprecipitation sequencing (RIP-seq) and RNA sequencing (RNA-seq). KGN cells transfected with IGF2BP2 overexpressing plasmids and nuclear factor 1 C-type (NFIC) siRNAs, were applied to CCK-8, EdU and TUNEL assays. IGF2BP2 was highly expressed in GCs from PCOS patients. As a RBP, it preferentially bound to the 3’and 5’UTRs of mRNAs with GGAC motif and a newly found GAAG motif. The overexpression of IGF2BP2 changed the transcriptome profile of KGN cells. IGF2BP2 functioned to regulate alternative splicing events (ASEs) and promote cell proliferation through inhibiting exon skipping events of NFIC. In conclusion, we demonstrated that IGF2BP2 promotes granulosa cell proliferation via regulating alternative splicing of NFIC in PCOS. The findings help to better understand the roles of IGF2BP2 in the pathogenesis of PCOS.

overall_design: Immunoprecipitation and high-throughput sequencing of IGF2BP2 in KGN cells.

first: Feiyan

last: Zhao

first: Liang

last: Wu

first: Qin

last: Wang

first: Xuehan


title: IGF2BP2-regulated alternative splicing of NFIC causes excessive granulosa cell proliferation in PCOS [RNA-seq]

overall_design: Over-expression of IGF2BP2 in KGN cells.


title: RNA sequencing data from 3T3 cells overexpressing hPARG

city: Grand Forks

first: Yaroslava

last: Karpova

state: ND

address: 501 Columbia Road

department: Biomedical Sciences

institute: University of North Dakota

summary: 3T3 malignant cell line with stable overexpression of PARG under Doxycycline induction was generated. Transcriptome analysis linked malignance reduction phenotype with changes in chemokine family and other genes' expression levels.

overall_design: 3T3 cells were transduced with lentivirus construct encoding PARG cDNA with cleavable mClover3 under TetOne Doxycycline inducible promoter. Cells were plated to single well of 6 well plate, grown at 37°C in 5% CO2 for 72 hours without or with 500ng/ml Doxycycline and RNA isolated.

first: Sarah

last: Johnson

first: Danping

last: Guo

first: Alexei

last: Tulin


title: IGF2BP2-regulated alternative splicing of NFIC causes excessive granulosa cell proliferation in PCOS


title: Mutant-SETBP1 activates transcription of Myc programs to accelerate CSF3R-driven myeloproliferative neoplasms

city: Portland

middle: Ann

last: Carratt

state: Oregon

address: 3181 S.W. Sam Jackson Park Road, Mail Code KR-HEM

institute: OHSU

summary: Colony stimulating factor 3 receptor (CSF3R) mutations lead to JAK pathway activation and are the molecular hallmark of chronic neutrophilic leukemia (CNL). Approximately half of CNL patients also have mutations in SET binding protein 1 (SETBP1). In this study, we developed models of SETBP1-mutant leukemia to understand the role that SETBP1 plays in CNL. SETBP1 mutations promote self-renewal of CSF3R-mutant hematopoietic progenitors in vitro and prevent cells from undergoing terminal differentiation. In vivo, SETBP1 mutations accelerate leukemia progression, leading to the rapid development of hepatosplenomegaly and granulocytosis. Through transcriptomic and epigenomic profiling, we found that SETBP1 enhances progenitor-associated programs—most strongly upregulating Myc and Myc target genes. In summary, we find that SETBP1 mutations promote aggressive hematopoietic cell expansion when expressed with mutant CSF3R through the upregulation of Myc-associated gene expression programs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A novel CNL cell line and patient sample cells were analyzed by multi-omic profiling including bulk RNA-seq, single cell CITE-seq and CUT&Tag

first: Garth

middle: L

last: Kong

first: Brittany

middle: M

last: Smith

first: Julia

middle: E

last: Maxson

first: Theodore

middle: P

last: Braun


title: Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patients

city: Kansas City

first: Scott

middle: T

last: Younger

state: MO

address: 2401 Gillham Road

institute: Children's Mercy Kansas City

summary: Clinical whole genome sequencing has enabled the discovery of potentially pathogenic noncoding variants in the genomes of rare disease patients with a prior history of negative genetic testing.  However, interpreting the functional consequences of noncoding variants and distinguishing those that contribute to disease etiology remains a challenge.  Here we address this challenge by experimentally profiling the functional consequences of rare noncoding variants detected in a cohort of undiagnosed rare disease patients at scale using a massively parallel reporter assay.  We demonstrate that this approach successfully identifies rare noncoding variants that alter the regulatory capacity of genomic sequences.  In addition, we describe an integrative analysis that utilizes genomic features alongside patient clinical data to further prioritize candidate variants with an increased likelihood of pathogenicity.  This works represents an important step towards establishing a framework for the clinical interpretation of noncoding variants.

sample_organism:
Homo sapiens
other sequences

platform_organism:
Homo sapiens
other sequences

overall_design: MPRA (massively parallel reporter assay) screening the impact of rare genetic variants on the regulatory capacity of genomic sequences in cultured human cells and bulk RNA-seq following CRISPR-mediated perturbation of transcription factors/variant sites.


title: Homeostasis imbalance of YY2 and YY1 promotes tumor growth by manipulating ferroptosis

city: Chongqing

first: Yanjun

middle: Chongqing

last: Li

state: Chongqing

address: 174 Shazheng Street

institute: Chongqing University

summary: Ferroptosis is a type of programmed cell death caused by disruption of redox homeostasis, and is closely linked to amino acid metabolism. Yin Yang 2 (YY2) and its homolog Yin Yang 1 (YY1) are members of the YY family with high homology, especially in their zinc-finger domains. Furthermore, they share consensus DNA binding motif. In contrast with the oncogenic YY1, increasing evidences have demonstrated the tumor suppressive effect of YY2; however, at present, little is known about its biological and pathological functions. Here we found that YY2 induces tumor cells ferroptosis and subsequently, suppresses tumorigenesis, by inhibiting SLC7A11 transcription, leading to the decreased glutathione biosynthesis. Furthermore, we reveal that YY2 and YY1 bind competitively to SLC7A11 promoter and antagonistically regulate tumor cells ferroptosis, thus suggesting the molecular mechanism underlying their opposite regulation on tumorigenesis. Moreover, we showed that mutations of YY2 zinc-finger domains in clinical cancer patients abrogated YY2/SLC7A11 axis and tumor cells ferroptosis. Together, these results provide a new insight regarding the regulatory mechanism of ferroptosis, and a mechanistic explanation regarding the tumor suppressive effect of YY2. Furthermore, our findings demonstrate that homeostasis between YY1 and YY2 is crucial for maintaining redox homeostasis in tumor cells.

overall_design: 6 samples

first: Vivi

last: Kasim

first: Shourong


title: ATAC-seq in WT, p53-ko, Ezh2-ko primary macrophages

city: Shanghai

first: Jia

last: Yuan

address: Yueyang road 320, Xuhui, Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: Assess chromatin accessibility in WT, p53-ko, Ezh2-ko primary macrophages using ATAC-seq.

overall_design: ATAC-seq was performed on 50000 cells in WT, p53-ko, Ezh2-ko primary macrophages

first: Yichuan

last: Xiao

first: Qingchen

last: Zhu


title: CHIP-seq in WT, p53-ko, Ezh2-ko primary macrophages

summary: We immunoprecipitated chromatin in primary macrophages using antibodies against Ezh2, p53, H3K27ac, H3K27me3 and Sirt1 to identify the potential binding genes.

overall_design:
Examination of binding activities using indicated antibodies in different macrophages
Please note that each processed data was generated from both ChIP and input samples, and is linked to the corresponding ChIP sample records.


title: CHIP-seq and ATAC-seq in WT, p53-ko, Ezh2-ko primary macrophages


title: A Unique Estrogen-Sensitive Cell Population Drives Abdominal Muscle Fibrosis in an Inguinal Hernia Mouse Model

city: Chicoago

first: Serdar

last: Bulun

state: IL

address: 303 E Superior Street

department: Obstetrics & Gynecology

institute: Northwestern Feinberg School of Medicine

summary: We performed single cell analysis on lower abdominal muscle tissues in wild-type and a humanized aromatse mice with scrotal hernias

overall_design: Examination of 3 different WT and Aromhum lower abdominal muscle tissues

first: Tanvi

last: Potluri


title: Intratumoral heterogeneity, cell of origin and microenvironment in retinoblastoma [scRNA-seq]

city: Guangzhou

first: Cheng

last: Wu

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

summary: Retinoblastoma (RB) is the most common primary intraocular malignancy of childhood. The diverse malignant and immune cells in tumors determine tumor progression, but the intratumoral heterogeneity, tumor microenvironment and their impact in RB remain poorly characterized. Here, we conducted transcriptomic profiles of around 70,000 cells from tumor samples of seven RB patients with pathological and clinical measurements. Fifteen cell types were identified where the majority were cone precursor-like (CP-like) and MKI67+ cone precursor (MKI67+ CP) cells. These cells expressed markers of cone precursor, suggesting that RB originated from cone precursor cells. The conversion of CP-like to MKI67+ CP led to the loss of photoreceptor function and increased cell proliferation ability in RB. By integrative copy number variation analysis, we found that two subtypes of MKI67+ CP cells were more malignant related to cell proliferation. The tumor microenvironment in RB was composed of three cell types, of which glial cells, including tumor-associated macrophages and astrocytes-like cells, created an immunosuppressive environment and promoted tumor growth and invasion by inhibiting the GALECTIN signaling pathway. Together, our study presents the first transcriptomic map of RB at a single-cell resolution and provides novel insights into the occurrence and progression of RB which will be important to the development of the future targeted therapy and immunotherapy.

overall_design: Single cells from seven independent retinoblastoma samples were captured in 10 batches (RB01, RB02, and RB03 samples repeated) using the 10X Chromium system.

first: Xie

last: Zhi

first: Wu

last: cheng


title: Expression data from human BPH1 and WPMY-1 cells treated with Rauwolfia vomitoria (RWF).

city: nanjing

first: jiakuan

last: liu

address: 12 xuefu road, pukou district

institute: nanjing university

summary:
Rauwolfia vomitoria extract is an herbal preparation of the root bark of a plant in the tropical forests of Africa, which could inhibit Benign prostatic hyperplasia (BPH). Characterizing the molecular alterations of BPH1 and WPMY-1 cells treated with RWF is important for understanding the molecular mechanisms of RWF inhibiting BPH.
We used microarrays to detail the RNA expression.

overall_design: 8 samples were analyzed, 2 replicates. BPH1 and WPMY-1 cells were treated with vehicle or RWF (250μg/ml). These cells were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Jiakuan

last: Liu

first: Jun

last: Yan


title: Transcriptome analysis of miniBacillus PG10 and its parental strain B. subtilis 168

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: miniBacillus PG10 lacks ~36% of dispensible genentic material and has been derived from B. subtilis 168 (Reuß et al. 2017; PMID: 27965289). We performed RNA-seq analysis on mid-to-late exponential cultures and stationary phase cultures that were grown in LB medium. We specifically analyzed differential gene expression levels of lipid metabolic genes to compare to the lipidomic profiles of the two strains.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: 12 samples; 3 replicates

first: Amanda

middle: Y

last: van Tilburg

first: Philipp

last: Warmer

first: Auke

last: van Heel

first: Uwe

last: Sauer

first: Oscar

last: P Kuipers


title: Cnot8 Eliminates Naïve Regulation Networks and Is Essential for Naïve-to-Formative Pluripotency Transition (PAIso-Seq)

city: Beijing

first: Lei

last: Li

state: Beijing

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: The transition of mammalian early epiblast at different phases is characterized by the differences of pluripotent states and developmental potential, involving extensive transcriptome changes. However, the role of post-transcriptional RNA degradation modulation in cell fate transition remains largely unexplored. Here, we report that deadenylase Cnot8 of Ccr4-Not complex specifically plays a role in naïve-to-formative transition of pluripotent stem cells (PSCs). Disruption of Cnot8 results in early embryonic lethality, accompanying with the increased expression levels of naïve transcription factors in mouse epiblasts. Cnot8 depletion leads to accumulated expression abundances and increased poly(A) tail lengths of massive transcripts including mRNAs of naïve regulation networks, impairing the naïve-to-formative pluripotency conversion. Mechanistically, Cnot8 interacts with Tob1 and Pabpc1 to guarantee the prompt mRNA deadenylation and degradation of naïve regulation networks at specific time. Together, these findings delineate the mechanism underlying PSC fate transition through global degradation of mRNAs for naïve regulation networks by Cnot8.

overall_design: totally four PAIso-seq library were constructed for the wildtype and Cnot8 KO    ESC cell line, each with two replications

first: Falong

last: Lu


title: Mapping of Single Nuclear Transcriptomic Responses Uncovers Plasticity of Subpopulation of Purkinje Neurons Driving Motor Learning

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

summary: Cellular diversification is a fundamental feature of the brain that is critical for physiological functions of the nervous system including perception, motor control, and learning and memory. Advances in single cell RNA-sequencing have led to characterization of transcriptomic profiles of distinct major types of neurons in the brain. However, how transcriptomic profiles diversify within a specific population of neurons and their links to function remain poorly understood. Purkinje neurons represent some of the most iconic cells in the brain with decades of research characterizing their anatomy, cell biology, physiology, and roles in plasticity, learning and memory, as well as in diseases of the nervous system. In this study, we deployed an approach of isolating nuclei tagged in specific cell types followed by cell sorting and single nuclear RNA sequencing to profile Purkinje neurons and their response to motor activity and learning in adult mice. We uncovered the molecular map of two major subpopulations of Purkinje neurons, identified by the hallmark genes Aldoc and Plcb4, which bear distinct transcriptomic features. Remarkably, Plcb4+, but not Aldoc+, Purkinje neurons display robust plasticity of gene expression in mice subjected to sensorimotor and learning experience with downregulation of gene clusters related to chromatin regulation and synaptic organization and upregulation of gene clusters related to neuronal activity and synaptic transmission and neuron-immune interactions. Using in vivo calcium imaging and optogenetics perturbation approaches, we show that activation of Plcb4+ Purkinje neuron plays a crucial role in associative motor learning. Upon integrating single nuclear RNA-seq datasets with weighted gene network analysis, we also identify a motor activity and learning specific gene module that includes components of the FGFR2-SOS1-MAPK signaling pathway in Plcb4+ Purkinje neurons. Knockout of FGFR2 in Plcb4+ Purkinje neurons in adult mice by a CRISPR approach dramatically disrupts motor learning. Our findings provide a platform for identification of subpopulations of neurons and define how diversification of Purkinje neurons in the cerebellum links to their responses to motor learning. Our study, and by extension similar studies in the human brain, will provide the foundation for understanding the selective vulnerability of Plcb4+ Purkinje neurons to neurological diseases.

overall_design: Exploration the diversification of Purkinje neurons in the cerebellum links to their responses to motor learning

first: Xiaoying

last: Chen

first: Yanhua

last: Du

first: Xiaoqing

last: Zhang

first: Azad

last: Bonni


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control and rhCYGB treated in MIA PaCa-2 cell line

city: Osaka

first: Hoang

middle: Viet

last: Dinh

state: Osaka-fu

address: 1-4-3 Asahimachi - Abeno-ku

department: Hepatology

country: Japan

institute: Osaka city university

summary:
Purpose: The goal of this study is to investigate the inhibitor effect of  Cytoglobin on pancreatic cancer
Method: mRNA profiles of control and  rhCYGB treated pancreatic cancer cells were generated by deep sequencing.
Results: The RNA-seq data  confirmed that extracellular matrix-encoding genes and cell cycle regulated genes were down-regulated by the His-CYGB treatment.

overall_design: mRNA profiles of MIA PaCa-2 cells with or without rhCYGB treatment

first: Norifumi

last: Kawada

first: Le

last: Thuy

first: Dinh

middle: V

last: Hoang


title: Cnot8 Eliminates Naïve Regulation Networks and Is Essential for Naïve-to-Formative Pluripotency Transition (RNA-Seq)

overall_design: Total 24 RNA-seq libraries with 12 wild type and 12 Cnot8/7 KO from five differential time points


title: Simonsiella muelleri DSM 2579 RNA-Seq

status: Public on May 10 2022

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

summary: mRNA-Seq for differential gene expression analysis and delineation of chromosome interaction domains

overall_design: 3 conditions in biological triplicates (exponential growth (OD600 = 0.2), stationary growth (OD600 = 1), growth on solid medium for 24h)

first: Tobias

last: Viehboeck


title: CAF-1 Histone Chaperone is a Repressor of Mixed Cellular States in Myeloid Progenitors [scRNA-seq]

city: Pasadena

first: David

middle: Eugene

last: Frankhouser

state: CA

address: 1500 E Duarte Rd

department: Population Sciences

institute: City of Hope

summary: To characterize the cell identity of CAF-1 depleted Hoxa9-granulocyte-macrophage progenitors (Hoxa9-GMPs) and address whether CAF-1 suppression in Hoxa9-GMPs leads to either a heterogeneous or a mixed lineage state, we conducted single cell transcriptome analysis before and after the Hoxa9-GMPs commit to differentiation in both CAF-1 suppression and Hoxa9 inactivation conditions.

overall_design: Single-cell mRNA profiles of Hoxa9-GMPs at 0h, 48hrs and 96hrs upon CAF-1 suppression or Hoxa9 inactivation by high throughput sequencing.

first: Yiming

last: Guo

first: Sihem

last: Cheloufi

first: Russell

last: Rockne


title: Marker Frequency Analysis of Simonsiella muelleri DSM 2579

summary: Investigation of replication dynamics (detection of origin of replication, bidirectionality, …)

overall_design: 3 conditions (early exponential (OD600 = 0.3), late exponential (OD600 = 0.6), stationary growth (OD600 = 1))


title: Cystathionine gamma-lyase is required for the heat shock protein 70-driven penile neurovascular regeneration and erectile function recovery

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

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

department: Urology

country: South Korea

institute: Inha university hospital

summary: Neurovascular dysfunction in penis is a fundamental reason of erectile dysfunction. Diabetes mellitus is one of the major causes of erectile dysfunction and leads to a poor response to oral phosphodiesterase-5 inhibitors. Heat shock protein 70 (Hsp70), a ubiquitous molecular chaperone exist in all living organisms, is known to play a role in cell survival and neuroprotection. Here, we report an effectiveness of Hsp70 in mediating neurovascular regeneration in diabetic conditions. Using Hsp70-Tg mice or Hsp70 protein administration, we demonstrate that overexpression of Hsp70 in diabetic mice restores erectile function through enhanced penile angiogenesis and neural regeneration. We found that cystathionine gamma-lyase (Cse) is a novel target of Hsp70-driven penile angiogenesis and neural regeneration. Hsp70-Cse triggered SDF1/HO-1/PI3K/Akt/eNOS/NF-κB p65 pathways involved in angiogenesis and neural regeneration. Coimmunoprecipitation and His-Tag pull down assay using mouse cavernous endothelial cells treated with Hsp70 showed the physical interaction between Hsp70 and Cse, and solid-phase binding assay revealed a high-affinity Hsp70-Cse binding with an apparent dissociation constant of 1.8 nmol/L. We provide a novel and solid evidence for Cse-dependent mechanism of Hsp70, which mediates Hsp70-induced neurovascular regeneration and the restoration of erectile function under diabetic conditions.

overall_design: Control (normal glucose) (n=3), Hg (high glucose) (n=4) and Hspto (high glucose+Hsp70) (n=4)

first: Guo

middle: N

last: Yin

first: Ghatak

last: Kalyan

first: Ji-Kan

last: Ryu

first: Jun-Kyu

last: Suh


title: Post-transcriptionally regulated genes are essential for pluripotent stem cell survival

city: Kyoto

first: Mio

last: Iwasaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

type: Non-coding RNA profiling by high throughput sequencing

summary: The effects of transcription factors on the maintenance and differentiation of pluripotent stem cells (PSCs) have been well studied. However, the importance of post-transcriptional regulatory mechanisms, which cause the quantitative dissociation of mRNA and protein expression, is still little known. Here, by combining transcriptome and proteome profiling, we identified 228 post-transcriptionally regulated genes with strict upregulation at the protein amounts in PSCs. Among them, we found that 84 genes were vital for the survival of PSCs and HDFs, including 20 genes that were specifically necessary for the survival of PSCs. These 20 proteins were upregulated only in PSCs and not in differentiated cells derived from the three germ layers. Subcellular fractionation of the mRNA showed that the expression of most of the 20 proteins was regulated at the mRNA localization stage from the nucleus to the cytoplasm, but their translation efficiency was constant. Together, these results revealed that post-transcriptionally regulated genes have a crucial role in PSC survival.

overall_design: Whole and subcellular fractionated human pluripotent stem cell line in feeder free condition (N=3),   Whole and subcellular fractionated human dermal fibroblast (N=3)

first: Kazutoshi

last: Takahashi

first: Chikako

last: Okubo


title: Tethering distinct molecular profiles of single cells by their lineage histories to investigate sources of cell state heterogeneity

status: Public on May 12 2022

city: Seattle

first: Anna

last: Minkina

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Gene expression heterogeneity is ubiquitous within single cell datasets, even among cells of the same type. Heritable expression differences, defined here as those which persist over multiple cell divisions, are of particular interest, as they can underlie processes including cell differentiation during development as well as the clonal selection of drug-resistant cancer cells. However, heritable sources of variation are difficult to disentangle from non-heritable ones, such as cell cycle stage, asynchronous transcription, and measurement noise. Since heritable states should be shared by lineally related cells, we sought to leverage CRISPR-based lineage tracing, together with single cell molecular profiling, to discriminate between heritable and non-heritable variation in gene expression. We show that high efficiency capture of lineage profiles alongside single cell gene expression enables accurate lineage tree reconstruction and reveals an abundance of progressive, heritable gene expression changes. We find that a subset of these are likely mediated by structural genetic variation (copy number alterations, translocations), but that the stable attributes of others cannot be understood with expression data alone. Towards addressing this, we develop a method to capture cell lineage histories alongside single cell chromatin accessibility profiles, such that expression and chromatin accessibility of closely related cells can be linked via their lineage histories. We call this then leverage this indirect “coassay” approach "THE LORAX" and leverage it to explore the genetic and epigenetic mechanisms underlying heritable gene expression changes. Using this approach, we show that we can discern between heritable gene expression differences mediated by large and small copy number changes, trans effects, and possible epigenetic variation.

overall_design: Single cell RNA-seq (sci-RNA-seq), single cell ATAC-seq (sci-ATAC-seq), and targeted transcript capture encoding lineage relationships alongside both single cell methods. Cell line: HEK293.

first: Junyue

last: Cao

first: Jay

last: Shendure


title: Irisin enhances chondrogenic differentiation of human mesenchymal stem cells via Rap1/PI3K/AKT axis.

first: Taiqiu

last: Chen

state: Guangdong

address: 33, Yinfeng Road

institute: Sun yat-sen university

summary:
Collectively, our study reveals that irisin can enhance chondrogenic differentiation of hMSCs via the Rap1/PI3K/AKT pathway, suggesting that irisin possesses prospects in cartilage regeneration.
Collectively, our study reveals that irisin can enhance chondrogenic differentiation of hMSCs via the Rap1/PI3K/AKT pathway, suggesting that irisin possesses prospects in cartilage regeneration.

overall_design: To further explore the possible mechanisms accounting for the role of irisin on the chondrogenic differentiation of hMSCs, RNA sequencing was performed in hMSC-induced cartilage tissue between controls and irisin-treated groups on day 7.

first: Wenjie

last: Gao


title: Marker Frequency Analysis of Alysiella filiformis DSM 16848

first: Silvia

last: Bulgheresi

first: Tobias

last: Viehboeck


title: Single-cell RNA-seq of human kidney organoids

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

summary: We used scRNA-Seq  (and other biological experiments) to study the impact of a high oscillatory glucose regime in the differentiation and metabolic status of human kidney organoids further emulating early hallmarks of the diabetic kidney. To study the interplay between those changes and SARS-CoV-2 infection we  assessed the effect of early stages of infection (1 day post infection) in normoglicemic (5 mM), hyperglicemic (5-25 mM oscillatory regime) and differentiating (11 mM) conditions. We retrieved metabolic changes and an upregulation of inflammatory related processes upon infection, whilst there was not an impact in the viability of the different cell types in the kidney organoids. Also, we studied the differences between ACE2 CRISPR/Cas9 knockouts and ACE2 WT organoids, using single cell RNA sequencing to resolve cell-type specific and cell proportion changes.

first: Nuria

last: Montserrat


title: Psychrotolerant bacterium Sphingomonas glacialis AAP5 harvests light energy using both  proton-pumping xanthorhodopsins and bacteriochlorophyll-based reaction centers

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: Bacterium Sphingomonas glacialis AAP5 isolated from the alpine lake Gossenköllesee contains genes for anoxygenic phototrophy as well as proton-pumping xanthorhodopsin. Here we show that AAP5 expresses xanthorhodopsin when illuminated at temperatures below 16°C. In contrast bacteriochlorophyll-containing reaction centers are expressed between 4 and 22°C in the dark. Thus, cells grown at lower temperature under natural light-dark cycle produced both photosystems. The purified xanthorhodopsin contains carotenoid nostoxanthin serving as an auxiliary antenna and performs the standard photocycle. The xanthorhodopsin-containing cells reduced upon illumination their respiration, increased their ATP synthesis and produced more biomass. This documents that the harvested light energy was utilized in the metabolism, which can represent a competitive advance under carbon-limiting conditions. The presence of Sphingomonas bacteria with dual phototrophy was verified in the metagenomes collected from lake Gossenköllesee. This unique trait may represent a metabolic advantage in alpine lakes where photoheterotrophic organisms facelimited organic substrates, low temperature, and extreme changes in irradiance.

overall_design: Samples from three independent cultures were withdrawn. Each of the three replicate cultures were sampled for three consenquent days. Each day, samples were taken 1 h and 6 h after the switch to light and 1 h and 6 h after the switch to dark phase of cultivation

first: Karel

last: Kopejtka

first: David

last: Kaftan

first: Alastair

last: Gardiner

last: Bína

first: Christopher

last: Bellas

first: Astrid

last: Dröge

first: Michal

last: Koblížek


title: Cnot8 Eliminates Naïve Regulation Networks and Is Essential for Naïve-to-Formative Pluripotent Transition

first: Lei

last: Li

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

overall_design: Refer to individual Series


title: Manipulating Cholesterol Metabolism by oncolytic virus suppresses metastasis of triple-negative breast cancer [cell line]

city: Nanjing

first: Jie

last: Dong

address: Hankou road 22

institute: Nanjing University

summary: To investigate the effect of ApoA1 mediated cholesterol efflux on the gene expression of 4T1 cells

overall_design: ApoA1 over-expressed 4T1 and wild type 4T1 were cltured for 48h. mRNA were collected for RNA sequencing.

first: Dong

last: Jie

first: Kong

last: Lingkai


title: Manipulating Cholesterol Metabolism by oncolytic virus suppresses metastasis of triple-negative breast cancer [tumors]

summary: To investigate the effect of  ADV or AAV encoding ApoA1 treatment on the gene expression of 4T1 tumor in vivo

overall_design: Mice burden with breat cancer were treated by ADV-CON, ADV-ApoA1, AAV-CON or AAV-ApoA1.Tumor mRNA were collected for RNA sequencing.


title: Genome-wide transcripts in NMuMG cells expressing Osr2

city: Tsukuba, Ibaraki

first: Ken

last: Nishimura

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: Analysis of NMuMG cells expressing Osr2 or treated with TGF-ß. Results provide insight into a novel function of Osr2 in EMT induction.

overall_design: Two replicates of total RNA were isolated from NMuMG cells transduced with the Osr2-expressing retroviral vector for 3 days (Day3) or 9 days (Day9) as well as those treated with or without TGF-b (TGFb or Control, respectively) for 2 days. Library construction and RNA-seq were performed by Illumina sequencing platform (Annoroad Gene Technology). Sequence reads were mapped to the mouse genome (GRCm38.p6) using STAR aligner (v2.7.3a) with default parameters. The read counts were calculated by featureCounts (v2.0.0) with the gene model from Ensemble (Mus_musculus GRCm38.75.gtf) at gene level to obtain TPM (Transcripts Per Million). The gene count data was normalized by variance stabilizing transformations (VST) using DESeq2.

first: Akihiro

last: Kuno


first: Mio

last: Iwasaki

overall_design: Human pluripotent stem cell line in feeder free condition, N=6  Human embryonic stem cell line in feeder free condition, N=3  Human dermal fibroblast, N=6

first: M

last: Narita


title: The influence of age and sex on the pre-treatment immune microenvironment of a  carcinogen induced murine model of bladder cancer

city: Kingston

first: Madhuri

last: Koti

state: Ontario

address: 10 Stuart Street

department: Department of Biomedical and Molecular Sciences

country: Canada

institute: Queen's University

summary: The incidence of urothelial carcinoma of the bladder is four times higher in males than females; however, females tend to present with a more aggressive disease, a poorer response to immunotherapy and suffer worse clinical outcomes. Recent findings have demonstrated sexual dimorphism in the tumor immune microenvironment of non-muscle invasive bladder cancer and associated clinical outcomes. However, a significant gap in knowledge remains with respect to the current pre-clinical modeling approaches and more precisely recapitulating these differences towards improved therapeutic design. Based on the similarities in mucosal immune physiology between humans and mice, we evaluated the sex and age-related immune alterations in healthy murine bladders. Bulk-RNA sequencing and multiplex immunofluorescence based spatial immune profiling of healthy murine bladders from male and female mice of age groups spanning young to old showed a highly altered immune landscape that exhibited sex and age associated differences, particularly in the context of B cell associated responses. Spatial profiling using markers specific to macrophages, T lymphocytes, B lymphocytes, activated dendritic cells, high endothelial venules, myeloid cells and the PD-L1 immune checkpoint showed sex and age associated differences. Bladders from healthy older female mice showed a higher number of tertiary lymphoid structures (TLSs) compared to both young female and male equivalents. Spatial immune profiling of N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN) carcinogen exposed male and female bladders from young and old mice revealed a similar frequency of TLS formation, sex differences in the bladder immune microenvironment and, age differences in latency of tumor induction. These findings support the incorporation of sex and age as factors in pre-clinical modeling of NMIBC and will potentially advance the field of immunotherapeutic drug development to improve clinical outcomes in NMIBC.

overall_design: Bulk RNA sequencing of bladders from 3, 6, 9, 12, 15, and 18 month old male and female C57BL/6 mice, differential expression and pathway analysis to find age and sex based differences

first: Ali

last: Hamade

first: Deyang

first: Kathrin

last: Tyryshkin

first: Minqi

last: Xu

first: Stephen

last: Chenard

first: Gwenaelle

last: Conseil

first: Priyanka

last: Yolmo

first: Robert

last: Siemens


title: Genome-wide transcripts in reprogramming cells expressing Osr2

summary: Analysis of reprogrammed MEFs expressing Osr2. Results provide insight into an importance of Osr2 downregulation during the reprogramming.

overall_design: Total RNA were isolated from reprogrammed MEFs expressing Osr2 or kusabira orange treated with or without 10 µM SB431542.Libraries were sequenced on an Illumina NovaSeq 6000. Sequence reads were mapped to the mouse genome (GRCm38.p6) using STAR aligner (v2.7.3a) with default parameters. The read counts were calculated by featureCounts (v2.0.0) with the gene model from Ensemble (Mus_musculus GRCm38.75.gtf) at gene level to obtain TPM (Transcripts Per Million).


title: Massively Parallel Characterization and Prediction of Disease-Associated Branch Site Variants that Perturb RNA Splicing

city: Taipei

first: Chien-Ling

last: Lin

address: 128 Academia Road, Section 2

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: It is estimated that 10-30% of disease-associated genetic variants affect splicing. Splicing variants may generate deleteriously altered gene product and are potential therapeutic targets. However, experimental diagnosis for splicing variants is time-consuming and reliable computational prediction tools have not been established, especially for the 3’ end of introns. The major challenge lies in the redundant and ill-defined branch site motif therein. Here, we carried out unbiased massively parallel splicing assays on 5,307 disease-associated variants overlapped with branch sites. We observed that 11.0% (455 out of 4,154 valid comparisons) of candidate variants showed a consistent pattern of altered splicing across four experimental replicates, among which 244 candidates (6.1%) presented more than two-fold changes in the use of noncanonical splice sites and these are named high-confidence (HC) significant candidates.

overall_design: A total of 5,307 BS variants are reported in the Human Gene Mutation Database (HGMD), the public archive of interpretations of clinically relevant variants (ClinVar), the database of single nucleotide polymorphisms (dbSNP), or the Catalogue of Somatic Mutations in Cancer (COSMIC), all of which provide overlapping data on the most informative BS position 0 (i.e., the branchpoint), as well as the -2 or -3 positions of experimentally discovered branchpoints. We synthesized paired oligos containing the wildtype (WT) or mutant (mt) BS and their affiliated exons in bulk, ligated them into three-exon splicing minigenes, and then transfected them into human embryonic kidney cells (HEK293T) to examine the splicing outcome. An exonic barcode was associated with the intronic variant for genotype identification. The spliced product was recovered by reverse transcription and library-specific amplification, and then resolved by amplicon sequencing. Biased splicing efficiency and use of noncanonical splice sites by variants relative to their WT counterparts was identified by Fisher’s exact test.

first: Hung-Lun

last: Chiang

first: Yi-Ting

last: Chen

first: Yun-Ling

last: Wang


title: An RNA-sequencing transcriptome of the rodent Schwann cell response to peripheral nerve injury

city: Stanford

first: Tawaun

middle: Autry

last: Lucas

address: 1201 Welch Rd

institute: Stanford University

summary:
The important contribution of glia to mechanisms of injury and repair of the nervous system is increasingly recognized.  In stark contrast to the central nervous system (CNS), the peripheral nervous system (PNS) has a remarkable capacity for regeneration after injury. Schwann cells are recognized as key contributors to PNS regeneration but the molecular underpinnings of the Schwann cell response to injury remain incompletely understood.
To gain insight into the acute SC injury response, we provide an RNAseq database of Schwann cells purified acutely from the naïve and injured rodent sciatic nerve at 3, 5, and 7 days post injury. Bioinformatic analysis provides validation of cell purity and dataset integrity as well as identification of discrete modules of genes that follow distinct patterns of regulation in the first days after injury and their corresponding molecular pathways.
Our dataset provides a helpful resource for further deciphering the SC injury response and provides a depth of transcriptional data that can complement the findings of recent single cell sequencing approaches. In addition, as more data becomes available on the response of CNS glia to injury, we anticipate that this dataset will provide a valuable platform for understanding key differences in the PNS and CNS glial responses to injury and for designing approaches to ameliorate CNS regeneration.

overall_design: RNA profiling of rat Schwann cells after sciatic nerve crush from uncrushed/naïve, 3 days, 5 days, and 7 days post nerve crush

first: Amanda

last: Brosius Lutz

first: Glenn

last: Carson

first: Marion

last: Buckwalter

first: Steven

last: Sloan


title: Next Generation Sequencing Facilitates Quantitative Analysis of U87-PLV03 and U87-GPR17 Transcriptomes

city: Fujian Province, China

first: huiqing

last: Liu

address: State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen ,Fujian Province, China

institute: Xiamen University

summary: GPR17 over-expression inhibits glioma cell proliferation and induces apoptosis by raising ROS levels, and mechanistically inhibits the transcription of RNF2, leading to reduced histone H2A monoubiquitination. Here, To identify the genes mediating the effects of GPR17 and RNF2 on ROS level, we performed RNA-Seq of WT and U87-GPR17 cells and RNF2 ChIP-Seq of WT and U87-shGPR17 cells.

overall_design: U87-PLV03 cells and U87-GPR17 cells

first: Chen

last: Ying

first: Han


title: GPR17


title: Genome-wide binding of RNF2 in control and GPR17 knock-down U87-MG cells

overall_design: RNF2 DNA binding in control and GPR17 knock-down U87-MG cells


title: Genes related to microtubule functions were downregulated in sinhcaf mutant FG follicles and eggs

city: Wuhan

first: Binbin

last: Tao

address: No. 7 Donghu South Road

institute: Institute of Hydrobiology

summary: Transcriptome sequencing (RNA-seq) analysis uncovered that 1238 genes were upregulated, 923 genes were downregulated in sinhcaf mutant FG follicles, compared to wild type FG follicles. Loss of sinhcaf in mature eggs resulted in upregulation of 904 genes, and downregulation of 911 genes. Downregulated genes in sinhcaf mutant FG follicles and eggs were classified by gene ontology (GO) analysis, then the top 30 GO terms with highest -log10P values were screened out, and at least two downregulated genes were included in each biological processes, cellular components or molecular function term. Microtubules and microtubule-based processes were included in the top 30 GO terms.

overall_design: RNA sequencing was performed on five biological replicates for mature egg, four biological replicates for FG follicle of wild type and sinhcaf mutant zebrafish. Each biological replicate was a pool of mature eggs or FG follicles from one female zebrafish.


title: RNA-seq in AGS-EBV, shRNA

city: Changsha

first: siwei

last: Zhang

state: Hunan

address: 87 Xiangya Road

department: Department of Microbiology

institute: Central South University

summary: Gastric cancer is one of the most common cancers worldwide. Epstein-barr virus-associated gastric cancer accounts for about 10% of all gastric cancers. EBV itself expresses a variety of proteins and regulates the expression of host genes. In this study, we examined the knockdown of BC200 and eIF4A3 in AGS-EBV, respectively, and analyzed its effect on host mRNA expression.

overall_design: Total RNA was prepared using Trizol reagent from nine each independent cultures of AGS-EBV cells.

first: Siwei

first: Jing

last: Li


title: Exploring the potential mechanism of Zhuanggu Zhitong Capsule in the treatment of osteoporosis in ovariectomized rats based on the transcriptome

status: Public on May 09 2022

city: changsha，CHINA

first: Hai-ping

last: HUANG

address: 300 Xuesheng Road, Hanpu Science and Education Park, Yuelu District, Changsha, Hunan province, China

institute: Hunan University of Chinese Medicine

summary: Objective: To analyze the differentially expressed genes and related pathways of Zhuanggu Zhitong Capsule (ZGZTC) in the treatment of osteoporosis in ovariectomized rats based on transcriptome sequencing.  Methods: Eighteen SD female rats were randomly divided into sham operation group, model group and ZGZTC group, each with 6 rats. Intervention was started 1 week after the model was established. The experimental group was given ZGZTC (567mg/kg), and the sham operation group and model group were given (1ml/150g) volume of distilled water, once a day for 13 consecutive weeks. On the second day after the last administration, samples were taken and blood was collected from the abdominal aorta to prepare the corresponding group of serum. RNA-Seq sequencing was performed to screen differentially expressed genes and KEGG function Annotation analysis and GO enrichment analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for osteoporosis rats and ZGZTC treated rats

first: Huiping

first: Guomin


title: ScRNAseq analysis of EC sensitized mouse skin

city: Boston

first: Manuel

last: Leyva-Castillo

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: We performed single-cell RNA-seq to transcriptionally characterize the populations and gene expression in the skin of mice epicutaneously sensitized

overall_design: Balb/c mice were epicutaneously sensitized for 10 days. 2 days later the mouse skin was collected and enzymatically digested to generate a sjingle cell suspension. Barcoding and library preparation were done using  the 10x Genomics Chromium platform, with the Chromium Single Cell 3′ Library & Gel Bead Kit v2 and Chromium Single Cell 3′ Chip kit v2 according to the manufacturer’s instructions.

first: Juan

last: Leyva-Castiilo

first: Raif

last: Geha


title: Effect of TNF-α on gene expression of L929 cells

first: Ruiyu

last: Xiang

department: Institute of Dermatology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: To investigate the TNF-α in the regulation of L929 cells.We performed gene expression profiling analysis using data obtained from RNA-seq of L929 cells activated by TNF-α.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for L929 cells and L929 cells activated by TNF-α of 10ng/ml and actinomycin d of 1μg/ml.

first: Yong

last: Yang


title: A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model

city: Wako

first: Chiawen

last: Lin

state: Saitama

address: 2-1, Hirosawa

department: CBS

institute: RIKEN

summary: Immune dysregulation plays a key role in the pathogenesis of autism. Changes occurring at the systemic level, from brain inflammation to disturbed innate/adaptive immune in the periphery, are frequently observed in patients with autism; however, the intrinsic mechanisms behind them remain elusive. We hypothesize a common etiology may lie in progenitors of different types underlying widespread immune dysregulation. By single-cell RNA sequencing (sc-RNA seq), we trace the developmental origins of immune dysregulation in a mouse model of idiopathic autism. It is found that both in aorta-gonad-mesonephros (AGM) and yolk sac (YS) progenitors, the dysregulation of HDAC1-mediated epigenetic machinery alters definitive hematopoiesis during embryogenesis and downregulates the expression of the AP-1 complex for microglia development. Subsequently, these changes result in the dysregulation of the immune system, leading to gut dysbiosis and hyperactive microglia in the brain. We further confirm that dysregulated immune profiles are associated with specific microbiota composition, which may serve as a biomarker to identify autism of immune-dysregulated subtypes. Our findings elucidate a shared mechanism for the origin of immune dysregulation from the brain to the gut in autism and provide new insight to dissecting the heterogeneity of autism, as well as the therapeutic potential of targeting immune-dysregulated autism subtypes.

overall_design: Comparing the definitive hematopoietic process in yolk sac and AGM between B6 and autistic model of BTBR mice by sc-RNA seq

first: Chia-wen


title: Genome-wide transcriptome profiling of human trabecular meshwork cells treated with TGF-β2.

city: Buncrana

first: Breedge

last: Conwell

address: Cromore rd

institute: Ulster university

summary: we employed RNA-Seq to delineate the TGF-β2 induced changes in the transcriptome of normal primary human trabecular meshwork cells (HTM).

overall_design: Examine changes to gene expression in TGF-β2 treated human trabecular meshwork cells derived from patients

last: Callaghan

first: Karen

last: Lester

first: Brian

last: Lane

first: Xiaochen

last: Fan

first: Katarzyna

last: Goljanek-Whysal

first: David

middle: A

last: Simpson

first: Carl

last: Sheridan

first: Colin

last: Willoughby


title: CLT-seq as a universal homopolymer-sequencing concept reveals poly(A) tail-tuned ncRNA regulation

city: Shenzhen

first: Qiang

last: Su

state: None Selected

address: 1066 Xueyuan Street

institute: Shenzheng Uni

summary:
To more understand the poly(A) tail-tuned regulation in eukaryotic cells, we describe central limit theorem (CLT)-managed RNA-seq (CLT-seq) as a universal homopolymer-sequencing concept that features unbiased RNA-seq and facilitates accurate homopolymer base-calling.
We then performed transcriptome-wide poly(A)-tail profiling analysis using data obtained from oligo(dT)-primed RNA-seq of HEK293T and A549 cell lines.

overall_design:
Comparative poly(A)-tail profiling analysis of RNA-seq data for different cells.
The T12, T18, T30, T18V, T18VN, and T18VNN are adaptor-flanked oligo(dT) primers with anchor or without anchor base for poly(A) tail-specific reverse transcription. The sequence is as following:
T12: 5'-TACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGCGTAGCTTTTTTTTTTTT-3'
T18: 5'-TACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGCGTAGCTTTTTTTTTTTTTTTTTT-3'
T30: 5'-TACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGCGTAGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3'
T18V: 5'-TACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGCGTAGCTTTTTTTTTTTTTTTTTTV-3'
T12VN: 5'-TACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGCGTAGCTTTTTTTTTTTTTTTTTTVN-3'
T18VNN: 5'-TACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGCGTAGCTTTTTTTTTTTTTTTTTTVNN-3'


title: Convergence of SIRT1 and ATR signaling to modulate replication origin dormancy

city: Bethesda

first: Christophe

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

summary: During routine genome duplication, many potential replication origins remain inactive, or 'dormant'. Such origin dormancy is achieved, in part, by an interaction with the metabolic sensor SIRT1 deacetylase. We report here that dormant origins are a group of consistent, pre-determined genomic sequences that can be distinguished from baseline (i.e. ordinarily active) origins by their preferential association with MCM2, a component of the replicative helicase, phosphorylated on serine 108 (pS108-MCM2). pS108-MCM2 is a substrate of the ATR kinase, which is recruited to chromatin via an interaction with hyperacetylated TOPBP1 in cells undergoing replication stress or in cells devoid of SIRT1 deacetylase activity. In turn, S108-MCM2 phosphorylation enhances a second, DDK-dependent, S139-MCM2 phosphorylation, which triggers initiation of DNA replication at dormant origins. These observations suggest that replication origin dormancy and activation are regulated by distinct post-translational modifications on the MCM helicase that reflect a balance between SIRT1 activity and ATR signaling.

overall_design: Nascent strands were purified with the lambda exonuclease methods from HCT116 cells. Chromatin from HCT116 cells was subjected to ChIP-Seq with antibody directed against pT530-SIRT1, pS108-MCM2, pS40/41, pS53 and pS139-MCM2.

first: M

middle: I

last: Aladjem


title: Sex-specific Phenotypes modulated by activin in pancreatic cancer cachexia and mortality

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

summary: Cachexia frequently develops in patients with pancreatic ductal adenocarcinoma (PDAC) and contributes to cancer deaths.Sex differences have been observed in cancer cachexia; however, the underlying molecular mechanisms are far less addressed. We assessed sex difference in PDAC cachexia phenotypes in the KPC (Kras-G12D;Trp-R172H;Pdx1::Cre) genetically engineered mouse model of PDAC and profiled gene expression in the quadriceps skeletal muscles. Males with PDAC experienced earlier cachexia-onset than the female counterpart and activin blockade by ACVR2B/Fc reduced cachexia sympotomes in males but not females. PDAC induced earlier global transcritome alterations in males than females.

overall_design: Males and females were evaluated for PDAC tumor and cachexia initiation and progress and ACVR2B/Fc effects. Tumor and organ tissues were collected at early and late time points and the quadriceps muscles were subjected to molecular and transcriptome analysis.

first: Xiaoling

last: Zhong

first: Ashok

last: Narasimhan

first: Jianguo

last: Liu

first: Jun

last: Wan

first: Sheng

first: Yunlong

first: Amber

first: Emma

last: Doud

first: Leonidas

middle: G

last: Koniaris


title: IPMK physically binds to the SWI/SNF complex and modulates BRG1 occupancy

city: Daejeon

first: Sungwook

last: Han

address: Deahakro 291

department: Biological Science

institute: KAIST(Korea Advanced Institute of Science and Technology)

summary: Inositol polyphosphate multikinase (IPMK), a key enzyme in the inositol polyphosphate (IP) metabolism, is a pleiotropic signaling factor involved in major biological events, including transcriptional control. In the yeast, IPMK and its IP products promote the activity of the chromatin-remodeling complex SWI/SNF, which plays a critical role in gene expression by regulating chromatin accessibility. However, the direct link between IPMK and chromatin remodelers remains unclear, raising a question on how IPMK contributes to the transcriptional regulation in mammals. By employing unbiased screening approaches and in vivo/in vitro immunoprecipitations, here we demonstrated that mammalian IPMK physically interacts with the SWI/SNF complex by directly binding to SMARCB1, BRG1, and SMARCC1. Furthermore, we identified the specific domains required for the IPMK-SMARCB1 binding. Notably, using the CUT&RUN and ATAC-seq assays, we discovered that IPMK co-localizes with BRG1 and regulates BRG1 localization as well as BRG1-mediated chromatin accessibility in a genome-wide manner in mouse embryonic stem cells. Finally, our mRNA-seq analyses revealed that IPMK and SMARCB1 regulate the expression of a common gene set, validating a functional link between IPMK and the SWI/SNF complex. Together, these findings show that IPMK regulates promoter-targeting of the SWI/SNF complex and thereby contributes to SWI/SNF-meditated chromatin accessibility, transcription, and differentiation.

overall_design:
For RNA-seq experiment: Strand-specific mRNA-Seq of Control (EgfpKD) and IpmkKD in mouse embryonic stem cells (mESCs) and mouse embryonic fibroblasts (MEFs).
For ATAC-seq experiment: Genome-wide analysis of chromatin accessibility upon IPMK depletion in mESCs.
For CUT&RUN experiment: Genome-wide distributions of BRG1 upon IPMK depletion (siRNA-mediated and shRNA-mediated) in mESCs.

first: Jiyoon

last: Beon

first: Hyeokjun

last: Yang

first: Seung-Eun

last: Park

first: Kwangbeom

last: Hyun

first: Song-Yi

last: Lee

first: Hyun-Woo

last: Rhee

first: Jeong-Kon

last: Seo

first: Jaehoon

last: Kim

first: Seyun

first: Daeyoup


title: Transcriptomes of human oocytes during in vitro maturation

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

institute: Kyushu University

summary: We aimed to reveal gene expression profiles of human oocytes at each maturation stage by single cell RNA-seq analyses. We investigated transcriptomes of immature oocytes at the germinal vesicle (GV) stage, maturating oocytes at the metaphase I (MI) stage and in vitro matured oocytes at the metaphase II (MII) stage.

overall_design: In this study, transcriptomes for oocytes at different maturation stages were examined using single cell RNA-seq. Surplus oocytes, which are normally discarded as medical waste, were subjected to this study. Immature oocytes at the time of oocyte collection were used for in vitro maturation, and oocytes that reached the MII stage until 5.5-7 hours after the oocyte collection were used for infertility treatment. The remaining oocytes were regarded as surplus oocytes. Those were again subjected to incubation for in vitro maturation and their morphology was assessed during 7.5-9 hours after the oocyte collection. At this stage, oocytes at the GV, MI, and MII stages were collected and subjected to RNA-seq. Moreover, some remaining oocytes were further cultured for 15-16.5 hours and oocytes that reached each maturation stage at 24 hours after the oocyte collection were also used for RNA-seq analyses.


title: Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: We evaluated the chromatin structure around MyoD-bound genome regions during the cell cycle by chromatin immunoprecipitation sequencing.

overall_design: We performed RNA-seq and ChIP-seq in proliferative mouse C2C12 myoblasts during three phases (G1, S, G2/M) of the cell cycle.

first: Qianmei

last: Wu

first: Takeru

last: Fujii

first: Akihito

last: Harada

first: Kosuke

last: Tomimatsu

first: Atsuko

last: Miyawaki-Kuwakado

first: Kazumitsu

last: Maehara


title: ALDH RNA seq

city: Greenwood

first: Sneha

last: Mokashi

state: South Carolina

address: 113 Gregor Mendel Circle

institute: Greenwood Genetic Center

summary: Mono- and biallelic variants in the ALDH18A1 gene cause a spectrum of human disorders associated with cutaneous and neurological findings that overlap with both cutis laxa and spastic paraplegia.  ALDH18A1 encodes the bifunctional enzyme pyrroline-5-carboxylate synthetase (P5CS) that plays a role in the de novo biosynthesis of proline and ornithine.  Here we characterize a previously unreported homozygous ALDH18A1 variant (p.Thr331Pro) in four affected probands from two unrelated families, and demonstrate broad-based alterations in amino acid and antioxidant metabolism.  These four patients exhibit variable developmental delay, neurological deficits, and loose skin.  Functional characterization of the p.Thr331Pro variant demonstrated a lack of any impact on the steady-state level of the P5CS monomer or mitochondrial localization of the enzyme, but reduced incorporation of the monomer into P5CS oligomers. Using an unlabeled NMR-based metabolomics approach in patient fibroblasts and ALDH18A1-null human embryonic kidney cells expressing the variant P5CS, we identified reduced abundance of glutamate and several metabolites derived from glutamate, including proline and glutathione.  Biosynthesis of the polyamine putrescine, derived from ornithine, was also decreased in patient fibroblasts, highlighting the functional consequence on another metabolic pathway involved in antioxidant responses in the cell.  RNA sequencing of patient fibroblasts revealed transcript abundance changes in several metabolic and ECM-related genes, adding further insight into pathogenic processes associated with impaired P5CS function.  Together these findings shed new light on amino acid and antioxidant pathways associated with ALDH18A1-related disorders, and underscore the value of metabolomic and transcriptomic profiling to discover new pathways that impact disease pathogenesis.

overall_design: 2 genotypes- control and patient; fibroblasts derived from control and patient; 3 replicates per genotype

first: Richard

last: Steet


title: Differential antagonistic effects of finerenone and spironolactone on the aldosterone transcriptome in human kidney cells.

city: Le Kremlin-Bicêtre

first: Florian

last: Le Billan

address: 63, Gabriel Péri street

country: France

institute: INSERM

summary: Aldosterone, the main mineralocorticoid hormone in humans, controls, via gene transregulation, various renal functions including water and sodium reabsorption and potassium excretion. Dysregulations in the aldosterone signaling pathway lead to renal dysfunctions, including chronic kidney disease and renal fibrosis, that can be prevented or treated with mineralocorticoid receptor antagonists (MRAs). To understand the global effects of aldosterone on the human renal transcriptome, and how it is antagonized by the MRAs spironolactone and finerenone, we used RNA-sequencing on a human kidney cells HK-GFP-hMR. Our data provide the first complete transcriptome for aldosterone on a human renal cell line and support at the RNA level the benefit of finerenone for the treatment of kidney injury and fibrosis.

overall_design: Human Kidney HK-GFP-hMR cells were treated 3 h with 1:1000 ethanol (Vehicle, Veh), 10 nM aldosterone (Aldo), 1 μM spironolactone (Spiro), 1 μM finerenone (Fine), or a combinaison of the molecules (Aldo + Spiro, Aldo + Fine).

first: Say

last: Viengchareun

first: Peter

last: Kolkhof

first: Jérôme

last: Fagart

first: Marc

last: Lombès


title: Improved Biocompatibility of Amino-functionalized Graphene Oxide in Caenorhabditis elegans

city: Cologne

first: Bjoern

last: Schumacher

state: NRW

address: Joseph-Stelzmann-Strasse 26

department: Institute for Genome Stability in Ageing and Disease

country: Germany

institute: CECAD Cologne

summary: Graphene oxide (GO) holds high promise for diagnostic and therapeutic applications in nanomedicine but reportedly displays immunotoxicity, underlining the need for developing functionalized GO with improved biocompatibility. Here, we study the adverse effects of GO and amino-functionalized GO (GONH2) during Caenorhabditis elegans development and ageing upon acute or chronic exposure. Chronic GO treatment throughout the C. elegans development causes decreased fecundity and a reduction of animal size, while acute treatment does not lead to any measurable physiological decline. However, RNA-Seq data reveal that acute GO exposure induces innate immune gene expression. The p38 MAP kinase, PMK-1, which is a well-established master regulator of innate immunity, protects C. elegans from chronic GO toxicity, as pmk-1 mutants show reduced tissue-functionality and facultative vivipary. In a direct comparison, GONH2 exposure does not cause detrimental effects in the wild type or in pmk-1 mutants, and the innate immune response is considerably less pronounced. Our work establishes the enhanced biocompatibility of amino-functionalized GO in a whole-organism, emphasizing its potential as biomedical nanomaterial.

overall_design: Gene expression analysis in C. elegans upon 12 h treatment with either graphene oxide (GO) or amino-functionalized GO (GONH2)

first: Corvin

last: Rive

first: Giacomo

last: Reina

first: Prerana

last: Wagle

first: Alberto

last: Bianco

first: Lucia

last: Gemma-Delogu

first: Matthias

last: Rieckher

first: Björn


title: Ewing sarcoma cell lines

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

institute: Institut Curie

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

overall_design: Refer to individual Series


title: The role of Hoxb1 in NMPs and neural progenitors

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

institute: TU Dresden

summary: We found that, whereas Hoxb1 does not affect NMP specification per se, it promotes NMP survival through the upregulation of Fgf8 and other components of Fgf signaling as well as the repression of components of the apoptotic pathway. Additionally, it upregulates the expression of some, primarily anterior, Hox genes suggesting that it plays an active role in the early steps of AP specification. In hindbrain neural progenitors Hoxb1 synergizes with shh to repress the expression of dorsal markers, regulate the expression of ventral markers and direct the specification of facial branchiomotorneuron (FBM) - like progenitors. Additionally, Hoxb1 and shh synergize in regulating the expression of diverse signals and signaling molecules in neural progenitors, including the Ret tyrosine kinase receptor. Hoxb1 synergizes with GDNF to strengthen Ret expression and further promote the generation of facial branchiomotorneuron (FBM) – like progenitors

overall_design: Genome wide expression analysis in two contexts (A) WT and Hoxb1 null NMP cells (B) Neuronal progenitors expressing or not Hoxb1 in the presence or absence of SAG

first: Kristijan

last: Pazur


title: New, Potent, Small Molecule Agonists of Tyrosine Kinase Receptors Improve Dry Eye Disease

status: Public on May 08 2022

city: Houston

first: Cintia

middle: S.

last: de Paiva

state: TX

address: 6565 Fannin Street NC505G

department: Ophthalmology

institute: Baylor College of Medicine

summary:
Nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin3 (NT-3) bind to tyrosine kinase (Trk) receptors, TrkA, TrkB, and TrkC, respectively. This study investigated the efficacy of novel molecule agonists of Trk receptors in an in vivo model of dry eye disease.
Compared to vehicle, mice subjected to desiccating stress and treated with agonists pan and C1 showed improved corneal barrier function, while C1 also increased GC densities. NanoString analyses revealed upregulation of specific mRNA transcripts (Ptger4, Tnfaip3, Il1a and Ptger4, Tlr3, Osal1) in pan and C1 treated corneas compared to vehicle-treated corneas. Western blots showed pan and C1 decreased vehicle-induced NFkB nuclear translocation after DS for one day and increased PTGER4 and TNFAIP3 protein levels after 5 days of DS in corneal epithelium lysates.  These results were confirmed by immunostaining using antibodies for TNFAIP3 and PTGER4 in wholemount corneas. We conclude that small-molecule agonists of Trk receptors improve dry eye disease by decreasing NFkB activation and increasing protein expression of anti-inflammatory molecules TNFAIP3 and PTGER4. Surprisingly, the most efficacious small molecule agonists were not TrkA selective, but TrkC and panTrk, suggesting that wider exploration of TrkB and C and pan Trk agonists are warranted in efforts to treat dry eye disease.

overall_design: For this, small molecule TrkC agonist C1) and a pan-Trk agonist (pan) were synthesized.  C57BL/6J mice were subjected to desiccating stress (DS) and received bilateral eye drops of C1, pan or vehicle (2x/day). Dry eye signs, inflammation and expression of  Corneal barrier function, and conjunctival goblet cell (GC) densities were measured as part of the dry eye phenotype.  Corneal epithelial lysates were collected for either western blot or RNA extraction.  Extracted total RNAs were used for NanoString analyses.  Immunofluorescent staining was performed on wholemount corneas using anti-TNFAIP3 and anti-PTGER4 antibodies.

first: Zhiyuan

last: Yu

first: Shaon

last: Joy

first: Tianxiong

last: Mi

first: Ghasem

last: Yazdanpanah

first: Kevin

last: Burgess

middle: S


title: Manipulating Cholesterol Metabolism by oncolytic virus suppresses metastasis of triple-negative breast cancer

city: Nanjing

first: Jie

last: Dong

address: Hankou road 22

institute: Nanjing University


title: Whole-genome RNAsequencing of intestinal organoids and tumoroids

first: Silvia

last: Fre

address: 26 rue d’Ulm

department: Genetics and Developmental Biology

summary: In order to decipher the molecular responses of normal epithelial cells to the tumor secretome, we obtained the gene expression profiles of wildtype organoids exposed to either WT or tumor conditioned medium, along with the transcriptional signature of the tumoroids from which the corresponding tumor conditioned medium was derived.

overall_design: Three replicates of wildtype organoids (from 3 different mice) exposed for 24h to conditioned medium (wildtype or tumor organoids) and three replicates of  tumoroids (from 3 different mice) grown for 24h were used for the analysis. A total of 9 samples was analyzed (3 per condition).

first: Guillaume

last: Jacquemin

first: Wenjie

last: Sun


title: Risk SNP-mediated enhancer-promoter interaction drives keloid through lncRNA DEIK

city: Guangzhou

first: Chengcheng

last: Deng

address: No.2 lujing Road

institute: Dermatology Hospital, Southern Medical University

summary: Genetics is a major factor for keloid predisposition and the genome-wide association study (GWAS) has identified a single nucleotide polymorphism (SNP) rs873549 at 1q41 as a susceptibility locus. However, the functional significance of this locus in keloid pathogenesis remains elusive. Here, we found that rs1348270, an enhancer located SNP in strong linkage disequilibrium with rs873549, mediated looping with the promoter of a lncRNA DEIK (Down Expressed In Keloids, formerly RP11-400N13.1). The risk variant was associated with decreased enhancer-promoter interaction and DEIK expression. Mechanistically, downregulation of DEIK increased the expression of collagens and chondrocyte and osteocyte associated genes such as POSTN and COMP through upregulating BMP2. Furthermore, correlation analysis revealed that DEIK expression was inversely correlated with BMP2, POSTN and COMP expression in keloid and normal fibroblasts. These findings uncover new mechanisms underlying genetic factor-mediated keloid predisposition and identify potential targets for keloid therapies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for fibroblasts and its knockdown derivatives (siDEIK).

first: Zhili

last: Rong

first: Bin

last: Yang


title: Interferon regulatory factor 1 (IRF1) controls the metabolic programmes of low-grade pancreatic cancer cells

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute


title: TfR1 globally regulates transcription and alternative splicing

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: In the current study, to figure out the regulation pattern of TfR1, we knocked down TFRC expression level by shRNA in HeLa cells. RNA-sequencing (RNA-seq) was used to analyze the global transcript level and alternative splicing (AS) on knockdown-treated (KD) and normal control (NC) cell samples. 629 differentially expressed genes (DEGs) were identified between OE and NC, and Gene ontology (GO) and KEGG analysis for DEGs were carried out. It was found that multiple DEGs were involved in O-glycan processing, protein modification, response to hypoxia and ATP catabolic process, indicating the down-regulated expression of TfR1 extensively disturbed cell physiology.

overall_design: To explore the regulation pattern of TfR1, we knocked down TFRC by shRNA in HeLa cells and RNA-sequencing (RNA-seq) was carried out in knockdown-treated (KD) versus normal control (NC) cell samples.

last: Huang


title: mRNA transcriptome sequencing of bone marrow-derived macrophages (BMDMs) and dendritic cells (BMDCs) from Lyz2-Cre;Trpv2fl/fl and Trpv2fl/fl mice.

first: Yu-Yao

last: Guo

address: Donghu Road 115

institute: Wuhan University

summary: Femurs and tibias were dissected from Trpv2fl/fl and Lyz2-Cre;Trpv2fl/fl mice. Bone marrow was flushed from the bones, and the red blood cells were lysed with ACK lysis buffer. Debris was removed by passing cells through a 70 μM strainer and cells were counted via Countess II FL Automated Cell Counter. Approximately 5 × 106 bone marrow cells were cultured in 100 mm dishes in DMEM (Thermo Fisher Scientific, MA, USA) containing 10% heat-inactivated fetal bovine serum (FBS, Gibco, Thermo Fisher Scientific) and 1% streptomycin-penicillin at 37 °C in a humidified incubator gassed with 5% CO2. GM-CSF (20 ng/mL, Peprotech) and M-CSF (10 ng/mL, Peprotech) were added to the bone marrow cultures for differentiation of BMDCs and BMDMs, respectively. The medium was changed every 3 days. On day 7, cells were collected and homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. TruSeq Stranded mRNA LT Sample Prep Kit was used to synthesized the first strand cDNA through the action of random primers and reverse transcriptase, the second strand cDNA is synthesized with the first strand cDNA as the template, cDNA library construction followed by sequencing on an Illumina NovaSeq 6000 platform. RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with cutadapt, then aligned to Mus musculus GRCm38 genome with Ensembl. The numbers of counts were summarized at the gene level using HTseq.  Gene expression values were computed from fragments per kilo bases per million fragments (FPKM) values produced by addition of a pseudocount of 1 and log2 transformation of the results.

overall_design: BMDCs from Trpv2fl/fl mice (n=2) and Lyz2-Cre;Trpv2fl/fl mice (n=2) were used,respectively. BMDMs from Trpv2fl/fl mice (n=2) and Lyz2-Cre;Trpv2fl/fl mice (n=2) were used,respectively.

first: Yue

last: Gao

first: Bo

last: Zhong

first: Jing

last: Yao


title: Bidirectional regulation between AP-1 and SUMO genes modulates inflammatory signaling during Salmonella Typhimurium infection

city: PUNE

first: Girish

last: Ratnaparkhi

state: MH

address: Dr. Homi Bhabha Road Pashan Pune 411008

department: Biology

country: India

institute: Indian Institute of Science Education & Research

summary:
Purpose: To understand the role of SUMOylation of c-Fos in the differential regulation of target genes and altered cellular pathways upon STm infection. To address this, we performed a RNA-seq experiment with stable over expressing WT-FOS or SUMO-def-FOS in f10 c-FOS-Knock out MEFs upon STm infection.
Methods: Three biological replicates of c-FOS-KO-WT-FOS, c-FOS-KO-WT-FOS with salmonella infection, c-FOS-KO-SUMO-def-FOS and c-FOS-KO-SUMO-def-FOS with salmonella infection, cells were collected and total RNA was extracted according to kit's protocol. The total RNA was used to generate a cDNA library using Quantseq 3' mRNA kit.
Results: Transcriptional profiling revealed that genes involved in immune response, proliferation, metastasis etc. are differentially regulated in salmonella infected c-FOS-KO-SUMO-def-FOS MEFs compare to salmonella infected c-FOS-KO-WT-FOS MEFs.
Conclusions: Our study revealed the extensive transcriptomics analysis from c-FOS-KO-WT-FOS and c-FOS-KO-SUMO-def-FOS MEFs upon salmonella infection. We found that SUMOylation of c-Fos provides selectivity that causes differential regulation of target genes which are involved in immune response, proliferation etc. pathways of host.  Together, our findings illuminate an important regulatory role played by SUMOylated c-Fos upon STm infection.

overall_design: RNA-seq

first: Pharvendra

last: Kumar

first: C

last: Srikanth


title: SOX7 regulates MAPK/ERK-BIM mediated apoptosis in cancer cells

city: Singapore

first: SIQIN

last: ZHOU

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Here we showed that SOX7 was significantly downregulated in different cancer types, especially in lung and breast cancers. Low expression of SOX7 was associated with advanced stage of cancer with shorter overall survival. Cancer cells with loss of SOX7 promoted cell survival and colony formation, suppressed cellular apoptosis and produced a drug resistant phenotype against a variety of chemo/targeting therapeutic agents. Mechanistically, SOX7 induced cellular apoptosis through upregulation of genes associated with both P38 and apoptotic signaling pathway, as well as preventing the proteasome mediated degradation of pro-apoptotic protein BIM. Treatment of either a proteasome inhibitor MG132 or bortezomib, or with a p-ERK/MEK inhibitor U0126 attenuate the SOX7 promoted BIM degradation.

overall_design: mRNA profiles of Control (GFP) and SOX7 overexpressing H23 and H1299 cells, as well as SOX7 silenced PC14 cells were generated by microarray using  Illumina Human HT-12 v4 Expression BeadChip

first: Qiao-Yang

first: Ling-Wen

last: Ding

first: Kara

last: Johnson

first: Siqin

last: Zhou

first: Jeffrey

middle: W

last: Tyner

first: Henry

first: Ngan

middle: B

last: Doan

first: Jonathan

last: Said

first: Jin-Fen

last: Xiao

first: Xin-Yi

last: Loh

first: Xue-Bin

last: Ran

first: Nachiyappan

last: Venkatachalam

first: Zhentang

last: Lao

first: Ye

first: Liang

last: Xu

first: Li-Fei

last: Fan

first: Wenwen

last: Chien

first: De-Chen

last: Lin

first: H

last: Koeffler


title: Chd4 regulates intra-chromatin looping by concealing CTCF sites from B2 SINEs in mESCs

first: Sungwook

last: Han

address: Deahakro 291

summary: CTCF plays a critical role in maintaining the three-dimensional (3D) chromatin organization, which is important for gene regulation, as it allows distal regulatory elements to come into proximity with one another. However, the detailed mechanism responsible for establishing and maintaining the recruitment of CTCF remains elusive. Here, we use in situ Hi-C to show that the ATP-dependent chromatin remodeler, Chd4, regulates intra-chromatin looping by controlling chromatin accessibility to conceal aberrant CTCF-binding sites in mouse embryonic stem cells (mESCs). These aberrant CTCF-binding sites are embedded in B2 SINEs and are localized within the interior of chromatin loops. In the absence of Chd4, the aberrant CTCF-binding sites become accessible and improper CTCF recruitment occurs, resulting in disorganization of the 3D chromatin architecture and subsequent disruption of enhancer-promoter interactions and the transcription of the corresponding genes. These results indicate that Chd4 regulates adequate transcription of mESCs by securing the proper 3D chromatin organization.

overall_design: For in situ Hi-C experiment : Genome-wide chromatin conformation capture upon CHD4 loss (Chd4 knockdown using siRNA and auxin treatment for CHD4-mAID) in mouse embryonic stem cells (mESCs).  For MNase-seq experiment : Genome-wide analysis of nucleosomes upon CHD4 loss in mESCs.  For ATAC-seq experiment : Genome-wide analysis of chromatin accessibility upon CHD4 loss in mESCs.  For ChIP-seq experiment : Genome-wide distributions of various factors upon CHD4 loss in mESCs.  For CUT&RUN experiment : Genome-wide distributions of various factors upon CHD4 loss in mESCs.  For RNA-seq experiment : Strand-specific totalRNA-seq and mRNA-Seq upon CHD4 loss in mESCs.  For GRO-seq experiment : Genome-wide analysis of nascent transcripts upon CHD4 loss in mESCs.

first: Hosuk

last: Lee

first: Andrew

middle: J

first: Seung-Kyoon

last: Kim

first: Inkyung

last: Jung

first: Gou

last: Koh

first: Tae-Kyung

first: Daeyoup


title: Lack of apoA-I in apoEKO mice causes skin xanthomas, worsening of inflammation and increased coronary atherosclerosis in the absence of hyperlipidemia

status: Public on May 07 2022

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

institute: University of Milan

summary: High-throughput sequencing technologies were used to analyse the transcriptome of the spleen and axillary lymph node of apoE/apoA-I double deficient (DKO) mice, characterized by an almost complete HDL deficiency, and DKO mice overexpressing human apoA-I (DKO/hA-I), characterized by high HDL plasma levels. Mice were 30 weeks old and had been fed a normal laboratory diet.

overall_design: RNA-seq performed in spleen and axillary lymph node of apoE/apoA-I double deficient (DKO) mice and DKO mice overexpressing human apoA-I (DKO/hA-I), n=3 per experimental group, using the Illumina Genome Analyzer IIx. One diet (normal laboratory diet), one time point (30 weeks of age).

first: Marco

last: Busnelli

first: Stefano

last: Manzini

first: David

last: Horner

first: Giulia

last: Chiesa


title: Clinical associations of ESR2 (estrogen receptor beta; ERβ) expression across thousands of primary breast tumors

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

summary:
PURPOSE: Estrogen receptor alpha (ERα, encoded by ESR1) is a well-characterized transcription factor expressed in more than 75% of breast tumors and is the key biomarker to direct endocrine therapies. On the other hand, much less is known about estrogen receptor beta (ERβ, encoded by ESR2) and its importance in cancer. Previous studies had some disagreement, however most reports suggested a more favorable prognosis for patients with high ESR2 expression.
METHODS: To add further clarity to ESR2 in breast cancer, we interrogated a large population-based cohort of primary breast tumors (n=3207) from the SCAN-B study (Sweden Cancerome Analysis Network—Breast [SCAN-B], ClinicalTrials.gov identifier: NCT02306096). Spearman rank correlation was used to determine correlations between expression of ESR1 and ESR2. Kruskal-Wallis non-parametric test and Wilcoxon rank sum test were used to compare and plot expression of the ESR1 and ESR2 genes in various clinical groups such as PAM50 subtype and age groups in both the SCAN-B and TCGA cohorts. Transformed ESR2 expression data was divided into tertiles, with the first tertile defined as ESR2-high, and the bottom two tertiles at ESR2-low. Mann Whitney U test and Fisher’s exact test were used to evaluate significant differences in the clinicopathological variables for the ESR2-high and ESR2-low groups. Survival analysis was performed by Kaplan-Meier and Cox regression survival analyses that included a median follow-up of 6.2 years (IQR = 2.2).
RESULTS: Using RNA-seq data, we found that ESR2 is expressed at low levels overall with a slight inverse correlation to ESR1 expression (Spearman R = -0.18, p = 2.2e-16), and highest ESR2 expression in the basal- and normal-like PAM50 subtypes. ESR2-high tumors had favorable overall survival (p=0.006), particularly in subgroups receiving endocrine therapy (p=0.03) and in triple-negative breast cancer (p=0.01). These results were generally robust in multivariable analyses accounting for patient age, size, node status, and grade. Gene modules consistent with immune response were associated to ESR2-high tumors.
CONCLUSIONS: Taken together, our results indicate that ESR2 is generally expressed at low levels in breast cancer but associated with improved overall survival and may be related to immune response modulation.

overall_design:
Illumina paired-end RNA-sequencing and expression estimation using StringTie, were performed for the SCAN-B 3,207 BC cohort. Hormone receptor positive early breast tumors were defined as cases expressing estrogen (ERα) or progesterone (PR) receptors using an immunohistochemical staining cutoff ≥ 10% of neoplastic/BC cells as indicated by Swedish guidelines and HER2 status was assessed according to standard recommendations. Molecular subtyping was performed using the PAM50 gene list. Clinical/medical records were retrieved from the Swedish National Cancer Registry (NKBC).

Due to the patient consent, Swedish law, the potential that the sequencing data contains personally-identifiable information and hereditary mutations, and the right to privacy, the submitter cannot make available the raw sequence data in a public repository.

first: Hina

last: Dalal

first: Malin

last: Dahlgren

first: Sergii

last: Gladchuk

first: Christian

last: Brueffer

first: Sofia

middle: K

last: Gruvberger-Saal


title: Transcriptome analysis for CT mRNA treated BT-549 cells and negative control cells

city: Seoul

first: Hyeon-Cheol

address: 136, Changgyeonggung-ro,Jongro-gu

department: Research center

institute: BPgene Co., Ltd.

summary: We report the altered metabolite changes by processing CT mRNA in the TNBC cell line, BT-549. It was confirmed that the treatment of CT mRNA disrupted the synthesis of dTTP during nucleic acid metabolism, increasing the signal related to DNA damage in the cell, and that the energy metabolism and NADPH metabolism in the cell were changed for its recovery. The main energy sources, glucose metabolism and glutamine metabolism, are closely linked to the mitochondrial TCA cycle products. In the CT mRNA treatment group, intracellular nucleic acid depletion was observed to increase glutamine metabolism as a source of N source, and the pathway of aspartate utilization was observed. It was confirmed that it was expanded. As a result, a significant increase in the cysteine influx was observed according to the occurrence of ROS, and an effort to regulate the intracellular NADPH balance was observed through the change of metabolites over time. Finally, it was observed that the oncogenic pathway was significantly reduced in the CT mRNA-treated group compared with all untreated groups or controls with other substrate specificities. This study characterizes changes in intracellular metabolites caused by specific dTTP biosynthesis disturbances.

overall_design: Examination of T001 mRNA, 2 different nucleotidase and untreated cells

first: Bong-Seong

last: Koo

first: Jin-Sook

first: Dae-Ho


title: Transcriptome of peptidoglycan-associated lipoprotein mutant and wild-type A. baumannii strains

city: Chonqing

first: Xi

last: Zeng

address: Gaotanyan main street NO.30

department: Department of Microbiology and Biochemical Pharmacy

country: China

institute: Army Medical University

summary: We apply RNAseq of mutant and wild-type strains to study the role  of  peptidoglycan-associated lipoprotein in A. baumanni.

overall_design: Peptidoglycan-associated lipoprotein mutant was constructed from A. baumannii strain LAC-4. LAC-4 mutant and wild-type strains were cultured in 20ml TSB until OD600=0.6~0.8, and then the bacteria were collected and resuspended in 1ml PBS.

first: Yun

last: Shi


title: Expression data from control or drought stress of tomato

city: Bunkyoku-Yayoi

first: Hiroko

last: Asakura

state: TOKYO

address: １－１－１

institute: The University of Tokyo

summary:
In order to analyze changes in gene expression after drought stress, we used ripening fruits of MicroTom. By comparing with the control group, mRNA whose expression changes due to drought stress was extracted.
Using microarray analysis, we aimed to understand the overall expression change of mRNA in fruits after drought stress.

overall_design: Ripening Microtom were subjected to control or drought stress, and the mRNA expression in the fruit was compared between the two group.

first: Tomiko


title: MicroRNA-449a inhibits triple negative breast cancer by disturbing DNA repair and chromatid separation

status: Public on May 06 2022

city: Hannover

first: Marlies

last: Eilers

address: Kurze Halbe 12

institute: Medizinische Hochschule Hannover

summary: To identify target genes of microRNA-449a in triple negative breast cancer (TNBC) we transfected the TNBC cell line HCC38 with miRNA449a mimics.

overall_design: The HCC38 cell line was transfected with miRNA449a-mimics or the control AllStars (Qiagen). The array experiment was performed 48h after transfection.

first: Beate

last: Vajen

first: Britta

last: Skawran


title: PARP1 binds and regulates expression of extracellular matrix genes in renal tubular epithelial cells

city: Wu Han

first: Jing

last: Ke

address: No. 17 High-tech 6th Road, East Lake High-tech Development Zone, Wuhan, Hubei 430200, China.

institute: Renmin Hospital of Wuhan University


title: CDX2-induced intestinal metaplasia in human gastric organoids derived from induced pluripotent stem cells

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

summary: We induced an intestinal metaplasia in human gastric mucosa in vitro, followed by the overexpression of CDX2 gene using a tet-on system.

overall_design: Comparison of the gene expression of the gastric organoids, differenciated from iPSCs in the presence or absence of DOX.

first: Takahiro

last: Koide

first: Takashi

last: Aoi