title: Deceleration of the cell cycle underpins a switch from proliferative to terminal division in plant stomatal lineage

city: Austin

first: Keiko

middle: U

last: Torii

address: 2506 SPEEDWAY

institute: University of Texas at Austin

summary: We have previously identified genes that are induced by MUTE, key transcription factor for stomatal lineage fate commitment and symmetric cell division that create stomata surrounded by a pair of guard cells in Arabidopsis. To test whether these genes are indeed direct MUTE targets, we performed genome-wide MUTE ChIP-sequencing.

overall_design: Examination of MUTE binding sites in Arabidopsis seedling (scrm-D mutant background).

first: Soon-Ki

last: Han

first: Eundeok

last: Kim

first: Tomoaki

last: Sakamoto

first: Seisuke

last: Kimura


title: SINGLE CELL RNA SEQUENCING IDENTIFIES IGFBP5 AND QKI

status: Public on Feb 12 2022

city: PITTSBURGH

first: TORU

last: NYUNOYA

state: PA

address: NW628 UPMC MONTEFIORE, 3459 FIFTH AVENUE

country: USA

institute: UNIVERSITY OF PITTSBURGH

type: Expression profiling by high throughput sequencing

summary: Whole lung tissue transcriptomic profiling studies in chronic obstructive pulmonary disease (COPD) have led to the identification of several genes associated with the severity of airflow limitation and/or the presence of emphysema, however,  the cell types driving these gene expression signatures remain unidentified. T-distributed stochastic neighbor embedding and clustering of scRNA seq data revealed a total of 17 distinct populations. Among them, the populations with more differentially expressed genes in cases vs. controls (log fold change >|0.4| and FDR=0.05) were monocytes (n=1499); macrophages (n=868) and ciliated epithelial cells (n= 590), respectively. Using GSEA, we found that only ciliated and cytotoxic T cells manifested a trend towards enrichment of the previously reported 127 regional emphysema gene signatures (normalized enrichment score [NES] = 1.28 and =1.33, FDR= 0.085 and =0.092 respectively). Among the significantly altered genes present in ciliated epithelial cells of the COPD lungs, QKI and IGFBP5 protein levels were also found to be altered in the COPD lungs.

overall_design:
To determine cell specific transcriptomic changes in severe COPD, we conducted single-cell RNA sequencing (scRNA seq) on n= 29,961 cells from the peripheral lung parenchymal tissue of nonsmoking subjects without underlying lung disease (n=3) and patients with severe COPD (n=3). The cell type composition and cell specific gene expression signature was assessed. Gene set enrichment analysis (GSEA) was used to identify the specific cell types contributing to the previously reported transcriptomic signatures.

**Please note that all the control data is from PMID 31221805 [GSE128033]***

first: Xiuying

last: Li

first: Guillaaume

last: Noell

first: Tracy

last: Tabib

first: Alyssa

middle: D

last: Gregory

first: Humberto

middle: E

last: Bittar

first: Ravi

last: Vats

first: Tomasz

middle: W

last: Kaminski

first: John

last: Sembrat

first: Mark

last: Snyder

first: Divay

last: Chandra

first: Kong

last: Chen

first: Chubin

last: Zou

first: Yingze

last: Zhang

first: Prithu

last: Sundd

middle: F

last: McDyer

first: Frank

last: Sciurba

first: Mauricio

last: Rojas

first: Robert

last: Lafyatis

first: Steve

last: Shapiro

first: Rosa

last: Faner

first: Toru

last: Nyunoya


title: MicroRNA expression data from LCMV infected CD8 T cells

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary:
Investigating the role of microRNAs (miRs) in CD8 T cells responding to acutely resolved or chronic viral infection identified miR-29a as a key regulator of Tcell exhaustion cells
We used miRNA microarrays to understand the role in development of T cell exhaustion in setting of LCMV infection

overall_design: LCMV gp33 specific and naïve T cells were sorted and three replicates were used in miRNA microarray

first: Erietta

last: Stelekati

middle: J

last: Wherry


title: Altered serotonergic circuitry in SSRI-resistant major depressive disorder patient-derived neurons

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: The goals of this study are to generate and study serotonergic neurons from MDD patients that are selective serotonin reuptake inhibitor (SSRI) remitters and SSRI-nonremitters (NR).

overall_design: From patients (NR, R) and healthy controls (H),  serotonergic neurons were derived from iPSCs for further study

first: Krishna

middle: C

last: Vadodaria

first: Fred

middle: H

last: Gage


title: Molecular landscape of IDH-wildtype, H3-wildtype glioblastomas of adolescents and young adults (AYA)

city: Hong Kong

first: Kay Ka-Wai

last: Li

address: 5/F, Cancer Centre, Prince of Wales Hospital

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of IDH-wildtype, H3-wildtype AYA glioblastomas

overall_design: 50  IDH-wildtype, H3-wildtype AYA glioblastomas were examined with EPIC Illumina Infinium Human (850k) array

first: Kay

middle: K


title: RNA-sequencing of macrophages after stimulation of SLAMF7

status: Public on Feb 11 2022

city: Boston

first: Daimon

last: Simmons

state: MA

address: 75 Francis Street

institute: Brigham and Women's Hospital

summary: This study evaluated transcriptomic changes in monocyte-derived macrophages from healthy donors after stimulation with recombinant SLAMF7 or anti-SLAMF7 antibody, compared to macrophages without additional stimulation.

overall_design:
Monocyte-derived macrophages were pre-incubated with IFN-g (10 ng/ml) for 24 hours, then stimulated anti-SLAMF7 (10 ug/ml) or recombinant SLAMF7 (1 ug/ml) for an additional 4 hours. Lysates were harvested for RNA-sequencing using the Smart-seq2 protocol. Transcript were pseudoaligned and quantified using kallisto.

>>>Submitter states: The raw sequencing files (fastq) will be deposited on dbgap, per instructions from NIH <<<<

middle: P


title: Continuous activation of the IL-17F driven inflammatory pathway in acute and chronic digital dermatitis lesions in dairy cattle

city: Merelbeke

first: Anne-Sofie

last: Vermeersch

address: Salisburylaan 133

department: Internal medicine, reproduction and population medicine

country: Belgium

institute: Ghent University

summary: Objectives of the present study were to get a deeper insight into the course of the inflammatory pathways of digital dermatitis lesions in dairy cattle by investigating the gene expression patterns throughout the different clinical stages (M0 to M4.1) of the disease. Normal skin samples (M0) were used as a reference for comparing the gene expression levels in the other M-stages through RNA Seq-technology.

overall_design: 22 skin samples were obtained from 5 different M stages (M1, M2, M3, M4, M4.1) on 6 dairy farms with Holstein-Friesian cows. Five M0 samples and two M1 samples were harvested from Holstein-Friesian cattle postmortem at the local slaughterhouse.

first: Peter

last: Geldhof

first: Richard

last: Ducatelle

first: Yannick

last: Gansemans

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: Deforce

first: Geert

last: Opsomer


title: RAN-seq analysis comparing gene expression difference between control and Decr2 knock-down B16.SIY tumors

city: Chicago

first: shuyin

address: 5801 S Ellis Ave

institute: University of Chicago

summary:
Purpose: To undstand the mechanism by which Decr2 knock-down tumors were resistant to CD8+ T cell killing in vitro and anti-PD-L1 therapy in vivo, we performed RNA-seq analysis comparing Decr2-knockdown versus control B16.SIY cells
Methods: mRNA was isolated from Decr2 shRNAs (2 shRNA) and Control shRNA infected B16.SIY cells. mRNA profiles were generated by deep sequencing, in triplicate, using the Illumina HiSeq  platform. Alignment was performed using the Kallisto software.  All submitted samples passed quality control using the R package FastQC. Raw read counts were processed by TMM normalization followed by log2 transformation. Limma voom was used to identify differentially expressed genes between DECR2 knockdown and control cells.

overall_design: RNA-seq was performed to compare the mRNA expression level between  Decr2 shRNAs and Control shRNA infected B16.SIY cells.

first: Shuyin

first: Emily

last: Higgs


title: Transcriptome sequencing reveals two subtypes of cortisol-secreting adrenocortical tumors in dogs and identifies CYP26B1 as a potential new therapeutic target

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

summary: Cushing’s syndrome (CS) is a serious endocrine disorder that is rare in humans, but relatively common in dogs. In ~15-20% of cases, CS is caused by a cortisol-secreting adrenocortical tumor (csACT). To identify differentially expressed genes that can improve prognostic predictions after surgery and represent novel treatment targets, we performed RNA sequencing on csACTs (n=48) and normal adrenal cortices (NACs; n=10) of dogs. A gene was declared differentially expressed when the adjusted P-value was <0.05 and the log2 fold change was >2 or <-2. Between NACs and csACTs, 98 genes were differentially expressed. Based on the principal component analysis (PCA) the csACTs were separated in two groups, of which group 1 had significantly better survival after adrenalectomy (P=0.002) than group 2. Between csACT group 1 and group 2, 77 genes were differentially expressed. One of these, cytochrome P450 26B1 (CYP26B1), was significantly associated with survival in both our canine csACTs and in a publicly available dataset of 33 human cortisol-secreting adrenocortical carcinomas. In the validation cohort, CYP26B1 was also expressed significantly higher (P=0.012) in canine csACTs compared to NACs. In future studies it would be interesting to determine whether CYP26B1 inhibitors could inhibit csACT growth in both dogs and humans.

overall_design: whole transcriptome sequencing of canine cortisol-secreting adrenocortical tumor and normal adrenal cortices

first: Karin

last: Sanders

first: Hans

middle: S

last: Kooistra

first: Marieke

last: van den Heuvel

first: Michal

last: Mokry

first: Guy

last: Grinwis

first: Noortje

middle: A

last: van den Dungen

middle: G

first: Sara

last: Galac


title: Transcriptome analysis of small intestine and liver samples of control and LCWE-induced mice

city: Beijing

first: Feng

last: Wan

address: No. 8 Xishiku Street

country: China

institute: Peking University First Hospital

summary:
Purpose:Mucosal immune regulation is considered a key aspect of IgAN immunopathogenesis. Direct experimental evidence clarifying the role of intestinal mucosa attributes in IgAN is lacking.
Methods:Small intestine and liver mRNA profiles in control and LCWE-induced mice were generated by deep sequencing. 2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® . The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Illumina Novaseq 6000.
Results:The transcriptional signature showed that numerous genes were highly upregulated in the small intestines of the LCWE-induced mice compared with those in PBS mice. GO analysis of the small intestine revealed an over-representation of genes involved in the Fc gamma R-mediated phagocytosis, B cell receptor signaling pathway, NF-κB signaling pathway, and intestinal immune network for IgA production. The GO analysis of live samples revealed that genes involved in metabolic pathways, galactose metabolism, drug metabolism-other enzymes, and bile secretion were downregulated
Conclusions:The intestinal barrier was dysfunctional in the LCWE-induced mice and liver’s ability to clear IgA may be reduced.

overall_design: Small intestine and liver mRNA profiles of control and LCWE-induce mice

first: Hui

last: Wang

first: Manliu


title: RNA-sequencing of human monocytes with high and low expression of SLAMF7

first: Daimon

last: Simmons

summary: This study evaluated transcriptomic differences in cells with high and low expression of SLAMF7 in monocyte populations from blood and synovial fluid.

overall_design:
Monocyte populations based on expression of CD14 and CD16 were sorted based on high and low expression of SLAMF7. Lysates were harvested for RNA-sequencing using the Smart-seq2 protocol. Transcript were aligned using the Broad Institute pipeline with STAR alignment and quantification with RSEM.

>>>Submitter states: The raw sequencing files (fastq) will be deposited on dbgap, per instructions from NIH <<<<


title: Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [ATAC-seq 2]

city: GuangZhou

first: Hanwen

last: Yu

state: GuangDong

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-*Sen Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

institute: SUN YAT-SEN UNIVERSITY

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Totipotent cells have more robust developmental potency than any other cell types, giving rise to both embryonic and extraembryonic tissues. Stable totipotent cultures and deciphering the principles of totipotency regulation would be invaluable to understand cell plasticity and lineage segregation in early development. Our approach of remodeling the pericentromeric heterochromatin and re-establishing the totipotency-specific broad H3K4me3 domains promotes the pluri-to-totipotency transition. Our protocol establishes a closer match of mouse 2-cell (2C) embryos than any other 2C-like cells. These totipotent-like stem cells (TLSCs) are stable in culture and possess unique molecular features of the mouse 2C embryo. Functionally, TLSCs are competent for germline transmission and give rise to both embryonic and extraembryonic lineages at high frequency. Therefore, TLSCs represent a highly valuable cell type for studies of totipotency and embryology.

overall_design: We investigated chromatin state on the genome of  mESC, 2C::GFP+, 2C::GFP+/SGC, 2C::GFP+/SA cells and TLSCs using ATAC-seq.

first: Mingzhu

last: Yang

first: Xiu

first: Jichang


title: RNA-seq analysis with WT and Ninj2-deficient mouse oligodendrocytes.

city: Xiamen

first: yuxia

last: sun

address: Xiang'an South Road

institute: Xiamen University

summary: Loss of Ninj2 in oligodendrocytes reduced the population of Olig2+ oligodendrocytes. In order to elucidate the molecular basis underlying the dysmyelination induced by Ninj2 deletion, we performed RNA-Seq analysis with WT or Ninj2-deficient mouse oligodendrocytes to identify specific differentially expressed genes.

overall_design: RNA-Seq analysis with  WT or Ninj2-deficient mouse oligdendrocytes were performed. All RNA-Seq data were aligned to mm10 by Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 and StringTie(v1.3.3b) were used to generate gene counts. Differential expressed genes were identified using DESeq2 with fold change>2.0 and p<0.05.

first: Ying

last: Chen

first: Changqin

last: Liu


title: Loss of MBD2 Attenuates MLL-AF9-Driven Leukemogenesis By Reducing Leukemic Cell Cycling via CDKN1C

city: Wuhan

first: Kuangguo

last: Zhou

state: Hubei

address: 1095 Jiefang Avenue

institute: Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary:
Emerging evidence supports that MBD2, a DNA methylation reader, often participated in the transcriptional silencing of hypermethylated genes in cancer cells. Nevertheless, the role of MBD2 in AML remains elusive. Herein, by using MLL-AF9 murine model and human AML cell line, we observed that loss of MBD2 could delay the initiation and propagation of leukemia through serial transplantation experiments. MBD2 depletion significantly reduced the leukemia burden by decreasing the frequency of leukemic stem cells (LSCs), coupled with inhibiting leukemia proliferation, thereby allowing leukemia blasts develop to a more mature state reflecting normal myelopoiesis. Both gene expression analyses and bioinformatic studies revealed that MBD2 negatively modulated the genes related to myeloid differentiation and was necessary to sustain MLL-AF9 oncogenic induced gene programs.
We further demonstrated that MBD2 could promote LSC cell cycle progression through epigenetic regulation of CDKN1C transcription by binding to its promoter region. Taken together, our data suggested that MBD2 promotes AML development and could be a therapeutic target of myeloid malignancies.

overall_design: To investigate the mechanism underlying the longer latency of leukemogenesis caused by loss of MBD2,  leukemic cells were obtained from mice transplanted with Wide type (C1, C3, C4) or Mbd2-/- (M1, M3, M4) AML cells to microarray analysis on Affymetrix microarrays.

first: Jianfeng


title: Proximal and Distal Nephron-specific Adaptation to Furosemide

city: Stanford

first: Purvesh

last: Khatri

state: California

address: 279 Campus Dr. Beckman Center B235A

department: BMIR

institute: Stanford University

summary: scRNA seq analysis of furosemide-treated mice demonstrates maladaptive expression changes in specific cell types of the kidney nephron.

overall_design: mRNA profiles of mice treated for one week with either furosemide or vehicle

first: Aram

last: Krauson

first: Steven

last: Schaffert

first: Elisabeth

middle: M

last: Walczak

first: Jonathan

last: Nizar

first: Gwen

last: Holdgate

first: Sonali

last: Iyer

first: Ragwa

last: Elsayed

first: Alexandre

last: Gaudet

first: Vivek

last: Bhalla


title: Coexpression Gene Network Analysis reveals novel regulatory pathways involved in Porto-sinusoidal vascular disease pathophysiology

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Porto-sinusoidal vascular disease (PSVD) is a rare vascular liver disease of unknown etiology that causes portal hypertension. It usually affects young individuals and shorts live expectancy. The deregulated pathways involved in PSVD development are unknown and therefore we lack curative treatments. The purpose of this study was to better understand the biological pathology of PSVD integrating transcriptomic and clinical data by comprehensive network-based modeling with the final aim of uncovering altered biological processes in patients with PSVD.

overall_design: RNA-seq transcriptomic analysis  using  frozen livers from 8 PSVD, 8 liver cirrhosis (LC) and 8 Healthy subjects(HNL).

first: V

last: Hernandez-Gea

first: J

last: Garcia-Pagán


title: Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [ATAC-seq]

first: Hanwen

last: Yu

first: Mingzhu

last: Yang

first: Xiu

first: Jichang

last: Wang


title: Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [RNA-seq 2]

overall_design: RNA-seq were applied on mESC, 2C::GFP+, 2C::GFP+/SGC, 2C::GFP+/SA cells, and TLSCs to profile their transcriptomes.


title: Next-generation sequencing (NGS) facilitates quantitative analysis of differentially expressed genes in ethanol-fed murine livers after ethanol binge

status: Public on Feb 10 2022

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary:
Purpose: The goals of this study are to use NGS-derived liver transcriptome profiling (RNA-seq) and identify differentially expressed genes in damaged livers that were exposed to 5% ethanol-containing liquid diet and ethanol binge.
Methods: Liver mRNA profiles were generated from chronic ethanol feeding plus a single binge by deep sequencing, in duplicate, using Illumina Hiseq2500. qRT–PCR validation was performed using SYBR Green assay.
Results: Chronic ethanol feeding plus a single binge treatment was associated with 422 downregulated genes and 384 upregulated genes, whereas Yap1 null livers had 351 downregulated genes and 287 upregulated genes after ethanol/CCl4 induced liver damage.
Conclusions: This study provides detailed analysis of liver transcriptomes during hepatocyte damage caused by chronic ethanol feeding plus a single binge treatment, with biologic replicates, generated by RNA-seq technology.

overall_design: Liver mRNA profiles of 8-week-old C57BL6 that received 5% ethanol feeding with or without ethanol binge (5g ethanol/kg body weight) were generated by deep sequencing, in duplicate, using Illumina Hiseq2500.

first: Liya

last: Pi

first: Yang

last: Lu

first: Jinhui


title: Microarray expression profile of microRNAs in Esophageal Squamous Cell Carcinoma

first: Fen

last: Liu

address: Youanmenwai Street

department: Department of Epidemiology and Health Statistics

institute: Capital Medical University

summary: The purpose of this study is to explore the miRNAs expression profiles from esophageal squamous cell carcinoma (ESCC) and matched normal adjacent tissue.

overall_design: Four ESCC tissues and their paired adjacent normal tissues were used to profile miRNA expression with a microarray assay.

first: XuDong

last: Guo

first: YuanJie

last: Ding

first: Yi

last: Shen

last: Shao

first: WenQiang

last: Wei

first: XinQing

last: Li


title: Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [RNA-seq]


title: Transcriptional profiling of the Candida albicans response to the DNA damage stressing agent methyl methanesulfonate

city: Nantong

first: Jinrong

last: Feng

address: Qixiu Road

institute: Nantong University

summary: We explored the global transcription profile in response to MMS in C. albicans through RNAseq assay. Here, we identified 407 genes (log2 fold cut off 1.0, P<0.05) whose levels of transcription were significantly affected under the MMS treatment condition; 207 genes were upregulated, and 200 genes were down-regulated. GO term analysis revealed that a small portion of changed genes showed direct roles in DNA repair progress, but a large number of induced genes are involved in antioxidant responses, and some down-regulated genes are involved in nucleosome packing and nitrogen utilization. In addition, the changed transcription of some DNA repair genes, as well as antioxidants genes, are blocked by deleting RAD53. Taken together, treatment of the DNA damage agent MMS induces a global transcriptional change in C. albicans, but not only DNA damage response genes.

overall_design: We used 0.015% MMS to treat the Candida albicans cells and explored the global transcription profile in response to MMS in C. albicans through RNAseq assay.


title: Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [ChIP-seq]

overall_design: We investigated H3K79me2 and H3K79me3 landscape on the genome of  mESC, 2C::GFP+, 2C::GFP+/SGC, 2C::GFP+/SA cells, and TLSCs using ChIP-seq. ChIP-seq was performed  with the indicated antibody and Input as control.


title: circRNA expression files in invasive CRC cells

first: Benyu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

summary: To explore the role of circRNAs during CRC (colorectal cancer) metastasis, we isolated CRC cells from human sample and performed transwell assay. Then circRNA microArray analysis were performed and differentially expressed circRNAs were identified.

overall_design: Total RNAs from invasive and non-invasive CRC cells were isolated and used for microarray through human circular RNA Array V2.0.

first: Zhenzhen

last: Chen


title: Single-cell RNA sequencing identifies cells exhibiting sexually dimorphic gene expression in the brain of the mosquito, Aedes aegypti

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

summary: In this study, 10x Chromium technology was applied to quantify transcripts from single-cell nuclei of adult male and female brain of Aedes aegypti, a medically important mosquito vector that transmits yellow fever, dengue, chikungunya, and Zika viruses to humans.

overall_design: Single nuclei from male and female mosquitoes were used for  10x single cell 3' RNA-seq libraries, and the libraries were sequenced (20,000 per nucleus, paired-end single indexing reads) by Novaseq 6000.

first: Yingjun

last: Cui

first: David

last: Severson

first: Alexander

last: Franz


title: DNA methylation changes in glial cells implicate functional changes in oligodendrocytes, astrocytes and microglial cells in the normal appearing white matter of Multiple Sclerosis patients

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Background. Multiple Sclerosis is a chronic inflammatory disease of the central nervous system (CNS) characterized by autoimmune demyelination and subsequent neuro-axonal degeneration. Despite major progress in deciphering MS immunopathogenesis and treating early stages of disease, CNS-confined processes underpinning later progressive form of MS remain elusive, alluding to the poor accessibility to the target organ. We and others have demonstrated the reliability of profiling DNA methylation, a stable epigenetic marker of genome activity, in neuronal nuclei or bulk tissue to capture relevant molecular changes underlying MS neuropathology. In this study, we examined DNA methylation changes occurring in the normal appearing white matter (NAWM) glial cells of MS patients in comparison to white matter (WM) of non-neurological controls (NNC).  Results. We profiled DNA methylation in NeuN-negative nuclei of glial cells, isolated from 38 postmortem NAWM specimens of MS patients (n=8) in comparison to WM of NNC individuals (n=14), using Infinium MethylationEPIC BeadChip. We applied reference-free cell type deconvolution to further reduce cellular heterogeneity and identified 1,226 significant (genome-wide adjusted P-value < 0.05) differentially methylated positions (DMPs) between MS patients and controls. Functional annotation of the affected genes uncovered alterations of processes related to cellular motility, cytoskeleton dynamics, metabolic processes, synaptic support, neuroinflammation as well as signaling pathways, such as Rho, Wnt and TGF-β signaling. A fraction of these changes affected genes which displayed transcriptional differences in the brain of MS patients, as reported by publically available transcriptomic data. Gene ontology analysis of differentially methylated genes according to their constitutive cell type-specific expression in glial cells attributed alteration of cytoskeleton rearrangement and extracellular matrix remodelling to all glial cell types, while some processes, including ion transport, Wnt/TGF-β signaling and immune processes were more specifically linked to oligodendrocytes, astrocytes and microglial cells, respectively.  Conclusion. Our findings strongly suggest that NAWM glial cells are highly active, even in the absence of lesional insult, collectively exhibiting a multicellular reaction in response to diffuse inflammation.

overall_design: Case vs Control

first: Lara

last: Kular

first: Maja

last: Jagodic


title: Role of Zfp276 in oligodendrocyte differentiation

city: Erlangen

first: Melanie

last: Küspert

address: Fahrstraße 17

department: Institute of Biochemistry

summary: To identify target genes of the Zfp276 protein in oligodendrocytes in a genome-wide and unbiased approach, we performed RNA-Seq studies on primary mouse oligodendroglial cells (1°OGCs) that were differentiated 3 days in vitro. We compared samples generated from forebrains of mice that carried Sox10::Cre-mediated deletion of exons 2-5 of the Zfp276 gene (Zfp276cko) or Zfp276 fl/fl mice that were negative for the Cre-transgene (Ctrl). Each biological replicate was generated from 3 individuals of the same genotype at postnatal day P2-P4. Among others we detected substantial changes in the expression of genes associated with oligodendrocyte differentiation and myelination.

overall_design: We generated mRNA profiles of 3 days differentiated mouse primary oligodendrocytes which carried the Zfp276 fl/fl allele without (ctrl) or together with the Sox10::Cre allele (Zfp276cko) using the Illumina HiSeq 2500 platform.

first: Michael

last: Wegner


title: Single-cell transcriptomic interrogation of hematopoietic progenitors within the E11.5 AGM of the mouse

first: Sachin

last: Patel

address: 1 Blackfan Circle

institute: Children's Hospital, Boston

summary: To clarify the relationship between eMPPs and other progenitors, including pre-HSCs, within the AGM landscape, we performed single cell RNA-sequencing of hematopoietic progenitors within the E11.5 AGM.

overall_design: Three Bl6 E11.5 embryos, pooled, were used for the single-cell experiment. Three populations were sorted: AGM pre-HSCs and endothelial cells (Lin- cKit+ CD45lo/mid CD31+ VE-Cad+); AGM progenitors (Lin- cKit+ CD45+); and fetal liver progenitors (cKit+/high CD45+ CD41- and cKit+/high CD45+ CD41high were separately sorted and mixed before encapsulation). Lineage markers used here were Ter119, Gr1, CD19, and CD3. Single-cell encapsulation was performed using 10X Chromium single cell 3’ technology. Whole-transcriptome libraries were prepared using the 10X v3 protocol and sequenced on Illumina NextSeq500 paired-end 150 cycles (Read 1: 28 cycles; Index Read 1 (i7): 8 cycles; Read 2: 91 cycles).

first: Constantina

last: Christodoulou

first: Fernando

last: Camargo


title: Next-generation sequencing facilitates transcriptomes quantitative analysis of N2a cells transfected with RfxCas13d and targeting/non-targeting crRNA and of stably expressing RfxCas13d HEK293T cells transfected with target genes and corresponding crRNAs

first: Yunfei

state: China

address: 38 Xueyuan Road, Haidian District, Beijing

department: Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China

institute: Peking University

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7. [ChIRP-seq]

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

summary: The histone acetyltransferase p300 (also known as KAT3B) is a general transcriptional coactivator that introduces the H3K27ac mark on enhancers triggering their activation and gene transcription. Genome-wide screenings demonstrated that a large fraction of long non-coding RNAs (lncRNAs) plays a role in cellular processes and organ development although the underlying molecular mechanisms remain largely unclear. We found 122 lncRNAs that interacts directly with p300. In depth analysis of one of these, lncSmad7, is required to maintain ESC self-renewal and it interacts to the C-terminal domain of p300. lncSmad7 also contains predicted RNA-DNA Hoogsteen forming base pairing. Combined Chromatin Isolation by RNA precipitation followed by sequencing (ChIRP-seq) together with CRISPR/Cas9 mutagenesis of the target sites demonstrate that lncSmad7 binds and recruits p300 to enhancers in trans, to trigger enhancer acetylation and transcriptional activation of its target genes. Thus, these results unveil a new mechanism by which p300 is recruited to the genome.

overall_design: ChIRP-seq of lncSmad7 in wild type and lncSmad7 knock-out ES cells, 13 samples total: 2 wild type Odd set, 2 wild type Even set, 2 knock-out Odd set, 2 knock-out Even set,  3 wild type and 2 knock-out Input DNA as control samples.

first: Mara

last: Maldotti

first: Francesca

last: Anselmi

first: Ivan

last: Molineris

first: Annalaura

last: Tamburrini

first: Guohua

last: Meng

first: Isabelle

last: Polignano

first: Mirko

last: Scrivano

first: Fabiola

last: Campestre

first: Lisa

last: Simon

first: Stefania

last: Rapelli

first: Edoardo

last: Morandi

first: Danny

last: Incarnato

first: Salvatore

last: Oliviero


title: LRH1 can help reprogram sexual cell fate and is required for Sertoli cell development and spermatogonial stem cell maintenance in the mouse testis

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: The mammalian nuclear hormone receptors LRH1 and SF1 are close paralogs that can bind the same DNA site and play crucial roles in gonadal development and function. Lrh1 has been shown to be essential for follicle development in the ovary and also has been proposed to regulate steroidogenesis in the testis, but genetic analysis of its role in the male gonad has not been reported. Here we use conditional genetics to examine Lrh1 requirements in gonadal cell fate reprogramming and in normal development of the three major cell lineages of the mouse testis. Lrh1 expression is highly elevated by loss of the sex regulator Dmrt1, which triggers male-to-female transdifferentiation of Sertoli cells. We found that loss of Lrh1 suppresses this transdifferentiation, confirming that Lrh1 can act as a key driver in reprogramming sexual cell fate. In otherwise wild-type testes we found that Lrh1 is dispensable in Leydig cells but is required in Sertoli cells for their proliferation, for seminiferous tubule morphogenesis, for maintenance of the blood-testis barrier, for feedback regulation of androgen production, and for support of spermatogenesis. Expression profiling identified misexpressed genes likely underlying most aspects of the Sertoli cell phenotype. In the germ line Lrh1 is required for maintenance of spermatogonial stem cells (SSCs) and mutants progressively lose spermatogenesis. Reduced expression of the RNA binding factor Nxf2 likely contributes to the SSC maintenance defect. Unexpectedly, however, the Lrh1 mutant germ line can recover abundant spermatogenesis and fertility. This finding suggests the presence of a reserve stem cell population with different genetic requirements from the stem cells that normally support steady state spermatogenesis. Together our results demonstrate that Lrh1, like Sf1, is an essential regulator of testis development and function but has a distinct repertoire of functions.

overall_design: Conditional deletion of Lrh1 Nanos-Cre at P1 or Dhh-Cre at P3.  Each experiment has 4 replicates each for the control and experimental conditions.

first: Kellie

last: Agrimson

first: Vivian

last: Bardwell

first: David

last: Zarkower


title: Transcriptomic signature for precise prediction of 3HP related systemic drug reaction for latent tuberculosis infection treatment: A prospective study

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

country: Taiwan

institute: National Chiao Tung University

summary: Background: Systemic drug reaction (SDR) is a major safety concern of weekly rifapentine-based treatment (known as 3HP) for latent tuberculosis infection (LTBI). Understanding predictors of SDR and identifying risk subjects before treatment can improve public acceptance and cost-effective implement of LTBI program.  Methods: We first prospectively recruited 187 subjects receiving 3HP and randomly selected a pilot cohort for generating whole-blood transcriptomic data. After integrating the hierarchical systems biology model (HiSBiM) and a therapy-biomarker pathway approach, candidate genes were obtained and evaluated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Then, we developed interpretable machine learning models and established universal cut-off value (shapley additive explanations value) for each SDR prediction model. An independent cohort was used to evaluate the performance of these predictive models.  Findings: Based on the transcriptomic profile of the pilot cohort, a total of 19 candidate genes were identified. Among them, six were sieved out by RT-qPCR results of a small number of samples from the training cohort. By applying the SHAP values of various combinations of the 6 gene expression signature, and the best model consisted of three genes, had an G-mean of 0.959, sensitivity of 0.972 and specificity of 0.947 for the joint of the two cohorts, and worked well across different subgroups.

overall_design: Four groups: 8 samples before 3HP treatment from SDR group (SB), 8 samples after 3HP treatment from SDR group (SA), 8 samples before 3HP treatment from non-SDR group (NB), and 12 samples after 3HP treatment from non-SDR group (NA)

first: Hung

middle: L

last: Huang

first: Jung

middle: Y

last: Lee

first: Sing

first: Yu

last: Lo

first: I

last: Liu

first: Meng

middle: R

first: Chih

first: Jann

last: Wang

first: Jinn

first: Inn

last: Chong


title: Next-generation sequencing facilitates transcriptomes quantitative analysis of stably expressing RfxCas13d HEK293T cells transfected with target genes and corresponding crRNAs

first: Yunfei

last: Li

summary: To determine what effect the collateral activity of RfxCas13d has on cells, a HEK293T cell line stably expressing RfxCas13d (HEK293T-RfxCas13d) was constructed and then transfected with plasmids encoding target gene and corresponding crRNAs. After 24 hours of transfection, cells were collected and extracted for total RNA. Then, we performed RNA-seq to compare the differentially expressed genes between cells transfected with targeting crRNAs and non-targeting crRNA.

overall_design: mRNA profiles of stably expressing RfxCas13d HEK293T cells transfected with target genes and crRNAs.


title: Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [CUT&Tag]

first: Hanwen

last: Yu

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-*Sen Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

summary: Totipotent cells have more robust developmental potency than any other cell types, giving rise to both embryonic and extraembryonic tissues. Stable totipotent cultures and deciphering the principles of totipotency regulation would be invaluable to understand cell plasticity and lineage segregation in early development. Our approach of remodeling the pericentromeric heterochromatin and re-establishing the totipotency-specific broad H3K4me3 domains promotes the pluri-to-totipotency transition. Our protocol establishes a closer match of mouse 2-cell (2C) embryos than any other 2C-like cells. These totipotent-like stem cells (TLSCs) are stable in culture and possess unique molecular features of the mouse 2C embryo. Functionally, TLSCs are competent for germline transmission and give rise to both embryonic and extraembryonic lineages at high frequency. Therefore, TLSCs represent a highly valuable cell type for studies of totipotency and embryology.

overall_design: We investigated H3K4me1, H3K4me3, H3K27me3, H3K27ac and H3K9me2 landscape on the genome of  mESC and TPSC cells using CUT&Tag. CUT&Tag was performed  with the indicated antibody and IgG as control.

first: Mingzhu

first: Xiu

first: Jichang


title: The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7. [PAR-CLIP]

first: Andrea

last: Lauria

overall_design: PAR-CLIP of p300 in ES cells, 4 samples total: 2 biological replicates of PAR-CLIP with p300 antibody, 2 biological replicates of PAR-CLIP with IgG antibody as control.

first: Mara

last: Maldotti

first: Francesca

last: Anselmi

first: Guohua

last: Meng

first: Lisa

last: Simon

first: Stefania

last: Rapelli

first: Isabelle

last: Polignano

first: Edoardo

first: Annalaura

last: Tamburrini

first: Ivan

last: Molineris

first: Danny

first: Salvatore


title: Next-generation sequencing facilitates transcriptomes quantitative analysis of N2a cells transfected with RfxCas13d and targeting/non-targeting crRNA

first: Yunfei

summary: To determine whether target genes were specifically knocked down by RfxCas13d in N2a cells, we performed RNA-seq to compare the differentially expressed genes between cells transfected with targeting crRNAs and non-targeting crRNA.

overall_design: mRNA profiles of N2a cells cotransfected with RfxCas13d and targeting/non-targeting crRNAs.


title: Generation of cDC-like cells from human induced pluripotent stem cells via Notch signaling

status: Public on Feb 09 2022

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center


title: The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7. [ChIP-seq]

overall_design: ChIP-seq of H3K27ac in ES cells, 6 samples total: 2 wild type, 2 lncSMAD7-/-, 2 Input DNA as control samples.

last: Morandi

last: Incarnato

last: Oliviero


title: RNA-Seq analysis in liver tissues of Wild Type and Ezh2(K307R) mice.

city: Tianjin

first: Yan

last: Wang

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

institute: Tianjin Medical University

summary: The histone methyl transferase EZH2, a member of PRC2, is a master epigenetic regulator involved in histone H3 lysine 27 trimethylation and gene transcription repression. Here, we reported the K307 dimethylation of EZH2 could regulate its protein stability. Thus, to further investigate the biological significance of the K307 dimethylation of EZH2 and to explore its downstream regulated genes, we subsequently analyzed the genome-wide transcriptional targets of Ezh2K307R using an RNA sequencing (RNA-seq) approach in the livers of Ezh2K307R and WT mice.

overall_design: Examination the changes of gene expression in the liver tissue of Ezh2K307R point mutant mice.


title: The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7. [RNA-Seq]

overall_design: RNA-seq of ES cells, 8 samples total: 2 biological replicates of wild type, 2 biological replicates of lncSMAD7-/- not transfected, 2 biological replicates of lncSMAD7-/- transfected with lncSMAD7, 2 biological replicates of lncSMAD7-/- transfected with Smad7.


title: E12.5 Neural tube RNA-Seq

city: Dunedin

first: Lyvianne

last: Decourtye

address: 270 Great King Street

department: Anatomy

country: New Zealand

institute: University of Otago

summary: RNA-seq on E12.5 neural tube from WT and Lbx1Δ/Δ.

overall_design: WT or Lbx1Δ/Δ neural tubes from a same litter were pooled together and RNA was extracted.


title: The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7


title: Generation of cDC-like cells from human induced pluripotent stem cells via Notch signaling [RNA-Seq]

summary: Dendritic cells (DCs) play critical roles in regulating the innate and adaptive immune responses, and have long been a major focus of cancer immunotherapy. Accumulating evidence suggests that conventional type 1 DC (cDC1s) excel in cross-presentation of exogenous antigens on MHC-I molecules, and induction of antitumor CD8+ T cell immunity; however, obtaining large numbers of cDC1s is difficult. The use of reprogramming and differentiation technology is advantageous for obtaining unlimited numbers of autologous cDC1s especially for therapeutic interventions where repeated vaccinations are required. However, generation of cDC1s from human induced pluripotent stem cells (iPSCs) remains elusive.

overall_design: iPSC-derived DCs and PBMCs were stained with a master mix of antibodies for surface staining including Live/Dead Fixable Aqua Dead, XCR1, CLEC9A, CD11c and HLA-DR after Fc block with human IgG. CD11c+HLA-DR+CLEC9A+XCR1+ cells were sorted on BD FACSAria II. Total RNA was prepared from these sorted DCs using the miRNeasy mini kit (Qiagen).

first: Fumito

last: Ito

first: Kenichi

last: Makino


title: Mouse Mist1 and Lrig1 apc tumors

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: tumors, WT

overall_design: n=3,4 per condition (4)

first: Cherie'

last: Scurrah

first: Alan

last: Simmons


title: Mouse modeling dissecting macrophage-breast cancer communication uncovered roles of PYK2 in macrophage recruitment and breast tumorigenesis

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Macrophage infiltration in mammary tumors is associated with enhanced tumor progression, metastasis, and poor clinical outcome, and considered as target for therapeutic intervention. Here we used different genetic mouse models and show that ablation of the tyrosine kinase PYK2, either in breast cancer cells, only in the tumor microenvironment, or both, markedly reduced the number of infiltrating tumor macrophages and concomitantly inhibited tumor angiogenesis and tumor growth. Strikingly, PYK2 depletion only in macrophages was sufficient to induce similar effects. These phenotypic changes were associated with reduced monocyte recruitment and a substantial decrease in tumor-associated macrophages (TAMs). Mechanistically, we show that PYK2 mediates mutual communication between breast cancer cells and macrophages through critical effects on key receptor signaling. Specifically, PYK2 ablation inhibited Notch1 signaling and consequently reduced CCL2 secretion by breast cancer cells, and concurrently reduced the levels of CCR2, CXCR4, IL4R, and Stat6 activation in macrophages. These bidirectional effects modulate monocyte recruitment, macrophage polarization and tumor angiogenesis. PYK2 expression is correlated with infiltrated macrophages in breast cancer patients, and its significant effects on macrophage infiltration and their pro-tumorigenic phenotype suggest that PYK2 targeting can be utilized as an effective strategy to modulate TAMs and possibly sensitize breast cancer to immunotherapy.

overall_design: Bone marrow derived macrophages (BMDM) were differentiated from bone marrow cells extracted from WT and PYK2 KO mice. RNA was extratcted seven days after isolation. RNA-seq was performed on BMDM extracted from three mice from each group.

first: Anna-Katharina

last: Müller

first: Ulrike

last: Köhler

first: Yaron

last: Vinik


title: Generation of cDC-like cells from human induced pluripotent stem cells via Notch signaling [scRNA-seq]

overall_design: To investigate hiPSC-DC phenotypes,  Droplet-based 3’ end massively parallel scRNAseq was performed by encapsulating sorted live CD11c+HLA-II+ cells into droplets and libraries were prepared using Chromium Single Cell 3’ Reagent Kit V2 according to manufacturer’s protocol.


title: Differential Expression Analysis of a Histidine phosphotransferase RNAi mutant in Magnaporthe oryzae

city: Thrissur

first: Varsha

last: Mohanan

state: Kerala

address: St.Mary's College road, Chembukavu

department: Department of Biotechnology

country: India

institute: St.Mary's College, Thrissur

summary: Magnaporthe oryzae is notorious for its efficient evolution as a plant pathogen.  Analysis of well organised fungal pathogenic mechanisms would enable the scientific  understanding to fight against pathogens. Histidine phosphotransferase in fungal  systems are good targets for antifungals since they are component of SAPK pathway,  which is essential for survival of the fungus. The histidine Phosphotransferase YPD1  in M. oryzae is known to be light responsive and important for both asexual  reproduction as well as pathogenicity. In this study, the knock-down (KD) mutant of  YPD1 was highly sensitive to cell wall perturbing agents and were highly deficient in  laccase expression and activity. A RNA-seq transcriptome screening of KD mutant  compared to wild type revealed altered expression of about 146 genes important in  biotrophic and necrotrophic phases of the pathogen. About 96 genes were found to be  down regulated, of which several plant cell wall degrading genes vital for pathogenicity  and fungal cell wall maintenance genes important for growth and fungal development  were identified. Most of the genes identified are involved in biotrophic invasion and  metabolism. Our results explain the reason for the deficiency of the KD mutant in  asexual reproduction as well as pathogenicity. Analysis of differentially expressed  genes in the KD YPD1 mutant suggests that YPD1 can be a good target for  development of novel antifungal compounds, as YPD1 expression affects genes  required for pathogenicity.

overall_design: Two pooled samples of B157 and RA6 were analysed,  B157 is the wildtype control sample RA6 is the RNAi mutant of MoYPD1 in M.oryzae. There is no biological replicates

first: Pinal

last: Chandarana

first: Bishun

last: Prasad

first: Bharat

middle: B

last: Chattoo


title: CRISPR-based gene disruption coupled to targeted integration of novel, high-avidity, natural T cell receptors to WT1 for acute leukemia

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

institute: Consiglio Nazionale delle Ricerche

summary: Newly identified WT1-specific TCRs can be employed to generate an army of engineered lymphocytes with redirected specificity towards WT1-expressing malignancies.

overall_design: T cells specific for the tumor antigen WT1 were expanded by sequential stimulation of peripheral blood mononuclear cells harvested from healthy donors with a pool of overlapping peptides spanning the full length of the protein. Longitudinal monitoring of the TCR alpha/beta clonotypes fluctuations enabled the retrieval of the anti-WT1 TCRs.

first: Eliana

last: Ruggiero

first: Chiara

last: Bonini


title: RNA-sequencing of mouse melanoma cell lines WT31, B16F10 luc2, RET, D4M and HCmel12

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: In vitro cultured, sub-confluent (50 %) mouse melanoma cell lines WT31, B16F10 luc2, RET, D4M and HCmel12 were analyzed by RNA-seq.

overall_design: All used melanoma cell lines were from murine origin. The melanoma cell line B16F10 luc2 was purchased from Perkin Elmer (MA, USA). RET1 melanoma cells were generated from metallothionein-I (MT)/RET transgenic mice and kindly provided by V. Umansky (German Cancer Research Center (DKFZ), Heidelberg, Germany). The transformed melanoma cell line WT31 was derived from Tyr∷NrasQ61K/°; INK4a−/− mice and was a generous gift from O. Sansom (Beatson Institute for Cancer Research, Scotland). HCmel12 melanoma cells were established from a primary melanoma in HGF-CDK4(R24C) mice and kindly provided by T. Tüting (University of Magdeburg, Germany). The Dartmouth murine mutant malignant melanoma (D4M) is derived from Tyr::CreER;BrafCA;Ptenlox/lox mice and was generously provided by C. E. Brinckerhoff (Geisel School of Medicine at Dartmouth, NH, USA). After thawing the cells were not passaged more than three times. Thereafter, RNA was extracted at sub-confluency (50%) and prepared for RNA-sequencing.  The library preparation and the sequencing with an Illumina HiSeq 4000 sequencing system (Illumina, CA, USA) were then performed by BGI (Hongkong, China).

first: Sebastian

last: Wohlfeil

first: Verena

last: Häfele

first: Cyrill

last: Géraud

first: Carolina

last: Delatorre


title: CSN5 deletion in oligodendrocytes causes senescence-induced inflammation and neurodegeneration

city: Milan

first: Stefano

middle: Carlo

last: Previtali

state: Milan

address: via Olgettina,60

department: INSPE

institute: IRCSS San Raffaele Scientific Institute

summary: Oligodendrocytes are the primary target of demyelinating disorders in the CNS, which may evolve in neurodegeneration. DNA damage and oxidative stress are considered key pathogenic events, but the underlying molecular mechanisms remain unclear. Moreover, comprehensive animal models are lacking or do not fully recapitulate human diseases, complicating the path to effective treatments. Here we report that mice with cell autonomous deletion of the COP9 signalosome component CSN5 (Jab1) in oligodendrocytes develop DNA damage and defective DNA repair in myelinating glial cells. Interestingly, oligodendrocytes lacking Jab1 expression undergo a senescence-like phenotype that fosters chronic inflammation and oxidative stress. These mutants develop progressive CNS demyelination, microglia inflammation and neurodegeneration, with severe motor deficits and premature death. Notably, blocking microglia inflammation did not prevent neurodegeneration; whereas, deletion of p21CIP1 but not p16INK4a pathway ameliorated the disease. We suggest that senescence is key to sustaining neurodegeneration in demyelinating disorders and might represent a new potential therapeutic target.

overall_design: RNA-Seq of sorted oligodendrocyte (O1+ cells) from P40 mouse brain. 4 Sample per genotype are analyzed (Wt=Control, CnpCre:Jab1fl/fl = KO and p21-/-CnpCre:Jab1fl/fl= dKO) . Each sample derived from two different mouse brains

first: Cristina

last: Rivellini

first: Giorgia

last: Gullotta

first: Marco

last: Bacigaluppi

first: Giulia

last: Scotti


title: miRNA expression profiles in gastric diffuse large B cell lymphoma

city: Taipei

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

department: Pathology

institute: National Taiwan University

summary:
Background: Gastric diffuse large B-cell lymphoma (DLBCL) is often associated with Helicobacter pylori (H. pylori) infection. Early-stage gastric DLBCLs could be treated with H. pylori eradication therapy (HPET), and are classified into a sensitive group and a resistant group.
Methods: Genome-wide miRNA and mRNA profiles were performed on gastric DLBCLs that had been treated with HPET. MicroRNAs and mRNAs preferentially associated with resistance or sensitivity to HPET were identified. Pathway enrichment and a miR-centered bioinformatic approach were also used. The candidate markers were further evaluated with a luciferase assay and Western blotting in BJAB or U2932 lymphoma cell lines of B-cell origin. These markers were verified in an independent series, and clinical and pathological correlations were established.
Results: Genome-wide miRNA and mRNA profiles showed that the resistant group had higher levels of miR-155 and lower levels of DEPTOR (an inhibitor of mTOR) than the sensitive group. BJAB cells transfected with miR-155 also had lower DEPTOR and higher mTOR levels. Therefore, miR-155-mediated inhibition of DEPTOR with secondary activation of mTOR was a potential marker for resistance HPET. In contrast, pathway enrichment analysis showed that Toll-like receptor 5 (TLR5), the receptor for bacterial flagellin, was a potential marker for sensitivity to HPET. In an independent series, stronger expression of pS6K1 (a direct target of mTOR) was associated with the resistant group, and morphologic evidence of active gastritis was associated with the sensitive group.
Conclusions: These findings showed that miR-155 and TLR5 were markers for resistance and sensitivity to HPET. Furthermore, histological evaluation of active gastritis might be used as a surrogate marker to predict responsiveness to HPET in gastric DLBCL. These data also suggested the possibility that mTOR inhibitors might be used in gastric DLBCLs resistant to HPET.

overall_design:
Gastric diffuse large B-cell lymphomas (DLBCLs) are often associated with Helicobacter pylori (H. pylori) infection. Early-stage gastric DLBCLs can be treated with H. pylori eradication therapy (HPET). Uisng genome-wide miRNA expression profiling, miR155 was identified as a predictor of resisatnce to HPET.
Genome-wide miRNA expression profiling was performed in 9 cases of gastric DLBCLs sensitve to HPET and 8 cases of gastric DLBCLs resistant to HPET. The expression level of miR-155 was higher in the resistant group than the sensitive group. In BJAB cells, miR-155 inhibited DEPTOR, an inhibitor of mTOR. In a second cohort, activation of the miR-155-DEPTOR-mTOR pathway was identified in the resistant group.

first: Wei-Ting

last: Huang


title: mTOR and Toll-like receptor 5 in gastric diffuse large B-cell lymphoma as markers for resistance and sensitivity to H. pylori eradication therapy

overall_design:
Gastric diffuse large B-cell lymphoma (DLBCL) is often associated with H. pylori infection, and can be treated with H. pylori eradicatin therapy (HPET). Genome-wide mRNA profiling was performed in 8 gastric  DLBCLs sensitive to HPET, and 8 gastric DLBCL resistant to HPET.
Tissue blocks of 16 cases of gastric DLBCLs were retireved from the archives f the Department of Pathology at National Taiwan University Hospital. Total RNA was extracted from formalin-fixed paraffin-embedded tissue blocks, and mRNA profiling was performed. Differential expressed mRNAs between the sensitive and the resistant groups were compared.


title: miR-155 inhibits DEPTOR in gastric diffuse large B-cell lymphoma resistant to H. pylori eradication therapy

overall_design:
Gastric diffuse large B-cell lymphoma (DLBCL) is often associated with H. pylori infection, and can be treated with H. pylori eradication therapy (HPET). Both increased  miR155 and decreased DEPTOR were associated with resistance to HPET. MiR-155  inhibits DEPTOR when transfected into BJAB cells, supporting that miR-155 inhibits DEPTOR in gastric DLBCL resistant to HPET.
MiR-155 or an empty EGFP+ vector was transfected into BJAB cells. The EGFP+ cells were isolated with flow cytometry. Genome-wide mRNA profiling was performed.


title: miR-200 is associated with sensitivity of gastric diffuse large B-cell lymphoma to H. pylori eradication therapy

overall_design:
Gastric diffuse large B-cell lymphoma (DLBCL) is often associated with H. pylori infection, and can be treated with H. pylori eradication therapy (HPET). Increased miR-200 was associated with sensitivity to HPET. MiR-200 was transfected into U2932 cells to look for targets.
MiR-200 a, b, or c or an empty EGFP+ vector was transfected into U2932 cells. The EGFP+ cells were isolated with flow cytometry. Genome-wide mRNA profiling was performed.


title: Haploinsufficiency of the mouse Tshz3 gene leads to kidney dysfunction

city: Marseille

first: Laurent

last: Fasano

address: Parc Scientifique de Luminy

country: France

institute: CNRS-AMU

summary: Renal tract defects and autism spectrum disorder (ASD) deficits represent the phenotypic core of the 19q12 deletion syndrome caused by the loss of one copy of the TSHZ3 gene. While a proportion of Tshz3 heterozygous (Tshz3+/lacZ) mice display ureteral defects, no kidney defects have been reported in these mice. The purpose of this study was to characterize the expression of Tshz3 in adult kidney as well as the renal physiological consequences of embryonic haploinsufficiency of Tshz3 by analyzing the morphology and function of Tshz3 heterozygous adult kidney. Here, we described Tshz3 expression in the smooth muscle and stromal cells lining the renal pelvis, the papilla and glomerular endothelial cells (GEnCs) of the adult kidney. Histological analysis showed that Tshz3+/lacZ adult kidney had an average of 29% fewer glomeruli than wild type kidney. Transmission electron microscopy (TEM) of Tshz3+/lacZ glomeruli revealed ultrastructural defects. Compared to wild type, Tshz3+/lacZ mice showed no difference in their urine parameters but lower blood urea, phosphates, magnesium and potassium at 2 months of age. At the molecular level, transcriptome analysis identified differentially expressed genes related to inflammatory processes in Tshz3+/lacZ compare to wild type (WT; control) adult kidneys. Lastly, analysis of the urinary peptidome revealed 33 peptides associated with Tshz3+/lacZ adult mice. These results provide the first evidence that in the mouse Tshz3 haploinsufficiency leads to cellular, molecular and functional abnormalities in the adult mouse kidney.

overall_design: For RNA sequencing, Tshz3+/LacZ and wild-type mice kidneys were collected at 60 days-of-age. Dissected kidneys were stored in RNAlater solution (Qiagen) and kept frozen at -80 °C until RNA extraction.

first: Irene

last: Sanchez-Martin

first: Xavier

last: Caubit

first: Ahmed

last: Fatmi

first: Andy

last: Saurin

first: Thien

last: Vu


title: Ricolinostat promotes the generation of megakaryocyte progenitors from human hematopoietic stem and progenitor cells

city: Beijing

first: Jinhua

last: Qin

address: Taiping Road

institute: Beijing Institute of Transfusion

summary: Ex vivo production of induced megakaryocytes (MKs) and platelets from stem cells is an alternative approach for supplying transfusible platelets. However, it is still difficult to generate large numbers of MKs and platelets from cord blood hematopoietic stem cells. To optimize the differentiation efficiency of megakaryocytic cells from hematopoietic stem and progenitor cells (HSPCs), we first employed a platelet factor 4 (PF4)-promoter reporter and high-throughput screening strategy to screen for small molecules. We found that a small molecule, Ricolinostat, efficiently promoted the generation of CD34+CD41+ megakaryocyte progenitor cells (MkPs) and CD41+CD61+ MKs from cord blood HSPCs. Ricolinostat showed the capacity to enhance the cell fate commitment of MkPs from HSPCs and promoted the proliferation of CD34+CD41+ MkPs. Ricolinostat significantly increased the gene expression levels of key MK transcriptional factors, including HOXC6 and PCGF2. Notably, these megakaryocytic cells generated from Ricolinostat-induced HSPCs could differentiate into mature MKs and platelets. Additionally, RNA sequencing data suggested that Ricolinostat might enhance MkP fate mainly by inhibiting the secretion of IL-8 and decreasing the expression of IL-8 receptor CXCR2. Our study will help in the development of manufacturing protocols for large-scale generation of induced MKs and platelets for clinical application.

overall_design: CD34+CD41+ cells were sorted by flow cytometry on day 7. After 7 days of Ricolinostat treatment, the cells were collected and centrifuged at 2000 rpm.

first: Jianan

last: Jiang

first: Min

last: Zheng

first: Xuetao

last: Pei

first: Yanhua

last: Li


title: Monocytes from peripheral blood from mouse with and without tumour II

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

country: United Kingdom

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

summary: Monocytes from peripheral blood of tumour-bearing (B6Tg(MMTV-PyMT)634Mul/Lellj) or non-tumor-bearing C57BL/6JCrl mice were FACS sorted and single cells analysed by SMARTseq2

overall_design: Single cell transcriptomic data are presented from CD11b+ CD45+ CD115+ Lineage- (CD3- CD19-NK1.1-) monocytes from tumor-bearing B6Tg(MMTV-PyMT)634Mul/Lellj and non-tumor-bearing C57BL/6JCrl mice

first: Amy

last: Robinson

first: Jeffery

last: Pollard


title: Whole transcriptome resequencing of the cavernous tissue of the penis of rats

city: hangzhou

first: huang

last: jie

address: binwen Road

institute: Zhejiang University of Chinese Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: There is growing evidence that circular RNAs (circRNAs) play an important role in a variety of diseases, including erectile dysfunction (ED). Nevertheless, the role of circRNAs in cavernous nerve-damaging ED (CNI-ED) is unknown. Here, we aimed to discover new circRNAs, investigate their potential role in the pathogenesis of CNI-ED, and construct a circRNA-miRNA-mRNA network.
Methods: Twelve male Sprague Dawley rats were randomly divided into bilateral cavernous nerve crush (BCNC) and control groups. Four weeks after surgery, the spongy smooth muscle tissue of the rat penis was sequenced using high-throughput full transcriptome sequencing. We analyzed the expression profiles of circRNAs, miRNAs, and mRNAs in the two groups. Twenty circRNAs with significantly different expressions were selected for real-time polymerase chain reaction (RT-qPCR). The circRNA-miRNA-mRNA network was established using Cytoscape. Gene ontology (GO)-term and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the edgeR package.
Results:  RNA transcriptome sequencing showed that 4,587 circRNAs, 762 miRNAs, and 21,661 mRNAs were dysregulated in the BCNC group. The top 20 differentially expressed circRNAs were further verified via RT-qPCR. The ceRNA network contained 23 circRNA-miRNA pairs and 227 miRNA-mRNA pairs, including ten circRNAs, six miRNAs, and 227 mRNAs. GO analysis suggested that these ten circRNAs could regulate various processes, such as oxidation-reduction processes, lipid metabolic processes, apoptotic processes, and proteolysis. Furthermore, KEGG analysis of mRNAs in the ceRNA network showed that they were involved in energy metabolism and communication between cells. A protein‐protein interaction network was constructed with the 227 mRNAs, and five hub genes (Ccna2, Cxcl10, Pld1, Mapk11, and Mboat2) were identified. In addition, Using circRNADb, we found 12 circRNAs with protein-coding potential, three of which were highly conserved in humans and rats. Our study revealed a potential link between circRNAs, miRNAs, and mRNAs in CNI-ED, suggesting that circRNAs may contribute to the occurrence of ED by regulating the cellular energy metabolism in CNI-ED.

overall_design: There were 6 samples, 3 control groups and 3 model groups

first: Jianxiong

last: Ma

first: Huang

last: Jie


title: REV1 promotes lung tumorigenesis by activating the Rad18/SERTAD2 axis

city: Wuhan

first: hua

middle: xiao

address: Xinhua Road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: REV1 is the central member of the family of TLS polymerases, which participate in various DNA damage repair and tolerance pathways, including translesion DNA synthesis, and play a significant role in maintaining genomic stability. However, the role of REV1 in tumors is rarely reported. In this study, we found that the expression of REV1 was significantly upregulated in lung cancer tissues compared with matched adjacent tissues and was associated with poor prognosis. Functional experiments demonstrated that REV1 silencing decreased the growth and proliferation capacity of lung cancer cells. Mechanistically, REV1 upregulated the expression of SERTAD2 in a Rad18-dependent manner, thereby promoting lung carcinogenesis. A novel REV1 inhibitor, JH-RE-06, suppressed lung tumorigenesis in vivo and in vitro and was shown to be safe and well tolerated. Our study confirmed that REV1 is a potential diagnostic marker and therapeutic target for lung cancer and that JH-RE-06 may be a safe and efficient therapeutic agent for NSCLC.

overall_design: A549 cells transfected with Scrambled or SiRNAs targeting REV1 for 48 hours were analyzed by RNA-seq.

first: Yunshang

last: Chen

first: Xiaohua

first: Biyuan

last: Xing

first: Zhenyu

first: Gang

last: Wu


title: Knock down of LIMD2 inhibits the invasion and metastasis of ovarian cancer

city: Changchun

first: Lixin

address: 1266 Fujin Road

institute: Jilin University

summary: LIMD2 is involved in the invasion and metastasis of ovarian cancer. This study focused on  knock down of the LIMD2 in the A2780 ovarian cancer cells. The potential mechanism of the function of LIMD2 was analysised.

overall_design: Two target of LIMD2 was designed and transfected with lentivirus and detected with the RNA-seq.


title: Based on RNA-SEQ and experimental validation to explore the similarities and differences in catabolism and proliferation of chondrocyte inflammatory models between rats and mice.

city: shanghai

first: daofang

last: ding

address: 1200 Cai Lun Road,Zhangjiang Hi-TechPark,Pudong New Area

institute: Shanghai University of Traditional Chinese Medicine

summary: IL-1β promotes the proliferation of rat chondrocytes and inhibits the proliferation of mouse chondrocytes.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: To choose a suitable in-vitro cell model for studying OA, RNA samples from rats chondrocytes and mice chondrocytes were sequenced by using Illumina HiSeq 4000. From the sequence data, we further compared the growth properties of chondrocytes between rats and mice.

first: Daofang

last: Ding


title: Next generation sequencing of blood platelets and PBMCs in early and late stage of melanoma in mice

city: Xi'an

first: Yue

last: Yin

state: Shaanxi

address: No. 76, Yanta West Road

department: Histology and Embryology

institute: Guilin Medical University

summary: We report the application of next generation sequencing of blood platelets in an early-early melanoma mice model for screening early cancer biomarkers. By inoculating C57BL/6 mice with different numbers of B16F10 cells, we establish an early-early melanoma model. We find that mice inoculated with lower number of B16F10 cells develop tumors at a later time. Therefore the blood samples collected at day 14 post-injection before the formation of visible tumors are early-early cancer samples. The mRNA profiles of platelets from early-early group are distinct from those of control group and large tumor group. However, the mRNA profiles of PBMCs from early-early group are not so distinct from those of control group and large tumor group. This study provides a proof of concept strategy for future cancer biomarker screening and cancer immunology research.

overall_design: Platelet and PBMC mRNA profiles of different stages of melanomas in C57BL/6 mice


title: PHF6 and JAK3 mutations cooperate to drive T-cell acute lymphoblastic leukemia progression (ChIP-Seq)

city: Tianjin

first: shengnan

last: yuan

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders

summary: Chromatin immunoprecipitation sequencing (ChIP-seq) analysis of HA-PHF6-overexpressing (PHF6 OE) K562 cells showed that PHF6 directly bound to the ADGRB1 (BAI1) gene

overall_design: Examination of HA-PHF6-overexpressing (use a HA antibody) in K562 cells.

first: Shengnan

last: Yuan

first: Weiping


title: PHF6 and JAK3 mutations cooperate to drive T-cell acute lymphoblastic leukemia progression

summary:
Purpose: For RNA-Seq analysis of isogenic Phf6 WT and KO mouse T-ALL cells
Methods: Phf6 WT and KO mouse T-ALL cells were analyzed by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Results: Using an optimized data analysis workflow, we identified 2377 genes up-regulated and 3751 genes down-regulated （P < 0.05） in the BM cells from Phf6 WT and KO mice. Altered expression of 16 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes  may contribute to analyze PHF6 function.
Conclusions: Our study represents the first detailed analysis of  T-ALL cell transcriptomes with PHF6 deficiency and JAK3 mutation. Our results  suggested that Phf6 loss promoted JAK3M511I induced T-ALL progression by accelerating cell cycle and impairing T cell differentiation.

overall_design: BM cells from Phf6 WT and KO mice in the context of JAK3M511I


title: miR-155-regulated mTOR and Toll-like receptor 5 in gastric diffuse large B-cell lymphoma

first: Chung-Wu

last: Lin

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

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

overall_design: Refer to individual Series


title: Gene expression in tolerant and non-tolerant liver allografts

city: Toronto

first: Andrzej

last: Chruscinski

state: Ontario

address: 200 Elizabeth St.

country: Canada

institute: University Health Network

summary: Liver biopsy samples were obtained as part of the LITMUS trial (ClinicalTrials.gov NCT02541916). All samples were obtained from liver transplant recipients prior to immunosuppression withdrawal. Percutaneous liver biopsies were performed under local anaesthesia using an 18-gauge Jamshidi needle. A 0.5cm portion of the biopsy to be used for gene expression was stored in RNAlater (Qiagen) for 24 hours at 4 °C and then transferred to -80 °C. Specimens were thawed and transferred to a clean, RNase free microcentrifuge tube. Tissue samples were incubated in 600 ul of lysis buffer (Ambion) with 6 ul of 2-mercaptoethanol for 10 minutes. Tissue samples were then homogenized using a nuclease-free disposable pellet pestle (Kimble Kontes) and processed using the PureLink RNA Mini Kit (Ambion). RNA quality was evaluated using an Bioanalyzer 2100 (Agilent) and samples with RIN > 7 were submitted for sequencing and analysis at The Center for Applied Genomics (Toronto, Canada).

overall_design: Eight samples are from tolerant liver transplant recipients, and nine samples are from non-tolerant liver transplant recipients. All samples are liver biopsies obtained prior to immunosuppression withdrawal.


title: Time-course transcriptome analysis of in vitro differentiated Th17 cells from wild-type C57BL/6 mice

city: London

first: Gitta

last: Stockinger

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Purpose: to identify the effects and kinetics of a panel of polarizing cytokines on Th17 differentiation in vitro

overall_design: Naïve CD4 T cells were isolated from C57BL/6 mice and the cells were sort-purified and cultured in the presence of plate-bound αCD3 and plate-bound αCD28. Th17 differentiation was induced by culturing the cells in the presence of TGFβ , IL6 , IL21 and/or IL1β . Part of the cells was cultured without any polarizing cytokines, in “Th0” conditions. Three biological replicates of samples were collected at 0, 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 hours time points.

first: Helena

last: Ahlfors

first: Brigittta

first: Harri

last: Lähdenmäki

first: Sini

last: Rautio


title: Benefit and limitations of glioblastoma tissue slice cultures – an RNA sequencing study

city: Leipzig

first: Susann

last: Haehnel

address: Liebigstrasse 13

department: Institute of Anatomy

institute: University of Leipzig

summary: One of the major challenges in cancer research is to find models closely resembling the tumor within patients. Human tissue slice cultures represent a promising approach to display the patient's biology ex vivo. Recently, it was shown that these slices can be successfully analyzed by whole transcriptome sequencing as well as automated histochemistry, increasing their usability as preclinical model. Glioblastoma multiforme (GBM) is a highly malignant brain tumor with poor prognosis and little is known about its genetic background and heterogeneity regarding therapy success. In this study, tissue of 25 patients with primary GBM were processed into slice cultures and treated with standard therapy (irradiation and temozolomide). Total RNA sequencing and automated histochemistry were performed to display treatment-mediated effects at a transcriptional and histological level. Slice cultures from long-term survivors (OS > 24 months) exhibited higher apoptosis than cultures from patients with shorter OS. Proliferation within these slices was slightly increased in contrast to other groups, but not significant. Among all samples, 58 protein-coding genes were upregulated and 32 downregulated in treated vs. untreated slice cultures. In general, an upregulation of DNA damage-related and cell cycle checkpoint genes as well as enrichment of genotoxicity pathways and p53-dependent signaling was found after treatment. In conclusion, we demonstrate that treatment-mediated effects in GBM slice cultures can be determined by RNA sequencing and histological staining. The slice culture model reproduces knowledge from former studies regarding transcriptomic changes and its applicability is further improved by a comprehensible correlation with survival data of the patients.

overall_design:
total RNA of glioblastoma tissue slices from 25 patients were treated with temozolomide and x-irradiation or left untreated as control slices

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

first: Michael

last: Rade

first: Nicole

last: Kaiser

first: Kristin

last: Reiche

first: Dennis

last: Loeffler

first: Andreas

last: Horn

first: Conny

last: Blumert

first: Sven-Holger

last: Puppel

first: Felicitas

last: Rapp

first: Friedemann

first: Juergen

last: Meixensberger

first: Christof

last: Renner

first: Ingo

last: Bechmann

first: Wolf

last: Mueller

first: Frank

last: Gaunitz

first: Karsten

last: Winter


title: Inducible smooth muscle specific deletion of Yap1/Wwtr1 in mouse [Thoracic aorta RNA-seq]

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

institute: Lund University

summary: YAP and TAZ are transcriptional co-activators and downstream effectors of the Hippo pathway, which play crucial roles in organ size control and cancer pathogenesis. Genetic deletion of YAP/TAZ has revealed their critical importance for embryonic development of the heart, vasculature and gastrointestinal mesenchyme. The aim of this study was to determine the functional role of YAP/TAZ in adult smooth muscle cell in vivo.

overall_design: Thoracic aorta from 3 controls (Myh11CreERT2-negative-Yap1/Wwtr1 floxed) and 3 knockout (Myh11CreERT2-positive-Yap1/Wwtr1 floxed) were isolated and snap rozen in liquid nitrogen 7 days after the first (out of 5) tamoxifen injections


title: U87 glial-like cells gene and protein modulation under fluoride exposure

status: Public on Feb 08 2022

city: Belém

first: Bruna

last: Puty

state: Pará

address: Travessa Honório José dos Santos, 423, Jurunas

department: ICB

country: Brazil

institute: UFPA

summary: To investigate the molecular mechanism of F toxicity on glial cells we have performed a large transcriptomic and proteomic analysis over to two relevant fluoride doses. U87 glial-like cells were exposed to 0,095µg/mL and 0.22µg/ml for 10 days to mimic a chronic exposure to fluoride. A total of 62 genes and  209 genes were modulated after exposure to 0.095 and 0.22µg/ml respectively. The number of proteins modulates were 20 and 10 respectively. Gene Ontology annotation revealed changes on cellular metabolism and cell death regulation  pathways such as MAPK and ERK1/ERK2. Proteomics analysis have confirmed changes on energy metabolism and revealed changes on cytoskeleton components.

overall_design: Fluoride induced gene and protein expression on U87 glial cells were measured at 10 days after exposure to 0.095µg/mL and 0.22µg/mL. Three independent experiments were performed using different cells passages.

first: Leonardo

middle: O

last: Bittencourt

first: Leidiane

last: Alencar

first: Jéssica

last: Plaça

first: Aline

last: Dionizio

first: Marilia

last: Buzalaf

first: Edivaldo

last: Oliveira

first: Rafael

last: Lima


title: Transcriptional Sequencing of Salmonella enterica serovar Typhimurium wild typle and DsrA-deletion mutant Survival unfer LB or H2O2 conditions

city: Shanghai

first: Rui

last: Dong

address: Dongchuan Road

institute: Shanghai Jiao Tong University

summary: To elucidated the regulatory effect of DsrA on the oxidative resistance in Salmonella enterica serovar Typhimurium. RNA sample of wild-type and DsrA-deletion strain that grown in LB medium or H2O2 stress were extracted. Three biological replicates were carried out per sample. RNA sample was sequenced with Illumina HiSeq 4000 System. DESeq2 method was used to calculate the differentially expressed genes. qRT–PCR and gene mutation were used to validate RNA-seq result.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: wild-type in LB (WT_CK), wild-type in H2O2(WT_TREAT), dsrA mutant in LB(MT_CK), dsrA in H2O2 (MT_TREAT)  Three biological repetitions of each samle, totally 12 samples were conducted RNA sequncing.

first: Xianming

last: Shi


title: Single-cell transcriptome of Nicotiana attenuata corolla cells.

city: Daejeon

first: Moonyoung

last: Kang

address: Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: High-throughput single-cell RNA sequencing (scRNA-seq) identifies distinct cell populations based on cell-to-cell heterogeneity in gene expression. By examining the distribution of the density of gene expression profiles, we can observe the metabolic features of each cell population. Here, we employ the scRNA-seq technique to reveal the entire biosynthetic pathway of a flower volatile. The corolla of the wild tobacco Nicotiana attenuata emits a bouquet of scents that are composed mainly of benzylacetone (BA). Protoplasts from the N. attenuata corolla limbs and throat cups were isolated at three different time points, and the transcript levels of >16,000 genes were analyzed in 3,756 single cells. We performed unsupervised clustering analysis to determine which cell clusters were involved in BA biosynthesis. The biosynthetic pathway of BA was uncovered by analyzing gene co-expression in scRNA-seq datasets and by silencing candidate genes in the corolla. In conclusion, the high-resolution spatiotemporal atlas of gene expression provided by scRNA-seq reveals the molecular features underlying cell-type-specific metabolism in a plant.

overall_design: Examination of single cell transcriptome of flowers over three different timepoints (ZT8, ZT12, ZT16, one replicate for each timepoint), at which flower opens and starts to emit floral scents

first: Yuri

last: Choi

first: Hyeonjin

last: Kim

first: Sang-Gyu


title: Distinct silencer states determine epigenetic states of heterochromatin

city: Berkeley

first: Daniel

last: Saxton

state: CA

address: 100 University Ave

department: MCB

country: USA

institute: University of California Berkeley

summary: To identify the roles of silencers in generating and maintaining epigenetic states, we utilized FACS to sort cells that exhibited different epigenetic states, and ChIP to survey the chromatin architecture of a locus in these cells. Additional experiments involve modulation of silencing factors and phenotypic measurements such as transcription of the locus of interest and ChIP of silencing factors at that locus.

overall_design: Examination of silencing proteins Sir3 and Sir4, as well as histone modifications such as H4K16ac and H3K79me3

first: Jasper

last: Rine


title: Single cell RNA sequencing reveals deep homology of dental cell types across vertebrates

city: Atlanta

first: Larry

last: Young

state: GA

address: 954 Gatewood Rd NE

department: Department of Psychiatry

institute: Emory University


title: Nasally-delivered interferon-λ in mice protects against upper and lower respiratory tract infection of SARS-CoV-2 variants including Omicron

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has had devastating impacts on our global society. Although vaccines and monoclonal antibody countermeasures have reduced the morbidity and mortality associated with SARS-CoV-2 infection, variants with constellations of mutations in the spike gene threaten their efficacy. Therefore, antiviral interventions that are resistant to further virus evolution may be needed. Here, we show IFN-λ protects against SARS-CoV-2 B.1.351 (Beta) and B.1.1529 (Omicron) variants in three strains of conventional and human ACE2 transgenic mice. Prophylaxis or therapy with nasally-delivered IFN-λ2 limited infection of historical or variant (B.1.351 and B.1.1.529) SARS-CoV-2 strains in both the upper and lower respiratory tracts without causing excessive inflammation. In the lung, IFN-λ was produced preferentially in epithelial cells and acted on radio-resistant cells to protect against of SARS-CoV-2 infection. Thus, inhaled IFN-λ may have promise as a treatment for evolving SARS-CoV-2 variants that develop resistance to antibody-based countermeasures.

overall_design: RNA sequencing of lung homogenates of naive female K18-hACE2 mice (control) or mice treated with 2 μg of murine IFN-λ2 by intranasal routfor 1 (D+1) or 3 (D+3) days.

first: Zhenlu

last: Chong

first: Courtney

middle: E

last: Karl

first: Peter

middle: J

last: Halfmann

first: Yoshi

last: Kawaoka

first: Emma

last: Winkler

first: Michael

last: Diamond


title: Single cell RNA sequencing reveals deep homology of dental cell types across vertebrates [TJ]

summary: Here we use single nuclei RNA sequencing (snRNA-seq) of replacement teeth and adjacent oral lamina in Lake Malawi cichlids, species with lifelong whole-tooth replacement, to make two main discoveries. First, despite hundreds of millions of years of evolution, we demonstrate conservation of cell type gene expression across vertebrate teeth (fish, mouse, human). Second, we used an approach that combines marker gene expression and developmental potential of dental cells to uncover the transcriptional signature of stem-like cells in regenerating teeth. Our work underscores the importance of a comparative framework in the study of vertebrate oral and regenerative biology.

overall_design: Single nuclei RNA sequencing of replacement teeth and adjacent oral lamina in Lake Malawi cichlids

first: George

last: Gruenhagen

first: Talha

last: Mubeen

first: Chinar

last: Patil

first: Joseph

last: Stockert

first: Jeffrey

middle: T

last: Streelman


title: Single cell RNA sequencing reveals deep homology of dental cell types across vertebrates [JPOOL]


title: Transcriptional signatures of tumor infiltrating CAR-T cells

city: Boston

first: Aedin

last: Culhane

state: MA

address: 450 Brookline Ave

institute: DANA-FARBER CANCER INST

summary: We compared the second-generation (CD28, 4-1BB) with the third-generation (CD28-4-1BB) carbonic anhydrase IX (CAIX) targeted CAR constructs and investigated the antitumor effect of CAR-T cells with different CD4/CD8 proportion in vivo. The results demonstrated that anti-CAIX G36-4-1BB (BBζ) CAR-T cells exhibited superior efficacy compared to G36-CD28 (28ζ) and G36-CD28-4-1BB (28BBζ) CAR-T cells in a clear cell renal cell carcinoma (ccRCC) skrc-59 cell bearing NSG-SGM3 mouse model. Tumor infiltrating T cells were recovered and profiled via flow cytometry and 10X genomics single cell RNA sequencing (scRNAseq). We found that BBζ CAR-T cells upregulated human leukocyte antigen (HLA) II genes and cytotoxicity associated genes, while, downregulated inhibitory immune checkpoint receptor genes and differentiation of regulatory T cells (Tregs), leading to outstanding therapeutic efficacy in vivo. An increased memory phenotype, an elevated tumor infiltration, and a decrease in exhaustion related genes were observed in the CD4/8 mixture of untransduced T (UNT) cells compared to CD8 only ones, indicating that CD4/8 could be the favored cellular composition for CAR-T cell therapy with long-term persistence. In summary, these findings suggest that anti-CAIX BBζ CAR48 serves as a highly potent clinic translatable cell therapy for ccRCC with enhanced proliferation potential, increased functional capacity, diminished terminal differentiation, as well as durable immune surveillance

overall_design: Profile of anti-CAIX CAR-T cells and untransduced T cells, including BBz, 28z, 28BBz, UNT CD8 and UNT CD4/8.

first: Yufei

last: Wang


title: The Gene Expression Analysis of Peripheral Blood Monocytes from Psoriasis Vulgaris Patients with Different Traditional Chinese Medicine (TCM) Syndromes

city: Guangzhou

first: Yue

last: Lu

address: 232 Huandong Road, University Town, Guangzhou

institute: Guangzhou University of Chinese Medicine

summary: Psoriasis is chronic skin disease and an important health concern. Traditional Chinese Medicine (TCM) has shown great promise in the treatment of psoriasis. However, the correlation between TCM Syndromes and genomics of psoriasis has not been evaluated. Here, we analyzed gene expression profiling of monocytes from psoriasis vulgaris patients with different TCM syndrome types to reveal the molecular basis of different psoriasis syndromes. Of the 62 cases of psoriasis vulgaris recruited, 16, 23, and 23 cases were of blood-heat syndrome, blood stasis syndrome, and blood-dryness syndrome, respectively; 10 healthy controls were recruited as controls. Affymertix's Gene Chip ®clariom D gene chip was used to detect the gene expression profile of peripheral blood monocytes collected from recruited individuals. Compared with the healthy control group, 1570 genes were up-regulated and 977 genes were down-regulated in the psoriasis vulgaris patients group; 798 genes and 108 genes were up- and down-regulated in the blood-heat syndrome group respectively; 319 and 433 genes were up- and down-regulated in the blood-dryness syndrome group, respectively; and 502 and 179 genes were up-and down-regulated in the blood-stasis syndrome group. Our analyses indicated not only common differential genes and pathways between psoriasis syndrome groups and healthy controls, but also syndrome-specific genes and pathways. The results of this study link the three syndromes at the gene level and will be useful for clarifying the molecular basis of TCM syndromes of psoriasis.  Trial registration: ChiCTR, ChiCTR-TRC-14005185. Registered 8 August 2014, http://www.chictr.org.cn/showproj.aspx?proj=4390  Keywords: Gene chip, Gene expression, Psoriasis vulgaris, TCM syndrome type

overall_design: We analyzed gene expression profiling of monocytes from psoriasis vulgaris patients with different TCM syndrome types to reveal the molecular basis of different psoriasis syndromes. Of the 62 cases of psoriasis vulgaris recruited, 16, 23, and 23 cases were of blood-heat syndrome, blood stasis syndrome, and blood-dryness syndrome, respectively; 10 healthy controls were recruited as controls. Affymertix's Gene Chip ®clariom D gene chip was used to detect the gene expression profile of peripheral blood monocytes collected from recruited individuals.

first: Li

last: Li

first: Yuhong

last: Yan

first: Jianan

last: Wei

first: Danni

last: Yao

first: Jingjing

last: Wu

first: Hao

last: Deng

first: Jingwen

first: Shuyan

last: Ye

first: Haiming

last: Chen

first: Qubo

first: Ling

last: Han

first: Chuanjian

first: Yao

last: Qi

first: Hengjun

last: Gao


title: ChIP-seq data of CDYL in mouse dorsal root ganglia

city: Beijing

first: Zhao-wei'

last: Sun

address: 38 Xue Yuan Road

institute: Peking University Health Science Center

summary: We report that the epigenetic factor CDYL is crucial for pain processing.  CDYL downstreams in mouse dorsal root ganglia (DRG) are  mostly associated with neurological functions, including chemical synaptic transmission, regulation of membrane potential and ion transport. CDYL facilitates H3K27me3 deposition at the Kcnb1 intron region thus silencing Kv2.1 transcription. Loss function of CDYL enhances total Kv and Kv2.1 current density in DRG and knockdown of Kv2.1 reverses the pain-related phenotypes of Cdyl deficiency mice.

overall_design: Detection of CDYL downstreams in mouse primary sensory neurons

first: Zhao-wei

first: Yun


title: The effect of AML on platelets

city: Houston

first: Rebecca

last: Murdaugh

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Early diagnosis of acute myeloid leukemia (AML) in the pre-leukemic stage remains a clinical challenge, as pre-leukemic patients show no symptoms, lacking any known morphological or numerical abnormalities in blood cells. Here, we demonstrate that platelets with structurally abnormal mitochondria emerge at the pre-leukemic phase of AML, preceding detectable changes in blood cell counts or detection of leukemic blasts in blood. We visualized frozen-hydrated platelets from mice at different time points during AML development in situ using electron cryo-tomography (cryo-ET) and identified intracellular organelles through an unbiased semi-automatic process followed by quantitative measurement. A large proportion of platelets exhibited changes in the overall shape and depletion of organelles in AML. Notably, 23% of platelets in pre-leukemic cells exhibit abnormal, round mitochondria with unfolded cristae, accompanied by a significant drop in ATP levels and altered expression of metabolism-related gene signatures. Our study demonstrates that detectable structural changes in pre-leukemic platelets may serve as a biomarker for the early diagnosis of AML.

overall_design: Platelets were collected from control or AML mice and used for RNA-seq library generation. Both control and AML have 2 replicates. 3-4 mice were pooled for one sample.

first: Yu-Jung

last: Tseng

first: Daisuke

last: Nakada


title: Neurobehavioral abnormalities following prenatal psychosocial stress are differentially modulated by maternal environment

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: The goal of this study was to compare transcriptional profiles of the amygdala from control and (PS) prenatally stressed male and female offspring to elucidate sex-specific molecular mechanisms underlying behavioral and neuroendocrine abnormalities observed after in-utero psychosocial stress exposure. Amygdalar mRNA profiles of 28 day old control and PS male and female mice were generated by preparing sequencing libraries using the NEBNext Ultr II Directional RNA Library Prep Kit for Illumina. After indexing, enrichment through 8 cycles of PCR, and passing initial quality control metrics, individually indexed and compatible libraries were proportionally pooled and sequenced using Nextseq 550 sequencer. The sequencing setting of single read 1 × 85 bp to generate ∼50 M reads per sample was used. Differentially expressed genes (DEGs) were analyzed using RUVseq and EdgeR. Results were validated via qPCR We find psychosocial PS results in the emergence of anxiety-like behaviors, an altered behavioral coping strategy to stress, and anhedonia in male and female offspring. Neuroendocrine abnormalities, evidenced by acute stress-induced HPA axis hyperactivity, are only observed in PS female offspring. Our RNA-seq analysis reveals these phenotypic changes in PS offspring to be associated with sex-specific disturbances in genes associated with synaptic transmission, including genes associated with glutamatergic and GABAergic signaling in PS males, and upregulation of DBH, known to regulate NE synthesis, in PS females. Our study represents one of the first detailed analysis of amygdalar transcriptomes generated by RNA-seq comparing control vs prenatally stressed offspring, identifying sex-specific changes in response to in-utero psychosocial stress exposure.

overall_design: mRNA profiles of 28-day old control and PS (prenatally stressed) male and female mice

first: Sandra

middle: P

last: Zoubovsky

first: Joseph

last: Salomone

first: Louis

last: Muglia


title: Long non-coding RNA and mRNA expression analysis in liver of mice with Clonorchis sinensis infection

city: Harbin

first: Su

address: 157 Health Care Road, Nangang District

institute: Department of Parasitology, Harbin Medical University, Harbin, P. R. China

summary: We compared the expression of lncRNAs and mRNAs in the liver tissue of mice infected with C. sinensis, in order to further understand the molecular mechanisms of clonorchiasis.

overall_design: Mice were divided into two groups randomly with three mice per group, and each mouse in the infected group was orally infected with 100 metacercariae.The mice in both infected and control groups were sacrificed at 4 wpi,and then liver samples were selected for lncRNA microarray analysis.

first: Xue-li

last: Zhang

first: Xu

last: jiang

first: Xiang

last: Li

first: Jian

last: Ding

first: Li-jiao

last: Zuo

first: Shan-Shan

last: Duan

first: Rui

first: Bei-Bei

first: Xin-Yi

last: Hu

first: Yan-Nan

first: Xiao-Li


title: gp130/STAT3 signaling is required for homeostatic proliferation and anabolism in postnatal growth plate and articular chondrocytes [bulkRNA-seq]

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary: Growth of long bones and vertebrae is maintained postnatally by a long-lasting pool of progenitor cells. Little is known about the molecular mechanisms that regulate the output and maintenance of the cells that give rise to mature cartilage. Here we demonstrate that postnatal chondrocyte-specific deletion of a transcription factor Stat3 results in severely reduced proliferation coupled with increased hypertrophy, growth plate fusion, stunting and signs of progressive dysfunction of the articular cartilage. This effect is dimorphic, with females more strongly affected than males. Chondrocyte-specific deletion of the IL-6 family cytokine receptor gp130, which activates Stat3, phenocopied Stat3-deletion; deletion of Lifr, one of many co-receptors that signals through gp130, resulted in a milder phenotype. These data define a new molecular circuit that regulates chondrogenic cell maintenance and output and reveals a novel, hitherto unrecognized function of IL-6 cytokines in the skeletal system with direct implications for skeletal development and regeneration.

overall_design: mRNA sequencing for human fetal chondrocytes with and without STAT3 knock-down

first: Ben

last: Van Handel


title: gp130/STAT3 signaling is required for homeostatic proliferation and anabolism in postnatal growth plate and articular chondrocytes

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

overall_design: Refer to individual Series