title: Failure of digit tip regeneration in the absence of Lmx1b suggests Lmx1b functions disparate from dorsoventral polarity

city: Santander

first: Marian

last: Ros

address: 22nd Albert Einstein St.

institute: IBBTEC-CSIC-SODERCAN

summary: Mammalian digit tip regeneration is linked to the presence of nail tissue, but a nail-explicit model is missing. Here, we report that nail-less double-ventral digits of ΔLARM1/2 mutants that lack limb-specific Lmx1b enhancers, fail to regenerate. To separate the nail’s effect from the lack of DV polarity, we also interrogate double-dorsal double-nail digits and show that they regenerate. Thus, DV polarity is not a prerequisite for regeneration and the nail requirement is supported. Transcriptomic comparison between wild-type and non-regenerative ΔLARM1/2 mutant blastemas reveals differential up-regulation of vascularization and connective tissue functional signatures in wild-type versus upregulation of inflammation in the mutant. These results, together with the finding of Lmx1b expression in the postnatal dorsal dermis underneath the nail and uniformly in the regenerative blastema opens the possibility of additional Lmx1b roles in the progression of digit tip regeneration, in addition to the indirect effect of mediating the formation of the nail.

overall_design: RNA-seq from dissected blastema from amputated digit tips; stage: 12 or 14 days post amputation (dpa); mouse genotype: Wildtype (2 biological replicates) or ΔLARM1/2 (3 biological replicates)

first: A

last: Castilla-Ibeas

first: S

last: Zdral

first: L

last: Galán

first: E

last: Haro

last: Allou

first: V

last: Campa

first: J

last: Icardo

last: Mundlos

first: K

last: Oberg

first: M


title: IL-2 is inactivated by the acidic pH environment of tumors enabling engineering of a pH-selective mutein (RNA-Seq)

status: Public on Dec 02 2022

city: Lille

first: Suman

last: Mitra

address: 1 Place de Verdun

country: France

institute: INSERM

type: Expression profiling by high throughput sequencing

summary: Cytokines interact with their receptors in the extracellular space to control immune responses. How the physicochemical properties of the extracellular space influence cytokine signaling is incompletely elucidated. Here, we show that the activity of interleukin (IL)-2, a critical cytokine in T cell immunity, is profoundly affected by pH, limiting IL-2 signaling within the acidic environment of tumors. Generation of lactic acid by tumors limits STAT5 activation, effector differentiation and anti-tumor immunity by CD8+ T cells and renders high-dose IL-2 therapy poorly effective. Directed evolution enabled selection of a pH-selective IL-2 mutein (Switch-2). Switch-2 binds the IL-2 receptor subunit IL-2Ra with higher affinity, triggers STAT5 activation and drives CD8+ T cell effector function more potently at acidic pH than at neutral pH. Consequently, high-dose Switch-2 therapy induces potent immune activation and tumor rejection with reduced on-target toxicity in normal tissues. Finally, we find that sensitivity to pH is a generalizable property of a diverse range of cytokines with broad relevance to immunity and immunotherapy in healthy and diseased tissues.

overall_design: Activated human CD8+ T cells were rested O/N, transferred in complete media pH 7.5 or 6.5 and stimulated for 4 h with 10 nM IL-2 or Switch-2

first: Gaggero

last: Silvia

first: Leprohon

last: Malo

first: Mitra

last: Suman


title: IL-2 is inactivated by the acidic pH environment of tumors enabling engineering of a pH-selective mutein (scRNA-Seq)

overall_design: CD8+ TILs from B16.SIY tumor-bearing mice treated with PBS, Fc-IL-2 or Fc-Switch-2 were isolated by magnetic and FACS sorting and analysed by scRNAseq. For each sample, cells derived from 3 different mice were pulled together.


title: IL-2 is inactivated by the acidic pH environment of tumors enabling engineering of a pH-selective mutein

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: A Nuclear factor I-X mediated regulatory network governs the balance of hematopoietic stem and progenitor cells during hematopoiesis

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Place

department: Department of Hematology

country: USA

institute: St. Jude Children’s Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The transcription factor (TF), nuclear factor I-X (NFIX), is a positive regulator of hematopoietic stem and progenitor cell (HSPC) transplantation. Nfix-deficient HSPC exhibit a severe loss of repopulating activity, increased apoptosis and a loss of colony forming potential. However, the underlying mechanism remains elusive. Here, we performed cellular indexing of transcriptomes and epitopes by high-throughput sequencing (CITE-seq) on Nfix-deficient HSPC and observed loss of long-term hematopoietic stem cells (LT-HSC) and an accumulation of megakaryocyte and myelo-erythroid progenitors. The genome-wide binding profile of NFIX in primitive murine hematopoietic cells revealed its co-localization with other hematopoietic TFs such as PU.1. We confirmed the physical interaction between NFIX and PU.1 and unveiled that the two TFs co-occupy super-enhancers and regulate genes implicated in cellular respiration and hematopoietic differentiation. Our data support a model in which NFIX collaborates with PU.1 at super-enhancers to promote the differentiation of hematopoietic progenitors.

overall_design: scRNA-seq of NFIX WT and KO bone marrow cells, NFIX,PU.1 CHIP-seq, ATAC-seq, and H3K27ac ChIP-seq in HPC5 cells.

first: Megan

last: Walker

first: Yichao

last: Li

first: Yong

last: Cheng


title: YAMAT-seq of mature tRNA pools in the bacterium Escherichia coli str. K-12 substr. MG1655 and derivatives

city: Ploen

first: Jenna

last: Gallie

address: August-Thienemann Strasse 2

country: Germany

institute: Max Planck Institute for Evolutionary Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in 10 strain-medium combinations (all strains dervied from the model bacterium E. coli MG1655). The aim of the experiment was to investigate the effect of reducing tRNA gene copy number on mature tRNA pools in rich and poor media.

overall_design: Three replicates of five strains (MG1655 wildtype; MG1655 with glyVXY tRNA genes removed, MG1655 with leuVPQ tRNA genes removed, MG1655 with glyU tRNA gene removed, and MG1655 with thrW tRNA gene removed), in each of two media (rich: rich LB, and poor: M9 with 0.05% galactose). 30 samples total (5 strains x 2 media x 3 reps = 30 samples).

first: WingYui

last: Ngan

first: Parth

middle: K

last: Raval

first: Deepa

last: Agashe


title: RNASeq of RNA from blasted CD4+ T cells from individuals with TCF3 mutations and healthy controls

status: Public on Dec 01 2022

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr.

department: Dept. of Lab. Medicine

institute: NIH Clinical center

summary: RNA-seq was performed using RNA extracted from blasted CD4+ T cells from individuals with TCF3 (haploinsufficiency [HI], null, or dominant negative [DN] mutations and healthy controls for the following study groups: healthy controls (HC, n=4) and patients with TCF3 mutations (HI=4, null=1, DN=1 ). Libraries were prepared using the AmpliSeq for Illumina Transcriptome Human Gene Expression panel. RNA-seq was performed on the Illumina HiSeq 2500 (Illumina; AmpliSeq for Illumina/HiSeq 2500). Demultiplexed reads were mapped to the hg19 genome using the splice-aware aligner Tophat (Trapnell et al., 2009). Gene-level counts data were generated using the Rsubread feature counts a read summarization program that counts mapped reads for genomic features such as genes (Liao et al., 2019). Differential expression analysis was performed using R (v.3.5.3) and DESeq2 (v.1.22.2)(Love et al., 2014).

overall_design:
RNA sequencing was performed using the AmpliSeq for Illumina Transcriptome Human Gene Expression panel anf the Illumina HiSeq 2500 analyzer. We analyzed RNA samples extracted from enriched T cell blasts from healthy controls and patients with TCF3 mutations.
Submitter states that raw data files were lost due to server issues

first: Sergio

last: Rosenzweig

first: Hyesun

last: Kuehn

first: Jennifer

last: Stoddard

first: Shubham

last: Goel

first: Brigette

last: Boast


title: Gene expression profile at single cell level of periheral blood mono-nucleus cells (PBMC) in response to bacterial protein (PFOR) stimulation

city: Jinan

first: Ming

state: Shandong

address: Wenhuaxi Road #107

country: China

institute: Shandong University, Qilu Hospital

summary: We identified Pyruvate:Ferredoxin Oxidoreductase (PFOR) as a bioactive protein from Faecalibacterium prausnitzii. We usd single cell transcriptome sequencing to fully evaluate the PFOR's effect on PBMC.

overall_design: In this study, PBMCs samples were treated with the PFOR protein or its 2nd inactive peptide (as control) respectively. The scRNA-seq of 10× Genomics based on droplet capture technology was done by Novogene (Tianjin, China) according to their commercially standard protocol (Ni et al., 2021). Briefly, the harvested single cells and the gel beads with barcoded sequences and oil droplets were put in the machine together. These gel beads precisely capture the target cells, then cells were lysed, thus releasing a large quantity of RNA and barcoded sequences, which undergo reverse transcription producing the cDNA templates for sequencing. Bulk PCR amplification was then performed to establish a library, which was for 3’end sequencing at last.

first: Kai-ruo

last: Wang

first: Yi-xuan

last: Guo

first: Yuan-yuan

last: Liu


title: Deacetylation of HP1g enhances multiple myeloma drug resistance through DNA damage repair and liquid-liquid phase separation (ChIP-seq)

city: Tianjin

first: Zhiqiang

address: 22 Qixiangtai Rd

department: Pathophysiology

institute: Tianjin Medical University

summary: Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during drug resistance, but the underlying mechanisms are not fully understood. Here we demonstrate that HP1g coordinates histone H3 lysine 9 trimethylation (H3K9me3) to regulate chromatin dynamic and gene transcription during bortezomib resistance.Mechanistically, HP1g can interact with H3K9me3, its CD domain is responsible to read H3K9me3 to serve its function.

overall_design: Examination of binding of HP1g in wild type myeloma cells by ChIP-seq.

first: Xin

first: Sheng


title: PHD2 constrains the anti-tumor CD8+ T cell activity

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: The  PHD/HIF  pathway  has  been  implicated  in  a  wide  range  of  immune  and  inflammatory   processes, including in the oxygen‐deprived tumor microenvironment. To examine the effect of   HIF stabilization in anti‐tumor immunity, we deleted Phd2 selectively in T lymphocytes using the   cre/lox  system.  We  show  that  the  deletion  of  PHD2  in  lymphocytes  resulted  in  enhanced   regression  of  EG7‐OVA  tumors,  in  a  HIF‐1adependent  manner.  The  enhanced  control  of   neoplastic  growth  correlated  with  increased  poly‐functionality  of  CD8+ tumor‐infiltrating   lymphocytes,  i.e.  enhanced  expression  of  IFN‐g,  TNF‐a  and  granzyme  B.  Phenotypic  and   transcriptomic analyses point  to a key role of glycolysis in sustaining CTL activity in  the  tumor   bed  and  identifies  the  PHD2/HIF‐1  pathway  as  potential  target  for  intervention.

overall_design: PHD2-deltaT vs. WT

first: Charlotte

middle: B

last: Donnet

first: Valérie

last: Acolty

last: Azouz

first: Anaëlle

last: Taquin

first: Coralie

last: Henin

first: Sarah

middle: T

last: Cafarello

first: Sébastien

last: Denanglaire

first: Massimiliano

last: Mazzone

first: Guillaume

last: Oldenhove

first: Oberdan

last: Leo

first: Stanislas

last: Goriely

first: Muriel

last: Moser


title: Epigenome-wide Association Study of Physical Activity and Physiological Parameters in Discordant Monozygotic Twins

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: An epigenome-wide association study (EWAS) was performed on buccal cells from monozygotic-twins (MZ) reared together as children, but who live apart as adults. Cohorts of twin pairs were used to investigate associations between neighborhood walkability and objectively measured physical activity (PA) levels. Due to dramatic cellular epigenetic sex differences, male and female MZ twin pairs were analyzed separately to identify differential DNA methylation regions (DMRs). A priori comparisons were made on MZ twin pairs discordant on body mass index (BMI), PA levels, and neighborhood walkability. In addition to direct comparative analysis to identify specific DMRs, a weighted gene coexpression network analysis (WGCNA) was performed to identify DNA methylation sites associated with the physiological traits of interest. The pairs discordant in PA levels had epigenetic alterations that correlated with reduced metabolic parameters (i.e., BMI). The DNA methylation sites are associated with over fifty genes previously found to be specific to vigorous PA, metabolic risk factors, and sex. Combined observations demonstrate that behavioral factors, such as physical activity, appear to promote systemic epigenetic alterations that impact metabolic risk factors. The epigenetic DNA methylation sites and associated genes identified provide insight into PA impacts on metabolic parameters and the etiology of obesity.

overall_design:
Participants for this study were monozygotic twins recruited from the community-based Washington State Twin Registry. Participants in the current study previously participated in a study of objective measures of physical activity (PA) and locations among individuals residing in the Puget Sound area around Seattle between 2012 and 2015. Follow-up data collection was conducted in 2018 and 2019, 72 pairs completed follow-up collection out of the 144 pairs who completed the baseline study. Once participants were enrolled in the study, the study coordinator sent all study materials to the participant for remote data collection. Participants wore a Qstarz BT-Q1000XT (Qstarz International Co. Ltd, Taipei, Taiwan) GPS data logger and Actigraph GT3X+ accelerometer (Actigraph Inc. Pensacola, FL) attached to a belt worn around the waist for one week. They also completed questionnaires and provided a buccal sample, with 70 complete pairs provided buccal samples. Twins that were discordant for PA, walkability, and BMI were identified and used for the study. Male and female groups were separated for the analysis. The DNA was isolated from the buccal cells and used in a methylated DNA immunoprecipitation (MeDIP) protocol followed by next generation sequencing (MeDIP-Seq).

Please note that some samples were excluded from data analysis due to either sequence quality issues or a lack of twin pair discordance, and thus do not have the associated processed data. However, those sample are included in the records for completeness.

first: Glen

last: Duncan

first: Ally

last: Avery

first: Jennifer

middle: L

last: Thorson

first: Eric

last: Nilsson

first: Daniel

last: Beck


title: Enniatin B and beauvericin prevailing in fish  feed affect intestinal cell function and hematological processes in Atlantic salmon (Salmo salar) after acute exposure

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

summary: Unintentional use of mold-infested plant-based feed ingredients are sources of mycotoxins in fish feeds. The presence of the emerging mycotoxins ENNB and BEA in Norwegian commercial fish feeds and plant-based feed ingredients has raised concerns regarding the health effects on farmed Atlantic salmon (Salmon salar). Atlantic salmon pre-smolts were exposed to a non-lethal single-dose of BEA and ENNB, and total RNA sequencing of the intestine and liver was carried out to evaluate gut health and identify possible hepatological changes after a single-dose dietary exposure. ENNB and BEA did not give acute toxicity, however ENNB caused the onset of pathways linked to acute intestinal inflammation and BEA exposures caused the onset of hepatic hematological disruption. The prevalence and concentration of ENNB found in today's commercial feed could affect the fish health if consumed over a longer time-period.

overall_design: In vivo 12h acute exposure exposure

first: Sofie

last: Söderström

first: Liv

last: Søfteland

first: Veronika

last: Sele

first: Anne-Katrine

last: Lundebye

first: Marc

middle: H

last: Berntssen


title: Host-derived O-glycans inhibit toxigenic conversion by a virulence-encoding phage in Vibrio cholerae

city: Palo Alto

first: Benjamin

last: Wang

state: CA

address: 299 Campus Drive

institute: Stanford

summary: Pandemic and endemic strains of Vibrio cholerae arise from toxigenic conversion by the CTXφ bacteriophage, a process by which CTXφ infects non-toxigenic strains of V. cholerae. CTXφ encodes the cholera toxin, an enterotoxin responsible for the watery diarrhea associated with cholera infections. Despite the critical role of CTXφ during infections, signals that affect CTXφ-driven toxigenic conversion or expression of the CTXφ-encoded cholera toxin remain poorly characterized, particularly in the context of the gut mucosa. Here, we identify mucin polymers as potent regulators of CTXφ-driven pathogenicity in V. cholerae. Our results indicate that mucin-associated O-glycans block toxigenic conversion by CTXφ and suppress the expression of CTXφ-related virulence factors, including the toxin co-regulated pilus and cholera toxin, by interfering with the TcpP/ToxR/ToxT virulence pathway. By synthesizing individual mucin glycan structures de novo, we identify the Core 2 motif as the critical structure governing this virulence attenuation. Overall, our results highlight a novel mechanism by which mucins and their associated O-glycan structures affect CTXφ-mediated evolution and pathogenicity of V. cholerae, underscoring the potential regulatory power housed within mucus.

overall_design:
We performed RNA-seq to identify changes in gene expression in V. cholerae in response to a purified pool of mucin glycans.
Comparative RNA-seq comparing +/- mucin glycans

middle: X

first: Julie

last: Takagi

first: Katharina

last: Ribbeck


title: RNA binding protein HuR protects against NAFLD by suppressing long noncoding RNA H19 expression

city: Richmond

first: Huiping

last: Zhou

state: VA

address: 1220 East Broad Street

department: Department of Microbiology and Immunology

institute: Virginia Commonwealth University

summary: NAFLD has become the most common chronic liver disease worldwide. Human antigen R (HuR), an RNA-binding protein, is an important post-transcriptional regulator. HuR has been reported as a key player in regulating lipid homeostasis in the liver and adipose tissues by using tissue-specific HuR knockout mice. However, the underlying mechanism by which hepatocyte-specific HuR regulates hepatic lipid metabolism under metabolic stress remains unclear and is the focus of this study.

overall_design: Comparative gene expression profiling analysis for the livers of wild type mice and hepatocyte-specific HuR knockout mice fed Western Diet and sugar water.

first: Yanyan

first: Yun-Ling

last: Tai

first: Grayson

last: Way

first: Jing

last: Zeng

first: Derrick

last: Zhao

first: Lianyong

last: Su

first: Xixian

last: Jiang

first: Bo-Cheng

last: Cheng

first: Xuan

first: Emily

middle: C

last: Gurley

first: Jinze

last: Liu

first: Jinpeng

first: Weidong

last: Chen

first: Xiang-Yang

first: Arun

middle: J

last: Sanyal

first: Phillip

last: Hylemon


title: Formation of the Glomerular Microvasculature is Regulated by VEGFR-3

city: Chicago

first: Yalu

state: IL

address: 303 E. Superior St,

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Single cell RNAseq analysis of kidneys from P0 mouse demonstrated that expression of Vegfc by podocytes and mesangial cells is dispensable for glomerular development.

overall_design: Kidneys from wild type C3H/Hej mouse were harvested at P0.

first: Michael

last: Donnan

first: Dilip

last: Deb

first: Dorian

middle: S

last: Kaminski

first: Susan

last: Quaggin


title: Acquired MEN1 mutations mediate resistance to Menin inhibition [CHIP-seq]

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

summary: Acute leukemias driven by rearrangements of the Mixed Lineage Leukemia gene (MLLr) or mutants of Nucleophosmin (NPM1c) require the chromatin adapter protein Menin, encoded by the MEN1 gene, to sustain aberrant gene expression programs and maintain stem-like properties. In a phase I first-in-human clinical trial, the Menin-inhibitor SNDX-5613, designed to disrupt the Menin-MLL1 interaction, induced promising clinical responses in leukemia patients6. However, acquired drug resistance was observed in some cases. Here we characterized MEN1 variants that arise on therapy and mediate resistance to Menin inhibition in patients, xenograft models, and a base-editor screen. We show that resistance was associated with emergence of novel MEN1 mutations. These mutants blunted response by impairing drug-target binding, thereby preventing the eviction of Menin-MLL1 complexes from chromatin. Structural modeling revealed a unique interaction mode of the affected residues with the drug, providing the basis for structure-guided development of second-generation compounds. These studies are the first to demonstrate that a small molecule targeting a chromatin-binding protein exerts sufficient selection pressure to drive evolution of a narrow spectrum of escape mutants leading to sustained chromatin occupancy as a novel mechanism of drug resistance in cancer.

overall_design: ChIPseq analysis for characterization of novel MEN1-mutations as mediators of acquired Menin-inhibitor resistance in acute leukemia.

first: Charles

last: Hatton

first: Yanhe

last: Wen


title: Acquired MEN1 mutations mediate resistance to Menin inhibition.


title: ONECUT2 regulates RANKL-dependent Enterocyte and Microfold cell differentiation in the small intestine; a multi-omics study [ATAC-seq]

city: Nijmegen

first: Maria

middle: Victoria

last: Luna Velez

state: Gelderland

address: Geert Grooteplein Zuid, 30, Route 274

department: Molecular Biology

country: Netherlands

institute: Radboud University

summary: Microfold (M) cells reside in the intestinal epithelium of Peyer’s patches. Their unique ability to take up and transport antigens from the intestinal lumen to the underlying lymphoid tissue is key in the regulation of the gut-associated immune response. Here, we applied a multi-omics approach to investigate the molecular mechanisms that drive M cell differentiation in mouse small intestinal organoids. We generated a comprehensive profile of chromatin accessibility changes and transcription factor dynamics during in vitro M cell differentiation, allowing us to uncover numerous cell type-specific regulatory elements and associated transcription factors. By using single-cell RNA sequencing, we identified an M cell precursor population. We linked precursor-specific gene expression to transcription factor motif content in cis-regulatory elements with our newly developed computational tool SCEPIA, uncovering a high expression of and motif activity for the transcription factor ONECUT2. Subsequent in vitro and in vivo perturbation experiments revealed that ONECUT2 acts downstream of the RANK/RANKL signalling to support Enterocyte differentiation, thereby restricting M cell lineage specification. This study sheds new light on the mechanism regulating mucosal immunity and cell fate balance, and provides a powerful blueprint for investigation of cell fate switches in the intestinal epithelium.

overall_design: Bulk ATAC-sequencing analysis of mouse small intestinal organoids treated with RANKL for 6 days, or control organoids grown in conventional organoid culture medium. Replicates correspond to three independent differentiation experiments.

middle: V

first: Hannah

last: Neikes

first: Rebecca

middle: R

last: Snabel

first: Yarah

last: Quint

first: Chen

last: Qian

first: Aniek

last: Martens

first: Gert Jan

last: Veenstra

last: Freeman

first: Simon

last: van Heeringen

first: Michiel

last: Vermeulen


title: ONECUT2 regulates RANKL-dependent Enterocyte and Microfold cell differentiation in the small intestine; a multi-omics study


title: ONECUT2 regulates RANKL-dependent Enterocyte and Microfold cell differentiation in the small intestine; a multi-omics study [scRNA-seq]

overall_design: scRNA-sequencing analyses of mouse small intestinal organoids treated with RANKL for 9 days (3 x 384-well plates per day) or with RANKL+CSRM617 for 6 days (2 x 384-well plates per day).


title: ONECUT2 regulates RANKL-dependent Enterocyte and Microfold cell differentiation in the small intestine; a multi-omics study [bulk RNA-seq]

overall_design: Bulk RNA-sequencing analyses of mouse small intestinal organoids treated with RANKL for 6 days, alone or in combination with CSRM617, or control organoids grown in conventional organoid culture medium. Replicates correspond to three independent differentiation experiments.


title: ONECUT2 regulates RANKL-dependent Enterocyte and Microfold cell differentiation in the small intestine; a multi-omics study [ChIP-Seq]

overall_design: Bulk ChIP-sequencing (H3K27ac, ONECUT2) analysis of mouse small intestinal organoids treated with RANKL for 6 days, or control organoids grown in conventional organoid culture medium. Replicates correspond to three independent differentiation experiments.

first: Gert


title: Acquired MEN1 mutations mediate resistance to Menin inhibition [RNA-seq]

overall_design: RNAseq analysis for characterization of novel MEN1-mutations as mediators of acquired Menin-inhibitor resistance in acute leukemia.


title: Stakeholder Florida Pompano Larviculture Across Different Salinities Whole Body Transcriptomes

city: Fort Pierce

first: David

last: Bradshaw

state: FL

department: Aquaculture & Stock Enhancement

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

summary:
Introduction: A major economic impediment to the aquaculture of marine finfish in land-based recirculating systems is maintaining the system salinity at a range for optimal growth. Florida Pompano (Trachinotus carolinus) are warm water, euryhaline, marine finfish shown to be a suitable candidate for low-salinity culture. Due to its popularity among sport and commercial fishers, high market value, and ability to readily consume pelleted feeds, the Florida Pompano has become a renewed target for commercialized aquaculture. Although the Florida Pompano has been successfully grown at various salinities, its optimal growth salinity has not yet been established. Studies have shown culturing at different salinities has an effect on digestion rates, feed utilization, and lipid biosynthesis. Identifying the optimal salinity for growth would result in decreased energy expenditure on maintaining homeostasis, since osmoregulation is a highly demanding process. This would allow for energy to be spent on the efficient use of nutrients.
Methods: Our study was designed to determine how Florida Pompano larviculture at various salinities affects fish health with transcriptomics (RNA-seq) and fatty acid analysis. RNA-seq was used to identify genes actively transcribed and expressed at the time of sampling. After hatching in a salinity of ~ 30 ppt, larvae were reared in 345 L tanks at one of three salinities (10, 20, 30 ppt) in triplicate. Larvae samples for RNA-seq and fatty acid analysis were collected every three days until weaning. Samples for fatty acid composition were analyzed using a gas chromatography-mass spectrometry (GC/MS). RNA was extracted from homogenized whole-body samples using the Qiagen RNeasy Mini kit. Total RNA was sequenced on the Illumina HiSeq 4000 System. Raw sequences were filtered for low-quality sequences, aligned to the S. dumerili reference genome (NCBI Genome: 12614), and quantified. Each sampling day was compared across salinities to establish the differentially expressed genes (DEGs) between salinities.
Results & Discussion: The numbers of DEGS in pooled samples was minimal (less than 15 total in each comparison) and the number of DEGS at each dph was variable. There were no significant differences between pooled samples or at each dph according to PERMANOVA analysis, but each dph was statistically different on pairwise analysis. Gene set enrichment analysis revealed that there was a downregulation of immune related genes in lower salinities versus higher salinities suggesting larvae may be dealing with less stress at lower salinities. Most osmoregulation, fatty acid, and immune related genes tested were not significantly different across salinities. This is likely be cause the Florida pompano is euryhaline and has a tolerance to the salinities selected. There was an increase in the expression levels of several immune related genes that may indicate an increase exposure to pathogens at later days post hatch likely related to feeding schedule. There was also an increase in fatty acid biosynthesis genes that corresponded with levels of fatty acids indicating a possible synthesis of essential fatty acids from precursors.
Conclusions: From a transcriptomics perspective, the larvae did not show a negative response to lower salinities in comparison to higher salinities, which in fact showed upregulation of immune related genes. Further exploration of Florida pompano’s ability to biosynthesize essential fatty acids is necessary. This study will help enable the optimization of Florida Pompano larviculture using information on the optimal salinity and fatty acid content for growth and facilitate more cost-effective rearing methods.

overall_design: Three salinities in triplicate tanks with 30 ppt as control salinity, one fish taken from each tank at 7 timepoints across 3 to 24 days post hatch

first: Sahar

last: Mejri

first: Carlie

first: Laura

last: King

first: Veronica

last: Uribe

first: Gonzalo

last: Illán

first: Elizabeth

last: Allmon

first: Brandon

last: McHenry

first: Brent

last: Rupnik

first: Nicole

last: Kirchhoff

first: Martin

last: Riche

last: Sepúlveda

first: Paul

last: Wills


title: 10X Genomics single-cell RNA-Seq data set of CreER mice

city: Dallas

first: Tao

last: Wang

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Center

summary: The liver is organized into zones in which hepatocytes express different metabolic enzymes. The cells most responsible for liver repopulation and regeneration remain undefined because fate-mapping has only been performed on a few hepatocyte subsets. Fourteen mouse fate mapping strains were used to systematically compare distinct subsets of hepatocytes. During homeostasis, cells from both periportal zone 1 and pericentral zone 3 contracted in number, whereas cells from midlobular zone 2 expanded in number. These cells, which are sheltered from common injuries, also contributed to regeneration after pericentral and periportal injuries. Zone 2 repopulation was driven by the IGFBP2-mTOR-CCND1 axis. Hence, different regions of the lobule exhibit differences in their contributions to hepatocyte turnover, and zone 2 is the primary source of new hepatocytes during homeostasis and regeneration.

overall_design: Primary hepatocytes were isolated with a two-step collagenase perfusion method described previously. Cells were washed and resuspended in hepatocyte washing medium (Life, 17704024). Single cell libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagents Kit v3. For each sample, 8,000 hepatocytes were loaded to target ~5,000 cells after recovery according to the manufacturer's protocol. Single cell libraries were generated and sequenced using the 150 bp paired-end Illumina NextSeq500 in the UTSW Children’s Research Institute Sequencing Facility.   10X scRNA-seq data was preprocessed using the Cellranger v3.0.2 software. We used the mkfastq and count commands to process the 10x single-cell RNA-seq output into cells by gene expression count matrix, and used the aggr command to pool sequencing runs from 4 mice. All parameters were set to default except for the “force-cells” parameter, which was set to 4000.

first: Hao

last: Zhu


title: Transcriptional profiling of mouse Th17 cells treated with bacterial metabolites 3-oxo-lithocholic acid (3-oxoLCA) and isolithocholic acid (isoLCA)

city: Boston

first: Eunha

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Immunology

institute: Harvard Medical School

summary: We report transcriptional profiling of mouse Th17 cells activated and expanded in vitro in the presence of Th17-inhibitory bacterial metabolites 3-oxoLCA and isoLCA.

overall_design: Naïve CD4 T cells  from C57BL/6J mice were activated and expanded in Th17 polarization condition for 3 days in vitro. 3-OxoLCA and isoLCA were added 18 hours after T cell receptor (TCR) activation by anti-CD3 and anti-CD28 antibodies.

first: Donggi

last: Paik

first: Jun

last: Huh


title: Symptomatic Domoic Acid exposure in zebrafish

city: Seattle

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Domoic acid (DA) is a naturally produced neurotoxin synthesized by the marine diatom genus Pseudo-nitzschia. DA accumulates in filter-feeders such as shellfish, and can produce severe neurotoxicity when contaminated seafood is ingested. DA poisoning is a significant public health concern, and though seafood regulations have effectively minimized the human risk of severe acute poisoning, the effects of exposure at asymptomatic levels are poorly understood. The objective of this study was to determine the effects of exposure to symptomatic and asymptomatic doses of DA on gene expression patterns in the zebrafish brain. We exposed adult zebrafish to either a symptomatic (1.1 ± 0.2 μg /g) or an asymptomatic (0.31 ± 0.03 µg DA/g fish) dose of DA by intracelomic injection and sampled at 24, 48 and 168 h post-injection. Transcriptional profiling was done using Agilent and Affymetrix microarrays. Our analysis revealed distinct, non-overlapping changes in gene expression between the two doses. We found that the majority of transcriptional changes were observed at 24 hours post-injection with both doses. In response to symptomatic dose exposure, we observed 328, 5, and 1 genes were differentially expressed at 24, 48 and 168 hours post-injection, respectively. In contrast, 136, 12, and 28 genes were differentially expressed in the asymptomatic dose at the same time points. Pathway analysis revealed symptomatic DA exposure affected genes associated with pathways including cell adhesion, inflammation, and amyloid proteins. Among the pathways enriched among genes differentially expressed with asymptomatic exposure were circadian rhythms and endocrine signaling. Overall, these results suggest that transcriptional responses are specific to the DA dose and that asymptomatic exposure can cause long-term changes. Many of the differentially expressed genes are important players in neuronal, neuroimmune and neuroendocrine function. Further studies are needed to characterize the potential downstream neurobehavioral impacts of DA exposure.

overall_design: Wild-type zebrafish (Danio rerio, AB strain), approximately five months of age, were obtained from Oregon State University (Sinnhuber Aquatic Research Laboratory Corvallis, OR). Fish were maintained at the Northwest Fisheries Science Center (NWFSC, Seattle, WA) in a ZebTec stand-alone recirculating and continuously-monitored zebrafish rack system with UV sterilizer (Techniplast, Exton, PA). Water temperature was maintained at 26°C, and fish were kept on a 12:12 hr light:dark cycle and fed daily with BioVita fish feed (Bio-Oregon, Longview, WA).  Adult zebrafish were exposed to domoic acid (DA) or an identical volume of vehicle (PBS) via intracoelomic (IC) injection at one year of age. DA was purchased from Sigma Chemical Corp. (St. Louis, MO). The dose of DA used in this experiment was 1.1 ± 0.2 μg /g fish. Dose standard deviations represent slight differences in individual fish body weights. Injections were of 10μL volume delivered with 33-gauge needle in a custom-made auto-injector from Hamilton® (Reno, NV). After each injection, fish were observed for 30-45 minutes to note the instance of any neurobehavioral excitotoxic signs (e.g., circle- or spiral-swimming). This is considered to be a “symptomatic dose” as these fish showed behavioral symptoms soon after injection, which were ameliorated within five minutes. Each treatment consisted of 10-12 individual fish (biological replicates) per time period.

first: Alia

last: Hidayat

first: Kathi

last: Lefebvre

first: Theo

last: Bammler

first: Neel

last: Aluru


title: Mechano-regulated RNA binding protein hnRNPC contributes to RNA homeostasis in heart failure

city: Brno

first: Fabiana

last: Martino

address: Studentska

department: CTM

country: Czech Republic

institute: ICRC

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

overall_design: Refer to individual Series


title: Examination of Generational Impacts of Adolescent Chemotherapy: Ifosfamide and Potential for Epigenetic Transgenerational Inheritance

status: Public on Nov 30 2022

first: Michael

last: Skinner

summary: The current study was designed to use a rodent model to determine if exposure to the chemotherapy drug ifosfamide during puberty can induce altered phenotypes and disease in the grand-offspring of exposed individuals through epigenetic transgenerational inheritance. Numerous toxicant exposures during critical developmental windows can have generational impacts through this non-genetic inheritance mechanism. Pathologies such as delayed pubertal onset, kidney disease and multiple pathologies were observed to be significantly more frequent in the F1 generation offspring of ifosfamide lineage females. The F2 generation grand-offspring ifosfamide lineage males had transgenerational pathology phenotypes of early pubertal onset and reduced testis pathology. Reduced levels of anxiety were observed in both males and females from the exposure lineage in the transgenerational F2 generation grand-offspring. Differential DNA methylated regions (DMRs) were also identified in chemotherapy and control lineages sperm in the F1 and F2 generations. The transgenerational alterations in sperm epigenetics provides a molecular mechanism for the ancestral impacts of chemotherapy. Therefore, chemotherapy exposure can impact pathology and disease susceptibility in subsequent generations.

overall_design:
The transgenerational actions of control vehicle phosphate buffered saline (PBS) and ifosfamide (8.5mg/kg of body weight) treatments administered to pubertal male rats (F0 generation) once every three days for three treatments, starting at 26 days of age were investigated. Therefore, the F0 generation pubertal male was exposed to chemotherapy and as an adult bred to generate the F1 generation and F1 generation adult bred to generate the F2 generation for a transgenerational assessment. Analysis of sperm differential DNA methylation regions (DMRs) between F1 and F2 generation ifosfamide and control lineage animals was assessed with methylated DNA immunoprecipitation (MeDIP) followed by next generation sequencing (MeDIP-Seq).
Several samples do not have an associated processed data file

first: Ryan

middle: P

last: Thompson

first: Daniel

last: Beck

first: Eric

last: Nilsson

first: Millissia

last: Maamar

first: Margarett

last: Shnorhavorian


title: Mechano-regulated RNA binding protein hnRNPC contributes to RNA homeostasis in heart failure [RIP-Seq]

summary: Cardiac pathologies are characterized by intense remodeling of the extracellular matrix (ECM) that eventually leads to heart failure. Cardiomyocytes respond to the ensuing biomechanical stress by re-expressing fetal contractile proteins via transcriptional and post-transcriptional processes, like alternative splicing (AS). Here, we demonstrate that the heterogeneous nuclear ribonucleoprotein C (hnRNPC) is upregulated and relocates to the sarcomeric Z-disk upon ECM pathological remodeling. At this site, the protein participates to the localized translation of mRNAs encoding sarcomeric proteins. Alterations in hnRNPC expression and localization can be mechanically determined and affect the AS of numerous mRNAs involved in mechanotransduction and cardiovascular diseases. We thus propose that cardiac ECM remodeling serves as a switch in RNA metabolism by directly impacting an associated regulatory protein of the spliceosome apparatus. These findings offer new insights on the mechanism of mRNAs homeostasis mechanoregulation in disease conditions.

overall_design: RIP-seq : RNA immunoprecipitation of hnRNPC-RNA complexes in human failing heart (HF).

first: Ana

last: Perestrelo

first: Vaclav

last: Hejret

first: Helena

last: Durikova

first: Vladimir

last: Horvath

first: Francesca

last: Cavalieri

first: Frank

last: Caruso

first: Waleed

last: Albihlal

first: André

last: Gerber

first: Mary

middle: A

last: O’Connell

first: Stefania

last: Pagliari

first: Giancarlo

last: Forte


title: Hepatic Phosphatidylcholine Catabolism Driven by PNPLA7 and PNPLA8 Supplies Endogenous Choline to Replenish the Methionine Cycle with Methyl Groups III

city: Tokyo

first: Tetsuya

last: Hirabayashi

address: 2-1-6 Kamikitazawa, Setagaya-ku

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

summary: Choline supplies methyl groups for regeneration of methionine and the methyl donor S-adenosylmethionine in the liver. Here we demonstrate that the catabolism of membrane phosphatidylcholine (PC) into water-soluble glycerophosphocholine (GPC) by the phospholipase/lysophospholipase PNPLA8-PNPLA7 axis enables endogenous choline stored in hepatic PC to be utilized in methyl metabolism. PNPLA7-deficient mice show marked decreases in hepatic GPC, choline, and several metabolites related to the methionine cycle, accompanied by various signs of methionine insufficiency including growth retardation, hypoglycemia, hypolipidemia, increased energy consumption, reduced adiposity, increased FGF21, and an altered epigenetic methylation landscape. Moreover, PNPLA8-deficient mice recapitulate most of these phenotypes. In contrast to wild-type mice fed a methionine/choline-deficient diet, both knockout strains display a decreased hepatic triglyceride likely via reductions of lipogenesis and GPC-derived glycerol flux. Collectively, our findings highlight the biological importance of phospholipid catabolism driven by PNPLA8/PNPLA7 in methyl group flux and triglyceride synthesis in the liver.

overall_design: We compared gene expression in livers and white adipose tissues(WATs) using Pnpla7-/- (knockout) mice and Pnpla7+/+ (wild type) controls. Individual array samples were generated by pooling equal amounts of total RNA derived from livers and WATs of 5 animals at 4 weeks.

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: Hepatic Phosphatidylcholine Catabolism Driven by PNPLA7 and PNPLA8 Supplies Endogenous Choline to Replenish the Methionine Cycle with Methyl Groups


title: Hepatic Phosphatidylcholine Catabolism Driven by PNPLA7 and PNPLA8 Supplies Endogenous Choline to Replenish the Methionine Cycle with Methyl Groups II

overall_design: We compared gene expression in Pnpla7-/- (knockout) livers  with Pnpla7+/+ (wild type) controls. Individual array samples were generated by pooling equal amounts of total RNA derived from livers of 5 animals at 3 and 6 weeks.


title: Hepatic Phosphatidylcholine Catabolism Driven by PNPLA7 and PNPLA8 Supplies Endogenous Choline to Replenish the Methionine Cycle with Methyl Groups I

overall_design: We compared gene expression in Pnpla8-/- (knockout) livers  with Pnpla8+/+ (wild type) controls. Individual array samples were generated by pooling equal amounts of total RNA derived from livers of 5 animals at 8 weeks.


title: Trancriptional Profile of Mycobacterium tuberculosis Replicating at in Artificial Intraocular Fluid

city: New York

first: Michelle

middle: Beth

last: Ryndak

state: NY

address: 550 First Avenue

department: Pathology

institute: NYU Langone

summary: Intraocular tuberculosis (IOTB) is a significant cause of visual morbidity in TB-endemic countries. However, pathogenesis of Mycobacterium tuberculosis (M. tb) in the ocular compartment is poorly defined. IOTB is paucibacillary in a vast majority of patients although M. tb has been detected in both the retinal pigment epithelial (RPE) cells (Rao et al. 2006) and in the intraocular fluid (IOF) (Aggarwal et al., 2016; Bajgai et al., 2017) in some cases. In this study, we have examined the replication and whole genome transcriptome of M. tb in an IOF model (artificial IOF; AIOF) (Macri et al., 2015). Results show that, as reported for transcriptional profiles of M. tb in sputum (Sharma et al., 2017) and in a starvation model (PBS) (Betts et al., 2002), genes involved in active replication and aerobic respiration are either downregulated or not differentially expressed in the AIOF. In ARPE-19 cells (human RPE cell line), M. tb replicates poorly and exhibits a quiescent phenotype (Abhishek et al., 2018). As in sputum, PBS, and ARPE-19 cells, M. tb in AIOF downregulates genes of the DosR regulon indicating the suppression of dormancy. Importantly, genes encoding ESAT-6 and ESAT-6-like proteins are also downregulated or not differentially expressed in sputum, AIOF and ARPE-19 cells. This is stark contrast to the transcriptome of M. tb in alveolar epithelial cells (Ryndak et al., 2015) and in blood (Ryndak et al. 2014). These results paint a scenario wherein M. tb acquires a replicative and invasive phenotype when it infects a new host and disseminates systemically. However, M. tb acquires a quiescent phenotype upon reaching its final niche in an extrapulmonary site, the ocular environment.

overall_design: The global gene expression of M. tb H37Rv replicating in artificial intraocular fluid at Day 6 was compared to that of M. tb grown to log phase in Middlebrook 7H9 media.

first: Kamaljit

last: Kaur

first: Suman

last: Laal


title: Chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) detection of histone H3 lysine 14 acetylation (H3K14ac) and KAT7 (HBO1) in E14.5 mouse neural stem and progenitor cells (NSPCs)

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

summary: Tissue specific deletion of the gene encoding the histone acetyltransferase KAT7 (HBO1) in the developing mouse central nervous system using cre-recombinase expression driven by regulatory sequences of the nestin locus (NesCre transgene) resulted in defective cerebral cortex development, a complete failure of neural stem cells to give rise to neurons and oligodendrocytes during in vitro differentiation and a failure to express the neuronal differentiation program. KAT7 genome occupancy and histone H3 lysine 14 acetylation (H3K14ac) levels were assessed by ChIP-seq in proliferating Kat7 deleted vs. Kat7 intact neural stem and progenitor cells (NSPCs). KAT7 and H3K14ac were completely absent in the Kat7 deleted cells. IN KAT7 intact cells, KAT7 occupancy levels and H3K14ac levels within the body of genes correlated strongly and positively. Both were higher in genes that were expressed strongly than in genes with lower or no expression. However, KAT7 and H3K14ac were present in all genes including silent genes and in all other regions of the genome, including intergenic regions and regions decorated with histone H3 lysine 9 trimethylation (H3K9me3), an indicator of constitutive heterochromatin.

overall_design: KAT7 genome occupancy and H3K14ac levels assessed by ChIP-seq at passage 5 day 3 of proliferating Kat7lox/loxNesCreT/+ and Kat7+/+NesCreT/+ neural stem and progenitor cells (NSPCs) originally isolated at E14.5 cultured as floating colonies (neurospheres). NSPC isolates from 4 Kat7 intact and 3 Kat7 deleted animals per genotype were assessed for H3K14ac and NSPC isolates from 3 Kat7 intact and 1 Kat7 deleted animal per genotype were assessed for KAT7 occupancy. IgG controls were also assessed.

first: Anna

last: Quaglieri

first: Chris

last: Woodruff

first: Terence

last: Speed

first: Anne

middle: K

last: Voss


title: Distribution of histone H3 lysine 14 acetylation in the genome of proliferating and differentiating mouse neural stem cells (neurosphere cells) [CHIP-seq]

summary: Anti-H3K14ac ChIP-seq data of neural stem and progenitor cell (NSPC) isolates from wild-type E14.5 foetuses for each, proliferating and differentiating conditions. H3K14ac changed during differentiation. H3K14ac levels correlated positively with the activation of the neuronal and glial gene expression programs.

overall_design: H3K14ac ChIP-seq data of NSPCs isolates from 4 wild-type (WT) E14.5 foetuses grown in proliferating and differentiating conditions. For some assessments, normalisation to input was conducted. IgG controls and Kat7/Hbo1 deleted cells, which lack H3K14ac, were included as negative controls.

first: Gordon

last: Smyth


title: Mechano-regulated RNA binding protein hnRNPC contributes to RNA homeostasis in heart failure [RNA-Seq]

first: Fabiana

last: Martino

overall_design: RNA sequencing of : NHDFs transfected with a stealth siRNA negative control low GC and NHDFs transfected with hnRNPC1/C2 siRNA HSS179304 (KD1) and hnRNPC1/C2 siRNA HSS179305

first: Ana

last: Perestrelo

first: Vaclav

last: Hejret

first: Helena

last: Durikova

first: Vladimir

last: Horvath

first: Francesca

last: Cavalieri

first: Frank

last: Caruso

first: Waleed

last: Albihlal


title: Effects of loss of the histone lysine acetyltransferase KAT7 on mRNA levels in proliferating and differentiating mouse neural stem cells (neurosphere cells) [RNA-seq]

summary: RNA-seq data of neural stem and progenitor cell (NSPC) isolates from Kat7lox/loxNesCreT/+ and Kat7+/+NesCreT/+ E14.5 foetuses for each, proliferating and differentiating conditions. KAT7 and H3K14ac were not required for the continued transcription of genes that were actively transcribed at the time of loss of KAT7, but indispensable for the activation of repressed genes.

overall_design: RNA-seq data of NSPC isolates from 4 Kat7lox/loxNesCreT/+ and 4 Kat7+/+NesCreT/+ E14.5 foetuses for each, proliferating and differentiating conditions. NSPC isolates were kept in proliferating conditions for 3 passages and 3 days or differentiated for 3 days after passage 3.


title: RNA-seq analysis of  wild type and Tim-4 KO mice primary peritoneal macrophages

city: Jinan

first: Lifen

last: Gao

address: 44 Wenhua Xi Road, Jinan, Shandong, 250012 P. R. China

institute: Shandong University

summary: To investigate transcriptomic changes upon depletion of Tim-4 in macrophages

overall_design: We performed differential gene expression analysis using wild type and Tim-4 KO mice primary peritoneal macrophages

first: Wen

last: Liu

first: Yingchun

last: Wang


title: Effect of endothelial-specific endorepellin expression on gene expression of breast cancer allografts in Tie2CreER;ERKi mice

city: Philadelphia

first: Renato

middle: V.

last: Iozzo

state: PA

address: 1020 Locust Street

institute: Thomas Jefferson University

summary:
To explore the translational implications of endorepellin in breast cancer, we created a double transgenic, inducible Tie2CreER;ERKi mouse line that expresses recombinant endorepellin specifically from the endothelium. We investigated the therapeutic effects of recombinant endorepellin overexpression in an orthotopic, syngeneic breast cancer allograft mouse model.
Tamoxifen-induced expression of recombinant endorepellin specifically from the endothelium in Tie2CreER;ERKi mice markedly suppressed breast cancer allograft growth, hyaluronan deposition in the tumor proper and perivascular tissues, and tumor angiogenesis.

overall_design: To investigate the effects of endorepellin in the vasculature of triple-negative breast cancer in mice, we generated double transgenic mice expressing a tamoxifen-inducible endothelial-specific endorepellin knock-in gene, injected mice with either tamoxifen or control, and then injected syngeneic mouse breast cancer cells into the mammary fat pads. Breast tumor allografts were harvested at 22 days, RNA was extracted from tumor samples and sent for RNAseq analysis.

first: Carolyn

middle: G

last: Chen


title: HNF4a acts as upstream functional regulator of intestinal Wnt3 and Paneth cell fate

city: Sherbrooke

first: Francois

last: Boudreau

state: QC

address: 3201 Jean-Mignault

department: Immunology and Cell Biology

country: Canada

institute: Université de Sherbrooke

summary: Maturation of Paneth cells depends on canonical Wnt signaling, but few transcriptional regulators have been identified to this end. We showed that HNF4a plays a non-redundant and crucial role in supporting the growth and survival of small intestinal epithelial cultures when cultured ex vivo as organoids. Transcriptomic analyses revealed an autosomal function of HNF4a in Wnt3 transcriptional regulation and Paneth cell differentiation. We showed that Wnt3a supplementation reversed cell death and transcriptional changes caused by the deletion of Hnf4a in jejunal organoids.

overall_design: mRNA profiles of DMSO-treated (Control) and 4OHT-treated (Hnf4a-depleted) jejunal organoids, also treated with recombinant Wnt3A, at day 2 (3 replicates/condition)

first: Christine

last: Jones

first: Mariano

last: Avino


title: PCIF1-mediated deposition of 5-cap N6,2-O-dimethyladenosine in ACE2 and TMPRSS2 mRNA regulates susceptibility to SARS-CoV-2 infection

city: San Diego

first: Lingling

state: California

address: 9500 Gilman Dr

institute: University of California San Diego

summary: We applied m6Am-exo-seq and RNA-seq on lung cancer to profile the differentially expressed genes and compared the results with m6A-exo-seq

overall_design: To investigate the relationship between gene expression and m6Am modification on transcripts, differentially expressed genes (DEGs) are characterized by RNA-seq, m6Am modified transcripts are detected by m6A-exo-seq. Then DEGs and m6Am modified transcripts are intersected to obtain the genes whose expression are regulated by m6Am RNA modification

first: Tariq

last: Rana


title: TREM2-independent microgliosis promotes tau-mediated neurodegeneration in the presence of ApoE4

city: St Louis

first: Maud

last: Gratuze

state: Missouri

address: 660 S. Euclid Avenue

department: Neurology

institute: Washington University in St. Louis

summary: In addition to tau and Aβ pathologies, inflammation plays an important role in Alzheimer's disease (AD). Variants in APOE and TREM2 increase AD risk. ApoE4 exacerbates tau-linked neurodegeneration and inflammation in P301S tau mice and removal of microglia blocks tau-dependent neurodegeneration. Microglia adopt a heterogeneous population of transcriptomic states in response to pathology, at least some of which are dependent on TREM2. Previously, we reported that knockout (KO) of TREM2 attenuated neurodegeneration in P301S mice that express mouse Apoe. Because of the possible common pathway of ApoE and TREM2 in AD, we tested whether TREM2 KO (T2KO) would block neurodegeneration in P301S Tau mice expressing ApoE4 (TE4), similar to that observed with microglial depletion. Surprisingly, we observed exacerbated neurodegeneration and tau pathology in TE4-T2KO versus TE4 mice, despite decreased TREM2-dependent microgliosis. Our results suggest that tau pathology-dependent microgliosis, that is, TREM2-independent microgliosis, facilitates tau-mediated neurodegeneration in the presence of ApoE4.

overall_design: The hippocampi of three mice per experimental group were dissociated and the cell nuclei were labelled with the myeloid lineage-determining transcription factor PU.1 and sorted for subsequent single nuclei RNA-seq analysis

first: Johannes

last: Schlachetzki

first: Christopher

last: Glass

first: David

middle: M

last: Holtzman


title: Inhibition of Eicosanoid Degradation Mitigates Fibrosis of the Heart

city: Aurora

first: Timothy

last: McKinsey

state: CO

department: Medicine

institute: University of Colorado Anschutz Medical Campus

summary: Background: Organ fibrosis due to excessive production of extracellular matrix (ECM) by resident fibroblasts is estimated to contribute to >45% of deaths in the Western world, including those due to cardiovascular diseases such as heart failure (HF).  Here, we screened for small molecule inhibitors with a common ability to suppress activation of fibroblasts across organ systems.       Methods:  High content imaging of cultured cardiac, pulmonary and renal fibroblasts was employed to identify non-toxic compounds that blocked induction of markers of activation in response to the profibrotic stimulus, TGF-β.  SW033291, which inhibits the eicosanoid-degrading enzyme, 15-hydroxyprostaglandin dehydrogenase (15-PGDH), was chosen for follow-up studies with cultured adult rat ventricular fibroblasts (ARVFs) and human cardiac fibroblasts (CFs), and for evaluation in mouse models of cardiac fibrosis and diastolic dysfunction.  Additional mechanistic studies were performed with CFs treated with exogenous eicosanoids.     Results:  Nine compounds, including SW033291, shared a common ability to suppress TGF-β-mediated activation of cardiac, pulmonary and renal fibroblasts.  SW033291 dose-dependently inhibited TGF-β-induced expression of activation markers (e.g. α-smooth muscle actin and periostin) in ARVFs and normal human CFs, and reduced contractile capacity of the cells.  Remarkably, the 15-PGDH inhibitor also reversed constitutive activation of fibroblasts obtained from explanted hearts from patients with HF.  SW033291 blocked cardiac fibrosis induced by angiotensin II (Ang II) infusion and ameliorated diastolic dysfunction in an alternative model of systemic hypertension driven by combined uninephrectomy (UNX) and deoxycorticosterone acetate (DOCA) administration.  Mechanistically, SW033291-mediated stimulation of ERK1/2 mitogen-activated protein kinase signaling was required for SW033291 to block CF activation.  Of the 12 exogenous eicosanoids that were tested, only 12-hydroxyeicosatetraenoic acid (12[S]-HETE), which signals through the G protein-coupled receptor (GPCR), GPR31, recapitulated the suppressive effects of SW033291 on CF activation.      Conclusions:  Inhibition of degradation of eicosanoids, arachidonic acid-derived fatty acids that signal through GPCRs, is a potential therapeutic strategy for suppression of pathological organ fibrosis. In the heart, we propose that 15-PGDH inhibition triggers CF-derived autocrine/paracrine signaling by eicosanoids, including 12(S)-HETE, to stimulate ERK1/2 and block conversion of fibroblasts into activated cells that secrete excessive amounts of ECM and contribute of HF pathogenesis.

overall_design: Transcriptomic profiling by RNA sequencing was performed using RNA from cultured primary adult rat ventricular fibroblasts treated with TGF-beta and SW033291, alone or in combination, for 48 hours (n = 4 biological replicates for each condition)

first: Marcello

last: Rubino

first: Joshua

last: Travers

first: Alaina

middle: L

last: Headrick

first: Blake

middle: T

last: Enyart

first: Madeleine

middle: E

last: Lemieux

first: Maria

last: Cavasin

first: Jessica

last: Schwisow

first: Elizabeth

last: Hardy

first: Keenan

last: Kaltenbacher

first: Marina

middle: B

last: Felisbino

first: Eric

last: Jonas

first: Amrut

last: Ambardekar

first: Michael

last: Bristow

first: Keith

last: Koch


title: High-Throughput Transcriptome Profiling of Single Nuclei and Single Synapses Using Single-Cell Total-RNA-Seq

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

overall_design: Refer to individual Series


title: Next generation sequencing quantitative analysis of C3H10T1/2 cells treated with purmorphamine, DMSO, purmorphamine and Picoberin or DMSO and Picoberin for 24h, 48h, 96h or 7 days

city: Dortmund

first: Jana

last: Flegel

state: NRW

address: Otto-Hahn-Straße 11

department: Chemical Biology

institute: Max Planck Institute of Molecular Physiology

summary:
Purpose: Analysis of the differential gene expression of C3H10T1/2 cells undergoing Hedgehog (Hh) induced osteoblast differentiation compared to unstimulated (DMSO treated) cells and investigation of the differential gene expression caused by Picoberin, a highly potent inhibitor of Hh induced osteoblast differentiation (Comparison of purmorphamin + Picoberin treated C3H10T1/2 cells with purmorphamin + DMSO treated cells)
Methods: 80 % confluent C3H10T1/2 cells were treated either with 1.5 µM purmorphamine + DMSO, only DMSO, 1.5 µM purmorphamine + 1 nM Picoberin, 1.5 µM purmorphamine +100 nM Picoberin or DMSO + 100 nM Picoberin for 24h, 48h, 96h or 7 days.
Results: Picoberin inhibits osteoblast differentiation

overall_design: In total 60 samples were analyzed. 5 treatment conditions with 4 timepoint for each treatment condition and 3 biological replicates per condition and timepoint

first: Herbert

last: Waldmann

first: Slava

last: Ziegler

first: Christian

last: Woehler

first: Bruno

last: Hüttel


title: A Systems Biology Approach To Disentangle the Direct and Indirect Effects of Global Transcription Factors on Gene Expression in Escherichia coli

city: Uppsala

first: Ankita

last: Pal

address: Husargatan 3

department: Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

summary: We report high-throughput RNA sequencing of WT,  ΔfnrΔarcA  (FA),  ΔfnrΔihf (FI) and ΔarcAΔihf (AI) strains  in the exponential phase under anaerobic fermentative conditions

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA was extracted from two biological replicates of WT, ΔfnrΔarcA (FA), ΔfnrΔihf (FI) and ΔarcAΔihf (AI) strains in the exponential phase under anaerobic fermentation conditions, grown in glucose minimal media conditions. RNA sequencing was done using Illumina HiSeq 4000 platform.

first: Mahesh

middle: S

last: Iyer

first: K

last: Venkatesh


title: Effect of SRP54 depletion on mRNA expression in cultured human cells

city: Lubbock

first: Andrey

last: Karamyshev

address: 3601 4th Street

department: Cell Biology and Biochemistry

institute: Texas Tech University Health Sciences Center

summary: Regulation of Aberrant Protein Production (RAPP) is a recently discovered protein quality control pathway that monitors proteins during their synthesis at the ribosome and degrades their mRNA if the proteins are not able to interact with their natural partners. In this study we induced RAPP by knockdown of SRP54, a Signal Recognition Particle subunit, and studied its effect at the full transcriptome level. The mRNA expression levels of many secretory and membrane proteins were decreased demonstrating the generality of the pathway. The RAPP activation leads to dramatic upregulation of the specific network of ribosome-associated HSP70/40/90 chaperones (HSPA1A, DNAJB1, HSP90AA1, and others), increased ribosome associated ubiquitination, and change in expression of RPS27 and RPS27L suggesting ribosome rearrangement. The results demonstrate a complex nature of mRNA and protein quality control at the ribosome.

overall_design: Two experimental condition (treated and control cells).  Treatment:  HeLa Tet-On cells were transfected with siRNA for SRP54 to knockdown SRP54. Control:  HeLa Tet-On cells were transfected with control siRNA. Each experimental condition included three independent biological replicates.

first: Sneider

last: Guarnizo


title: Matrix from Urine Stem Cells Boosts Tissue-Specific Stem Cell Mediated Functional Cartilage Reconstruction

status: Public on Nov 29 2022

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Articular cartilage has a limited capacity to self-heal once damaged. Tissue-specific stem cells are a solution for cartilage regeneration; however, ex vivo expansion resulting in cell senescence remains a challenge as a large quantity of high-quality tissue-specific stem cells are needed for cartilage regeneration. Our previous report demonstrated that decellularized extracellular matrix (dECM) deposited by human synovium-derived stem cells (SDSCs), adipose-derived stem cells (ADSCs), urine-derived stem cells (UDSCs), or dermal fibroblasts (DFs) provided a solution to rejuvenate human SDSCs in proliferation and chondrogenic potential. This study focused on the evaluation of ex vivo rejuvenation of rabbit infrapatellar fat pad-derived stem cells (IPFSCs) by the abovementioned dECMs to be used in functional cartilage repair in a rabbit osteochondral defect model and the potential cellular and molecular mechanisms underlying this rejuvenation. We found that dECM rejuvenation promoted rabbit IPFSCs’ cartilage engineering and functional regeneration in both in vitro and in vivo models, particularly for the dECM deposited by UDSCs, which was further confirmed by proteomics data. RNASeq analysis indicated that both mesenchymal-epithelial transition (MET) and inflammation-mediated macrophage activation and polarization are potentially involved in the dECM-mediated promotion of IPFSCs’ chondrogenic capacity, which needs further investigation.

overall_design: Rabbit IPFSCs grown on four varied dECMs deposited by human ASCs, DFs, SDSCs, and USCs or tissue culture plastic (PL) were incubated in a pellet culture system with chondrogenic induction medium for 21 days. Both cell and pellet samples were used for RNASeq analyses.

first: Ming

last: Pei

first: Yixuan

first: Sheng

last: Zhou

first: Elmira

last: Mikaeliagah

first: Christopher

last: Erickson

first: Benjamin

last: Giertych

first: Halima

last: Akhter

first: Lei

last: Wang

first: Amanda

last: Stewart

first: Joshua

last: Parenti

first: Bin

first: Sijin

last: Wen

first: Sotcheadt

last: Sim

last: Quenneville

first: Kirk

middle: C

last: Hansen


title: tRNA senses cellular nutrient status and senescence via amino acid acylation

city: Ibaraki

first: Tomonori

last: Kimura

state: Osaka

address: 7-6-8 Saito-Asagi

department: Center for Rare Disease Research

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

summary: We profiled the cellular tRNA charging landscape using next-generation sequencing and identified a subset of tRNA that sense nutrients. The charging levels of tRNAGln were exclusively and significantly decreased in response to amino acid starvation.

overall_design: 3 biological replicates of tRNA from TIG-1 cells under amino acid starvation or amino acid roch condition are analyzed

first: Yusuke

last: Tsukamoto

first: Yumi

last: Nakamura

first: Makoto

last: Hirata

first: Ryuichi

last: Sakate


title: Transcriptomic analyses of astrocyte heterogeneity within white matter tracts

city: Oxford

first: Amélie

last: Julé

address: Roosevelt Drive, Headington

country: United Kingdom

institute: Kennedy Institute of Rheumatology (KIR)

summary: Astrocytes are broadly categorized as protoplasmic or fibrous, with the former localized to synaptically dense gray matter regions and the latter associated with axons in the white matter. Much of what we know about astrocyte form and function is derived from the study of protoplasmic astrocytes, whereas fibrous astrocytes remain relatively unexplored. We investigated the transcriptome of uninjured fibrous astrocytes in the mouse from three regions: unmyelinated optic nerve head (ONH), myelinated optic nerve proper (ONP), and corpus callosum (CC).

overall_design: Comparative transcriptomic analyses of white matter astroctyes isolated from the ONH, ONP and CC at steady-state (untreated mice)

first: Arpan

last: Guha Mazumder

first: Paul

last: Cullen

first: Daniel

last: Sun


title: High-Throughput Transcriptome Profiling of Single Nuclei and Single Synapses Using Single-Cell Total-RNA-Seq [Hs]

first: Chenghang

last: Zong

summary: We developed the first droplet-based single-cell total-RNA-seq method. We refer to this platform as Multiple Annealing and Tailing-based Quantitative scRNA-seq in Droplet (MATQ-Drop). With the detection of nascent RNA species, we showed that the cell atlas of human brain samples could be effectively constructed based on nascent RNA species. Furthermore, we observed that only lncRNA species are sufficient to construct the cell atlas, suggesting that MATQ-Drop allows a large-scale identification of the cell-type-specific lncRNA species. Beyond total-RNA profiling for single nuclei, we also showed that MATQ-Drop could be used to profile the transcripts in different neuronal sub-compartments. Based on transcriptome profiling, we were able to determine different types of sub-compartments—in particular, synapses. Here we have referred to the transcriptome of individual synapses as the synaptome, and we identified different subtypes of pre-synapses and post-synapses. Furthermore, between pre-synapses and post-synapses, as well as between pre-synapses and the nuclei, we were able to identify different functional enrichments. Our result unveils unprecedented new insights about gene expression in individual synapses. It also demonstrates the feasibility of using MATQ-drop to profile the transcriptome of sub-cellular compartments.

overall_design: MATQ-Drop single-cell total-RNA-seq of Hoechst-positive nuclei and Hoechst-negative subneuronal compartments isolated from frozen human brain tissues

first: Muchun

last: Niu


title: SYF2 Suppression Mitigates Neurodegeneration in Models of Diverse Forms of ALS

status: Public on Nov 23 2022

city: Los Angeles

first: Justin

last: Ichida

state: CA

address: 1425 San Pablo Street, BCC 209

department: Department of Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

summary: RNA sequencing analysis of human induced motor neurons generated from a C9ORF72 ALS patient line and its isogenic control, treated with siRNA targetting SYF2. The goal of this study is to evaluate the process of SYF2 suppression in rescuing ALS motor neuron degeneration.

overall_design: We determine the effect of SYF2 suppression on induced motor neurons from ALS patients and controls. Motor neurons are derived from induced pluripotent stem cells.

last: K Ichida


title: Structure of the human DICER-pre-miRNA complex in a dicing state

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

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


title: Structure of the human DICER-pre-miRNA complex in a dicing state II

summary: Dicer plays a key role in small RNA biogenesis by processing double-stranded RNAs (dsRNAs). Human DICER (hDICER) is specialized in processing of small hairpins such as pre-microRNAs (pre-miRNAs) with a limited activity towards long dsRNAs, unlike its homologs in lower eukaryotes and plants which cleave long dsRNAs. While the mechanism of long dsRNA cleavage has been well documented, our understanding of pre-miRNA processing is limited due to lack of the structure of hDICER in a catalytic state. Here we report the cryo-electron microscopy structure of hDICER bound to pre-miRNA in a dicing state, uncovering the structural basis for pre-miRNA processing.

overall_design: AQ-seq (bias-minimized sRNA-seq) libraries were constructed using total RNAs as described in our previous study (Kim et al., 2019).

first: Young-Yoon

last: Lee

first: Hansol

first: V

middle: N

first: Soung-Hun

last: Roh


title: Taxonomy of fibroblasts and progenitors in the synovial joint at single-cell resolution

city: Aberdeen

first: Fraser

last: Collins

address: Foresterhill

department: Institute Of Medical Sciences

institute: University of Aberdeen

summary:
Objectives. Fibroblasts in synovium include fibroblast-like synoviocytes (FLS) in the lining and Thy1+ connective-tissue fibroblasts in the sub-lining. We aimed to investigate their developmental origin and relationship with adult progenitors.
Methods. To discriminate between Gdf5-lineage cells deriving from the embryonic joint interzone and other Pdgfrα-expressing fibroblasts and progenitors, adult Gdf5-Cre;Tom;Pdgfrα-H2BGFP mice were used and cartilage injury was induced to activate progenitors. Cells were isolated from knees, sorted by fluorescence-activated cell-sorting based on developmental origin, and analysed by single-cell RNA-sequencing. Flow cytometry and immunohistochemistry were used for validation. Clonal-lineage mapping was performed using Gdf5-Cre;Confetti mice.
Results. In steady state, Thy1+ sub-lining fibroblasts were of mixed ontogeny, while Thy1-Prg4+ lining fibroblasts predominantly derived from the embryonic joint interzone. The latter included Prg4-expressing progenitors distinct from molecularly defined FLS. Clonal-lineage tracing revealed compartmentalisation of Gdf5-lineage fibroblasts between lining and sub-lining. Following injury, lining hyperplasia resulted from proliferation and differentiation of Prg4-expressing progenitors, with additional recruitment of non-Gdf5-lineage cells, into FLS. Consistent with this, a second population of proliferating cells, enriched near blood vessels in the sub-lining, supplied activated multipotent cells predicted to give rise to Thy1+ fibroblasts, and to feed into the FLS differentiation trajectory. Transcriptional programmes regulating fibroblast differentiation trajectories were uncovered, identifying Sox5 and Foxo1 as key FLS transcription factors in mice and humans.
Conclusions. Our data blueprint a cell atlas of mouse synovial fibroblasts and progenitors in healthy and injured knees, and provide novel insights into the cellular and molecular principles governing the organisation and maintenance of adult synovial joints.

overall_design: Gdf5-lineage (Tom+) and non-Gdf5-lineage Pdgfrα (GFP+) cells were isolated from steady-state and injured synovial joints taken from  adult Gdf5-Cre;Tom;Pdgfrα-H2BGFP mice

first: Anke

middle: J

last: Roelofs

first: Rebecca

last: Symons

first: Karolina

last: Kania

first: Ewan

last: Campbell

first: Elaina

last: Collie-Duguid

first: Anna

middle: H

last: Riemen

first: Susan

last: Clark

first: Cosimo

last: De Bari


title: High-Throughput Transcriptome Profiling of Single Nuclei and Single Synapses Using Single-Cell Total-RNA-Seq [Mm]

first: Chenghang

overall_design: MATQ-Drop single-cell total-RNA-seq of Hoechst-positive nuclei and Hoechst-negative subneuronal compartments isolated from WT and 5XFAD mouse hippocampus


title: ΔNp63/p73 drive metastatic colonization by controlling a regenerative epithelial stem cell program in quasi-mesenchymal cancer stem cells

city: Cambridge

first: Arthur

middle: W.

last: Lambert

address: 455 Main street

institute: Whitehead Institute

summary: p63/p73 are master transcriptional regulators of ITGB4-hi cancer stem cells and are required to maintain CSCs in a quasi-mesenchymal state and for metastatic colonization

overall_design: RNA-seq of control (NT) ITGB4-hi cells and p63 KO, p73 KO, and p63/p73 (double KO, dKO) cells.  RNA-seq was performed on biolgical triplicates.

first: Arthu

last: r Lambert

first: Robert

last: Weinberg

first: Bingbing

last: Yuan


title: Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing

status: Public on Nov 26 2022

city: Chicago

first: Jon

last: Staley

institute: University of Chicago

summary: Long introns with short exons in vertebrate genes are thought to require spliceosome assembly across exons (exon definition), rather than introns, thereby requiring transcription of an exon to splice an upstream intron. Here, we developed CoLa-seq (co-transcriptional lariat sequencing) to investigate the timing and determinants of co-transcriptional splicing genome wide. Unexpectedly, 90% of all introns, including long introns, can splice before transcription of a downstream exon, indicating that exon definition is not obligatory for most human introns. Still, splicing timing varies dramatically across introns, and various genetic elements determine this variation. Strong U2AF2 binding to the polypyrimidine tract predicts early splicing, explaining exon definition-independent splicing. Together, our findings question the essentiality of exon definition and reveal features beyond intron and exon length that are determinative for splicing timing.

overall_design: Investigation of branch point usage and the timing of co-transcriptional lariat formation in k562 cells

first: Yi

last: Zeng

first: Yang

middle: I

last: Li

first: Jonathan


overall_design: single-cell RNA-seq of tdTom+ carcinoma cells isolated from the lungs of NSG mice 3 days after tail-vein injection. ITGB4-hi control (NT) or p63/p73 knockout (dKO) cells were injected into mice (n=5).  Three days later lungs was dissected, dissociated, and pooled together for each group.  tdTom+ carcinoma cells were isolated by flow cytometry and immediated processed for single-cell RNA-seq.

last: Lamber

first: Sumeet

last: Gupta


title: Gene expression changes in mouse hippocampus after overnight exposure to corticosterone

status: Public on Nov 24 2022

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

summary: The aim of the experiment was to test the effect of elevated level of corticosterone on hippocampal transcriptome after 12 hours of treatment during active phase to mimic the effect of a day-long stress. Additionally, we also tested the decay time of transcriptomic response during resting period when the level of glucocorticoids returns to the baseline. Our study shows that transcriptomic responses to glucocorticoids are heterogenous in terms of the decay time with some genes displaying persistent changes in expression during 9 hours of rest.

overall_design: This is an analysis of 48 hippocampal RNA samples. Vehicle and corticosterone-treated animals were compared at 3 time-points: 1, 5 or 9 hours post-treatment. There are 8 biological replicates in each comparison.

first: Aneta

last: Jaszczyk

first: Alicja

last: Majewska

first: Grzegorz

middle: R

last: Juszczak


overall_design: RNA-seq of rescue experiment in ITGB4-hi cells with knockout of p63/p73 (double KO, dKO).  dKO cells were engineered to ectopically express a control empty vector (EV), dNp63, TAp73, or both dNp63/TAp73 (dual).  ITGB4-lo cells were engineered to express a control empty vector (EV) or dNp63.   RNA-seq was performed on biolgical duplicates.


title: Needling on Trigger Point Promotes Muscle Regeneration after Bupivacaine Injection Induced Gastrocnemius Muscle Injury via RNA sequencing analysis

status: Public on Nov 22 2022

city: Beijing

first: Xiaodong

last: Liu

address: 11 E 3rd N ring RD

institute: Beijing University of Chinese Medicine

summary:
Purpose: We used RNA sequencing to investigate the effect of acupuncture treatment on regeneration after myotoxic muscle injury
Methods:Methods:Gastrocnemius muscle mRNA profiles of 6-7 months-old WT(wild-type), Sham(Saline injeciton), Injury(0.5% Bupivacaine injecion) and Acup(1-time needling 24 hour after bupivacaine injection site) mice were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The sequence reads that passed quality filters were analyzed with DESeq2 R package to identify differently expressed genes with padj<0.05. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Needling on trigger point once could change genetic expressions. Acupuncture once up regulated 623 genes and down regulated 65 genes compared to Injury muscle. Acupuncture 24 hours after injury promotes muscular regeneration.
Conclusions: Our research first reported that 1-time needling 24 hours after muslce injury can promote muslce regeneration which will provide novel therapeutic targets for treatment of  myofasical pain syndrome

overall_design: Gastrocnemius muslce mRNA profiles of 6-7 months-old  mice were generated by deep sequencing, in triplicate, using Illumina Hiseq.

first: Linqing

last: Miao


title: Microarray analysis of bovine macrophages cell line (BoMac) after infection with Bovine Immunodeficiency Virus

status: Public on Nov 21 2022

city: Pulawy

first: Magdalena

last: Materniak-Kornas

address: Partyzantow 57

department: Biochemistry

institute: National Veterinary Research Institute

summary: Bovine Immunodeficiency Virus (BIV) is a member of Retroviruses family which is natural pathogen of cattle, prevalent worldwide. The significance of BIV infection in cattle has not been clearly established and it is still unknown whether BIV induces a specific syndrome or whether it renders animals more susceptible to other infections. To gain insight into host response to BIV infection the pattern of gene expression in bovine macrophage cells (BoMac) was analyzed using BLO Plus microarrays from CAFG, Michigan State University ( GEO GPL9176).

overall_design: BoMac cells was infected in vitro with BIV using supernatant harvested from FBL/BIV FL112. Microarrays were hybridized using the two color hybridization method with total RNA extracted from BoMac and BoMac BIV cells at 24h post infection. Dye swap analysis was performed for each set of control and infected cultures.

first: Marzena

last: Rola-Łuszczak

first: Piotr

last: Kubiś

last: Pluta

first: Marlena

last: Smagacz

first: Jacek

last: Kuźmak


title: Inorganic polyphosphate abets silencing of a sub-telomeric gene cluster in fission yeast

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: This RNA-Seq analysis compares gene expression of the vtc4∆ mutant contrasting to the wild-type fission yeast (Schizosaccharomyces pombe).

overall_design: 1 test samples and 1 control sample was processed (each sample has 3 replicate experiments)

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Discovering Haematoma-Stimulated Circuits for Secondary Brain Injury after Intraventricular Haemorrhage by Spatial Transcriptome Analysis

status: Public on Nov 19 2022

city: Chengdu

first: Jiayidaer

last: Badai

address: No. 24, South Section 1, First Ring Road, Wuhou District

institute: Sichuan University

summary: Intraventricular haemorrhage (IVH) is one of the common complications after various acute brain injuries, leading to severe mortality and mobility, with great burdens on economics and society. Recently, a CLEAR III trial (NCT00784134) employing alteplase effectively cleared intraventricular haematoma but did not demonstrate adequate neuro behavioural benefits for patients. Therefore, the present study sought to investigate the pathophysiology of how these haematoma stimulations in ventricles cause neurological dysfunction. An autologous blood stereotactic injection model was employed to establish and mimic secondary IVH in mice, followed by our innovated spatial transcriptome sequencing-based bioinformatic algorithm to investigate the 3D spatial brain regions affected by the primary stimulation of haematoma in the ipsilateral ventricle after IVH, as well as related cell-cell communication strength and pathway analysis. These data illustrate that the three main 3D global pseudospace-time trajectory bundles represent the main neural circuits from the lateral ventricle to the hippocampus and primary cortex induced by experimental intraventricular haematoma stimulation. Further analysis indicated a rapid response in the primary cortex, as well as a direct and integrated effect on the hippocampus after IVH. To the best of our knowledge, this is the first study to interrogate secondary brain injury after IVH by using spatial transcriptome sequencing and bioinformatics analysis. These data could provide more helpful information on the pathophysiological mechanism of IVH in patients after acute brain injury, as well as for the bioinformatics analysis strategies for similar studies in the future.

overall_design: We collected wild-type C57/BL6 mouse brains, which were classified into the no-surgery group (control), the needle-puncture group without blood injection (sham), and the needle-puncture group with blood injection at 1st, 3rd and 7th day. Then, these brains were frozen on dry ice in OCT.Frozen brains were then sectioned coronally at 10 μm on a cryostat and mounted on 10x Genomics Visium spatial transcriptome slides. The tissue locations of the library patches started from the emergence of the lateral ventricle with 20 μm intervals and a 10 μm margin of error.

first: Le

last: Zhang

first: Guan

last: Wang

first: Xufang

last: Ru

first: Wenkai

last: Song

first: Yujie

last: You

first: Jiaojiao

last: He

first: Suna

last: Huang

first: Hua

last: Feng

first: Runsheng

last: Chen

first: Yi

last: Zhao


title: m7G-quant-seq: Quantitative Detection of RNA Internal N7-Methylguanosine

status: Public on Nov 18 2022

first: Li-Sheng

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

summary: Methods for the precise detection and quantification of RNA modifications are critical to uncover functional roles of diverse RNA modifications. The internal m7G modification in mammalian cytoplasmic tRNAs is known to affect tRNA function and impact embryonic stem cell self-renewal, tumorigenesis, cancer progression, and other cellular processes. Here, we introduce m7G-quant-seq, a quantitative method that accurately detects internal m7G sites in human cytoplasmic tRNAs at single-base resolution. The efficient chemical reduction and mild depurination can almost completely convert internal m7G sites into RNA abasic sites (AP sites). We demonstrate that RNA abasic sites induce a mixed variation pattern during reverse transcription, including G → A or C or T mutations as well as deletions. We calculated the total variation ratio to quantify the m7G modification fraction at each methylated site. The calibration curves of all relevant motif contexts allow us to more quantitatively determine the m7G methylation level. We detected internal m7G sites in 22 human cytoplasmic tRNAs from HeLa and HEK293T cells and successfully estimated the corresponding m7G methylation stoichiometry. m7G-quant-seq could be applied to monitor the tRNA m7G methylation level change in diverse biological processes.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
[dataset1] 20 samples (Sample 1-20): "Treated" samples for m7G-quant-seq to study the variation patterns at HeLa 18S rRNA m7G1639, under five RTs and different dNTP/dATP ratios.
[dataset2] 6 samples (Sample 21-26):  Calibration curves for estimating internal m7G methylation fractions, under HIV RT and 1mM dNTP.
[dataset3] 8 samples (Sample 27-34): Duplicates for m7G-quant-seq "Treated" and "Input" samples to reveal tRNA m7G46 methylation fractions in HeLa and HEK293T cells, under HIV RT and 1mM dNTP.

first: Cheng-Wei

last: Ju

first: Chang

last: Liu

first: Chuan


title: The B-cell CLL/lymphoma 7 (BCL7) protein family members drive gene expression changes via interactions with the Brahma Related Gene 1 (BRG1) Helicase-Sant Associated domain (HSA) domain [LongTerm]

status: Public on Nov 17 2022

city: RTP

first: Nicholas

last: Dietrich

state: NC

address: 111 TW Alexander

department: ESCBL

institute: NIH

summary: The SWI/SNF complex remodels chromatin in an ATP-dependent manner through the ATPase subunits BRG1 and Brm Chromatin remodeling alters nucleosome structure to change gene expression. However, aberrant remodeling and gene expression can result in cancer. We identified a family of SWI/SNF complex members, the BCL7 proteins, as critical components to drive BRG1-dependent gene expression changes. The BCL7 proteins have been implicated in B-cell lymphoma, but the characterization of their functional role within the SWI/SNF complex has not been fully explored. This study implicates their critical function alongside BRG1 to cause large scale changes in gene expression. Mechanistically, the BCL7 proteins bind to the HSA domain of BRG1 and require this domain for stable protein expression and binding to chromatin. These results provide a link between the HSA domain and the formation of a stable functional SWI/SNF remodeling complex through the interaction with the BCL7 proteins. The data shown here highlights the importance of proper formation of the SWI/SNF complex to drive critical biological functions, as losses of members that were once considered minor accessory components can cause severe loss of complex function.

overall_design: Adrenacorticoid carcinoma cells were generated to inducibly express respective constructs and harvested for RNA-seq.

first: James

last: Ward

first: Trevor

middle: K

last: Archer


title: Cell-Type Specific Profiling of Histone Post-Translational Modifications in the Adult Mouse Striatum

city: Philadelphia

first: Shuo

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Histone post-translational modifications (hPTMs) regulate gene expression via changes in chromatin accessibility and transcription factor recruitment. At a given locus, the coordinated enrichment of several distinct hPTMs regulate gene expression in response to external stimuli. However, neuronal hPTMs have been primarily characterized in bulk brain tissue and/or tissue pooled across subjects. This obscures both cell-type and individual variability, features essential to understand individual susceptibility to psychiatric disease. To address this limitation, we optimized a hybrid protocol, ICuRuS, to profile both activating and repressive hPTMs in a single neuronal subtype from a single mouse. We report here profiling of striatal medium spiny neuron (MSN) subtypes, genetically defined by expression of Adenosine 2a Receptor (A2a) or Dopamine Receptor D1 (D1), which differentially regulate reward processing and pathophysiology. Using ICuRuS, we defined genome-wide, A2a- or D1-specific combinatorial hPTM profiles, and discovered regulatory epigenomic features at genes implicated in neurobiological function and disease.

overall_design: 50K and 500K N2a CUT&RUN for H3K4me3 and H3K27me3. A2a and D1 neurons isolated via INTACT are subject to CUT&RUN for H3K4me3 and H3K27me3 with different antibodies.

first: Marco

middle: D

last: Carpenter

first: Delaney

last: Fischer

first: Allison

last: Bond

first: Kyle

last: Czarnecki

first: Morgan

last: Woolf

first: Hongjun

first: Elizabeth

middle: A

last: Heller


title: The B-cell CLL/lymphoma 7 (BCL7) protein family members drive gene expression changes via interactions with the Brahma Related Gene 1 (BRG1) Helicase-Sant Associated domain (HSA) domain [BCL7 knockdown]

middle: M


title: The B-cell CLL/lymphoma 7 (BCL7) protein family members drive gene expression changes via interactions with the Brahma Related Gene 1 (BRG1) Helicase-Sant Associated domain (HSA) domain [CUT&RUN]


title: The enhanced functionality of low-affinity CD19 CAR T cells is associated with activation priming and a polyfunctional cytokine phenotype

city: London

first: Eduardo

last: Gomez Castaneda

address: 30 Guilford Street

department: Institute of Child Health

institute: UCL

summary: We have compared a low-affinity second-generation anti-CD19 CAR (CAT) with the high-affinity FMC63 CAR used in tisagenlecleucel to understand the unknown molecular mechanisms that drive different CAR T cell treatment outcomes. CAT cells are characterized by a faster antigen dissociation rate and present an enhanced in vivo expansion and anti-tumor efficacy, showing lower toxicity to patients and a long-term persistence in a Phase I clinical study. To understand this improved CAT cells behaviour, we performed a systematic in vitro characterization of the transcriptomic (RNA-seq) and protein (CyTOF) changes between the two groups. The analysis focused on T cells expressing low-affinity vs high-affinity anti-CD19 CARs following stimulation with CD19-expressing cells. Our results show that CAT potent and long-term anti-tumour responses may be sustained by the establishment of a CAR T cells self-reinforcing circuit activated through cytokines polyfunctional crosstalk. This study may inform the design of versatile CAR T cells, capable of balancing safety and efficacy.

overall_design: Comparing a high- and a low-affinity anti-CD19 CAT T cells

last: Gomez-Castaneda

first: Ilaria

last: Michelozzi

first: Sergi

last: Castellano

first: Alice

last: Giustacchini


title: The B-cell CLL/lymphoma 7 (BCL7) protein family members drive gene expression changes via interactions with the Brahma Related Gene 1 (BRG1) Helicase-Sant Associated domain (HSA) domain [24 hours]


title: The  ATAC epigenomic profiling of Capitella teleta development

status: Public on Nov 16 2022

first: Yan

last: Liang

state: London

address: mile end road

department: SBBS

institute: Queen Mary Univerisity of London

summary: Capitella teleta is a model specie in marine annelids research, to gain insight into its development, we performed time-course ATAC-seq ranging from 64 cell to stage 8 larvae, to profiling the gene regulation dynamics

overall_design: Collected the  fresh samples from the 64 cells to the stage 8 larvae stages, profiling the genomic regulatory dynamics

first: Chema

last: Martin


title: The adult tissue transcriptome of Owenia fusiformis

summary: Owenia fusiformis is an ancestral sister group to the annelids, it has a unique "head larvae" type named mitraria larvae. To identify the gene expressed in different tissues, especially the gene expressed in head region, we dissected the 5 female worms and 1 male worm to get 9 different tissues, and extracted their RNA. The sequencing were performed on BGISEQ-500 platform, and the mapping were done with Kallisto and normalization was performed with DEseq2.

overall_design: We dissected 5 female worms to get the head and tail tissues; 1 female worm to get the gut, muscle and overy tussues; 1 male worm to get the cheate, testis, blood vessel and muscle tissues.


title: The B-cell CLL/lymphoma 7 (BCL7) protein family members drive gene expression changes via interactions with the Brahma Related Gene 1 (BRG1) Helicase-Sant Associated domain (HSA) domain

first: Nicholas

overall_design: Refer to individual Series


title: The differentially expressed lncRNAs (DELs) and mRNAs (DEMs) in Collagen-induced arthritis rats compared with normal rats.

city: Changsha

first: Yuqi

last: Wen

address: Xiangya Road

institute: Xiangya Hospital Central South University

summary: To determine te lncRNA expression profile in collagen-induced arthritis rats and normal rats, we uesed lncRNA microArray analysis form Arraystar to examine the expression of lncRNAs in CIA and normal rats' synovial tissues.

overall_design: Synovial tissues from rats were distributed into two experimental groups: CIA group and normal group, then perform lncRNAs chips by Arraystar Rats lncRNAs chip (Arraystar)

first: Xingui

last: Xiong


title: High-throughput and high-sensitivity full-length single-cell RNA-seq analysis on third-generation sequencing platform

status: Public on Nov 15 2022

first: Zhenyu

last: Liu

address: Peking University, No.5 Yiheyuan Road, Haidian District, Beijing, China

department: Biomedical Pioneering Innovation Center

institute: Peking University

summary:
We developed SCAN-seq2, a high-throughput and highly sensitive single-cell RNA sequencing method based on the TGS platform. Our study demonstrated that SCAN-seq2 improves upon the previous method, SCAN-seq, in terms of sensitivity and throughput. By using reference-guided assembly of single-cell data, we were able to identify thousands of novel full-length RNA isoforms, including cell type-specific expression patterns of pseudogenes. We also accurately determined V(D)J rearrangement events in T and B cells. Lastly, we found that treatment of HepG2 and Hela cells with the spliceosome inhibitor Isoginkgetin (IGG) resulted in a subpopulation of cells with distinct apoptosis features.

Our study provides a promising new tool for single-cell transcriptome research. The source code for SCAN-seq2 data analysis pipelines is available at https://github.com/liuzhenyu-yyy/SCAN-seq2 .

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus

overall_design: Single-cell full-length transcriptome profiling of 6 human cell lines and 3 mouse cell lines.

first: Yuhan

last: Liao

first: Yu

last: Zhang

first: Fuchou

last: Tang


title: The developmental transcriptome profiling of Capitella teleta

summary: Capitella teleta is a model specie in marine annelids research, to gain insight into its development, we performed time-course RNA-seq ranging from 64 cell to stage 7 larvae, to profiling the gene expression dynamics

overall_design: Collected the  fresh samples ranging from the 64 cells to the juvenile stages, profiling the gene expression.

first: Allan

last: Carrillo-Baltodano