title: Comparative transcriptomic experiment of Amycolatopsis japonica in order to investigate EDDS production changes

city: Tuebingen

first: Mehmet

middle: Direnc

last: Mungan

address: Auf der Morgenstelle, 28

institute: University of Tuebingen

summary: Here we report the effect of two comparative transcriptomics experiments effect on EDDS producing biosynthetic gene cluster. The goals of this study are to compare RNA sequencing derived transcriptomes of Amycolatopsis japonica at 24 hours in zinc treated and control culture conditions in combination with control and zur regulator deleted strains, in order to target other genes for the overexpression of EDDS cluster.

overall_design: RNA-Sequencing has been conducted at 24th hour of Amycolatopsis Japonica using Illumina NextSeq 500 System. In the first experiment two conditions were: zinc treated cultures wild type versus zur knockout strain. In the second experiment two conditions were: zur knockout strains vs control strains in normal culture conditions. Both experiments are conducted in triplicates. Corresponding fastq files trimmed by fastp, mapped by Hisat2 and the BAM files were generated via samtools. Read count per gene is summarized by featureCounts and differentially expressed genes were generated by DESeq2 package.

first: Simone

last: Edenhart


title: Functional genomic and transcriptomic analysis of ptychodera and the origin of vertebrate genomic traits

status: Public on Feb 26 2022

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

type: Expression profiling by high throughput sequencing

summary: Signaling pathways control a large number of gene regulatory networks (GRNs) during animal development, acting as major tools for body plan formation [Pires-daSilva & Sommer, Nat. Rev. Genet. 4, 39-49 (2003)]. Remarkably, in contrast to the large number of transcription factors present in animal genomes, only a few of these pathways operate during development [Sanz-Ezquerro, Münsterberg & Stricker, Front. Cell Dev. Biol. 5, 76 (2017)]. Moreover, most of them have been largely conserved during metazoan evolution [Babonis & Martindale, Philos. Trans. R. Soc. B 372, 20150477 (2017)]. How evolution has generated a vast diversity of animal morphologies with such a limited number of tools is still largely unknown. Here, we show that gain of interconnectivity between signaling pathways, and the GRNs they control, may have critically contributed to the origin of vertebrates. We perturbed the retinoic acid, Wnt, FGF and Nodal signaling pathways during gastrulation in the invertebrate chordate amphioxus and zebrafish and compared the effects on gene expression and cis-regulatory elements (CREs). We found that multiple developmental genes gain response to these pathways through vertebrate-specific CREs. Moreover, in contrast to amphioxus, many of these CREs responded to multiple pathways in zebrafish, which reflects their high interconnectivity. Furthermore, we found that vertebrate-specific cell types are more enriched in highly interconnected genes than tissues with more ancient origin. Thus, the increase of CREs in vertebrates integrating inputs from different signaling pathways probably contributed to gene expression complexity and to the formation of new cell types and morphological novelties in this lineage.

sample_organism:
Xenopus tropicalis
Ptychodera flava

platform_organism:
Xenopus tropicalis
Ptychodera flava

overall_design:
RNA-seq and ATAC-seq for different treatments that stimulate/inhibits signaling pathways in zebrafish, xenopus tropicalis, amphioxus and ptychodera flava during embryonic development
This submission corresponds to RNA-seq component of Ptychodera flava and Xenopus tropicalis data.

first: Martin

last: Franke

first: Alberto

last: Pérez-Posada

first: Che-Yi

last: Lin

first: Cindy

last: Chou

first: Yi-Hsien

last: Su

first: Jr-Kai

last: Yu


title: RNAseq analysis of adipose tissue transcriptomes from wild-type and FNIP1 adipocyte specific knockout (FNIP1-AKO) mice

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

country: China

institute: Nanjing University

summary: Activation of thermogenesis in brown and beige adipocytes upon activation by external stimuli burns fuel energy as heat. Owing to its remarkable benefits on metabolic health and its demonstrated presence in adult humans, beige adipocytes holds great promise to combat obesity and metabolic diseases. Folliculin interacting protein 1 (FNIP1) is an adaptor protein originally identified through its interaction with folliculin (FLCN) and AMPK. To investigate the physiological role of FNIP1 in adipose tissue in vivo, we generated adipocyte-specific FNIP1 deficient mice (referred to as FNIP1-AKO) by crossing mice bearing a conditional Fnip1 allele with introns 5 and 6 floxed (Fnip1 lox/lox) with the adiponectin promoter–driven Cre mice. We performed transcriptome analysis by whole-genome gene expression profiling experiments in inguinal white adipose tissue (iWAT) from both wild-type (WT) and FNIP1-AKO mice. We were particularly interested in the subset of genes that were up-regulated in the FNIP1-AKO mice. Gene ontology (GO) analysis revealed that the primary up-regulated genes were mitochondrial and lipid metabolism-related genes. Gene expression validation studies demonstrated that a broad array of genes involved in thermogenic and mitochondrial oxidative program was induced in FNIP1-AKO iWAT. Together, the transcriptional profiling results indicate that loss of FNIP1 activate thermogenic program in white adipocytes.

overall_design: Inguinal white adipose tissue mRNA profiles of 8-week-old WT and FNIP1-AKO mice were generated by deep sequencing, in duplicate, using Illumina HiSeq 4000.

first: Yujing

last: Yin


title: Pooled CRISPR/Cas9 screen for genes that contribute to ribosome biogenesis and turnover

city: Dallas

first: Michael

last: Buszczak

state: Texas

address: 5323 Harry Hines Boulevard

department: Molecular Biology

country: USA

institute: University of Texas Southwestern Medical Center

summary: While features of ribosome assembly are shared between species, our understanding of the diversity, complexity, dynamics, and regulation of ribosome production in multicellular organisms remains incomplete. To gain insights into ribosome biogenesis in human cells, we performed a genome wide loss of function screen combined with differential labeling of pre-existing and newly assembled ribosomes. These efforts identified two functionally uncharacterized genes, C1ORF09 and SPATA5. We provide evidence that these factors, together with CINP and SPATA5L1, control a late step of human pre-60S maturation in the cytoplasm. Loss of either C1ORF109 or SPATA5 impairs global protein synthesis. These results link ribosome assembly with neurodevelopmental disorders associated with recessive SPATA5 mutations. Based on these findings, we propose the expanded repertoire of ribosome biogenesis factors likely enables multicellular organisms to coordinate multiple steps of ribosome production in response to different developmental and environmental stimuli.

overall_design: A genome-scale CRISPR/Cas9-mediated loss of function screen for ribosome biogenesis/turnover factors was performed in HEK293T cells with endogenous RPL28-SNAP tagging. The pre-existing and newly produced ribosomes were differentially labeled with red and green fluorescence for FACS enrichment.

first: Chunyang

last: Ni

first: Jeon

last: Lee


title: Gain of gene regulatory network interconnectivity at the origin of vertebrates [RNA-seq]

summary: Signaling pathways control a large number of gene regulatory networks (GRNs) during animal development, acting as major tools for body plan formation. Remarkably, in contrast to the large number of transcription factors present in animal genomes, only a few of these pathways operate during development. Moreover, most of them are largely conserved along metazoan evolution. How evolution has generated a vast diversity of animal morphologies with such a limited number of tools is still largely unknown. Here we show that gain of interconnectivity between signaling pathways, and the GRNs they control, may have played a critical contribution to the origin of vertebrates. We perturbed the retinoic acid, Wnt, FGF and Nodal signaling pathways during gastrulation in amphioxus and zebrafish and comparatively examined its effects in gene expression and cis-regulatory elements (CREs). We found that multiple developmental genes gain response to these pathways through novel CREs in the vertebrate lineage. Moreover, in contrast to amphioxus, many of these CREs are highly interconnected and respond to multiple pathways in zebrafish. Furthermore, we found that vertebrate-specific cell types are more enriched in highly interconnected genes than those tissues with more ancestral origin. Thus, the increase of CREs in vertebrates integrating inputs from different signaling pathways probably contributed to gene expression complexity and the formation of new cell types and morphological novelties in this lineage.

sample_organism:
Branchiostoma lanceolatum
Danio rerio

platform_organism:
Branchiostoma lanceolatum
Danio rerio

overall_design: RNA-seq experiments in zebrafish and amphioxus embryos after modifying different signaling pathways

first: Alejandro

last: Gil-Gálvez

first: Sandra

last: Jiménez-Gancedo

first: Rafael

middle: D

last: Acemel

first: Stephanie

last: Bertrand

last: Schubert

first: Héctor

last: Escrivá

middle: J

first: José

middle: L

last: Gómez-Skarmeta


title: A single-cell liver atlas of relapsing human malaria

status: Public on Feb 25 2022

city: Paris

first: Liliana

last: Mancio-Silva

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

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

sample_organism:
Plasmodium vivax
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gain of gene regulatory network interconnectivity at the origin of vertebrates

first: Juan

last: Tena

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Branchiostoma lanceolatum
Danio rerio
Xenopus tropicalis
Ptychodera flava


title: A single-cell liver atlas of relapsing human malaria [Bulk-seq]

summary: Malaria-causing Plasmodium vivax parasites can linger in the human liver for weeks to years, and then reactivate to cause recurrent blood-stage infection. While an important target for malaria eradication, little is known about the molecular features of the replicative and non-replicative states of intracellular P. vivax parasites, or their human host-cell dependencies and the host responses to them. Here, we leverage a bioengineered human microliver platform to culture patient-derived P. vivax parasites in primary human hepatocytes and conduct transcriptional profiling. By coupling enrichment strategies with bulk and single-cell analyses, we captured both parasite and host transcripts in individual hepatocytes throughout the infection course. We define host- and state-dependent transcriptional signatures and identify previously unappreciated populations of replicative and non-replicative parasites, sharing features with sexual transmissive forms. We find that infection suppresses transcription of key hepatocyte function genes, and that P. vivax elicits an innate immune response that can be manipulated to control infection. Our work provides an extendible framework and resource for understanding host-parasite interactions and reveals new insights into the biology of P. vivax dormancy and transmission.

overall_design: Time-course bulk RNA-Seq of Plasmodium vivax-infected human hepatocytes over 11 days, in the presence or absence of a Pi4K inhibitor

last: Gural

first: Sangeeta

middle: N

last: Bhatia


title: VIVA1: A more Invasive Subclone of MDA-MB-134VI Invasive Lobular Carcinoma Cells With Increased Metastatic Potential in Xenograft Models

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

summary: Invasive Lobular Carcinoma (ILC) is the second most common type of breast cancer next to invasive ductal carcinoma (IDC). Few research tools exist to study ILC metastasis in vivo, with only one cell line reported to grow in xenograft models.  We thus set out to isolate and characterize ILC cells with increased invasive properties and establish a xenograft model that spontaneously metastasized from the orthotopic site.  MDA-MB-134VI ILC cells were placed in Matrigel transwells for 7-days. Migrated cells were isolated and expanded to create the VIVA1 cell line. VIVA1 cells were tested in vitro for ILC marker expression and relative proliferative and invasive ability compared to parental MDA-MB-134VI cells. An intraductally injected orthotopic xenograft model was used to assess primary and metastatic tumor growth in vivo. Similar to MDA-MB-134VI, VIVA1 cells retained expression of ER and lacked expression of E-cadherin, however showed increased invasion in vitro. Following intraductal injection, VIVA1 and MDA-MB-134VI cells had similar primary tumor growth similar survival kinetics. However, macrometastases were apparent in 6/10 animals at clinical endpoint in VIVA1 injected animals. RNA-seq analysis showed gene expression changes consistent with differences in cell migration and survival. Cells from the primary orthotopic tumor (VIVA-LIG43) were isolated and re-injected intraductally, which led to tumor growth in the mammary glands with a more rapid onset than the parental VIVA1 cells.

overall_design: polyA mRNA sequencing of 134VI and VIVA (n=2) cell lines

middle: P

first: Christina

last: Addison


title: Gain of gene regulatory network interconnectivity at the origin of vertebrates [ATAC-seq]

overall_design: ATAC-seq experiments in zebrafish and amphioxus embryos after modifying different signaling pathways


title: A single-cell liver atlas of relapsing human malaria [scRNA-seq]

platform_organism:
Plasmodium vivax
Homo sapiens
Mus musculus

overall_design: Time-course single-cell RNA-Seq of Plasmodium vivax-infected human hepatocytes over 14 days, in the presence or absence of a Pi4K inhibitor

first: Marc

last: Wadsworth II

first: Alex

middle: K

last: Shalek


title: Genome-wide repair maps of nucleotide excision repair in Drosophila and S2 cells.

city: Chapel Hill

first: Aziz

last: Sancar

state: NC

address: 120 Mason Farm Rd. CB#7260

institute: University of North Carolina at Chapel Hill

summary: We report the application of single-molecule-based sequencing technology (XR-seq) for high-throughput profiling of nucleotide excision repair in Drosophila four developmental stages and S2 cells. By obtaining over six billion bases of sequence from UV and cisplatin damage antibodies immunoprecipitated excision DNA, we generated genome-wide nucleotide excision repair  maps of Drosophila Embryo, Larva, Pupa , two gender of adults and S2 cells . We find that Drosophila performs transcription-coupled repair (TCR) at all its developmental stages. S2 cell carry out TCR response to both UV and Cisplatin damage. Finally, we show that XPC repair factor is required for both global and transcription-coupled repair in Drosophila. This study provides the mechanism of nucleotide excision repair of Drosophila in vivo and vitro response to UV and Cisplatin damage.

overall_design: Examination of TCR in all Drosophila whole life cycle and gender abd the function of XPC repair factor.

first: Zhenxing

last: Liu

first: Nazli

last: Deger

first: Xuemei

last: Cao

first: Christopher

last: Selby

first: Saygin

last: Gulec

first: Hiroaki

last: Kawara

first: Evan

middle: B

last: Dewey

first: Li

last: Wang

first: Yanyan

last: Yang

first: Sierra

last: Archibald

first: Ogun

last: Adebali

first: Jeff

last: Sekelsky


title: Whole hippocampus RNA seq on (SCDi Cayman 10566) and Vehicle (DMSO) in 10 month old WT and 3xTg-AD mice

city: Villejuif

first: Gaël

last: Moquin-Beaudry

address: 114, rue Édouard-Vaillant

institute: Gustave Roussy

summary: RNA was extracted from microdissected hippocampi from 10-month old DMSO or SCDi (Cayman 10566) ICV treated WT or 3xTg-AD mice.

overall_design: 28 day ICV infusion of DMSO or SCDi (Cayman 10566)

first: Laura

last: Hamilton

first: Karl

last: LFernandes


title: SCD inhibition reverses immune, synaptic and behavioral deficits in an animal model of Alzheimer’s disease [scRNA-Seq]

summary: Early- and late-onset forms of Alzheimer’s disease (AD) share common features that include abnormalities in lipid metabolism, immune response and synaptic function. Of these, the role of lipids remains the least understood. Our study revealed that molecular functions related to Stearoyl-CoA Desaturase (SCD), the rate limiting enzyme in monounsaturated fatty acid synthesis were specifically altered in the hippocampus of 3xTg-AD (a model of early-onset AD). Remarkably, infusion of an SCD inhibitor (SCDi) reversed 40% of altered immune and synapse genes, rescue dendritic spine number and structure, recovered activity-associated immediate-early gene expression and restored learning and memory in 3xTg-AD mice. In addition, we employed single cell RNA sequencing to characterize the cellular landscape of microglia subpopulations within the 3xTg hippocampus and uncovered that SCDi reversed microglial activation and polarization. Together, we show that a single lipid enzyme, SCD, impinges on the core features of AD.

overall_design: For each treatment group the ipsilateral hippocampi from 4 animals were dissociated into single cells and pooled before staining with CD45 mutiplexing kit from BD Biosciences.

first: Karl.

last: Fernandes


title: A human pancreatic ECM hydrogel optimized for 3-D modeling of the islet microenvironment

city: Madison

first: Daniel

middle: M

last: Tremmel

state: WI

address: 1111 Highland Ave, WIMR 5168

institute: University of Wisconsin

summary: Human islets were cultured in suspension (S) (standard culture) for 2 days, or embedded in human pancreas hydrogel (H) (hP-HG) and cultured for 2 days. RNA-seq was performed to assess changes in gene expression as a result of the hydrogel treatment.

overall_design: Six samples are analyzed, two sets of three replicates. The S (suspension culture) samples are the control.


title: Differential expressed genes in biopsies from discarded human kidneys after one hour of normothermic perfusion

status: Public on Feb 24 2022

city: Cambridge

first: Sarah

last: Hosgood

address: Addenbrooke's hospital, Hills road

department: Department of Surgery

country: United Kingdom

institute: University of Cambridge

summary: Nanostring nCounter Organ Transplant Panel data on 4 cortex biopsies from discarded human kidneys analysing the differential expressed genes after one hour of normothermic perfusion

overall_design: Human kidneys were placed one hour onto normorthermic machine perfusion after a period of static cold storage. Wedge biopsies of cortex were taken before and after NMP and stored in RNA later.

first: Nina

last: Jordan


title: SCD inhibition reverses immune, synaptic and behavioral deficits in an animal model of Alzheimer’s disease [bulk RNA-Seq]

overall_design: RNA was extracted from microdissected hippocampi from untreated 8-month old or 10-month old DMSO or SCDi ICV treated WT or 3xTg-AD mice. For the 8 month (8M) comparision 4 mice from each strain were compared. For the 10 month comparision all groups has 4 mice except WT-S that only had 3.


title: SCD inhibition reverses immune, synaptic and behavioral deficits in an animal model of Alzheimer’s disease


title: mRNA seq after hypothermia treatment of crush injury of the pre-chiasmatic optic nerve

city: Wenzhou City

first: Yu

last: Zhonghao

state: Zhejiang Province, China

address: 270 Xueyuan West Road

institute: The Eye Hospital, School of Ophthalmology & Optometry

type: Non-coding RNA profiling by high throughput sequencing

summary: Transcriptomic changes in the pre-chiasmatic optic nerve, retrobulbar optic nerve of goats 1 day after hypothermia treatment of optic nerve crush injury

overall_design: optic nerve mRNA profiles of hypothermia-treatment injured site and uninjured site

first: Zhonghao

last: Yu

first: Lanfang

last: Sun

first: Yikui

last: Zhang

first: Tian

last: Xia

first: Meng

last: Zhou

first: Ke

last: Li


title: Anti-tumor Effect and Action Mechanism of Exosomes Derived from Toxoplasma gondii-Infected Dendritic Cells in Mice Colorectal Cancer

city: Guangzhou

first: shilan

last: zhu

address: wuShan street

institute: South China Agricultural University

summary: Toxoplasma gondii is an obligate intracellular protozoan with anti-tumor activity against a variety of cancers. However, the therapeutic effect of T. gondii on colorectal cancer is unclear, and using direct Toxoplasma infection in immunotherapy involves safety concerns. This study investigated the anti-tumor effect and mechanism of exosomes derived from dendritic cells (DC) infected with T. gondii (Me49-DC-Exo). We used the density gradient centrifugation to isolate exosomes from uninfected DCs (DC-Exo) and T. gondii Me49-infected DCs (Me49-DC-Exo). The isolated exosomes were identified by transmission electron microscopy, nanoparticle tracking analysis, and western blotting. Me49-DC-Exo significantly inhibited tumor growth and reduced the proportion of M2 macrophages in the blood of tumor-bearing mice. In vitro, Me49-DC-Exo suppressed macrophage (RAW264.7) polarization to M2 phenotype. miRNA sequencing revealed that multiple miRNAs in Me49-DC-Exo were differentially expressed compared with DC-Exo. miR-182-5p, miR-155-5p, miR-125b-2-3p, and miR-155-3p were up-regulated, while miR-9-5p was significantly down-regulated. Transfecting mimics or inhibitors of these differential miRNAs into RAW264.7 cells showed that miR-155-5p promoted M1 macrophage polarization while inhibiting M2 macrophage polarization. Bioinformatics prediction and dual-luciferase reporter assay confirmed the suppressor of cytokine signaling 1 (SOCS1) as a direct target of miR-155-5p. Silencing SOCS1 gene expression in RAW264.7 cells increased CD86 + CD206 - M1 macrophage proportion and inducible nitric oxide synthase and tumor necrosis factor-α mRNA levels. However, arginase1 and transglutaminase 2 expression levels decreased. These results suggest that the exosomes inhibit macrophage polarization to M2 phenotype and regulate SOCS1 expression by delivering functional miR-155-5p. These findings provide new ideas for colorectal cancer immunotherapy.

overall_design: miRNA Profiles of exosomes from uninfected DCs (DC-Exo) and T. gondii Me49-infected DCs (Me49-DC-Exo)

first: Shilan

last: Zhu

first: Jinmiao

last: Lu


title: Influence of the downregulation of the MARS lncRNA (AT5G00580) of the response to Abscisic acid (ABA) in Arabidopsis

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

institute: CNRS

summary: We analyze the effect of the downexpression of the lncRNA MARS (AT5G00580) on the transcriptome in response to ABA treatment. 12 DAS seedlings were harvested and total RNA extracted for RNA sequencing.

overall_design: RNA-seq experiments (polyA+ RNA) in triplicates for each condition (before or after 4h after ABA spray) and genotype (Col-0 and RNAI-MARS-1 lines).

first: Aurélie

last: Christ

last: Roulé

first: Martin

last: Crespi


title: DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers [Drosophila oligo UMI-STARR-seq]

city: Wien

first: Bernardo

last: de Almeida

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary: Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood and enhancer de novo design is considered impossible. Here we built a deep learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. The model learned relevant TF motifs and higher-order syntax rules, including functionally non-equivalent instances of the same TF motif that are determined by motif-flanking sequence and inter-motif distances. We validated these rules experimentally and demonstrated their conservation in human by testing more than 40,000 wildtype and mutant Drosophila and human enhancers. Finally, we designed and functionally validated synthetic enhancers with desired activities de novo.

sample_organism:
Drosophila melanogaster
synthetic construct

overall_design: UMI-STARR-seq was performed in S2 cells using an oligo library (containing 23,959 Drosophila enhancer sequences and their motif-mutant sequences) with two core promoters each representing housekeeping and developmental transcription programs. All experiments were performed in 3 biological replicates.

first: Franziska

last: Reiter

first: Michaela

last: Pagani

first: Alexander

last: Stark


title: DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

summary:
Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood and enhancer de novo design is considered impossible. Here we built a deep learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. The model learned relevant TF motifs and higher-order syntax rules, including functionally non-equivalent instances of the same TF motif that are determined by motif-flanking sequence and inter-motif distances. We validated these rules experimentally and demonstrated their conservation in human by testing more than 40,000 wildtype and mutant Drosophila and human enhancers. Finally, we designed and functionally validated synthetic enhancers with desired activities de novo.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Drosophila melanogaster
Homo sapiens
synthetic construct


title: DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers [Human oligo UMI-STARR-seq]

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Human UMI-STARR-seq was performed in HCT-116 cells using an oligo library (containing 22,900 human enhancer sequences and their motif-mutant sequences). All experiments were performed in 2 biological replicates.


title: Coinduction of DNA Uptake and Fermentative Metabolism in Staphylococcus aureus During Infection

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

summary: Pathogens that grow during infections must cope with the reactive oxygen species (ROS) released by host immune cells. Among the different strategies to prevent oxidative damage during infections, pathogenic bacteria have evolved mechanisms to reduce respiration and other cellular processes that are particularly sensitive to free radicals, obtaining energy preferentially by undergoing to fermentative metabolism. As fermentation produces fewer ATP per glucose than respiration, bacteria ensure an appropriate supply of energy by increasing the glycolytic flux. The opportunistic human pathogen Staphylococcus aureus is one such microbe but the underlying mechanism that enables S. aureus to induce fermentation during infections is still unclear. Here we show that the ComK-like regulator of natural competence that is present in many gram-positive bacteria is crucial to redirect S. aureus metabolism to fermentation during infection. ComK is cryptic in laboratory conditions but highly induced during infections or in response to infection-related cues, such as ROS. ComK induces the glycolytic flux and glucose consumption rate, a key step to redirect ATP production to fermentation. This licenses fermenting S. aureus to reduce oxidative damage while increasing DNA uptake by natural transformation. As a consequence, a comK-defective mutant shows an accumulation of ROS as well as DNA mutations that lower bacterial survival. This mutant shows no distinctive phenotype in laboratory conditions but is unable to cause infection in vertebrates or invertebrate infection models. ComK-mediated synchronization of natural transformation to fermentative metabolism may allow S. aureus, and probably other gram-positive bacteria, to use the fermentation acid end products to eliminate bacterial competitors while assimilating their DNA. Assimilated DNA may serve as a source of nucleotides for DNA repair or to promote genetic variability, thereby enabling a successful host colonization of this bacterium.

overall_design: Transcriptomic analysis of two different Staphylococcus aureu strains

first: Daniel

last: Lopez

middle: U

first: Ana

last: Yepes

first: Mar

last: Cordero


title: Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons

city: Würzburg

first: Chase

middle: Lawrence

last: Beisel

address: Josef-Schneider Straße 2

department: Helmholtz-Institute for RNA-based Infection Research (HIRI)

institute: Helmholtz Centre for Infection Research (HZI)

summary: We report the PAMs of diverse type I-E CRISPR- Cas systems and the type I-C and the type I-F1 CRISPR-Cas systems from Xanthomonas albilineans. Furthermore, we report PAMs of two type I-B CRISPR transposons (CASTs) and the Vibrio cholerae type I-F CAST. For identification of the PAMs, we used a cell-free TXTL-based PAM screen we named PAM-DETECT. By adding a 5N randomized PAM library and plasmids encoding for Cascade genes and gRNAs, recognized PAMs were bound by Cascade and protected from cleavage by a restriction enzyme that has it's recognition site within the target region. By amplifying the non-cleaved target plasmid, we used next-generation sequencing to analyze the enrichment of functional PAMs of the studied CRISPR-Cas systems. We additionally assessed the insertion sites of crRNA-dependent and crRNA-independent transposition of the Rippkaea orientalis type I-B CAST in TXTL and E. coli.

sample_organism:
Escherichia coli
synthetic construct

platform_organism:
Escherichia coli
synthetic construct

overall_design: PAMs for 12 different type I-E CRISPR systems, one type I-C, one type I-F1 system, two type I-B CASTs and one type I-F1 CAST were determined. Insertion points for crRNA-dependent and crRNA-independent transposition were assessed for one type I-B CAST.

last: Wimmer

first: Ioannis

last: Mougiakos

first: Frank

last: Englert


title: DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers [Drosophila genome-wide UMI-STARR-seq]

platform_organism:
Drosophila melanogaster
synthetic construct

overall_design: Genome-wide UMI-STARR-seq was performed in S2 cells using two core promoters each representing housekeeping and developmental transcription programs. All experiments were performed in 2 biological replicates.


title: Newly defined human hematopoietic stem cell populations

status: Public on Feb 23 2022

city: Frankfurt

first: Florian

last: Buettner

state: Germany

address: Theodor-Stern-Kai 7

department: DKTK Frankfurt

institute: DKFZ

summary: Transcriptomic profiling (RNA-seq) of primitive human progenitor populations CD34+CD38-CD45RA-CD90-EPCR-; hereafter CD90-EPCR- MPP.

overall_design:
Purpose: To characterize the transcriptomic profile of the human CD90-EPCR- MPP progenitor population.
Methods: Cells were obtained from human cord-blood and flow-sorted using the surface antigens described. 5 CD90-EPCR- biological replicates were used to extract total RNA and quality was verified (RIN >8).
Libraries were prepared using 20-25 ng/sample of starting RNA. All samples were sequenced two independent times.
Conclusions: This study represents the analysis of transcriptomes from a human progenitor population, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles of other human blood stem/progenitor populations.

first: Fernando

last: Anjos-Afonso

first: Dominique

last: Bonnet


title: Autophagy in age-related macular degeneration using Vldlr KO mouse model of retinopathy

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

summary: Autophagy plays vital housekeeping neuronal functions but is not believed to fuel energy metabolism. Autophagy regulation by lipids nutrient sensors have not been identified. Cone photoreceptors’ very-low-density lipoprotein receptor (Vldlr) expression facilitates the uptake of triglyceride-derived fatty acid. In Vldlr-/- mice, we identify free fatty acid receptor 1 (Ffar1) as a suppressor of transcription factor EB (Tfeb), a master regulator of autophagy. Tfeb, in turn, governs the expression of PGC1 and Sirtuin-3, leading to reduced -ketoglutarate (-KG). We recently showed that low -KG in Vldlr-/- photoreceptors drives Vegfa expression and neovascularization reminiscent of a subset of age-related macular degeneration (AMD). Metabolomics of human AMD vitreous and Vldlr-/- retinas identified a similar Krebs cycle metabolite signature. Improving autophagy in AMD-like mice rescued the neovascular phenotype and vision. Dysregulated autophagy may therefore compound the energy failure of photoreceptors contributing to neovascular AMD and could be a driving force in other neovascular diseases.

overall_design: Dissociated cells from 1 C57B6 WT P14 mouse retina and 3 Vldlr KO mouse retina were processed by single cell RNAseq using the DROPseq technology. UMI count matrix data for cells from 2 C57B6 WT P14 retina replicates from Macosko et al, Cell 2015 (replicate 5 and 8, 3000 cells per replicate) were used as reference for DROPseq validation protocol and then conjugated with our the in-house WT replicate.

first: E

last: Heckel

first: G

first: S

last: Pundir

first: J

last: Sung-Kim

first: N

last: Kim

first: C

last: Clish

first: F

last: Wünnemann

first: L

last: Smith

last: Andelfinger

middle: S

last: Joyal


title: Genome-wide expression profiling of melanoma cells (cancer cell lines and patient derived xenograft tumor models) treated with ARN22089 inhibitor

city: Irvine

first: Anand

last: Ganesan

state: CA

address: 839 Health Science Ct.

department: Dermatology

institute: University of California, Irvine

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

overall_design: Refer to individual Series


title: HDAC6 inhibitor ACY241 evokes transcriptional changes in tumor-associated T cells and macrophages

city: Tampa

first: Dennis

last: Adeegbe

state: FL

address: 13131 USF Magnolia Drive

department: Immunology

institute: Moffitt Cancer Center

summary: While HDAC inhibitors have shown promise in hematologic cancers, their efficacy remains limited in solid cancers. In the present study, we evaluated the immunomodulatory properties of the HDAC6 inhibitor, Citarinostat (ACY241) on lung tumor immune compartment in  Kras and p53 mutant autochthonous murine model of non-small cell lung cancer. Tumor-bearing mice were treated with ACY241 or vehicle as controls after which tumor-associated effector T cells (CD3+CD25low/-)  macrophages CD11b+CD11cdimGr-1-) were sorted from lung tumors and subjected to RNA-sequencing. We found that the effect of ACY241 was most pronounced on macrophages compared to T cells. Over 4, 450 genes were differentially expressed in T cells while over 5, 650 genes were differentially regulated in tumor-associated macrophages upon ACY 241 treatment. Among the most upregulated genes are those encoding costimulatory molecules Tnfrsf9, Cd40, Cd80, Cd83; MHC proteins H2-Ab1, H2-DMb1, as well as related proteins Cd1d1, Cd74, Ctsa, and Tpp1. A number of chemokine genes such as Cxcl12, Ccl4, and Ccl22 were also differentially expressed. Furthermore, several downregulated gene transcripts include Tgfbr3, Cd274, Nos, Pdcd4, and Tnfsf10. Our findings suggest that HDAC6 while primarily considered a cytoplasmic protein, has measurable transcriptional activity that is revealed through its inhibition in tumor-associated immune cell subsets..

overall_design: Tumor-associated macrophages and conventional T cells were isolated from lung tumors of Kras and p53 mutant genetically engineered mouse model of non-small cell lung cancer. Samples were processed for bulk RNA-sequencing.

first: Andrew

last: Schultz


title: Genome-wide expression profile of human melanoma cell line WM3248 treated with ARN22089 at 0, 4, 6 µM dosing for 24 h

summary: To determine pathways engaged by ARN22089 in melanoma cells in-vitro; identify transcripts that are up- or down-regulated in the presence of ARN22089.

overall_design: Human melanoma cell line (WM3248) were treated with 0, 4, and 6 µM of ARN22089 for 24 h and harvested cells after treatment and performed RNA extraction and purification.

first: Linh

last: Vuong


title: TCF-1 mediates 3D genome reconfiguration during T cell development

city: Philadelphia

first: Wenliang

last: Wang

state: PENNSYLVANIA

address: 421 Curie Boulevard

institute: University of Pennsylvania


title: Genome-wide expression profile of human melanoma patient derived xenograft (PDX) tumors that were treated with ARN22089 at 0 (vehicle), 10 mg/kg and 25 mg/kg IV in NSG mice (NOD.Cg-Prkdcscid IL2rgtm1Wjl/SzJ)

summary: To determine the long-term ARN22089 treatment on tumor growth

overall_design: Inoculated mice with one BRAF mutant PDX that was known to have consistent growth properties. Mice were treated with ARN22089 with 0, 10 mg/kg, or 25 mg/kg IV BIW until control tumors reached endpoint.

first: Jessica

last: Flesher


title: Intron-mediated induction of phenotypic heterogeneity

city: Köln

first: Martin

last: Lukačišin

state: Deutschland

address: Zülpicher Straße 47a

department: Institute for Biological Physics

institute: Universität zu Köln

summary: Introns are universally present in the nuclear genomes of eukaryotes. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein (RP) genes differing primarily in their introns. Despite recent findings on the role of RP introns under stress and starvation, understanding the contribution of introns to ribosome regulation remains challenging. Here, combining isogrowth profiling with single-cell protein measurements, we found that introns can mediate inducible phenotypic heterogeneity conferring a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low Rps22B protein levels resulted in prolonged survival under sustained starvation, while high Rps22B levels enabled cells to grow faster after transient starvation. Further, yeast growing at high sugar concentrations – similar to those in ripe grapes – exhibit bimodal Rps22B expression when approaching stationary phase. Differential intron-mediated regulation of RP genes thus provides a way to diversify the population when starvation looms in natural environments. Our findings reveal a new role for introns in inducing phenotypic heterogeneity in changing environments and suggest that duplicated RP genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness.

overall_design: RNA samples from treatments with single stressors were obtained from cultures with automated re-inoculation every 8 hours, with a total incubation time of 24 hours, to keep cultures in exponential phase and assure the drug effects have taken place. Strains were grown in YPD with a drug, either in a concentration gradient to select samples closest to 50% of growth inhibition (LiCl, Fenpropimorph, and Myriocin), or in a single concentration (0.4 M NaCl and glucose 20%). Fenpropimorph (Sigma Aldrich cat. No. 36772) was tested in a 0.5-1.5 µM gradient, sequenced samples were treated with 0.85 µM Fenpropimorph. Myriocin (Sigma Aldrich cat. No. 476300) gradient encompassed 0.25-0.75 µg/ml; 0.32 µg/ml Myriocin samples were sequenced. For each sample of extracted RNA, both ribodepleted total RNA and mRNA Seq libraries were prepared at the Cologne Center for Genomics (CCG) and sequenced using 2×100bp paired-end reads.

first: Adriana

last: Espinosa-Cantú

first: Tobias

last: Bollenbach


title: Transcriptomic study from total RNA extract from reconstructed Human Epidermis (RHE) at 3 time points and quatriplicats under Afatinib (100 nm) exposure versus vehicle

city: Issy-les-Moulineaux

first: Georgios

last: Stamatas

address: 1, rue Camille Desmoulins

department: Consumer Health R&D

institute: Johnson & Johnson Santé Beauté France

summary:
Effect of EGFR inhibitors on the epidermis
Epidermal Growth Factor inhibitors (EGFRi) used in oncology therapy modify the keratinocyte differentiation processes, impairing proper skin barrier formation and leading to Cutaneous Adverse Drug Reactions (CADR).

To uncover the molecular signatures associated with CADRs, we applied phospho-proteomic and transcriptomic assays on Reconstructed Human Epidermis (RHE) tissues exposed to a therapeutically relevant concentration of afatinib, a second EGFRi generation.

Following drug exposure, we observed an increased expression of gene families involved in keratinocyte differentiation, senescence, oxidative stress and alterations in the epidermal immune-related markers.

Furthermore, our results show that afatinib may interfere with Vitamin D3 (VD3) metabolism, acting via CYP27A1 and CYP24A1 to regulate calcium concentration through the PI3K/AKT pathway. Consequently, basal layer keratinocytes switch from a pro-proliferating to a pro-differentiative program, characterized by upregulation of biomarkers associated with increased keratinization, cornification, Th2 response and decreased innate immunity. Such effects may increase the skin susceptibility to cutaneous penetration of irritants and pathogens.

overall_design: Afatinib 100 nm Vs vehicule (DMSO) at 6 h, 24h, 72h

first: Thomas

last: Ondet


title: Next Generation Sequencing of in vitro mouse T-cell differentiation via VCAM-1

status: Public on Feb 22 2022

city: vancouver

first: Peter

middle: W

last: Zandstra

address: 2222 Health Sciences Mall

department: sbme

institute: ubc

summary:
Sample preparation and single-cell RNA-sequencing of in vitro T-cell differentiation
Method: 10X Chromium was used to prepare single-cell cDNA libraries, and Illumina Nextseq was used to 3’ sequence the samples

overall_design: Isolated fetal liver cells from decapitated E13.5 CD1 mouse embryos were subjected to TER-119 depletion by EasySep magnetic sorting (STEMCELL Technologies). Next, sorted HSPCs (Sca-1+ cKit+) cultured at 3.1 x10E3 HSPCs/cm2 (corresponding to 1000 cells/well) in DL4 (10 μg/mL) and VCAM-1 (2.32 μg/mL) coated 96-well plates

first: Tiam

last: Heydari

first: Matthew

middle: A

last: Langley

first: Cynthia

last: Fisher

first: Daniel

last: Aguilar-Hidalgo

first: Shreya

last: Shukla

first: Ayako

last: Yachie-Kinoshita

first: Michael

last: Hughes

first: Kelly

last: McNagny


title: A single-cell RNA-sequencing time course of liver colonisation by colorectal cancer metastases

city: Utrecht

first: Maria

middle: Christine

last: Heinz

address: Heidelberglaan 100

department: Molecular Cancer Research

country: Netherlands

institute: University Medical Center Utrecht

summary: Murine colorectal cancer cells were injected into the portal vein of NOD.Cg-PrkdcSCID Il2rgtm1Wjl/SzJ  mice. Liver metastatic cells were harvested at specific time points for single-cell RNA-sequencing (SORT-seq).

overall_design: Lgr5- or Lgr5+ cells were collected from RFP+ murine colorectal cancer organoids (genetic background VillinCre-ERT2; ApcFL/FL; KrasLSL-G12D/+; Tp53KO/KO; R26R-Confetti; Lgr5DTR-eGFP) by FACS and injected into the portal vein of recipient mice. After 1, 7, 13, and 27 days, livers were perfused with a collagenase cocktail and RFP+ metastatic cells were isolated by FACS and analysed by single-cell RNA-seq.

middle: C

first: Niek

last: Peters

first: Koen

last: Oost

first: Rik

middle: G

last: Lindeboom

first: Lisa

last: van Voorthuijsen

first: Arianna

last: Fumagalli

first: Gustavo

last: de Medeiros

first: Mirjam

last: van der Net

first: Joris

middle: H

last: Hageman

first: Ingrid

last: Verlaan-Klink

first: Inne

last: Rinkes

first: Martijn

last: Gloerich

first: Prisca

last: Liberali

first: Jacco

last: van Rheenen

first: Michiel

last: Vermeulen

first: Onno

last: Kranenburg

first: Hugo

last: Snippert


title: N6-methyladenosine-modified circRNA in the bovine mammary epithelial cells injured by Staphylococcus aureus and Escherichia coli

city: Wuhan

first: Changmin

last: Hu

state: Hubei

address: No.1 Shizishan Street

institute: Huazhong Agricultural University

type: Methylation profiling by high throughput sequencing

summary: Mastitis is a common disease that hinders the development of dairy industry and animal husbandry. It leads to the abuse of antibiotics, the emergence of super drug-resistant bacteria, and poses a great threat to human food health and safety. Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) are the most common pathogens of mastitis in dairy cows and usually cause subclinical or clinical mastitis. CircRNAs and N6-methyladenosine (m6A) play important roles in immunological diseases. However, the mechanisms by which m6A modifies circRNA in bovine mammary epithelial cells remain poorly understood. The aim of our study was to investigate m6A-modified circRNAs in bovine mammary epithelial cells (MAC-T cells) injured by S. aureus and E. coli. The profile of m6A-modified circRNA showed a total of 1599 m6A peaks within 1035 circRNAs in the control group, 35 peaks within 32 circRNAs in the S. aureus group, and 1016 peaks within 728 circRNAs in the E. coli group. Compared with the control group, 67 peaks within 63 circRNAs were significantly different in the S. aureus group, and 192 peaks within 137 circRNAs were significantly different in the E. coli group. Furthermore, we found the source genes of these differentially m6A-modified circRNAs in the S. aureus and E. coli groups with similar functions according to GO and KEGG analyses, which were mainly associated with cells injury, such as inflammation, apoptosis, and autophagy. CircRNA-miRNA-mRNA interaction networks predicted the potential circRNA regulation mechanism in S. aureus- and E. coli-induced cell injury. We found that the mRNAs in the networks, such as BCL2, MIF and TNFAIP8L2, greatly participated in the MAPK, WNT, and inflammation pathways. This is the first report on m6A-modified circRNA regulation of cells under S. aureus and E. coli treatment, and sheds new light on potential mechanisms and targets from the perspective of epigenetic modification in mastitis and other inflammatory diseases.

overall_design: Examining 3 conditions, each with 3 replicates


title: KMT2C Loss Promotes Small Cell Lung Cancer Metastasis through DNMT3A-mediated Epigenetic Reprogramming

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Small cell lung cancer (SCLC) is notorious for its early and frequent metastases, which contribute to it as a recalcitrant malignancy. To understand the molecular mechanisms underlying SCLC metastasis, we generated SCLC mouse models with orthotopically transplanted genome-edited lung organoids and performed multi-omics analyses. We found that loss of KMT2C, an H3K4 methyltransferase frequently mutated in extensive stage SCLC, promoted multiple-organ metastases in mice. Metastatic and KMT2C deficient SCLC displayed both histone and DNA hypomethylation. Mechanistically, KMT2C directly regulated the expression of DNMT3A, a de novo DNA methyltransferase, through histone methylation. Forced DNMT3A expression restrained metastasis of KMT2C deficient SCLC through repressing metastasis promoting MEIS/HOX genes. Further, S-(5’-Adenosyl)-L-methionine, the common cofactor of histone and DNA methyltransferases, inhibited SCLC metastasis. Thus, our study revealed a concerted epigenetic reprogramming of KMT2C and DNMT3A-mediated histone and DNA hypomethylation underlying SCLC metastasis, which suggested a new epigenetic therapeutic vulnerability.

overall_design: Small cell lung cancer (SCLC) is a neuroendocrine lung malignancy characterized with rapid progress and heavy metastasis. To understand the molecular mechanisms underlying its unique pathology, we developed a new strategy to rapidly generate driver-defined primary and orthotopical murine SCLC models with gene-edited lung organoids. Single cell transcriptome analyses of primary and metastatic SCLC revealed a metastasis trajectory associated with dysregulated epigenetic programs. Disruption of KMT2C, an H3K4 methyltransferase frequently mutated in human SCLC of extensive stage, promoted the growth and metastasis of SCLC in mice. Interestingly, KMT2C loss resulted in significantly reduced DNA methylation through directly regulating the expression of DNMT3A. Ectopically expressing DNMT3A or treatment with S-adenosyl methionine repressed the metastasis of KMT2C-deficient SCLC. These epigenetic reprogramming exaggerated SCLC metastasis partially through upregulating Meis/Hox genes. Taken together, our study revealed an unprecedented synergistic histone and DNA hypomethylation in SCLC.

first: Xiangyu

first: Xuelan

last: Chen

first: Feifei

first: Jingyao

first: Yu

last: Liu

first: Chong


title: Liver colonisation by colorectal cancer metastases requires YAP-controlled plasticity at the micrometastatic stage

first: Maria

last: Heinz

summary: Human engineered CRC organoids were equipped with the intestinal stem cell reporter STAR reflecting transcriptional activity of ASCL2. Successfully growing organoids display heterogeneous STAR expression and grow into big structures, while growth-compromised organoids stay small and are either entirely STAR-pos or STAR-neg.

overall_design: Organoids were grown from single cells (APCKO/KO; KRASG12D/-; TP53KO/KO; SMAD4 KO/KO) for 12 days. Then, big and small organoids were size-separated from this culture, subcultures were dissociated to single cells, and STAR-high, STAR-mid, and STAR-neg cells were collected by FACS. Samples were processed for bulk RNA-seq.

first: Niek

last: Peters

first: Koen

last: Oost

first: Rik

last: Lindeboom

first: Lisa

last: van Voorthuijsen

first: Arianna

first: Gustavo

first: Mirjam

first: Joris

last: Borel Rinkes


title: Suppression of colorectal cancer by ketogenic diet and beta-hydroxybutyrate

first: Patrick

last: Lundgren

state: PA

address: 302 Johnson Pavilion, 3610 Hamilton Walk


title: Transcriptional profiling of the endophytic fungus Pestalotiopsis sp. 9143 and its endohyphal bacterium Luteibacter mycovicinis 9143

city: Tucson

first: David

last: Baltrus

state: AZ

address: 1140 E. South Campus Drive

institute: University of Arizona

summary: The fungal endophyte Pestalotiopsis sp. 9143 was found naturally infected with the endohyphal bacterium Luteibacter mycovicinis 9143. The fungus can be cured of the bacterium by culturing on antibiotics and the bacterium can be isolated from the fungus by culturing at high temperatures or mechanical disruption. This study investigates the transcriptomes of both partners cultured indepedently (axenically) and in coculture. The goal was to understand the changes in gene expression that accompany partner presence in order to identify genes and pathways that may facilitate the interaction.

sample_organism:
Luteibacter mycovicinus
Pestalotiopsis sp. 9143b

overall_design: Three bioreplicates each of Pestalotiopsis sp. 9143 in pure culture, of L. mycovicinis 9143 in pure cultures, and of cocultured fungus and bacterium. Fungal and bacterial RNA was sequenced and analyzed separately.

first: Morgan

middle: E

last: Carter

first: Justin

last: Shaffer

first: Joseph

last: Spraker

first: A

last: Arnold


title: CDK12 promotes tumorigenesis but induces vulnerability to therapies inhibiting folate one-carbon metabolism in breast cancer.

city: Milan

first: Salvatore

last: Pece

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology IRCCS,

summary: Cyclin-dependent kinase 12 (CDK12) overexpression is implicated in breast cancer, but whether it has a primary or only a cooperative tumorigenic role is unclear. Here, we show that transgenic CDK12 overexpression in the mouse mammary gland per se is sufficient to drive the emergence of multiple and multifocal tumors, while, in cooperation with known oncogenes or chemical carcinogens, it promotes earlier tumor onset and metastasis. Integrative transcriptomic, metabolomic and functional data revealed that enhanced glycolysis and hyperactivation of the serine-glycine-one- carbon network are metabolic hallmarks inherent to CDK12-induced tumorigenesis, which impose distinct metabolic dependencies in CDK12-transformed mammary epithelial cells. Consistently, in the retrospective analysis of adjuvant and neoadjuvant breast cancer patient cohorts and in prospective preclinical studies using primary-derived human breast tumor xenografts, CDK12-overexpressing breast cancers showed a more favorable disease course in response to methotrexate- based chemotherapy targeting CDK12-induced metabolic alterations, while appearing intrinsically refractory to other types of chemotherapy. Even more clinically relevant, in patients with hormone receptor-negative and lymph node-positive breast cancer who were randomized in an adjuvant phase III trial to 1-year low-dose metronomic methotrexate-based maintenance chemotherapy or no chemotherapy after standard adjuvant treatments, a high CDK12 status predicted a dramatic reduction in distant metastasis rate in the chemotherapy-treated vs. not-treated arm. Thus, by coupling tumor progression with metabolic reprogramming, CDK12 creates an actionable vulnerability for breast cancer therapy and might represent a suitable companion biomarker for targeted antimetabolite therapies in naturally occurring human breast cancers.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA profile of CDK12 overexpressing vs Wild Type human breast epithelial MCF-10A cell line, and CDK12 kncock-in vs Wild Type mouse PyMT breast tumor organoids.

last: Filippone

first: Daniela

last: Gaglio

first: Roberta

last: Bonfanti

first: Francesco

last: Tucci

first: Elena

last: Ceccacci

first: Rosa

last: Pennisi

first: Marcella

last: Bonanomi

last: Jodice

first: Micol

last: Tillhon

first: Francesca

last: Montani

first: Giovanni

last: Bertalot

first: Stefano

last: Freddi

first: Manuela

last: Vecchi

first: Angelo

last: Taglialatela

first: Mauro

last: Romanenghi

last: Romeo

first: Nadia

last: Bianco

first: Elisabetta

last: Munzone

last: Sanguedolce

first: Gianluca

last: Vago

first: Giuseppe

last: Viale

first: Pier

last: Di Fiore

first: Saverio

last: Minucci

first: Lilia

last: Alberghina

first: Marco

last: Colleoni

first: Paolo

last: Veronesi

last: Tosoni


title: The effect of 22-bulge of pre-miRNAs on DICER cleavage in human cells.

status: Public on Feb 21 2022

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: The experiments were conducted to examine the effects of 22-bulge of pre-miRNAs on DICER cleavage in human cells.

overall_design: HCT116 cells were transfected with pCDNA3 plasmids expressing pri-miRNA-216a containing 22-3p-bulge or 22-5p-bulge or 22-mismatch or nobulge. Small RNA sequencing libraries of the transfected HCT116 cells generated using NEBNext® Small RNA Library Prep Set for Illumina® (NEB).

first: Tuan

first: Trung

middle: D

first: Trinh

middle: T

last: Anh

first: Sheng

last: Bao


title: The effect of 22-bulge of pre-miRNAs on DICER cleavage in human cells

overall_design: HCT116 cells were transfected with pCDNA3 empty, pCDNA3 wild-type or SNP-containing pri-miRNA plasmids. Small RNA sequencing libraries of the transfected HCT116 cells generated using NEBNext® Small RNA Library Prep Set for Illumina® (NEB).


title: Genome-wide promoter assembly mechanisms in E. coli measured at single base resolution

city: Ithaca

first: B. Franklin

last: Pugh

state: NY

address: 465 Biotechnology Building

institute: Cornell University

summary: When performed at single bp resolution, the genome-wide location, occupancy level, and structural organization of DNA binding proteins provides mechanistic insights into genome regulation. Here we use ChIP-exo to provide the first high resolution view of the epigenomic organization of the E. coli transcription machinery and nucleoid structural proteins when cells are growing exponentially and upon rapid reprogramming (acute heat shock). We suggest that indirect readout of DNA shape at the flanks of cognate motifs provide major contributions to site specificity at promoter positions -35/-24 and -10/-12. We examined the site specificity of three sigma factors (RpoD/70, RpoH/32, and RpoN/54), RNA polymerase (RNAP or RpoA, B, C) and two nucleoid proteins (Fis and IHF). Our results confirm and refine reports that RpoD binds most annotated promoters, whereas RpoH and RpoN bind a much smaller subset, each through their cognate motifs. However, only upon heat shock does RpoH becomes active for RNAP recruitment. In contrast, upon heat shock RpoD remains active at its cognate promoters (including at heat shock genes), whereas RpoN remains inactive at its cognate promoters. RpoN binds ~1,000 non-annotated RpoN motifs, which may reflect a large number of condition-specific transcription units. Occupancy patterns of sigma factors and RNAP suggest a common promoter recruitment mechanism that differs from the long-standing views that sigma and RNAP are co-recruited as a complex, and also simultaneously dissociate from promoters. Our findings suggest that sigma factors are recruited and/or maintained at most promoters via an RNAP-independent mechanism. When RNAP arrives, it dwells for a relatively short time before clearing the promoter, leaving sigma behind. Taken together these findings add new dimensions to how sigma factors achieve promoter specificity through DNA sequence and shape and redefine mechanistic steps in regulated promoter assembly in E. coli.

overall_design: Genome-wide analysis of E. coli transcription factors using ChIP-exo

first: Jordan

last: John

first: Javaid

last: Jabbar

first: Nitika

last: Badjatia

first: Matthew

middle: J

last: Rossi

first: B

last: Franklin Pugh


title: Dnmt3a-Mutant Hematopoietic Stem cells are resistant to inflammatory stress

city: St Louis

first: Grant

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

summary: Dnmt3a-mutant mouse HSCs, but not control HSCs are able to maintain clonality during type II inteferson signaling. To investigate the molecular mechanism of this observation, we investigated IFNg-incuded changes in DNA methylome of mouse HSCs in a mouse model. In the model, we transplanted 10% CD45.2 donor BM cells, 10% CD45.1/2-GFP competitors and 80% CD45.1 BM cells into CD45.1 recipients. In the treatment group, we transplated the CD45.1 BM cells with the genotype of IFNgrKO; rtTA-M2; Tet-O-IFNg to induce a chronic IFNg exposure. A physiological relevant level of IFNg was induced by 1250ppm doxycycline chow every other week during 5-24 weeks post-transplant. In the control group, we transplanted CD45.1 cells with the genotype of IFNgrKO; rtTA-M2. All the mice in the control group were also on the same schedule of doxycycline chow. Recipients were sacrificed 26-weeks post-transplant and 3x10^5 donor derived BM cells from each group were sorted for gDNA extraction. Consistent with literature, our results showed a gradient loss of DNA methylation from Dnmt3a-HET to Dnmt3a-KO compared to Vav-cre controls. Chronic IFNg exposure, however, did not change the global DNA methylation levels. All the IFNg-induced changes were locus-specific. We conclud that IFNg-induced changes in DNA methylome cannot explain the protection of Dnmt3a-mutant HSCs against type II inteferon signaling.

overall_design:
Whole genome-wide bisulphite sequencing. Mice of different genotypes (Vav-cre: Control; Vav-cre;Dnmt3af/f: 3aKO) were retro-orbitally injected with two doses of 10ug of recombinant mouse IFNg with 24h apart. Mice were sacrificed for bone marrow cell harvest 2h post the second injection. Gender-, age-, genotype- matched mice recieved volume-equivalent PBS as control groups. Bone marrow cells were stained with lineage markers, as well as antibodies against cKIT and EPCR. Lin-cKIT+EPCR+ cells were sorted and used for scRNA-seq library construction. Data were processed with CellCounter and analyzed with Seurat 3.0.
Hematopoietic stem cells (HSCs) were sorted from Vav-CRE:Control, Vav-CRE:Dnmt3a-KO, Vav-CRE:Tet2-KO mice (treated with IFNg or PBS) for RNA-seq to determine gene expression

first: Christine

middle: R

last: Zhang

first: Elizabeth

middle: L

last: Ostrander

first: Jiameng

last: Sun

first: Cates

last: Mallaney

first: Emily

last: Haussler

first: Hamza

last: Celik

first: Ostap

last: Kuhkar

first: Jacob

last: Fairchild

first: Won

middle: K

last: Koh

first: Katherine

middle: Y

last: King

first: Paul

last: Gontarz


title: Comparison of gene expression in murine FoxP3+ T regulatory cells isolated from TNBC claudin-low model (T11) treated with anti-PD-1 with untreated tumors

city: Chapel Hill

first: Jonathan

last: Serody

address: 125 Mason Farm Rd.

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: We hypothesized that the expression of PD-1 on Tregs would lead to enhanced suppressive function of Treg and worsen anti-tumor immunity during PD-1 blockade.  To evaluate this, Tregs were isolated from claudin-low tumors and functionally evaluated ex vivo.  We compared transcriptional profiles of Tregs isolated from tumor bearing mice with or without a-PD-1 therapy using RNA-Seq.  We found several genes associated with survival and proliferation pathways, for example Jun, Fos, and Bcl2, were significantly upregulated in Tregs exposed to a-PD-1 treatment.

overall_design: RNA expression in FoxP3 Treg cells isoated from 150 mm^2 tumors from untreated and treated with anti-PD-1 mice

first: Sarah

last: Vick

first: Oleg

middle: V

last: Kolupaev

first: Charles

middle: M

last: Perou


title: The effect of 22-bulge of shRNAs on DICER cleavage in human cells

first: Duc

last: Nguyen

summary: The experiments were conducted to examine  the effects of 22-bulge on DICER cleavage in human cells.

overall_design: HEK293T cells were transfected with 22-bulge or nobulge variants of some shRNAs. Small RNA sequencing libraries of the transfected HEK293T cells generated using NEBNext® Small RNA Library Prep Set for Illumina® (NEB).

first: Tuan

first: Trung

first: Trinh

last: Anh

first: Sheng

last: Bao


title: Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria

city: Clayton

first: Stephanie

middle: Irene

last: Studniberg

state: VIC

address: 19 Innovation Walk

department: Microbiology

country: Australia

institute: Monash Biomedicine Discovery Institute

summary: To define the impact of asymptomatic malaria, we pursued a systems approach integrating antibody responses, mass cytometry, and transcriptional profiling of individuals experiencing symptomatic and asymptomatic P. falciparum infection. Defined populations of classical and atypical memory B cells and a TH2 cell bias were associated with reduced risk of clinical malaria. Despite these protective responses, asymptomatic malaria featured an immunosuppressive transcriptional signature with upregulation of pathways involved in the inhibition of T cell function, and CTLA-4 as a predicted regulator in these processes.

overall_design: We performed RNA-seq analysis of bulk PBMCs on a cohort of 17 individuals experiencing either symptomatic (n=6) or asymptomatic (n=5) malaria and healthy immune controls (n=6). Raw data are available upon request, subject to approval by the Walter and Eliza Hall Institutional Data Access Committee (dataaccess@wehi.edu.au) to ensure preservation of patient confidentiality.

middle: I

first: Diana

middle: S

last: Hansen

first: Alexandra

last: Garnham

first: Wei

last: Shi


title: Molecular mechanisms of zinc toxicity in the potworm Enchytraeus crypticus, analysed by high-throughput gene expression profiling

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

institute: MicroLife Solutions

summary: Zinc (Zn) is known to be relatively toxic to some soil-living invertebrates including the ecologically important enchytraeid worms. To reveal the molecular mechanisms of zinc toxicity we assessed the gene expression profile of Enchytraeus crypticus (Enchytraeidae), exposed to the reproduction effect concentrations EC10 and EC50, over 4 consecutive days, using a high-throughput microarray (species customized). Three main mechanisms of toxicity to Zn were observed: 1) Zn trafficking (upregulation of zinc transporters, a defence response to regulate the cellular zinc level), 2) oxidative stress (variety of defence mechanisms, triggered by Reactive Oxygen Species (ROS) generated by Zn), and 3) effects on the nervous system (possibly the primary lesion explaining the avoidance behaviour and also why enchytraeids are relatively susceptible to Zn). The adverse outcome at the organism level (reproduction EC50) could be predicted based on gene expression (male gonad development, oocyte maturation), with Zn at the EC50 affecting processes related to higher stress levels. The gene expression response was time-specific and reflected the cascade of events taking place over-time. The 1 to 4 days of exposure design was a good strategy to capture the sequence of events towards zinc adverse outcomes in E. crypticus.

overall_design: a single channel, interwoven loop design was used testing pools of 10 adult animals per sample to two concentrations of zinc (EC10 and EC50) or controls for 1,2,3 and 4 days

first: S

last: I Gomez

first: T

first: C

middle: A

last: van Gestel

first: N

last: van Straalen

first: A

last: Soares

middle: F

last: Roelofs

first: M

last: Amorim


title: The high-throughput DICER cleavage assays on 23296 shRNA variants

summary: The high-throughput DICER cleavage assays were conducted shRNA variants containing different sequences. We showcase a comprehensive cleavage activity of DICER on different shRNAs containing different secondary structures.

overall_design: 23296 shRNA variants were processed by DICER in vitro. The original substrates and cleaved products were cloned and sequenced.

first: Shengm


title: Effects of ‘Candidatus Liberibacter solanacearum’ haplotypes A and B on tomato gene expression and geotropism

status: Public on Feb 20 2022

city: College Station

first: Kyle

last: Harrison

address: 2475 TAMU

department: Entomology

institute: Texas A&M University

summary: The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of solanaceous crops such as tomato (Solanum lycopersicum L.) in the U.S. and vectors the disease-causing pathogen ‘Candidatus Liberibacter solanacearum’ (or Lso). Lso disease symptom severity is dependent on Lso haplotype: tomato plants infected with Lso haplotype B experience more severe symptoms and higher mortality compared to plants infected with Lso haplotype A. By characterizing the molecular differences in the tomato plant’s responses to Lso haplotypes, the key components of LsoB virulence can be identified and, thus, targeted for disease mitigation strategies. To characterize the tomato plant genes putatively involved in the differential immune responses to Lso haplotypes A and B, RNA was extracted from tomato ‘Moneymaker’ leaves three weeks after psyllid infestation. Gene expression levels were compared between uninfected tomato plants (i.e., controls and plants infested with Lso-free psyllids) and infected plants (i.e., plants infested with psyllids infected with either Lso haplotype A or Lso haplotype B). Furthermore, expression levels were compared between plants infected with Lso haplotype A and plants infected with Lso haplotype B. A whole transcriptome analysis identified 578 differentially expressed genes (DEGs) between uninfected and infected plants as well as 451 DEGs between LsoA- and LsoB-infected plants. These DEGs were primarily associated with plant defense against abiotic and biotic stressors, growth/development, plant primary metabolism, transport and signaling, and transcription/translation. These gene expression changes suggested that tomato plants traded off plant growth and homeostasis for improved defense against pathogens, especially when infected with LsoB. Consistent with these results, tomato plant growth experiments determined that LsoB-infected plants were significantly stunted and had impaired negative geotropism. However, it appeared that the defense responses mounted by tomatoes were insufficient for overcoming the disease symptoms and mortality caused by LsoB infection, while these defenses could compensate for LsoA infection.  The transcriptomic analysis and growth experiments demonstrated that Lso-infected tomato plants underwent gene expression changes related to abiotic and biotic stressors, impaired growth/development, impaired plant primary metabolism, impaired transport and signaling transduction, and impaired transcription/translation. Furthermore, the transcriptomic analysis also showed that LsoB-infected plants, relative to LsoA-infected, experienced more severe stunting, had improved responses to some stressors and impaired responses to others, had poorer transport and signaling transduction, and had impaired carbohydrate synthesis and photosynthesis.

overall_design: Tomato gene expression levels were measured in plants infested with psyllid vectors infected with a virulent pathogen (Lso) haplotype (LsoB) and compared to plants infested with psyllid vectors infected with a non-virulent haplotype (LsoA). These expression levels were also compared to uninfested control plants and plants infested with uninfected psyllid vectors.

first: Julien

middle: G

last: Levy

first: Cecilia

last: Tamborindeguy


title: RNA-Seq of MSK-PCa3 prostate cancer organoids upon knockdown of FOSL1, YAP, TAZ, or YAP/TAZ

city: New York

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: Transcriptome analysis of prostate cancer patient derived organoid MKS-PCa3 upon knockdown of FOSL1, YAP, TAZ, or YAP/TAZ mediated by siRNAs

overall_design: Transcriptome analysis was performed in MSK-PCa3 cells treated with siFOSL1, siYAP, siTAZ, or siYAP/TAZ for 48 hours

first: Ekta

last: Khurana

first: Chen

last: Wong

first: Duo

last: Xu


title: FUS-CHOP and ISWI chromatin remodeling in human myxoid liposarcoma

first: Ian

middle: Johnathan

last: Davis

state: North Carolina

address: 450 West Dr.

department: Genetics

summary: We identified novel protein-protein interactions between FUS-CHOP, a fusion oncoprotein that drives myxoid liposarcoma, and SNF2H, the ATPase subunit of the imitation switch (ISWI) chromatin remodeling complex. We used antibodies for FUS-CHOP, SNF2H, and H3K27ac to profile localization of these proteins and histones marks  on chromatin in human MLPS cell lines and show that colocalization of FUS-CHOP and SNF2H occurs at new enhancers marked by H3K27ac.

overall_design: ChIP-seq and CUT&RUN performed using antibodies for FUS-CHOP, H3K27ac, and SNF2H in human fusion positive myxoid liposarcoma (DL221 and MLS402) and human fusion negative liposarcoma cell lines (SW872).  RNA-seq on DL221,  MLS402 and SW872.

first: Mark

first: Joseph

middle: P

last: Foster II

middle: C

last: Lock

first: Nathan

middle: H

last: Leisenring

first: Andrea

last: Daniel

first: Robert

middle: W

last: Floyd

first: Eric

first: David

last: Kirsch


title: Regulation of Chromatin Accessibility by the Histone Chaperone CAF-1 Sustains Lineage Fidelity

city: Riverside

first: Sihem

last: Cheloufi

state: California

address: 3401 Watkins Dr.

department: Biochemistry

institute: University fo California Riverside

summary: To study the gene expression changes upon Hoxa9 inactivation and CAF-1 suppression, we performed RNA-seq analyses at 24 hours using Hoxa9-Granulocyte-macrophage progenitor cells (Hoxa9-GMPs).

overall_design: mRNA profiles of Hoxa9-GMPs at 0h and 24hrs upon CAF-1 suppression or Hoxa9 inactivation by Illumina sequencing.

first: Fei

last: Ji

first: Ruslan

last: Sadreyev

last: Sykes

first: Konrad

last: Hochedlinger


summary: To study the gene expression changes upon CAF-1 deletion, we performed RNA-seq analyses in isolated HSPCs after 48 hours of Chaf1b deletion.

overall_design: mRNA profiles in 2 reps of control HSPCs or HSPCs upon 48hrs of CAF-1 deletion .

first: Reuben

last: Franklin

first: Andrew

last: Volk


title: Astroblastomas exhibit radial glia stem cell lineages and differential expression of imprinted and X-inactivation escape genes [Nanostring]

city: Louisville

first: Norman

last: Lehman

state: Kentucky

address: CTRB Room 307, 505 South Hancock St.

institute: The University of Louisville

summary: Astroblastoma (AB) is an unusual brain tumor of unknown origin. We performed a clinicogenomic analysis of AB-like tumors.

overall_design: Twenty-six primary tumor samples were analyzed for microRNA expression by Nanostring.

first: N


summary: To study the expression and chromatin profiles upon Hoxa9 inactivation and CAF-1 suppression, we performed ATAC-seq and RNA-seq analyses at 24 hours using Hoxa9-Granulocyte-macrophage progenitor cells (Hoxa9-GMPs).

overall_design: chromatin accessibility profiles of Hoxa9-GMPs at 0h and 24hrs upon CAF-1 suppression or Hoxa9 inactivation by Illumina sequencing.


summary: To study the chromatin profiles upon Hoxa9 inactivation and CAF-1 suppression, we performed ChIP seq analyses at 48 hours using Hoxa9-Granulocyte-macrophage progenitor cells (Hoxa9-GMPs).

overall_design: TF binding and histone modifications of Hoxa9-GMPs at 0h and 48hrs upon CAF-1 suppression or Hoxa9 inactivation.

first: Shiyang

last: He

first: Jernej

last: Murn

first: Rui

last: Lu

first: Xinyue

last: Zhou


title: Single Cell RNA Seq Reveals a Distinct Immune Landscape in Vulnerable Coronary Plaques.

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

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

department: Division of Cardiovascular Medicine, Department of Internal Medicine

country: Japan

institute: Kobe University Graduate School of Medicine

summary: We observed a unique compositional difference between the stable and vulnerable plaques. Neutrophils, mast cells, and IL1B inflammatory macrophages were detected only in vulnerable plaques.

overall_design: Single Cell RNA Seq of human coronary plaques

first: Tomoya

last: Yamashita


title: Astroblastomas exhibit radial glia stem cell lineages and differential expression of imprinted and X-inactivation escape genes [methylation]

summary: Astroblastoma (AB) is an unusual brain tumor of unknown origin. We performed an integrated clinicogenomic analysis of 36 AB-like tumors. Lesions with MN1-BEND2 fusions demonstrated decreased promoter methylation and increased expression of IGF2-H19 and DLK1-DIO3 imprinted region genes. They also relatively overexpressed genes highly expressed during fetal brain development prior to 25 post-conception weeks (pcw), including genes enriched in ventricular zone radial glia (vRG), and generally presented in young children. Other tumors highly expressed MAP kinase pathway, PI3K pathway and X-inactivation escape genes. These and a third group of tumors tended to occur in young adults and showed enriched expression of outer radial glia (oRG) and truncated radial glia (tRG) genes, and genes highly expressed after 25 pcw.  Many of the latter are involved in axonal migration or synaptic plasticity and are implicated in autism, schizophrenia and other cognitive disorders. Findings suggest that AB-like tumors arise in the context of epigenetic and genetic changes in neural progenitors during fetal and later brain development: early ependymal tumors with MN1-BEND2 fusions (EET-MN1) from vRG-derived progenitor cells, and MAPK/PI3K and classic astroblastomas from oRG- and tRG-derived progenitors, respectively. Lastly, we found that like EET-MN1, immature ependymal cells express IGF2 and may represent an important source of this growth factor in the fetal lateral ventricular zone neural stem cell niche.

overall_design: Infinium MethylationEpic BeadChip methylDNA analysis of 17 rare astroblastoma-like tumors. These were subjected to tSNE analysis with 21 samples (also included here) from our previous study (GEO  accession 125450) for a total of 38 tumor DNA methylation profiles in our study.


title: Astroblastomas exhibit radial glia stem cell lineages and differential expression of imprinted and X-inactivation escape genes.

overall_design: We studied 28 archived FFPE samples of histologically diagnosed rare tumors known as atroblastomas and 4 archived FFPE samples of the histologically similar tumor known as papillary tumor of thepineal reqion (PTTR) by RNAseq in order to biologically characterize tumors histologically diagnosed as astroblastomas. Although there were no replicates In RNAseq examined samples, RNAseq expression data results were validated by Affymetrix cDNA gene chip array in a large subset of the samples.


title: Gene expression changes induced by FOSL1, YAP, and TAZ overexpression in LNCaP Prostate Cancer Cells

first: Yu

last: Chen

summary: Transcriptome analysis of LNCaP cells upon overexpression of FOSL1, YAP, and TAZ

overall_design: Transcriptome analysis was performed in LNCaP cells stably expressing FOSL1, YAP, YAP/FOSL1, TAZ, or TAZ/FOSL1

first: Ekta

last: Khurana

first: Chen

last: Wong

first: Duo

last: Xu


first: Sihem

last: Cheloufi

summary: To study the expression and chromatin profiles upon Hoxa9 inactivation and CAF-1 suppression, we performed ATAC-seq and RNA-seq analyses at 48 hours using Hoxa9-Granulocyte-macrophage progenitor cells (Hoxa9-GMPs).

overall_design: mRNA/chromatin profiles of Hoxa9-GMPs at 0h and 48hrs upon CAF-1 suppression or Hoxa9 inactivation by Illumina sequencing.

first: Fei

last: Ji

first: David


title: Astroblastomas exhibit radial glia stem cell lineages and differential expression of imprinted and X-inactivation escape genes [Affymetrix]

overall_design: Sixteen AB-like tumors, four PTPR, six PXA and twenty-two control normal brain samples were analyzed. No replicates were possible due to limited available material from these rare tumors, however, the Affymetrix data was validated by comparison to RNAseq data for the same AB-like tumor and PTPR samples. Tumor sample types were compared to each other and to controls.


title: Gene expression data of cancer cell lines treated with inhibitors of G9a and EZH2

city: Brisbane

first: Francesco

last: Casciello

state: Queensland

address: 300 Herston road

institute: QIMR Berghofer Medical Research Institute

summary: Epigenetic modifications modulate gene expression and, when deregulated, contribute to the development and progression of cancer. G9a (EHMT2) and EZH2 are two histone methyltransferases commonly upregulated in several cancer types, leading to the silencing of tumor suppressor genes. We performed high throughput sequencing of a breast cancer cell line (MDA-MB-231), an ovarian cancer cell line (CAOV3) and a melanoma cell line (D14) treated with a G9a inhibitor (UNC0642), EZH2 inhibitor (GSK126) and their combination.

overall_design: MDA-MB-231, CAOV3 and D14 cells were treated with Vehicle (DMSO), UNC0642 (5 µM), GSK126 (10 µM) for 8 hours. RNA was then extracted and libraries were prepared using the Illumina Total RNA Stranded (Ribo-zero Gold) kit.

first: Gregory

last: Kelly

first: Jason

last: Lee


title: Single cell profiling of salamander heart under homeostasis and after cryoinjury.

city: Stockholm

first: Kenneth

last: Chien

state: State...

address: A6 Biomedicum

department: CMB

country: Sweden

institute: Karolinska Insitute

summary: Heart disease is the leading cause of mortality worldwide due to the limited regenerative capacity of the mammalian heart. Myocardial infarction causes massive cardiomyocyte apoptosis that is replaced by a fibrotic scar. In contrast to mammals, certain vertebrates such as fish and amphibians can regenerate cardiac muscle without scarring. Here, we established a cryoinjury model in the salamander species, Pleurodeles waltl. We performed single-cell RNA sequencing to profile the salamander heart and identified CLDN6 as a specific marker of epicardium, the outermost mesothelial layer enclosing the heart. Notably, lineage tracing experiments showed differentiation of CLDN6+ epicardium-derived cell intermediates into cardiomyocytes in response to injury. Additionally, scRNA-seq experiments suggested a differentiation trajectory that describes epicardial cell to myocyte conversion. Furthermore, ablation of these intermediates with Clostridium perfringens enterotoxin (CPE) blocked cardiac regeneration.

overall_design: scRNA-seq of salamander heart tissue - sham, 7 days post cryoinjury (dpci), 14 dpci, 28 dpci.

first: Elif

last: Eroglu

first: Yat-Long

last: Tsoi

first: Ahmed

last: Elewa

first: Andras

last: Simon


summary: To study the gene expression changes upon Hoxa9 inactivation and CAF-1 suppression, we performed RNA-seq analyses at 48 hours using Hoxa9-Granulocyte-macrophage progenitor cells (Hoxa9-GMPs).

overall_design: mRNA profiles of Hoxa9-GMPs at 0h and 48hrs upon CAF-1 suppression or Hoxa9 inactivation by Illumina sequencing.

first: Ruslan

last: Sadreyev

last: Sykes

first: Konrad

last: Hochedlinger


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

overall_design: Refer to individual Series


title: Monocytes transition to monocyte-macrophages within the inflamed vasculature via CCR2 on monocytes and endothelial TNFR2

status: Public on Feb 19 2022

city: Boston

first: Vijayashree

last: Sathyanarayana Mysore

state: MA

address: 77 avenue Louis Pasteur

department: Pathology

institute: BWH-Harvard University

summary: Our study reports the CCR2 dependent functional specialization of monocytes into immature macrophages occurs within the TNF-TNFR2 activated vasculature and establishes a chemokine-based autocrine, feed-forward loop that may aplify the inflammation and renal injury.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
Monocytes and the endothelial cell co-cultures along with monocytes on plastic were harvested and subjected to 10X. Sample populations were stained with Total-Seq A hashtag antibodies #1 - #10. The populations were pooled together and were loaded onto the 10X Chromium controller.
Please note that individual sample information is provided in the sample_info.txt

last: Mysore

first: Tanya

last: Mayadas


title: Plasma exosomes transfer miR-885-3p targeting AKT/NFκB signaling pathway to improve the sensitivity of intravenous glucocorticoid therapy against Graves ophthalmopathy

city: harbin

first: jingxue

last: sun

state: heilongjiang

address: 246 xuefu road

institute: The Second Affiliated Hospital of Harbin Medical University

summary: Graves ophthalmopathy (GO), a manifestation of Graves' disease, is an organ-specific autoimmune disease. Intravenous glucocorticoid therapy (ivGCs) is the first-line treatment for moderate-to-severe and active GO. However, ivGCs is only effective in 70-80% of GO patients. Insensitive patients who choose 12 weeks ivGCs were not only delayed in treatment, but also took the risk of adverse reactions of glucocorticoids. At present, there is still a lack of effective indicators to predict the therapeutic effect of ivGCs. Therefore, the purpose of this study is to find biomarkers that can determine the sensitivity of ivGCs before the formulation of treatment, and to clarify the mechanism of its regulation of ivGCs sensitivity. This study first characterized the miRNA profiles of plasma exosomes by miRNA sequencing to identify miRNAs differentially expressed between GO patients with significant improvement (SI) and non-significant improvement (NSI) after ivGCs treatment. According to the function of the target genes, we screened 10 differentially expressed miRNAs. Results showed that compared with NSI patients, mir-885-3p was up-regulated and mir-4474-3p and mir-615-3p were down regulated in the exosomes of SI patients. Based on statistical difference and miRNA function, mir-885-3p was selected for follow-up study. In vitro functional analysis of exosomes mir-885-3p showed that exosomes from SI patients (SI-exo) could transfer mir-885-3p to orbital fibroblasts (OFs), up-regulate the GRE luciferase reporter gene plasmid activity and the level of glucocorticoid receptor (GR), down-regulate the level of inflammatory factors, and improve the glucocorticoid sensitivity of OFs. In addition, we found that high levels of mir-885-3p could inhibit AKT/NFκB signaling pathway, up‐regulate the GRE plasmid activity and GR level, and down‐regulate the level of inflammatory factors of OFs. Moreover, the improvement of glucocorticoid sensitivity by mir-885-3p transmitted by SI-exo can also be inhibited by AKT/NFκB agonist. Finally, through the in vivo experiment of GO mouse model, we further determined the relationship between exosomes mir‐885‐3p sequence, AKT/NFκB signaling pathway, and glucocorticoid sensitivity. As a conclusion, plasma exosomes deliver mir‐885‐3p and inhibit AKT/NFκB signaling pathway to improve the glucocorticoid sensitivity of OFs. Exosomes mir-885-3p can be used as a biomarker to determine the sensitivity of ivGCs in GO patients.

overall_design: Examination of the differential expression of exosomes miRNAs between Graves ophthalmopathy sensitive to intravenous glucocorticoid therapy and patients insensitive to  intravenous glucocorticoid therapy.

first: Jingxue

last: Sun

first: Jiaxing

last: Wei

first: Yaguang

last: Zhang

first: Jingjing

last: Li

first: Jian

first: Jiazhuo

last: Yan

first: Min

last: Guo

first: Jun

last: Han

first: Hong

last: Qiao


title: Paternal high-fat diet altered sperm 5'tsRNA-Gly-GCC is associated with enhanced gluconeogenesis in the offspring

status: Public on Feb 18 2022

city: Shanghai

first: Yunfang

address: 1239 Siping Road

department: Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology

institute: Tongji University

summary: In this study, we aimed to find out how the sperm tsRNA involved in paternal high-fat diet induced abnormal gluconeogenesis of F1 offspring, and explore the underlying molecular mechanism of its regulation.

overall_design: We performed small RNA sequencing to obtain a profile of small RNA in spermatozoa from the CD-F0 and HFD-F0 groups

first: Bin

last: Wang

first: Lin

last: Xia

first: Dan

last: Zhu

first: Hongtao

last: Zeng

last: wei

first: Likui

last: Lu

first: Weisheng

first: Yajun

last: Shi

first: Jingliu

last: Liu

first: Miao


title: LiMe genes and ER-Breast cancer

city: Chicago

first: Seema

middle: Ahsan

last: Khan

state: IL

address: 303 E. Superior Street, 4-111

institute: Northwestern University

summary: MCF-10 A cells were allowed to grow in high fatty acid environment to see what happens to the lipid metabolism and  oncogenic pathways.

overall_design:
MCF10A treated with octanoate
------------------------------
Artificial Intelligene (www.artificialintelligene.com)

first: Sivangi

last: Yadav


title: Genome-wide replication fork directionality measured by strand-specific sequencing of Okazaki fragments in chicken lymphoma cells (DT40).

city: Paris

first: Chunlong

last: Chen

address: 26 rue d’Ulm

institute: Institut Curie

overall_design: Here we provide strand-specific sequencing of Okazaki fragments (OK-seq) and measurement of DNA replication fork directionarity (RFD)  in DT40 cells. RFD reveals the proportion of rightward- and leftward-oriented forks in every genomic locus and allows a quantitative analysis of replication initiation, progression and termination along the genome.

first: Chun-Long

first: Nataliya

last: Petryk

first: Olivier

last: Hyrien


title: Mesothelial cell-derived antigen-presenting cancer-associated fibroblasts induce expansion of regulatory T cells in pancreatic cancer

city: Dallas

first: Huocong

last: Huang

state: TX

address: 6000 Harry Hines Blvd NB8.212

department: Department of Surgery

institute: UT Southwestern Medical Center

summary: Recent studies have identified a unique cancer-associated fibroblast (CAF) population called antigen-presenting CAFs (apCAFs). apCAFs are characterized by the expression of MHC II molecules, suggesting a function in regulating tumor immunity. Here by integrating multiple single cell RNA sequencing studies and performing robust lineage tracing assays, we found that apCAFs are derived from mesothelial cells. During pancreatic cancer progression, mesothelial cells form apCAFs by down-regulating mesothelial features and gaining fibroblastic features, a process induced by IL-1 and TGFβ. apCAFs directly ligate and induce naïve CD4+ T cells into regulatory T cells (Tregs) in an antigen-specific manner. Moreover, targeting the mesothelial cell marker mesothelin by a monoclonal antibody can effectively inhibit mesothelial cell to apCAF transition and the Treg formation induced by apCAFs. Taken together, our study elucidates an important but neglected cell type that regulates tumor immunity and may lead to targeted therapies that can overcome immune evasion in cancer.

overall_design: Examination of parental PanMeso cells and sorted PanMeso cells from tumors


title: Rapid and efficient adaptation of the dTAG system in mammalian development reveals stage specific requirements of NELF

first: Abderhman

last: Abuhashem

address: Rockefeller Research Labs, 430 E 67th St

department: Developmental Biology Program

institute: Sloan-Kettering Institute for Cancer Research

summary: mRNA expression profile of late 2-cell mouse embryos cultured +/- dTAG-13 to degrade NELFB from the zygote stage.

overall_design: Zygotes were retrieved from homozygouse Nelfb-dTAG females post natural mating with homozygous males. Zygotes were culture for 30 hours +/- 500nM dTAG-13 in KSOM medium, then collected for SMART-seq

first: Anna-Katerina

last: Hadjantonakis


title: The RNA sequencing analysis of  corylin ameliorating cellular senescence in HUVECs

city: Taoyuan City

first: chunhao

last: feng

address: No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan (R.O.C.)

department: Graduate Institute of Natural Product

country: Taiwan

institute: Chang Gung University

summary:
Purpose: To understand the mechanism by which corylin ameliorates cellular senescence in HUVECs, we used RNA sequencing to analyze transcriptome differences.
Methods: RNA was collected from HUVECs and extracted by TRIzol (T9424, Sigma, USA). The extracted RNA samples were sent to Genomics (Taipei, Taiwan) for analysis, and a library was constructed. Briefly, after quality control of raw reads, mRNA was purified using reverse transcriptase and a random primer to synthesize single-strand cDNA, and dUTP was used in place of dTTP to generate double-stranded cDNA. A single ‘A’ nucleotide was added to the 3’ end of ds cDNAs. Then, multiple indexing adapters were ligated to the 5’ and 3’ ends of ds cDNA. PCR was used to selectively amplify the DNA fragments with adapters on both ends. The library was validated on an Agilent 2100 Bioanalyzer and Real-Time PCR System.
Result: We found 433 shared transcripts between S/Y and S+C/S. By comparing the KEGG pathway annotation, we found shared pathways between the two groups associated with cellular senescence, the cell cycle, DNA replication, and the p53 signaling pathway. We next decoded the transcriptome differences in those pathways. Numerous transcripts were shifted in S/Y, such as a reduction in cyclin protein, replication factor, DNA helicase, cell proliferation signals, and an increase in SASP, indicating that HUVECs are in the senescent state. Furthermore, we found that the transcriptome pattern of senescent cells treated with corylin was similar to that of young cells. Most importantly, we found that eukaryotic translation initiation factor 4E (eIF4E)-binding protein 1 (4E-BP1) downregulated and Rho upregulated with corylin treatment, which are the downstream mTOR1 and mTOR2 pathways respectively. Additionally, we found that corylin decreased mTOR1 and p70S6k phosphorylation in U2OS cells . Taken together, these data reveal that corylin ameliorates cellular senescence.
Conclusions: By comparing the KEGG pathway annotation, we found shared pathways between the two groups associated with cellular senescence, the cell cycle, DNA replication, and the p53 signaling pathway. We next decoded the transcriptome differences in those pathways. Numerous transcripts were shifted in S/Y, such as a reduction in cyclin protein, replication factor, DNA helicase, cell proliferation signals, and an increase in SASP, indicating that HUVECs are in the senescent state.

overall_design: RNA sequencing to analyze transcriptome differences in three different groups: proliferating cells (Y), senescent cells (S), senescent cells with corylin treatment (S+C)


title: Olig2 Defines a Unique Subset of Neural Stem Cells That Produce Specific Olfactory Bulb Interneuron Subtypes in the Subventricular Zone of Postnatal and Adult Mice

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Distinct neural stem cells reside in different regions of the subventricular zone and generate multiple olfactory bulb interneuron subtypes in the adult mouse brain. This study shows that the basic helix-loop-helix type transcription factor Olig2 defines a ventrally enriched subset of NSCs in the early postnatal and adult SVZ and plays an important role in the subtype specification of olfactory bulb interneurons produced by adult NSCs.

overall_design: E18.5, P14 and adult mouse NSCs were analyzed using 10X single-cell rna-seq

first: Kenneth

last: Campbell

first: Masato

last: Nakafuku


title: Mogrol attenuates osteoclast formation and bone resorption by inhibiting the TRAF6/MAPK/NF-κB signaling pathway in vitro and protects against osteoporosis in postmenopausal mice

city: Xiamen

first: Chen

last: Yongjie

state: Fujian

address: Xiang'an East street

department: Orthopedics Surgery

institute: Xiang'an Hospital of Xiamen University

summary: Osteoporosis is a serious public health problem that results in fragility fractures, especially in postmenopausal women. Because the current therapeutic strategy for osteoporosis has various side effects, a safer and more effective treatment is worth exploring. It is important to examine natural plant extracts during new drug design due to low toxicity. Mogrol is an aglycon of mogroside, which is the active component of Siraitia grosvenorii and exhibits anti-inflammatory, anticancer and neuroprotective effects. Here, we demonstrated that mogrol dose-dependently inhibited osteoclast formation and function. To confirm the mechanism, RNA sequencing (RNA-seq), real-time PCR (RT–PCR), immunofluorescence and Western blotting were performed. The RNA-seq data revealed that mogrol had an effect on genes involved in osteoclastogenesis. Furthermore, RT–PCR indicated that mogrol suppressed osteoclastogenesis-related gene expression, including CTSK, ACP5, MMP9 and DC-STAMP, in RANKL-induced bone marrow macrophages (BMMs). Western blotting demonstrated that mogrol suppressed osteoclast formation by blocking TNF receptor-associated factor 6 (TRAF6)-dependent activation of the mitogen-activated protein kinase (MAPK)/nuclear factor-B (NF-κB) signaling pathway, which decreased two vital downstream transcription factors, the nuclear factor of activated T cells calcineurin-dependent 1 (NFATc1) and c-Fos proteins expression. Furthermore, mogrol dramatically reduced bone mass loss in postmenopausal mice. In conclusion, these data showed that mogrol may be a promising procedure for osteoporosis prevention or therapy.

overall_design: Study the effect of mogrol on osteoclast differentiation and its meachnism

first: Ji

last: Guangrong

first: Xu

last: Ren