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

first: Takayuki

last: Morimoto

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

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

first: Tsutomu

last: Nakazawa

first: Ryosuke

last: Matsuda

first: Fumihiko

last: Nishimura

first: Mitsutoshi

last: Nakamura

first: Shuichi

last: Yamada

first: Ichiro

last: Nakagawa

first: Young

last: Park

first: Takahiro

last: Tsujimura

first: Hiroyuki

last: Nakase


title: Regulation of translation by site-specific ribosomal RNA methylation.

status: Public on Aug 16 2021

city: Copenhagen

first: Anders

middle: Henrik

last: Lund

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen,BRIC

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Subtypes in human pancreatic ductal adenocarcinoma based on niche factor dependency show distinct drug treatment responses

status: Public on Aug 07 2021

city: Fukuoka

first: Kenoki

last: Ohuchida

address: 3-1-1, Maidashi, Higashi-ku

department: Surgery and Oncology

country: Japan

institute: Kyushu University

summary: BACKGROUND & AIMS: Pancreatic ductal adenocarcinoma (PDAC) is characterized by abundant stroma in which microenvironmental (niche) factors promote PDAC progression. In mouse models, reduction of the stroma increased the proportion of poorly differentiated PDAC with a worse prognosis. Here, we aimed to clarify the effects of stroma on PDAC that may define the PDAC phenotype and induce distinct therapeutic responses. METHODS: The molecular features of PDAC based on differentiation grade were clarified by genome and transcriptome analysis using PDAC organoids (PDOs). We identified the dependency on niche factors that might regulate the differentiation grade. A three-dimensional co-culture model with cancer-associated fibroblasts (CAFs) was generated to determine whether CAFs provide niche factors essential for differentiated PDAC. PDOs were subtyped based on niche factor dependency, and the therapeutic responses for each subtype were compared. RESULTS: The expression profiles of PDOs differed depending on the differentiation grade. Consistent with the distinct profiles, well differentiated types showed high niche dependency, while poorly differentiated types showed low niche dependency. The three-dimensional co-culture model revealed that well differentiated PDOs were strongly dependent on CAFs for growth, and moderately differentiated PDOs showed plasticity to change morphology depending on CAFs. Differentiated PDOs upregulated the expression of mevalonate pathway-related genes correlated with the niche dependency and were significantly more sensitive to simvastatin than poorly differentiated PDOs. CONCLUSIONS: Our findings suggest that CAFs maintain the differentiated PDAC phenotype through secreting niche factors and induce distinct drug responses. These results may lead to the development of novel subtype-based therapeutic strategies.

overall_design: To characterize transcriptional phenotypes of differentiation grades, gene expression microarray analysis of eight PDOs established from resected specimens from PDAC patients was performed. well differentiated (Grade1) PDOs, No. 565, 571, 585; moderately differentiated (Grade2) PDOs, No. 573, 578, 580; poorly differentiated PDOs, No. 497, 501.

first: Tomohiko

last: Shinkawa


title: Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs

status: Public on Aug 15 2021

city: Paris

first: Vanessa

last: Ribes

address: 15 rue Helene Brion

country: France

institute: Institut Jacques Monod

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hallmarks of the alveolar subclass of Rhabdomyosarcoma are chromosomal translocations that generate PAX3-FOXO1 or PAX7-FOXO1 chimeric transcription factors. Both PAX-FOXO1s drive related cell transformation in animal models, yet the two mutations are associated with distinct pathological manifestations in patients. To evaluate the mechanisms underlying these differences, we generated isogenic fibroblast lines expressing either PAX-FOXO1 paralog. Mapping their genome recruitment using CUT&Tag revealed that the two chimeric proteins have distinct DNA binding preferences. Furthermore, PAX7-FOXO1 causes stronger de novo transactivation of its bound regions than PAX3-FOXO1, resulting in greater transcriptomic dynamics involving genes regulating cell shape and cycle. Consistently, PAX3-FOXO1 accentuates fibroblast cellular traits associated with contractility and surface adhesion and limits entry to M phase. Instead, PAX7-FOXO1 pushes cells to adopt an amoeboid-like shape, reduce S phase entry and provokes more genome instabilities. Altogether, our results demonstrate that PAX7-FOXO1 has a greater chromatin remodelling and transactivating abilities and is more deleterious to cells than PAX3-FOXO1. Altogether our results argue that the diversity in rhabdomyosarcoma manifestation stems, in part, from the diverging transcriptional activity of PAX3-FOXO1 and PAX7-FOXO1. Furthermore, PAX7-FOXO1 pronounced deleterious effects provides an explanation for the low frequency of the translocation generating this factor in Rhabdomyosarcoma patients.

overall_design: CUT&Tag and RNA sequencing were performed on control or PAX3-FOXO1 or PAX7-FOXO1 expressing human foreskin fibroblasts

first: Line

last: Manceau

first: Julien

last: Richard Albert

first: Pier-Luigi

last: Lollini

first: Maxim

middle: C

last: Greenberg

first: Pascale

last: Gilardi-Hebenstreit


title: SIRT1 in mouse heart development

status: Public on Aug 23 2021

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

summary: The goal of this project is to investigate the role of SIRT1, the most conserved mammalian NAD+-dependent protein deacetylase, in the regulation of heart development. SIRT1 is important for heart development and functions. However, the underlying molecular mechanisms remain undefined. In this study, we analyzed the gene expression profiles in E18.5 WT and SIRT1 KO mouse hearts.

overall_design: Total RNA were extracted from 4 pairs of E18.5 WT and SIRT1 KO mouse hearts, and gene expression profiles were analyzed using Agilent Whole Mouse Genome 4x44 multiplex format oligo arrays (014868) (Agilent Technologies, Santa Clara, CA), following the Agilent 1-color microarray-based gene expression analysis protocol.

first: Xiaoling

last: Li

first: Yi

last: Fang


title: RNA seq analysis of MC38CEA cells with diminished ADAM17 expression due to Crispr/Cas9 gene editing or control cells

status: Public on Aug 03 2021

city: Kraków

first: Joanna

last: Bereta

address: Gronostajowa 7

department: Cell Biochemistry

country: Poland

institute: Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University

summary: The goal of this study was to compare transcriptomes of cells with reduced and normal levels of ADAM17, unstimulated or stimulated with IL1b and IFNg

overall_design: The cells were electroporated with Cas9 mRNA and after four hours electroporated with in vitro transcribed sgRNAs targeting Adam17 or EGFP (control).  The cells were left unstimulated or were stimulated with  human recombinant (hr) IL1b (10 ng/ml) and  mouse recombinant (mr) IFNg (10 ng/ml) for six hours and RNA was isolated.

first: Maria

last: Czarnek


title: The virulome of Streptomyces scabiei in response to cello-oligosaccharides elicitors

status: Public on Aug 08 2021

city: Liège

first: Sinaeda

last: Anderssen

address: Allée du six aout

country: Belgium

institute: Université de Liège

summary: We provide a manually-curated genome mining analysis of the bacterial plant pathogen Streptomyces scabiei. The expression of the deduced biosynthetic gene clusters was assessed by a RNAseq approach, and their potential to be induced by the virulence elicitors cellobiose and cellotriose was estimated by comparing mRNA levels before and after elicitor addition. Finally, we performed metabolomic analyzes to evaluate how the production of known specialized metabolites responds to virulence elicitors, in correlation (or not) with the transcriptomic data

overall_design:
mRNA levels of S. scabiei 87-22 in a minimal medium with maltose as carbon source suppl. with cellobiose or cellotriose. Two Elicitors, three time points in three replicates (18 samples). Each sample has several fastq raw read files, corresponding to different reads (paired-end, so R1 and R2), as well as different sequencing lanes (4 in total, L001/L002/L003/L004).
mRNA levels of S. scabiei 87-22 or ∆cebR in the rich ISP2 medium. Two strains, two time points with three replicates (12 samples). Each sample has several fastq raw read files, corresponding to different reads (paired-end, so R1 and R2), as well as different sequencing lanes (4 in total, L001/L002/L003/L004).

first: Benoit

last: Deflandre

first: Beatrice

last: Bonometti

first: Latifa

last: Karim

first: Wouter

last: Coppieters


title: Innate, translation-dependent silencing of an invasive transposon in Arabidopsis

city: San Francisco

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

type: Non-coding RNA profiling by high throughput sequencing

summary: Co-evolution between hosts' and parasites' genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence-degeneration and, ultimately, loss-of-autonomy of most transposable elements (TEs). Recognition of newly-invasive plant TEs, by contrast, involves an innate antiviral-like silencing response. To investigate this response's activation, we studied the single-copy element EVADÉ (EVD), one of few representatives of the large Ty1/Copia family able to proliferate in Arabidopsis when epigenetically-reactivated. In Ty1/Copia-elements, a short subgenomic mRNA (shGAG) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full-length genomic flGAG-POL. We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly-nuclear flGAG-POL. During this process, an unusually intense ribosomal stalling event coincides with mRNA breakage yielding unconventional 5'OH RNA fragments that evade RNA-quality-control. The starting-point of sRNA production by RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6), exclusively on shGAG, occurs precisely at this breakage point. This hitherto-unrecognized "translation-dependent silencing" (TdS) is independent of codon-usage or GC-content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against EVD de novo invasions that underlies its associated sRNA pattern.

overall_design: Ribo-seq and sRNA-seq were performed on RNA from inflorescence tissue of EVD and GFP-EVD-GUS overexpressing plants. NanoPare and SMART-seq2 was perfomed on wild-type (Col-0) and ddm1-2 inflorescence tissue.

first: Rajeswaran

last: Rajendran

first: Marieke

last: Trasser

first: Gregory

last: Schott

first: Verónica

last: Barragán-Borrero

first: Arturo

last: Marí-Ordóñez

first: Olivier

last: Voinnet


title: Loss of TREM2 reduces hyperactivation of progranulin deficient microglia but not lysosomal pathology

status: Public on Jul 30 2021

city: Munich

first: Anika

last: Reifschneider

address: Feodor-Lynen-Straße

country: Germany

institute: LMU

summary: GRN haploinsufficiency causes frontotemporal lobar degeneration and results in microglial hyperactivation, lysosomal dysfunction and TDP-43 deposition. To understand the contribution of microglial hyperactivation to pathology we evaluated genetic and pharmacological approaches suppressing TREM2 dependent transition of microglia from a homeostatic to a disease associated state.  Trem2 deficiency in Grn KO mice led to a reduction of microglia activation. To explore antibody-mediated pharmacological modulation of TREM2-dependent microglial states, we identified antagonistic TREM2 antibodies.  Treatment of macrophages from GRN-FTLD patients with these antibodies allowed a complete rescue of elevated levels of TREM2 together with increased shedding and reduction of TREM2 signaling. Furthermore, antibody-treated PGRN deficient hiMGL showed dampened microglial hyperactivation, reduced TREM2 signaling and phagocytic activity, however, lack of rescue of lysosomal dysfunction. Similarly, lysosomal dysfunction, lipid dysregulation and glucose hypometabolism of Grn KO mice were not rescued by TREM2 ablation. Furthermore, NfL, a biomarker for neurodegeneration, was elevated in the Grn/Trem2 KO. These findings suggest that microglia hyperactivation is not necessarily contributing to neurotoxicity, and instead demonstrates that TREM2 exhibits neuroprotective potential in this model.

overall_design: In this study we analyzed gene expression in total RNA isolated from whole brain of adult mice. We compared the expression profile of Trem2 knockout mice , Grn knockout mice, and Grn/Trem2 double knockout mice (for each genotype n=4, 6 month) to wild type mice (n=4, 6 months).

first: Anja

last: Capell


title: RNA seq analysis of MC38CEA cells transduced with pLKO1 vectors encoding shRNAs targeting Adam17 or control shRNA

status: Public on Aug 01 2021

overall_design: The cells were transduced with pLKO vectors from MISSION® library encoding shRNA targeting mouse ADAM17:  SL2 (TRCN0000031953) or control non-targeting shRNA: SHC016. Transduced cells were selected with puromycin. The cells were left unstimulated or were stimulated with  human recombinant (hr) IL1b (10 ng/ml) and  mouse recombinant (mr) IFNg (10 ng/ml) for six hours and RNA was isolated. Note: Control shRNA, SHC016, is cytotoxic and its expression leads to elimination of shRNA-coding casette (personal observation).


title: MiR-124 attenuates angiogenesis via the p38/MAPK and PI3K/AKT signaling pathways in acute myocardial infarction

status: Public on Jul 27 2021

city: Weihai

first: Yang

last: Liu

state: Shandong

address: No.3 Mishan East Rd,Wendeng District

department: Department of Critical Care Medicine

country: China

institute: Weihai Central Hospital，Shangdong,China

summary: Due to its rapid onset and high mortality, acute myocardial infarction (AMI) is considered as one of the most fatal diseases among heart diseases. Therefore, exploring its potential pathogenesis and developing effective treatment approaches for AMI have become a research hotspot in the medical community. In the present study, clinical blood samples from patients with AMI were analyzed and the results showed that the expression of microRNA (miR)-124 was significantly increased in peripheral blood of patients with AMI compared with healthy subjects. In addition, miR-124 overexpression notably promoted the apoptosis of HUVECs and attenuated their proliferative ability. Based on these findings, RNA from HUVECs was extracted and sequenced to investigate the changes in the gene expression profile triggered by miR-124 overexpression. The upregulated genes were enriched in several signaling pathways such as PI3K/AKT, while the downregulated ones were mainly enriched in metabolic-related signaling pathways. Additionally, the chromosomal location analysis revealed that the differentially expressed genes (DEGs) were distributed in all chromosomes, except the Y sex chromosome. Furthermore, the characteristic profile of DEGs mediated by miR-124 overexpression was analyzed via Connectivity Map analysis. The analysis revealed that anisomycin and sanguinarine, two agonists of the p38/MAPK signaling pathway involved in the inhibition of angiogenesis, exerted the highest enrichment scores. Additionally, Gene Set Enrichment Analysis demonstrated that DEGs were mainly enriched in the PI3K/AKT signaling pathway, thus inhibiting angiogenesis. Collectively, the present results indicated that miR-124 overexpression could promote AMI by affecting angiogenesis.

overall_design: mRNA profile changes between mir124 over-expression huvec and normal huvec

first: Weimin

last: Ma

first: Xin

last: Zhang


title: A structural role for histone methyltransferase MET-2 represses transcription independent of H3K9me catalysis

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

institute: Institute of Molecular Biology


title: The novel RNA binding protein IMP2 drives a stromal-Th17 cell inflammatory circuit in autoimmune neuroinflammation

status: Public on Jul 23 2021

city: Pittsburgh

first: Sarah

last: Gaffen

state: PA

address: 200 lothrop street

institute: University of Pittsburgh

summary:
Posttranscriptional control of Ccl2 in stromal cells by IMP2 is required to permit IL-17-driven progression of EAE pathogenesis.
Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome (build mm10) and identified potential differentially regulated transcripts in the lymph nodes of EAE Imp2 KO mice (n=3) compared to EAE WT mice (n=3) with an absolute fold change ≥1.5, p value <0.05 and RPKM in WT mice >1. Altered expression of potential genes was confirmed with qRT–PCR.

overall_design: Imp2 WT and KO mice were subjected to EAE. Inguinal Lymph nodes were harvested at Day 7. RNA was extracted with tryzol and  subjected to RNA-seq using illumina Plateform

first: Bechara

last: Rami

first: Gaffen

last: Sarah


title: Development  depression-associated biomarkers research

status: Public on Aug 17 2021

city: Shanghai

first: Ting

last: Zhou

address: No.6600, Nanfeng highway, Fengxian District

institute: Fengxian Hospital, Southern Medical University


title: RNA-Seq of MSK-PCa series of Patient Derived Organoids and Xenografts

status: Public on Aug 04 2021

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: Transcriptome profiling analysis was performed in 22 human prostate cancer organoids, 6 patient-derived xenografts (PDXs) and 7 cell lines.

overall_design:
Transcriptome analysis of patient derived prostate cancer organoids and xenografts

Please note that the "totalDf_rlog.csv" is a gene expression analysis of all our 33 uploaded RNA-seq data as well as publicly available RNA-seq from GEO:

LNCaP: SRR7651716; GSM3321040
VCaP: SRR7651717
22Rv1: SRR7651715; GSM3321039
C4-2: SRR7179610; GSM3145590
DU145: SRR7651718; GSM3321042
H660: SRR7651720; GSM3321044
PARCB1: SRR7651704; GSM3321028
PARCB3: SRR7651706; GSM3321030
PARCB6: SRR7651708; GSM3321032
PARCB8: SRR7651709; GSM3321033
MSKEF1 (MSKPca4): SRR7651719; GSM3321043

and the following data columns belong the samples as below:
BM110 -> MSKPCa18
BM111 -> MSKPCa19
ST262 -> MSKPCa20
ST278 -> MSKPCa22
ST280 -> MSKPCa24

first: Ekta

last: Kharuna

first: Brett

last: Carver

first: Zeda


title: A structural role for histone methyltransferase MET-2 represses transcription independent of H3K9me catalysis [RNA-seq]

summary: Packaging genomic regions into silenced heterochromatin is critical to maintain organismal viability and tissue identity. Methylation of histone H3 on lysine 9 (H3K9me) marks heterochromatin. Here we show that in addition to catalyzing H3K9me, the C. elegans histone methyltransferase MET-2 (SETDB1-like) has a second non-catalytic function that can itself contribute to gene repression.  We find that subnuclear concentrates, or foci, of MET-2 correlate with efficient HMT activity, yet foci composed of catalytic-deficient MET-2 are also able to mediate transcriptional silencing.  Genetic ablation of met-2 or physiological disruption of MET-2 foci by heat stress results in loss of silencing coincident with an increase in histone acetylation. Restoration of catalytically deficient MET-2 foci mitigates H3K9 and H3K27 hyperacetylation, gene derepression, and infertility, demonstrating a structural role for foci of a conserved heterochromatic histone methyltransferase in gene silencing independent of its enzymatic activity.

overall_design: Total RNAseq of RNA isolated from early C. elegans embryos (~1-300 cell stage) in N2 (Bristol), met-2(n4256) III, and met-2(gw1660) mutants cultured at 20°C, or exposed to 37°C for 1hr. Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using RNeasy kit (QIAGEN 74104) including DNase treatment. Depletion of ribosomal RNA was done for 5 ľg of total RNA with Ribo-Zero Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator kit (Zymo Research R1015) according to corresponding manufacturers instructions.

first: Colin

last: Delaney

first: Stephen

middle: P

last: Methot

first: Veronique

last: Kalck

last: Seebacher

first: Daniel

last: Hess

first: Susan

middle: M

last: Gasser


title: A structural role for histone methyltransferase MET-2 represses transcription independent of H3K9me catalysis [ChIP-seq]

overall_design: ChIP experiments of H3K27ac and H3K9me2 in wild-type (N2), met-2(n4256) III and met-2(gw1660) III. Libraries were prepared from chromatin IP and input samples using the NEBNext ultra DNA library prep kit for Illumina (NEB # 7370) and the NEBNext Multiplex Oligos for Illumina (NEB # E7335), according to the manufacturers recommendations. No size selection was performed during sample preparation and the libraries were indexed and amplified using 12 PCR cycles, using the recommended conditions. After a final cleanup with Agencourt AmPure XP beads (Beckman # A63881), the library size distribution and concentrations were determined using a BioAnalyzer 2100 (Agilent technologies) and Qubit (Invitrogen) instrument, respectively. The final pools were prepared by mixing equimolar amounts of all individual indexed libraries and then sequenced on a HiSeq 2500 (Illumina) in Rapid mode (Paired-End 50).


title: Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Neurodegeneration-associated mutations affect the dynamics of transient cytoplasmic stress granule (SG). However, it is unclear if and how aberrant SG behavior is linked to the downstream formation of protein aggregates and other molecular defects that persist after stress subsides. Using subcellular fractionation combined with RNA-seq (CeFra-seq) we characterize the global mRNA localization landscape in human pluripotent stem cell-derived motor neuron (PS-MN). Using CeFra-seq and quantitative proteomics, we find that transient stress leads to a widespread reshaping of mRNA and protein localization that recapitulates key molecular phenotypes of Amyotrophic Lateral Sclerosis (ALS). While the substantial reorganization of the global mRNA localization landscape is largely reversible in wild type PS-MNs, we find that cells harboring ALS-linked mutations in HNRNPA2B1 are unable to recover and display a delayed-onset increase in neuronal cell death in response to stress. Our findings reaffirm the importance of stress-induced molecular mechanisms in the formation of molecular disease pathology of ALS and highlight the importance of targeting SG-relevant molecular mechanisms in the development of therapeutic strategies.

overall_design: Analysis of global mRNA localization in stem cells, stem cell-derived motor neurons and stem cell-derived motor neurons exposed to cellular stress and/or harboring ALS-associated mutations in HNRNPA2B1

first: Sebastian

last: Markmiller

first: Shashank

last: Sathe

first: Kari

middle: L

last: Server

first: Amit

last: Fulzele

first: Neal

last: Cody

first: Julie

last: Bergalet

first: Ashkan

last: Javaherian

first: Sara

last: Broski

first: Steve

last: Finkbeiner

first: Eric

middle: J

last: Bennett

last: Lécuyer

middle: W


title: Cortical organoids model early brain development disrupted by 16p11.2 CNV in autism

status: Public on Jul 31 2021

first: Lilia

last: Iakoucheva

state: California

address: 9500 Gilman Drive, MC0603

department: Psychiatry

institute: University of California San Diego

summary:
Reciprocal deletion and duplication of 16p11.2 is the most common copy number variation (CNV) associated with Autism Spectrum Disorder (ASD) and other developmental disorders, and has significant effect on brain size. We used cortical organoids derived from ASD cases to investigate neurodevelopmental pathways dysregulated by dosage changes of 16p11.2 CNV. We show that organoids recapitulate patients’ macrocephaly and microcephaly phenotypes. Deletions and duplications have “mirror” effects on cell proliferation, maturation and synapse number, consistent with “mirror” effects on brain development in humans. Neuronal migration was decreased in both, deletion and duplication organoids. Transcriptomic and proteomic profiling revealed synaptic defects and neuronal migration as key drivers of 16p11.2 functional effect. We implicate upregulation of small GTPase RhoA involved in regulation of cytoskeletal dynamics, neuron migration and neurite outgrowth as one of the pathways impacted by the 16p11.2 CNV in ASD. Treatment with the RhoA inhibitor Rhosin rescued neuron migration, but not synaptic defects. This study identifies pathways dysregulated by the 16p11.2 CNV during early neocortical development using cortical organoid models.

Grant ID: Simons Foundation, #345469
Grant Title: Translational dysregulation of the RhoA pathway in autism
Affiliation: University of California San Diego
Name: Lilia M. Iakoucheva; Alysson R. Muotri

overall_design: Bulk RNA-seq of 108 samples of patient-derived iPSCs, 1 month old and 3 months old cortical organoids with 16p11.2 deletions, duplications and controls was performed

first: Jorge

last: Urresti

first: Alysson

middle: R

last: Muotri


title: mtDNA sequencing of aged muscle stem cells (mouse)

status: Public on Jul 29 2021

city: Dallas

first: Prashant

last: Mishra

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

type: Genome variation profiling by high throughput sequencing

summary: We report mitochondrial genome (mtDNA) sequences in purified mouse muscle stem cells at different ages. This study identifies changes in the mitochondrial genome of muscle stem cells during aging.

overall_design: Muscle stem cells were purified from wild-type mice of different ages (4 mice per age group). Total DNA was extracted, and the mitochondrial DNA was sequenced.

first: Xun

last: Wang


title: Mapping the 3D genome and epigenome in SARS-CoV-2 infected human cells

city: HOUSTON

first: Ruoyu

state: Texas

address: 6431 Fannin St

institute: UTHealth McGovern Medical School

summary: Many viruses can significantly impact host chromatin, but such roles of SARS-CoV-2 are unknown. Here, we characterized the three-dimensional (3D) genome architecture and epigenome landscapes in human cells after SARS-CoV-2 infection, revealing remarkable restructuring of host chromatin architectures.

overall_design: We utlizied Hi-C 3.0, spike-in calibrated ChIP-Seq to map the alterations of 3D genome and epigenome in SARS-CoV-2 infected human cells

first: Wenbo

last: Li

first: Joo-Hyung

last: Lee


title: RNA-seq of wild-type and Cox10-/- muscle stem cells (mouse)

summary: We report the transcriptome changes in purified mouse muscle stem cells in response to deletion of the Cox10 gene.  This study identifies changes in the muscle stem cell population in response to mitochondrial dysfunction.

overall_design: A floxed-Cox10 allele combined with Pax7-Cre (ERT2) driver were used to induce Cox10 deletion in muscle stem cells of adult animals, via administration of tamoxifen. Two days after tamoxifen administration, muscle stem cells were purified from wild-type (control) and Cox10-/- animals.


title: An integrated approach to identify environmental modulators of genetic risk factors for complex traits

status: Public on Jul 09 2021

city: Los Angeles

first: Brunilda

last: Balliu

address: 621 Charles Young Drive South

department: Computational Medicine

institute: UCLA

summary: Complex traits and diseases can be influenced by both genetics and environment. However, given the large number of environmental stimuli and power challenges for gene-by-environment testing, it remains a critical challenge to identify and prioritize specific disease-relevant environmental exposures. We propose a novel framework for leveraging signals from transcriptional responses to environmental perturbations to identify disease-relevant perturbations that can modulate genetic risk for complex traits and inform the functions of genetic variants associated with complex traits. We perturbed human skeletal muscle, fat, and liver relevant cell lines with 21 perturbations affecting insulin resistance, glucose homeostasis, and metabolic regulation in humans and identified thousands of environmentally responsive genes. By combining these data with GWAS from 31 distinct polygenic traits, we show that the heritability of multiple traits is enriched in regions surrounding genes responsive to specific perturbations and, further, that environmentally responsive genes are enriched for associations with specific diseases and phenotypes from the GWAS catalog. Overall, we demonstrate the advantages of large-scale characterization of transcriptional changes in diversely stimulated and pathologically relevant cells to identify disease-relevant perturbations.

overall_design: Examination of gene expression changes in three human cell lines in response to 21 metabolic perturbations


title: Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition from transcriptomic and proteomic profiles in Dingyuan pigs

status: Public on Jul 08 2021

city: Beijing

first: Pan

last: Zhang

address: No. 2, Yuanmingyuan West Road, Beijing

institute: China Agricultural University

summary: Purpose: This study conducted RNA-Seq analysis on Dingyuan pig individuals with different intramuscular fat content and backfat thickness, in order to find genes that specifically regulate subcutaneous fat and intramuscular fat deposition in pigs

overall_design: we used RNA Seq and TMT-based proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and intramuscular fat deposition in Dingyuan pigs. We found 191 differential genes (DEGs) in the HBF (high back fat thickness) group and LBF (low back fat thickness) group. In the HIMF (high intramuscular fat) and LIMF (low intramuscular fat) groups, we found 85 DEGs . The enrichment analysis of GO and KEGG showed that DEGs  of the BF group are mainly involved in various metabolic pathways such as carbohydrates, amino acids, esters and fatty acids, while the DEGs of the IMF group are involved in a wide range of signal pathways, including metabolic pathways, the insulin and the synthesis and degradation of ketone bodies, longevity, and some disease-related pathways. Among the genes related to the metabolic pathways of carbohydrates, amino acids, esters and fatty acids, we have found 26 candidate genes that specifically regulate subcutaneous fat deposition and 7 genes specifically regulate intramuscular fat deposition in Dingyuan pigs.Our data provide insights for analyzing the mechanism of pig fat deposition

first: Bo

first: Hao

first: Qinggang


title: Saturated fatty acids promotes β-cell toxicity by disabling intracellular lipid droplet formation through S-acylation of FIT2

city: Singapore

first: Yusuf

last: Ali

address: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

summary: Palm and coconut oils are linked to cardiovascular disease and diabetes because of their high saturated fatty acid (SFA) content but exactly how exogenous SFAs, but not unsaturated fatty acids (UFA), are toxic to cells remains unknown. In insulin-producing, β-cells of the Islets of Langerhans, loss of which exacerbates diabetes, we found that SFAs but not UFAs were toxic because they disable a highly conserved lipid droplet biogenesis machinery. We show that palmitate (a major SFA of these oils), but not palmitoleic or oleic, S-acylates the highly conserved ER-resident FITM2 protein, required for lipid coalescence and droplet budding from the ER. The S-acylation marks FITM2 for ubiquitination and proteosomal degradation, leaving SFAs within the ER instead safe sequestration within lipid droplets. ER-stress ensues with rapid induction of ER stress leading to β-cell apoptosis. Specific deletion of FITM2 in β-cells disrupts calcium signaling and key β-cell TFs and exacerbates high fat diet-induced ER stress and diabetes. Rescue by overexpression ameliorates ER-stress and β-cell apoptosis thus demonstrating an important link between lipid species and cell ability to sequester them away from the ER in the form of lipid droplets.

overall_design: Pancreatic islet mRNA profiles of 12 week old wild type (WT) and β-cell specific FIT2 knockout (β-FIT2KO, KO) mice were generated with the Illumina NextSeq, in quintuplicate

first: Jia

middle: N

last: Foo


title: RNA sequencing of wildtype and catalytic knockouts of TUT4/7

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

summary: TUT4 and TUT7 are terminal uridyl transferases that adds uridine bases to the 3′ end of RNAs such as miRNAs and mRNAs. The overall aim of this experiment was to identify differentially regulated mRNAs and miRNAs in catalytic knockouts of TUT4/7 relative to the wildtype. Catalytic mutants of TUT4/7 was generated in the prostate cancer cell line DU145 and the ovarian cancer cell line IGROV1. As the miRNA regulation by TUT4/7 depends on the oncoprotein LIN28A, LIN28A was lentivirally integrated in the LIN28A- DU145-derived lines and control. IGROV1 endogenously expresses LIN28A.  We report that excluding the let-7 family, miRNAs do not depend on LIN28A for TUT4/7-mediated regulation. As the entire miRNA is captured in a read, we provide the isomiR landscape in the presence and absence of TUT4/7. Loss of uridylated isomiRs results in a simultaneous gain in adenylated isomiRs. Finally, we report cell line specific miRNA-mRNA regulation.

overall_design: Identification differentially regulated genes and comparison of isomiR profiles in TUT4/7 catalytic knockouts and the wildtypes of DU145 and IGROV1 cell lines

first: Ragini

last: Medhi

middle: A

last: Miska


title: A MKP-MAPK protein phosphorylation cascade controls vascular disease resistance in plants

status: Public on Jul 01 2021

first: hui

last: lin

address: Shanghai fenfglinroad 300

institute: National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences,

summary: Vascular plant diseases, such as rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) and crucifer black rot caused by Xanthomonas campestris pv. campestris (Xcc), cause huge yield loss of crops worldwide. However, how plants operate vascular defense against these obligate pathogens remains elusive. In this study, we used both Arabidopsis and rice pathosystems to address the long-standing question.  We found that the loss of function mutation of Arabidopsis mitogen-activated protein kinase (MAPK) phosphatase 1 (MKP1) lost the non-host resistance to Xoo and supported Xoo to grow in the leaf veins, which also enhanced susceptibility to Xcc. MKP1 regulates the MPK3-mediated phosphorylation of the transcription factor MYB4 that functions in vascular lignification. Importantly, the MKP-MAPK cascade-mediated lignin biosynthesis is also conserved in rice through regulating OsMYB102 and OsMYB108, which control rice vascular resistance to adapted Xoo. Interestingly, the Arabidopsis and rice mutants enhanced resistance to the mesophyll cell pathogens most likely through upregulating salicylic acid biosynthesis, Pseudomonas syringae (P. syringae) and Xanthomonas oryzae pv. oryzicole (Xoc), respectively; strongly suggesting that this immune mechanism is likely specific to the obligate vascular pathogens. Therefore, our study uncovers a previously unrecognized vascular-specific and lignin-based immune mechanism, shedingshedding new sight on tissue-specific immunity in plants, as well as providing a practical approach for improvement of disease resistance against vascular pathogens in crops

overall_design: arabidopsis mRNA profiles of 4-week old wild type and mutant

first: Zuhua

last: He


title: Gene expression in the tomato trichome collected from af mutant and its complemented lines

city: East Lansing

first: koichi

last: Sugimoto

state: MI

address: 612 Wilson Rd

institute: Michigan State University

summary: We report the effect of chalcone isomerase deficiency on gene expression of glandular cells of type VI trichome in tomato leaves.

overall_design: Four independent sample collections from three genotypes.

first: Koichi

first: Gregg

last: Howe


title: Regulation of translation by site-specific ribosomal RNA methylation [RiboMeth-Seq]

status: Public on Aug 16 2021

city: Copenhagen

first: Anders

last: Lund

address: Ole Maaløes Vej 5

institute: University of Copenhagen,BRIC

summary: We report that 2’-O-methylation levels at subset of positions in human ribosomal RNA are variable between cell types and conditions, and that the degree of methylation at distinct sites is responsive to key cellular pathways. MYC overexpression results in increased methylation at a particular rRNA site (18S:C174). We find that this methylation is important for modulating translation of distinct mRNAs, leading to phenotypic changes including modulation of cell proliferation rate. Thus, differential rRNA 2’-O-methylation can give rise to ribosomes with specialized function.

overall_design: RiboMeth-seq (RMS) analysis of 11 indicated cell lines or conditions. 3 replicate RMS libraries were produced for each cell line. A distinct bar-coded sequencing adapter was used for each library replicate. Triplicate libraries for each cell line were sequenced on individual Ion Proton chips. A compressed fastq file for each replicate per cell line analysed are available here. Additionally the processed data for each cell line is provided.

first: Martin

middle: D

last: Jansson

first: Sophia

last: Hafner

first: Disa

last: Tehler

middle: H


title: Transcriptomic profiles of type I/III interferon-responsive hair follicle subsets from WT with or without Poly:IC injection

city: Bethesda

first: Keisuke

middle: Chris

last: Nagao

state: Maryland

address: 9000 Rockville Pike, Bldg 10, Rm12N240B

institute: National Institute of Arthritis and Musculoskeletal and Skin Diseases

summary: Inflammation triggered by viral infections can obscure tissue function. We utilized a model of systemic anti-viral immunity and found distinct type I IFN responses within the epidermal compartments.

overall_design: Transcriptomic changes in sorted upper hair follicle subsets, infundibulum (IFD) and isthmus (ISM) from WT mice without Poly:IC and WT mice 1 day after intraperitoneal poly(I:C) injection.

first: Keiko

last: Sakamoto


title: CASowary: CRISPR-cas13 guide RNA predictor for transcript depletion

status: Public on Jun 30 2021

first: Rajneesh

last: Srivastava

state: Pennsylvania

address: 450 Technology Dr

department: Surgery, University of Pittsburgh

institute: McGowan Institute for Regenerative Medicine

summary: Recent discovery of the gene editing system - CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins (Cas), has resulted in its widespread use for improved understanding of a variety of biological systems, by enabling large-scale perturbation of the genomes and transcriptomes. Cas13, a lesser studied Cas protein, has been repurposed to allow for efficient and precise editing of RNA molecules. The Cas13 system utilizes base complementarity between a crRNA/sgRNA (crispr RNA or single guide RNA) and a target RNA transcript, to preferentially bind to only the target transcript. Unlike targeting the upstream regulatory regions of protein coding genes on the genome, the transcriptome is significantly more redundant, leading to many transcripts having wide stretches of identical nucleotide sequences. Transcripts also exhibit complex three-dimensional structures and interact with an array of RBPs (RNA Binding Proteins), both of which further limit the scope of effective target sequences. As a result, there currently exists no method to predict whether a specific sgRNA will effectively knockdown a transcript. Here we present a novel machine learning and computational tool, to predict the efficacy of a sgRNA. We used publicly available RNA knockdown data from cas13 characterization experiments1 for 555 sgRNAs targeting the transcriptome in HEK293 cells, in conjunction with transcriptome-wide protein occupancy information on RNA2. Our model utilizes a Decision Tree architecture with a set of 112 sequence and target availability features, to classify sgRNA efficacy into one of four classes, based upon expected level of target transcript knockdown. After accounting for noise in the training data set, the noise-normalized accuracy exceeds 90%. Additionally, highly effective sgRNA predictions have been experimentally validated using an independent RNA targeting cas system – CIRTS3, confirming the robustness and reproducibility of our model’s sgRNA predictions. In particular, several highly efficient sgRNA’s designed using our model against SMARCA4 gene exhibited strong agreement with experimental data supporting a 10-fold decrease in expression. Utilizing transcriptome wide protein occupancy information, CASowary can predict high quality guides for different transcripts in a cell specific manner. Applications of CASowary to whole transcriptomes should enable rapid deployment of CRISPR/Cas13 systems, facilitating the development of therapeutic interventions linked with aberrations in RNA regulatory processes.

overall_design: To test the efficacy of CASowary in designing potential sgRNAs, we generated the protein occupied sites in HeLa cells by implementing Protein Occupancy Profile-Sequencing (POP-seq) with three variants- NPOP-seq (no crosslinking), UPOP-seq (UV-crosslinking) and FPOP-seq (Formaldehyde crosslinking) as described previously by Srivastava et al, Sci Rep 11, 1175 (2021).

first: Mansi

first: Alexander

last: Krohannon

first: Sarath Chandra

last: Janga


title: Pan-genomic study of primary human retinoblastoma samples

status: Public on Jul 06 2021

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

summary:
Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, as well as genomic profiling of primary retinoblastoma samples. The patients whose tumors were studied had received no treatment prior to surgical enucleation.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series: 118 samples distincts
Expression profiling by array (62 samples distincts, 66 files with replicates)
Genome variation profiling by SNP array (44 samples by SNP 370k, 22 samples by SNP 610k and 28 samples by Cytoscan)
Methylation profiling by genome tiling array (70 samples distincts, 74 files with replicates)
Genome variation profiling by genome tiling array (51 samples by BAC 3k and 26 samples by BAC 5k)


title: RNA-seq of erythroid cells  from 40 hours post fertilization ddx41 mutant and sibling zebrafish

city: Bronx

first: Teresa

last: Bowman

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead-box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development.

overall_design: mRNA profiling of gata1-positive erythroid cells isolated from 40 hours post fertilization ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Four sibling control samples and three mutant samples were sequenced.

middle: V


title: A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer

status: Public on Jul 18 2021

first: Chen

last: Yang

address: Xietu Road

institute: Shanghai Cancer Institute

summary: We first treated LX-2 cells with vehicle or HHT (1μM and 5μM) for 6 hours. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or HHT-treated LX-2 cells.  HHT-induced expression changes were obtained based on the resultant data.

overall_design: Examination of the transcriptome changes of LX2 cells treated with homoharringtonine (HHT)


title: Exploratory Single Cell RNA Sequencing: Murine Ciliary Body Transcriptome

status: Public on Jul 10 2021

city: St. Louis

first: Steven

last: Bassnett

state: MO

address: McMillan Building, 517 S Euclid Ave

institute: WUSTL Ophthalmology

summary: Single cell RNA-seq was performed on dissected murine ciliary body samples, and the resulted sequencing data was used to assess the various cell types present within the dissected tissue

overall_design: Exploration of 2 separate WT samples

first: Jacob

last: Youkilis


title: Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2

status: Public on Jul 21 2021

city: Cambridge

first: John

middle: G

last: Doench

state: MA

address: 75 Ames St.

department: Genetic Perturbation Platform

institute: Broad Institute

summary: Numerous rationally-designed and directed-evolution variants of SpCas9 have been reported to expand the utility of CRISPR technology. Here, we benchmark PAM preferences, on-target activity, and off-target susceptibility of 11 variants of SpCas9 in cell culture assays with thousands of guides targeting endogenous genes. To enhance the coverage and thus utility of base editing screens, we demonstrate that the SpCas9-NG and SpG variants are compatible with both A>G and C>T base editors, more than tripling the number of guides and assayable residues. We demonstrate the performance of these technologies by screening for loss-of-function mutations in BRCA1 and Venetoclax-resistant mutations of BCL2, identifying both known and new insights into these clinically-relevant genes. We anticipate that the tools and methodologies described here will facilitate the investigation of genetic variants at a finer and deeper resolution for any locus of interest.

sample_organism:
Homo sapiens
unidentified plasmid

platform_organism:
Homo sapiens
unidentified plasmid

overall_design:
BRCA1 tiling library:
Base editor (BE): CBE and ABE
Cas9 variants: WT, NG, SpG
Cell lines: HAP1, Meljuso
Reference: pDNA
Number of replicates: 2 or 3
BCL2 tiling library:
Base editor (BE): CBE and ABE
Cas9 variants: Cas9-NG
Cell lines: MOLM13
Reference: pDNA (for Dropout arm) and untreated arm (for Venetoclax arm)
Number of replicates: 3
High-fidelity (HF) variant off-target library:
Cas9 variants: WT, eCas9-1.1, HiFi Cas9
Cell line: A375
Number of replicates: 2
PAM-flexible variant off-target library:
Cas9 variants: SpG, NG
Cell line: A375
Number of replicates: 2
PAM-mapping library:
Cas9 variants: WT, Cas9-HF1, eCas9-1.1, evoCas9, HypaCas9, xCas9-3.7, Cas9-VQR, Cas9-VRER, Cas9-NG, SpG
Cell line: A375
Number of replicates: 2

first: Annabel

middle: K

last: Sangree

first: Audrey

last: Griffith

first: Zsofia

last: Szegletes

first: Priyanka

last: Roy

first: Peter

last: DeWeirdt

first: Mudra

last: Hegde

first: Abby

last: McGee

first: Ruth

middle: E

last: Hanna


title: MYOCD is required for cardiomyocytes induction from human urine cells and fibroblasts through remodeling chromatin

status: Public on Jun 29 2021

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

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

overall_design: Refer to individual Series


title: Global alternative splicing analysis of mutations in two new spliceosome components KIN17 and PRCC in C. elegans

city: Santa Cruz

first: Alan

last: Zahler

address: 1156 High St.

department: MCD Biology

institute: UC Santa Cruz

summary: Mutant alleles of KIN17 (dxbp-1) and PRCC (prcc-1) were identifed in a forward genetic screen for suppressors of cryptic splice site activation

overall_design: Strains with cryptic splicing suppressor alleles in dxbp-1 ((M107I) or (K23N)) or prcc-1 ((I371F) or (null)) along with NMD mutant allele smg-4(az152) were compared to strains carrying the smg-4 mutant allele alone to identify changes in native gene alternative splicing

first: Sol

last: Katzman

first: Jessie

last: Lopez


title: Gene expression analysis of three tumor organoids (GAN-WT, GAN-p53 and GAN-KP) derived from gastric tumor in K19-Wnt1/C2mE (GAN) mouse.

status: Public on Jun 15 2021

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

institute: Nihon University

summary: To develop a syngeneic mouse model of metastatic gastric cancer, we established the tumor organoids from gastric tumor arising in GAstric Neoplasia (GAN) mice (GAN-WT) which express Wnt1 and the PGE2 synthesis enzymes COX-2 and microsomal prostaglandin E synthase-1 (mPGES-1) in the stomach epithelium. Furthemore,  GAN-WT organoids were genetically manupilated into p53 knockout organoids (GAN-p53KO) and KrasG12V-expressing GAN-p53KO organoids (GAN-KP).

overall_design: At first, we established the tumor organoids from gastric tumor arising in GAstric Neoplasia (GAN) mice (GAN-WT) . Then,  we  knockedout Trp53 by CRISPR/CAS9 system in GAN-WT cells and generated p53 knockout organoids (GAN-p53KO). Finally, we lentivirally transduced mutant KrasG12V into GAN-p53KO cells and  established GAN-KP cells. Total RNAs were isolated from each organoids and subjected to cDNA microarray analysis in quadruplicate.

first: Juntaro

last: Yamasaki

first: Yuki

last: Hirata

first: Hideyuki

last: Saya

first: Osamu

last: Nagano


title: p53-mediated neurodegeneration in the absence of the nuclear protein Akirin2

status: Public on Jun 25 2021

city: Iowa City

first: Ethan

last: Bahl

state: IA

address: 25 S Grand Ave

institute: University of Iowa

summary:
Purpose: We investigated the molecular function of the nuclear protein, Akirin2 (Aki2), in postmitotic excitatory cortical neurons and neural progenitor cells of the embryonic dorsal telencephalon.
Method: We performed total RNA-Sequencing on the cortex of P35 CaMK-Cre;Aki2fl/fl mice and age matched controls.  We compared this transcriptomic database to one obtained through total RNA-Sequencing of  E10.5 Emx1-Cre;Aki2fl/fl dorsal telencephalon and age-matched controls .
Results: We discovered slow degeneration through necroptosis in the Aki2 postmitotic forebrain mutants and dysregulation of many p53 target genes in both transcriptomics datasets. Reduction of the p53 gene in the CaMK-Cre;Aki2fl/fl line delays cell death; while knockout prevents it entirely.
Conclusion: This study provides insight into the molecular mechanisms of Aki2 function in cortical neurons and identifies p53 as a molecular mediator of neuronal death in the absence of Aki2. Futhermore, it identifies several candidate Aki2-dependent genes dysregulated in both transcroptomic datasets and many candidate Aki2 target genes that are context dependent.

overall_design: cortical mRNA profiles of three P35 CaMK-Cre;Ak2fl/fl and four littermate control mice; dorsal telencephalon mRNA profile of four E10.5 Emx1-Cre;Aki2fl/fl and four littermate controls

first: Stacey

last: Peek

last: Bosch

first: Brianna

last: Iverson

first: Preeti

last: Bais

first: Mrutyunjaya

last: Parida

last: Manak

first: Jacob

last: Michaelson

first: Robert

last: Burgess

first: Joshua

last: Weiner


title: The transcriptome and genome-wide mapping of KANSL1 binding sites

status: Public on Jun 10 2021

first: Ting

last: Li

address: Taiping Road 27

institute: NCBA

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: RFX7-regulated transcriptome in U2OS

status: Public on Jun 17 2021

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: Identification of the RFX7-regulated transcriptome in Nutlin-3a and DMSO control treated U2OS cells

overall_design: RNA-seq (PolyA) from Nutlin-3a and DMSO control treated U2OS cells transfected with siControl or siRFX7

first: Konstantin

last: Riege

first: Steve

last: Hoffmann


title: KANSL1 ChIP-sequence analysis in HeLa cells

summary: We report the application of ChIP-sequence in HeLa cells. By obtaining over fifty million bases of sequence from chromatin immunoprecipitated DNA for each sample, we generated genome-wide chromatin-state maps of HeLa cells.

overall_design: Examination of KANSL1 target genes in HeLa cells.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kansl1-/- MEFs Transcriptomes

summary: We report the application of RNA-sequence in WT and Kansl1-deleted MEF cells with 3 biological replicates. We mapped over 42 million sequence reads per sample to the mouse genome (build mm10).

overall_design: mRNA profiles of WT and Kansl1-/- primary MEF cells


title: Alternative polyadenylation isoform abundance and stability of HEK293T cells

status: Public on May 31 2021

city: Philadelphia

first: Bin

last: Tian

address: 3601 Spruce Street

institute: the wistar institute

summary: mRNA isoform abundance and stability in HEK293T cells were examined by 4sU labeling and fractionation

overall_design: 3'READS libraries for analysis of alternative polyadenylation using total, 4sU labeled, and flow-through (FT) RNAs from HEK293T cells

first: Jihae

last: Shin


title: Identification of Pathological Transcription in Autosomal Dominant Polycystic Kidney Disease Epithelia

status: Public on Jul 15 2021

city: Freiburg

first: Sebastian

last: Friedrich

address: Hugstetter Str. 55

institute: University Hosptial Freiburg

summary:
Background: Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways.
Methods: Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways.
Results: Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways.
Conclusions: Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways.

overall_design: Transcriptomic profiling of mIMCD3 wild-type, Pkd1-/- and Pkd2-/- cells

first: Hannah

last: Müller

first: Caroline

last: Riesterer

last: Schüller

first: Katja

first: Carlotta

last: Wörner

first: Tilman

last: Busch

first: Amandine

last: Viau

first: E

last: Kühn

first: Michael

last: Köttgen

first: Alexis

last: Hofherr


title: Revisiting the Hayflick Limit: Insights from an Integrated Analysis of Changing Transcripts, Proteins, Metabolites, and Chromatin

status: Public on May 26 2021

city: Boston

first: David

last: Hendrickson

address: 725 Parsons

institute: Harvard

summary: Replicative senescence (RS) as a model has become the central focus of research into cellular aging in vitro. Despite decades of study, this process through which cells cease dividing is not fully understood in culture, and even much less so in vivo during development and with aging. Here, we revisit Hayflick’s original observation of RS in WI-38 human fetal lung fibroblasts equipped with a battery of high dimensional modern techniques and analytical methods to deeply profile the process of RS across each aspect of the central dogma and beyond. We applied and integrated RNA-seq, proteomics, metabolomics, and ATAC-seq to a high resolution RS time course. We found that the transcriptional changes that underlie RS manifest early, gradually increase, and correspond to a concomitant global increase in accessibility in nucleolar and lamin associated domains. During RS WI-38 fibroblast gene expression patterns acquire a striking resemblance to those of myofibroblasts in a process similar to the epithelial to mesenchymal transition (EMT). This observation is supported at the transcriptional, proteomic, and metabolomic levels of cellular biology. In addition, we provide evidence suggesting that t s conversion is regulated by the transcription factors YAP1/TEAD1 and the signaling molecule TGF-β

overall_design: WI-38 cells were grown and sampled during approach to replicative senescence for use in RNA-seq, scRNA-seq and ATAC-seq. Samples were matched with hTERT immortalized counterparts. Further controls for slowed growth (cell density) and DNA damage (radiation-RIS) were included for bulk RNA-seq.

first: Michelle

last: Chan


title: A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function with the Larp7 family member Pof8 in the biogenesis of telomerase

status: Public on May 22 2021

city: Mainz

first: Peter

last: Baumann

address: Ackermannweg 4

institute: Johannes Gutenberg University of Mainz

summary: We have identified two previously uncharacterized proteins involved in telomerase biogenesis. Both proteins are required for telomerase activity and telomere length maintenance. We named these proteins Thc1 (Telomerase Holoenzyme Component 1) and Bmc1 (Bin3/MePCE 1) based on structural and sequence similarities to the nuclear cap binding complex and the methyl phosphate capping enzyme (Bin3/MePCE) in metazoans, respectively. Thc1 and Bmc1 function together with Pof8 in recognizing telomerase RNA and promoting the recruitment of the Lsm2-8 complex and the catalytic subunit to assemble functional telomerase.

overall_design: Identification of undescribed fission yeast telomerase subunits by using Pof8, a telomerase constitutive member, as bait.

first: Diego

last: Páez-Moscoso

last: Ho

first: Katie

last: Hildebrand

first: Kristi

last: Jensen


title: DNA-loop extruding SMC complexes can traverse one another in vivo

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: Chromosome organization by structural maintenance of chromosomes (SMC) complexes is vital to living organisms. SMC complexes were recently found to be motors that extrude DNA loops. However, it remains unclear what happens when multiple complexes encounter one another in vivo on the same DNA and how interactions help organize an active genome. We created a crash-course track system to study SMC complex encounters in vivo by engineering the Bacillus subtilis chromosome to have defined SMC loading sites. Chromosome conformation capture (Hi-C) analyses of over 20 engineered strains show an amazing variety of never-before-seen chromosome folding patterns. Via 3D polymer simulations and theory, we find that these patterns require SMC complexes to bypass each other in vivo, as recently seen in an in vitro study. We posit that the bypassing activity enables SMC complexes to spatially organize a functional and busy genome.

overall_design: Hi-C and ChIP-seq experiments were performed on wild type and mutant cells of Bacillus subtilis PY79 growing in rich media.

first: X


title: SPAG9-JAK2 gene expression array in Ba/F3 cells

status: Public on May 18 2021

city: Kyoto

first: Azusa

last: Mayumi

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Pediatrics

institute: Kyoto Prefectural University of Medicine

summary: SPAG9-JAK2 is a novel fusion gene identified in a pediatric patient with Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL). In this study, we performed functional analysis of the SPAG9-JAK2 fusion to establish molecular targeted therapy. Ba/F3 cells expressing SPAG9-JAK2 generated by retroviral transduction (Ba/F3-SPAG9-JAK2), proliferated in the absence of IL-3, and exhibited constitutive phosphorylation of the tyrosine residues in the JAK2 kinase domain of the fusion protein and STAT3/STAT5. Mutation of tyrosine residues in the JAK2 kinase domain (SPAG9-JAK2 mut) abolished IL-3 independence, but had no influence on STAT3/STAT5 phosphorylation levels. Gene expression analysis revealed that Stat1 was significantly up-regulated in Ba/F3-SPAG9-JAK2 cells. STAT1 was also phosphorylated in Ba/F3-SPAG9-JAK2 but not SPAG9-JAK2 mut cells, suggesting that STAT1 is key for SPAG9-JAK2-mediated cell proliferation. Consistently, STAT1 induced expression of the anti-apoptotic proteins, BCL-2 and MCL-1, as did SPAG9-JAK2, but not SPAG9-JAK2 mut. Ruxolitinib abrogated Ba/F3-SPAG9-JAK2-mediated proliferation in vitro, but was insufficient in vivo. Venetoclax (a BCL-2 inhibitor) or AZD5991 (an MCL-1 inhibitor) enhanced the effects of ruxolitinib on Ba/F3-SPAG9-JAK2 in vitro. These findings suggest that activation of the JAK2-STAT1-BCL-2/MCL-1 axis contributes to SPAG9-JAK2-related aberrant growth promotion. BCL-2 or MCL-1 inhibition is a potential therapeutic option for B-ALL with SPAG9-JAK2 fusion.

overall_design: Ba/F3 cells were transduced with SPAG9-JAK2 fusion protein by the Retro-X Tet-On Advanced Inducible Expression System (Takara Bio), and Ba/F3 cells expressing SPAG9-JAK2 under doxycycline (DOX) dependent manner were established. To reveal which genes or pathways were affected by SPAG9-JAK2, Ba/F3 cells expressing SPAG9-JAK2 induced by DOX (Ba/F3-SPAG9-JAK2) or uninduced Ba/F3 cells (mock Ba/F3) were cultured in triplicate, and total RNA was extracted from Ba/F3-SPAG9-JAK2 or mock Ba/F3 48 hours later.

first: A

first: T

last: Tomii

last: Kanayama

last: Mikami

first: K

last: Tanaka

first: Y

last: Yoshida

first: I

last: Kato

first: M

last: Kawamura

last: Nakahata

first: J

last: Takita

first: H

last: Hosoi

last: Imamura


title: FK506 and Lactobacillus acidophilus Ameliorate Acute Graft-Versus-Host Disease by Modulating the T Helper 17/Regulatory T-Cell Balance

status: Public on May 11 2021

city: Seoul

first: Mi-La

last: Cho

address: 222,Banpo-daero, Seocho-gu

country: South Korea

institute: The Catholic University of Korea

summary: Graft-versus-host disease (GvHD) is critical complication after allogeneic hematopoietic stem cell transplantation (HSCT). The immunosuppressants given to patients undergoing allogeneic HSCT disturb the microbiome and the host immune system, potentially leading to dysbiosis and inflammation. The intestinal microbiome is a target for the development of novel therapies for GvHD. We determined the effect of the combination of tacrolimus (FK506) and Lactobacillus acidophilus on GvHD.

overall_design: mRNA expression profiles of the '12 wild type samples' by Illumina Hi-seq 2500.

first: Jin-ah

last: Baek


title: SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence

status: Public on May 20 2021

city: New York

first: Gregory

last: Brittingham

address: 435 East 30th street

department: Cell Biology

institute: NYU Institute for Systems Genetics

summary:
Purpose: It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH-sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in S. cerevisiae.
Methods: We performed RNA sequencing analysis to determine the extent of the requirement for theSNF5 QLC in the activation of glucose-repressed genes. Total RNA was extracted from WT, ΔQ-snf5 and HtoA-snf5 strains during exponentially growth (+Glu) and after 4 hours of glucose starvation. Next, Poly-A selection was performed using Dynabeads and libraries were performed following manufactures indications. Sequencing of the 32 samples was performed on an Illumina Hi-seq on two lanes. RNA-seq data were aligned to the University of California, Santa Cruz (UCSC), sacCer2 genome using Kallisto (0.43.0,http://www.nature.com/nbt/journal/v34/n5/full/nbt.3519.html) and downstream visualization and analysis was done using R (3.2.2). Differential gene expression analysis, heat maps and volcano plots were created using DESeq2 where a wald test was used to determine differentially expressed genes and Euclidean distance to calculate clustering for heat maps.
Conclusions: We found that pH changes and the SNF5 QLC are required for correct transcriptional reprogramming upon carbon starvation, but the dependencies are nuanced.

overall_design:
S.cerevisiae cells were grown in glucose or starvation conditions with the following genotypes: WT, delta-Q, HtoA-snf5 or starved at pH7.
Analysis scripts available: https://github.com/gbritt/Kallisto_DESeq2_Scripts_RNASeq_12.18.17

first: Liam

last: Holt

first: Juan

middle: I

last: Gutierrez


title: RFX7-regulated transcriptome in HCT116

first: Martin

last: Fischer

summary: Identification of the RFX7-regulated transcriptome in Nutlin-3a and DMSO control treated HCT116 cells

overall_design: RNA-seq (PolyA) from Nutlin-3a and DMSO control treated HCT116 cells transfected with siControl or siRFX7

first: Konstantin

last: Riege

first: Steve

last: Hoffmann


title: mRNA-seq analysis of RAGE knock-in (RageAHA/AHA) and RAGE-/- mice

city: Buffalo

first: Ding

last: Xu

address: 3435 Main St.

department: Oral Biology

institute: University at Buffalo

summary: Cell surface heparan sulfate (HS) plays an essential role in RAGE signaling by inducing RAGE oligomerization. To understand the physiological significance of HS-induced RAGE oligomerization in vivo, we generated RAGE knock-in mice (RageAHA/AHA) by introducing point mutations to specifically disrupt HS–RAGE interaction. The RAGE variant expressed by RageAHA/AHA mice demonstrated normal ligand-binding but greatly impaired capacity of HS-binding and oligomerization. To grasp the full scale of the alteration in gene expression caused by knocking out Rage, we performed a RNAseq analysis of mature neutrophils and lung from WT, RageAHA/AHA and Rage-/- mice. The overall number of differently regulated genes (DEGs) in Rage-/- neutrophils were almost 2.5 times higher than in RageAHA/AHA neutrophils (603 vs. 247). In contrast, the number of DEGs were much less in lungs compared to neutrophils in both strains (202 DEGs in Rage-/- lungs and merely 31 DEGs in RageAHA/AHA lungs),  however the difference between the two genotypes was even more dramatic in lungs (7-fold) than we observed in neutrophils (2.5-fold). By comparing transcriptomes of neutrophils and lung tissues from RageAHA/AHA and Rage-/- mice, we present clear evidence that complete deficiency of RAGE had much broader impact on global gene expression compared to point mutations of RAGE.

overall_design: PMN and lung mRNA profiles of  wild type (WT), RAGE knock-in (RageAHA/AHA) and RAGE-/- mice

first: Miaomiao

last: Li

first: Christophe

last: Langouët-Astrié


title: Anabolic Factors and Myokines Improve Differentiation of Human Embryonic Stem Cell Derived Skeletal Muscle Cells

city: Sydney

first: Travis

last: Ruan

address: Parramatta Road

country: Australia

institute: University of Sydney

summary: Skeletal muscle weakness is linked to many adverse health outcomes. Current research to identify new drugs has often been inconclusive due to lack of adequate cellular models. We have previously developed a scalable monolayer system to differentiate human embryonic stem cell (hESC) into mature skeletal muscle cells (SkMCs) within 26 days without cell sorting or genetic manipulation. Here, building on our previous work, we show that differentiation and fusion of myotubes can be further enhanced using the anabolic factors testosterone (T) and follistatin (F) in combination with a cocktail of myokines (C). Importantly, combined TFC treatment significantly enhanced both hESC-SkMC fusion index and expression of various skeletal muscle markers including the protein Myosin Heavy Chain (MyHC). Transcriptomic and proteomic analysis revealed oxidative phosphorylation as the most up-regulated pathway, suggesting energy metabolism is coupled to enhanced muscle differentiation. This cellular model will be a powerful tool for studying in vitro myogenesis and for drug discovery to further enhance muscle development or treat muscle diseases.

overall_design: Examination of hESC derived SkMC treated with anabolic factors and myokines

first: Dylan

last: Harney

first: Di

last: Xiao

first: Koay

last: Yen

first: Lipin

last: Loo

first: Mark

last: Larance

first: Pengyi

last: Yang

first: Leslie

last: Caron

first: Greg

last: Neely


title: Level of polyadenylated RNAs during regeneration of adult zebrafish brain

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

institute: Centre de recherche en transplantation et immunologie

summary: For its remarkable ability to heal injuries of the adult central nervous system, the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes, a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of mRNAs, their splice variants and regulatory long non-coding RNAs and their putative targets.

overall_design: RNA sequencing of injured and control adult zebrafish telencephalic hemisphere

last: Gourain

first: Olivier

last: Armant

first: Uwe

last: Straehle


title: MicroRNAs involved in regeneration of adult zebrafish brain.

summary: For its remarkable ability to heal injuries of the adult central nervous system, the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes, a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets.

overall_design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere


title: An integrated genomics approach towards deciphering human genome codes shaping HIV proviral transcription and fate

status: Public on May 05 2021

city: Dallas

first: Ivan

last: D'Orso

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

summary: HIV integrates semi-randomly into the genome of immune cells and thus proviruses that persist in patients under long-term, highly active suppressive therapy can be detected in various positions (inside and outside) and orientations (same, convergent and divergent) respective to genes, promoters, and enhancers. Thus, this integration landscape heterogeneity can influence HIV transcription activity thereby dictating proviral fate (active vs latent). However, the effect of the integration site to proviral transcription activity has so far remained elusive. Here we integrate open-source, large-scale datasets including epigenetics, transcriptome, and 3D genome architecture to interrogate the chromatin states, transcription activity landscape, nuclear sub-compartments, and topological associated domains around HIV integration sites in CD4+ T cell-based models to decipher ‘codes’ in the human genome shaping proviral transcription. As part of this integrated approach, here we collect nucleosome occupancy profiles in Jurkat CD4+ T cells.

overall_design: Nucleosome occupancy profiles in the Jurkat derivative J-Lat 10.6 T cell line.

last: D’Orso

first: Holly

last: Ruess


title: Reduced frequencies and functional impairment of dendritic cell subsets and non-classical monocytes in MDS

status: Public on May 01 2021

city: Utrecht

first: Nathalie

last: van Leeuwen-Kerkhoff

state: The Netherlands

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

summary: In myelodysplastic syndromes (MDS) the immune system is involved in pathogenesis as well as in disease progression. Dendritic cells (DC) are key players of the immune system by serving as regulators of immune responses. Their function has been scarcely studied in MDS and most of the reported studies didn’t investigate naturally occurring DC subsets. Therefore, we here examined the frequency and function of DC subsets and slan+ non-classical monocytes in various MDS risk groups. Frequencies of DC as well as of slan+ monocytes were decreased in MDS bone marrow (BM) compared to normal bone marrow (NBM) samples. Transcriptional profiling revealed down-regulation of transcripts related to pro-inflammatory pathways in MDS-derived cells as compared to NBM. Additionally, their capacity to induce T cell proliferation was impaired. Multidimensional mass cytometry showed that whereas healthy donor-derived slan+ monocytes supported Th1/Th17/Treg differentiation/expansion their MDS-derived counterparts also mediated substantial Th2 expansion. Our findings point to a role for an impaired ability of DC subsets to adequately respond to cellular stress and DNA damage in the immune escape and progression of MDS. As such, it paves the way toward potential novel immunotherapeutic interventions.

overall_design: Genome-wide transcriptional analysis of cDC2 and slan+ monocytes from healthy donor- and MDS-derived bone marrow.

first: Theresia

last: Westers

first: Pino

last: Poddighe

first: Giovanni

last: Povoleri

first: Jessica

last: Timms

first: Shahram

last: Kordasti

first: Tanja

last: de Gruijl

first: Arjan

last: van de Loosdrecht


title: Next Generation Sequencing Facilitates Quantitative Analysis of pancreatic tissue transcriptomes from KrasG12D;Pdx1-Cre and miR-301a-/-;KrasG12D;Pdx1-Cre mice treated with caerulein

status: Public on Jun 11 2021

city: Guangzhou

first: Xiaodong

last: Ma

state: Guangdong

address: Rm406,Building 29, South China Normal University

institute: South China Normal University

summary: Purpose: we used next generation sequencing to analyze gene expression profiles of pancreatic tissues from KrasG12D;Pdx1-Cre and miR-301a-/-;KrasG12D;Pdx1-Cre mice treated with caerulein. The goals of this study are to compare the different gene expression profiles of pancreatic tissue between KrasG12D;Pdx1-Cre and miR-301a-/-;KrasG12D;Pdx1-Cre mice treated with caerulein.

overall_design: KrasG12D;Pdx1-Cre and miR-301a-/-;KrasG12D;Pdx1-Cre mice were administered 8-hourly intraperitoneal injection of 50μg/kg caerulein. Mice were sacrificed at 7 days after the first caerulein injection and total RNA was extracted. mRNA profiles were generated by deep sequencing by using novaseq 6000 sequencing platform. The reads were mapped to the mouse reference genome (GRCm38) by STAR software (Version 2.5.1), annotation from GENCODE version vM21 was used. Differential gene expression was performed using DESeq2. qRT–PCR validation was performed using SYBR Green assays


title: High throughput RNA sequencing to identify genes up regulated by the transcription factor ATF-4

first: Jin

last: Meng

address: 1 Joslin Place

institute: Joslin Diabetes Center

summary: We report RNA sequencing (RNA-seq) data  WT, atf-4 loss-of-function mutants, and ATF-4 OE worms under non-stressed conditions. Three independent biological replicates were prepared for each sample, and worms were harvested at L4 stage.

overall_design: Examination of gene expression profiles in WT, atf-4 loss-of-function mutants, and ATF-4 OE C. elegans.

first: Collin

last: Ewald


title: Nuclear and cytoplasmic RNA exosomes and PELOTA limit miRNA-induced secondary siRNA production

status: Public on Apr 28 2021

city: København N

first: Peter

last: Brodersen

address: Ole Maaløes Vej 5

department: Department of Biology

institute: University of Copenhagen

summary: In this study, we aim at understanding which RNA degradation pathways are involved in keeping the secondary siRNA production in check in Arabidopsis thaliana. We have sequenced small RNAs from various T-DNA insertation single mutants and compared their capability of producing ectopic secondary siRNAs from endogenous miRNA targets. The mutants used in the work stem from three library pools from three different experiments. Libraries from all three experiments are submitted together here. The experiments can be distinguished by their title and their tag:experiment. There is a matrix of normalized reads from each pool of library as well called normalizedExp1.txt, normalizedExp2.txt and normalizedExp3.txt

overall_design: Libraries Exp.1: small RNA seq data from three mutant lines (ski2-5, ski3-5, cer7-3) and a wild type line. All lines are ecotype Col-0. There are technical replicates of each sample. Libraries in Exp.2: small RNA seq data from 6 mutant lines (ski2-5, pel1-1, pel1-2, hen2-5, rrp4, rrp45a) and a wild type line. All lines are ecotype Col-0. There are three biological triplicates of each sample except for pel1-1 that does not have a replicate. Libraries in Exp.3: small RNA seq data from three mutant lines (ski2-5, hen2-4, sop1-5) and a wild type line. All lines are ecotype Col-0. There are biological triplicates of each sample.

first: Maria

last: Vigh

first: Axel

last: Thieffry

first: Laura

last: Arribas-Hernandéz


title: Age-dependent modulation the microvasculature by human microenvironment and serum

status: Public on May 19 2021

city: San Diego

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: The functional decline of the vascular niches is linked to several disorders, including neurodegeneration and bone loss. However, the causes of this decline are poorly understood. A key signature of aging is the progressive damage of the microvasculature, but a clear picture of its determinants and therapeutic targets in a human context is lacking. We designed/validated a novel approach based on long-living human microvascular networks to study the age-dependent modulation of the endothelium by microenvironment and serum. Young fibroblasts restored the barrier function of aged endothelial cells, an effect counteracted by old serum. Among the involved factors, ANGPTL4 played a key role in restoring cell-cell junctions and vascular barrier. Once validated, we employed this strategy to identify potential targets involved in the degeneration of the Blood Brain Barrier (BBB) in Alzheimer Disease (AD) patients. Using serum from AD as well as from age-matched healthy donors, we demonstrated that PTP4A3 played a critical role in the regulation of vascular permeability and that its inhibition restored the functionality of the BBB exposed to serum from AD patients. We believe our strategy will be an invaluable tool to identify and therapeutically modulate the aging signature of the endothelium in the context of age-related diseases.

overall_design: Human skin endothelial cells were co-cultured with human fibroblasts from young or old donors. Human skin endothelial cells were also co-cultured with human fibroblasts from young donors and incubated with medium containing human serum from young or old donors. Human brain endothelial cells were co-cultured with human brain pericytes and astrocytes and incubated with serum from AD patients or age-matched healthy donors. Global gene expression changes were measured by mRNA-Seq in a paired design.

first: Simone

last: Bersini

first: Rafael

last: Arrojo Drigo

first: Martin

last: Hetzer

first: Maxim

last: Shokhirev

first: Ling

last: Huang


title: Effects of karrikins and the strigolactone analogue GR24 on the transcriptome of Brachypodium distachyon seedlings

status: Public on May 07 2021

city: CRAWLEY

first: Mark

last: Waters

state: WA

address: 35 Stirling Hwy

department: School of Molecular Sciences

institute: The University of Western Australia

summary: Objective: to compare and contrast the effects of exogenous application of karrikins KAR1 and KAR2, and the strigolatone analogue rac-GR24, on gene expression in shoot tissue of seedlings of Brachpodium distachyon (false brome). The experiment compared the effects on three genotypes: wild type Bd21-3, and two mutant alleles for the Brachypodium orthoologue of the karrikin receptor KARRIKIN INSENSITIVE2 (KAI2; Bradi1g15880.1). These alleles were designated Bdkai2-1 and Bdkai2-2.

overall_design: Four treatments (mock, 1 µM KAR1, 1 µM KAR2, 10 µM rac-GR24) were applied to three genotypes (WT Bd21-3, Bdkai2-1, Bdkai2-2) in triplicate, for a total of 36 samples. Three-day-old seedlings were transferred to liquid growth medium in 250 mL conical flasks for 24 hours, and then treated by addition of 1:1000 dilution of acetone (mock), 1 mM KAR1, 1 mM KAR2 or 10 mM rac-GR24 (all dissolved in acetone). Shoot material was collected after four hours of treatment and frozen in liquid nitrogen prior to extraction of total RNA.

middle: T

first: Vilmos

last: Soos

first: Norbert

last: Incze


title: Transcriptional profiling of Schizosaccharomyces pombe cells after deletion and overexpression of transcription factor Atf1 and Pcr1

status: Public on Jun 03 2021

city: Kolkata

first: Geetanjali

last: Sundaram

address: 35 Ballugunje circular road

country: India

institute: University of Calcutta

summary: The leads obtained in our analysis indicates how Atf1-Pcr1 can regulate the differential gene expression

overall_design: Differential gene expression studies were carried out following over-expression experiments  in a series of S. pombe  transformants. Here we conducted an analysis to put forth the altered gene expression pattern in conditions where certain genes were over-expressed in presence or absence of another gene(s), as compared to physiological conditions.

first: S

last: Basu

first: P

last: Sarkar

first: G


title: RNA-seq data for: Reduced ech-6 Expression Attenuates Fat-induced Premature Aging in C. elegans

status: Public on Apr 30 2021

city: Lausanne

first: Yasmine

last: Liu

address: Station 19 CH-1015 Lausanne

department: Laboratory of intergrative systems physiology

country: Switzerland

institute: EPFL

summary: Deregulated energy homeostasis represents a hallmark of aging and results from complex gene-by-environment interactions. Here, we discovered that reducing the expression of the gene ech-6 encoding enoyl-CoA hydratase remitted fat diet-induced deleterious effects on lifespan in Caenorhabditis elegans, while a basal expression of ech-6 was important to survival under normal dietary conditions. Lipidomics revealed that supplementation of fat in ech-6-silenced worms had marginal effects on lipid profiles, suggesting an alternative fat utilization for energy production. Transcriptomics further suggest a causal relation between the lysosomal pathway, energy production, and the longevity effect conferred by the interaction between ech-6 and high-fat diets. Indeed, enhancing energy production from endogenous fat by overexpressing lysosomal lipase lipl-4 recapitulated the lifespan effects of high-fat diets on ech-6-silenced worms. Collectively, these results reveal that the gene ech-6 modulates metabolic flexibility and may be a target for promoting metabolic health and longevity.

overall_design: In total 16 C. elegans samples were sequenced. Worm samples consisted of total RNA of whole worms, perfomed in quadruplicate for treatment (ech-6 RNAi) and P-80 supplementation.

first: Arwen

last: Gao

first: Reuben

middle: L

last: Smith


title: Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq

status: Public on Apr 19 2021

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

institute: University of Colorado Anschutz Medical Campus

summary: We have developed Halo-seq, an RNA proximity labeling method that allows the quantification of subcellular transcriptomes. We have demonstrated the efficacy of Halo-seq here by using it to quantify chromatin-proximal, nucleolar, and cytoplasmic transcriptomes. In Halo-seq, RNA molecules in close proximity to a spatially restricted protein are specifically marked and biotinylated, facilitating their separation from bulk cellular RNA and their quantification.

overall_design: Input and streptavidin-pulldown RNA samples from several Halo-seq experiments.

first: Robert

last: Spitale


title: New roles for Hoxc8 in the establishment and maintenance of motor neuron identity

first: Catarina

last: Catela

state: Illinois

address: Abbott Hall 402,

department: Neurobiology

institute: University of Chicago

summary: Comparison of the transcriptome of embryonic day 12 motor neurons and postnatal day 8 motor neurons. Comparison of the transcriptome of motor neurons without Hoxc8 protein and control littermates. Comparison of the transcriptome of postnatal day 8 motor neurons from the brachial, thoracic and lumbar regions of the spinal cord.

overall_design: RNA sequencing of motor neurons at different developmental stages, in different topographical regions of the spinal cord as well as RNA sequencing of embryonic motor neurons lacking Hoxc8 protein.

first: Paschalis

last: Kratsios

first: Yifei

last: Weng

first: Jihad

last: Aburas

first: Xiaoxi

last: Zhuang

first: Kailong

last: Wen


title: The transcriptomic profile of monocytes from patients with Sjögren’s Syndrome is associated with inflammatory parameters and is mimicked by circulating mediators

first: Ana

middle: Pinheiro

last: Lopes

state: Utrecht

address: Heidelberglaan 100

institute: University Medical Center Utrecht

summary: Primary Sjögren’s syndrome (pSS) is a systemic autoimmune disease characterized by infiltration of the exocrine glands and prominent B cell hyperactivity. Considering the key role of monocytes in promoting B cell hyperactivity, we performed RNA-sequencing analysis of CD14+ monocytes from patients with pSS, non-Sjögren’s sicca (nSS), and healthy controls (HC). We demonstrated that the transcriptomic profile of pSS patients is enriched in intermediate and non-classical monocyte profiles, and confirmed the increased frequency of non-classical monocytes in pSS patients by flow-cytometry analysis. Weighted gene co-expression network analysis identified four molecular signatures in monocytes from pSS patients, functionally annotated for processes related with translation, IFN-signaling, and toll like receptor signaling. Systemic and local inflammatory features significantly correlated with the expression of these signatures. Furthermore, genes highly associated with clinical features in pSS were identified as hub-genes for each signature. Unsupervised hierarchical cluster analysis of the hub-genes identified four clusters of nSS and pSS patients, each with distinct inflammatory and transcriptomic profiles. One cluster showed a significantly higher percentage of pSS patients with higher prevalence of anti-SSA autoantibodies, interferon score, and erythrocyte sedimentation rate compared to the other clusters. Finally, we showed that the identified transcriptomic differences in pSS monocytes were induced in monocytes of healthy controls by exposure to serum of pSS patients. Representative hub-genes of all four signatures were partially inhibited by interferon-a/b receptor blockade, indicating that the circulating inflammatory mediators, including type I interferons have a significant contribution to the altered transcriptional profile of pSS-monocytes. Our study suggests that targeting key circulating inflammatory mediators, such as type I interferons, could offer new insights into the important pathways and mechanisms driving pSS, and holds promise for halting immunopathology in Sjögren’s Syndrome.

overall_design: RNA-sequencing of pheripheral blood isolated CD14+ monocytes from patients with primary Sjögren’s syndrome (pSS; n=14) , non-Sjögren’s sicca (nSS; n=8), and healthy controls (HC; n=14).

first: A

middle: P

first: C

last: Bekker

first: M

last: Hillen

middle: C

last: Hinrichs

last: Pandit

last: Kruize

first: T

last: Radstake

first: J

last: van Roon


title: A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription

status: Public on Apr 20 2021

city: Chengdu

first: jin

last: long

address: Hui ming

institute: Sichuan Agricultural University

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

sample_organism:
Gallus gallus
Macaca mulatta
Homo sapiens
Canis lupus familiaris
Felis catus
Sus scrofa
Ovis aries
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus
Cavia porcellus

overall_design: Refer to individual Series


title: Differential gene expression between the uL22 K90D mutant variant and wild type uL22 containing cells

status: Public on Apr 06 2021

city: Huntsville

first: Luis

middle: Rogelio

last: Cruz

state: Alabama

address: 301 Sparkman Drive

department: Biological Sciences

institute: University of Alabama in HUntsville

summary: We show that a single change in uL22 in the ribosomal exit tunnel can have a profound impact on gene expression, suggesting further investigation given that changes in the K90 have been clinically isolated and linked to antibiotic resistance in several species.

overall_design: Examination of differential gene expression between a r-protein uL22 mutant and wild type E. coli.

middle: R

last: Cruz-Vera

first: Elizabeth

last: Franklin


title: Transcriptome analysis of normal control and miR-412-3p overexpressing in 786-0 cells

status: Public on May 25 2021

city: Jinhua

first: Weiqiang

last: Lin

state: Zhejiang

address: Shangcheng street N1

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

summary: To explore the signaling network involving circDVL1, miR-412-3p, and its targets in ccRCC, we used RNA sequencing (RNA-seq) to identify potential miR-412-3p target genes in miR-412-3p overexpressing and control cells. RNA-seq data identified 392 mRNAs that were downregulated in miR-412-3p overexpressing 786-O cells

overall_design: Transcriptome level expression profile of circRNAs in 2 different ccRCC serum samples


title: Selective Inhibitors of mTORC1 Activate 4EBP1 and Suppress Tumor Growth

status: Public on Apr 05 2021

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: The clinical benefit of current mTOR inhibitors is limited, perhaps reflecting their intrinsic pharmacological profiles. Rapamycin analogs selectively inhibit mTORC1, but fail to suppress phosphorylation of the mTORC1 substrate 4EBP1, a translational repressor that is a key driver of oncogenic mTORC1 signaling. mTOR kinase active-site inhibitors fully suppress mTORC1 and phosphorylation of its substrates, but are active against mTORC2 and additional kinases, potentially contributing to tolerability limitations. The prototype bi-steric inhibitor RapaLink-1 exploits the selective mTORC1 interactions of rapamycin and the broad mTOR kinase inhibitory effects of an active-site inhibitor, through covalent linkage of the two pharmacophores to achieve complete mTORC1/2 inhibition. We demonstrate that the anti-proliferative activity of RapaLink-1 is dependent upon mTORC1 and suppression of 4EBP1 phosphorylation. Using a rational design strategy, we tuned the affinities of the rapamycin core and ATP-mimetic moieties to create novel bi-steric inhibitors with enhanced mTORC1 selectivity and potency against 4EBP1 phosphorylation. mTORC1-selective bi-steric compounds produced durable inhibition of 4EBP1 phosphorylation in vitro and in vivo, and drove tumor regressions at well-tolerated doses in xenograft models of breast cancer.

overall_design: 4 biological replicates of MCF7 cells under one of the following conditions: Starvation, Full serum + DMSO, Full serum + MLN0128, Full serum + RMC-4627, Full serum + RMC-4745. RMC-4627 and RMC-4745 are selective inhibitors of mTORC1 developed within this study. For one of the biological replicate (replicate 1), we provided 2 technical replicates (1A and 1B)

first: Hui

last: Liu

first: Julie

last: Lorent


title: Single-cell transciptionnal landscape of SF3B1 mutated MDS

status: Public on Apr 26 2021

city: Paris

first: Olivier

last: Kosmider

state: Ile de france

address: 22 rue Méchain

department: Reproduction and cancer

institute: Institut Cochin

summary: To characterize early human hematopoiesis in SF3B1 mutated myelodysplastic syndroms, we performed Single-cell RNA-seq on CD34+ HSPC bone marrow cells.

overall_design: Single-cell RNA-seq of human bone marrow CD34+ cells from SF3B1 mutated MDS and age matched controls

first: Charles

last: Dussiau


title: T3-Dependent Transcriptional Programming by TR-beta Requires SWI/SNF Chromatin Remodelers (RNA-Seq)

status: Public on Apr 01 2021

city: Minneapolis

first: Noelle

last: Gillis

state: Minnesota

address: 2231 6th ST SE, CCRB

institute: University of Minnesota

summary: We used an integrated genomics approach to profile and characterize the cistrome of TR-beta, map changes in chromatin accessibility, and capture the transcriptomic changes in response to T3 in a normal thyroid cell line. Our data demonstrates that T3 promotes significant shifts in TR-beta genomic occupancy, which are associated with differential chromatin accessibility, and differential recruitment of SWI/SNF chromatin remodelers.

overall_design: Epigenetic and transcriptomic anlaysis a of thyroid hormone receptor beta binding and regulation of chormatin accessibility in normal thyroid cells in the presence and absence of thyroid hormone.

first: Seth

last: Frietze

first: Frances

last: Carr