title: Integrative multi-omics reveals analogous developmental neurotoxicity mechanisms between perfluorobutanesulfonic acid and perfluorooctanesulfonic acid in zebrafish

status: Public on Apr 04 2023

city: Seoul

first: Eun Ki

last: Min

address: 232, Gongneung-ro, Nowon-gu

department: Environmental engineering

institute: Seoul National University of Science and Technology

summary: The molecular mechanism of perfluorobutanesulfonic acid (PFBS), an alternative to legacy perfluorooctanesulfonic acid (PFOS), remains to be understood. Therefore, we conducted a developmental toxicity evaluation on zebrafish embryos exposed to PFBS and PFOS and assessed neurobehavioral changes at concentrations below each point of departure (POD) determined by embryonic mortality. Using transcriptomics, proteomics, and metabolomics, biomolecular perturbations in response to PFBS were profiled and then integrated for comparison with those for PFOS. Although PFBS (7525.47 M POD) was approximately 700 times less toxic than PFOS (11.42 M POD), similar alteration in behavioral assessment and neurochemical analysis was observed at the corresponding ratios of low and high concentrations. Multi-omics analysis revealed that the PFBS neurotoxicity mechanism was associated with oxidative stress, lipid metabolism, and glycolysis/glucogenesis. The commonalities in developmental neurotoxicity-related mechanisms between PFBS and PFOS interconnected by knowledge-based integration of multi-omics included the calcium signaling pathway, lipid homeostasis, and primary bile acid biosynthesis. Despite being less toxic than PFOS, PFBS exhibited similar dysregulated molecular mechanisms, suggesting that chain length differences do not affect the intrinsic toxicity mechanism. Overall, carefully managing potential toxicity of PFBS can secure its status as an alternative to PFOS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for zebrafish (Danio_rerio)

first: Ki-Tae

last: Kim


title: Investigation into SATB2 DNA-binding sites and the effect of SATB2 removal on the transcriptome of skeletal muscle satellite cells

status: Public on Apr 06 2023

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Induction of lineage-specific gene programs are strongly influenced by alterations in local chromatin architecture. However, key players that impact this genome reorganization remain largely unknown. In our associated paper, we found that the removal of special AT-rich binding protein 2 (SATB2), a nuclear protein that binds matrix attachment regions, is a key event in initiating myogenic differentiation. This study included ChIP-seq analyses to assess the genetic binding sites of SATB2 prior to differentiation and categorize their respective roles within the cell. Furthermore, transcriptome analyses using RNA-seq was conducted on C2C12 cells treated with control siRNA and siRNA against SATB2 prior to differentiation. This was done to assess the changes in transcript expression following the loss of SATB2.

overall_design: For the ChIP-seq experiments, the cells that were used were C2C12 skeletal muscle myoblasts in the proliferation phase. The control for the ChIP experiments was a pulldown using a mouse IgG instead of the mouse SATB2 antibody. The ChIP-seq analysis was done on n = 2 independent samples. For the RNA-seq experiments, we used C2C12 skeletal muscle myoblasts in the growth stage. The control for this experiment was C2C12 cells that were treated with control siRNA, while the experimental condition was C2C12 cells that were treated with siRNA against SATB2. These experiments were done at an n=3 on independent samples.

first: Ryan

middle: A

last: Bell

first: Mohammad

middle: H

last: Al-Khalaf

first: Alphonse

last: Chu

first: F

middle: J

last: Dilworth

first: Lynn

last: Megeney


title: Integrated multi-omics analysis reveals the underlying molecular mechanism for developmental neurotoxicity of perfluorooctanesulfonic acid in zebrafish

country: South Korea

summary: Limited studies on multi-omics have been conducted to comprehensively investigate the molecular mechanism underlying the developmental neurotoxicity of perfluorooctanesulfonic acid (PFOS). In this study, the locomotor behavior of zebrafish larvae was assessed under the exposure to 0.1–20 μM PFOS based on its reported neurobehavioral effect. After the number of zebrafish larvae was optimized for proteomics and metabolomics studies, three kinds of omics (i.e., transcriptomics, proteomics, and metabolomics) were carried out with zebrafish larvae exposed to 0.1, 1, 5, and 10 μM PFOS. More importantly, a data-driven integration of multi-omics was performed to elucidate the toxicity mechanism involved in developmental neurotoxicity. In a concentration-dependent manner, exposure to PFOS provoked hyperactivity and hypoactivity under light and dark conditions, respectively. Individual omics revealed that PFOS exposure caused perturbations in the pathways of neurological function, oxidative stress, and energy metabolism. Integrated omics implied that there were decisive pathways for axonal deformation, neuroinflammatory stimulation, and dysregulation of calcium ion signaling, which are more clearly specified for neurotoxicity. Overall, our findings broaden the molecular understanding of the developmental neurotoxicity of PFOS, for which multi-omics and integrated omics analyses are efficient for discovering the significant molecular pathways related to developmental neurotoxicity in zebrafish.

first: Hyojin

last: Lee


title: Expression profiles of salivary gland MSC or wharton's jelly MSC, and their extracellular vesicles

status: Public on Apr 05 2023

first: Donghyun

address: 50-1, Yonsei-ro, Seodaemun-gu

institute: Yonsei University College of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: MSCs from salivary gland or wharton's jelly were subjected to gene expression analysis, and their extracellular vesicles were used for exosomal miRNA profiling.

overall_design: RNAseq from 2 different MSCs and miRNAseq from 2 different MSC's derivative extracellular vesicle (n=3).

first: Kyung

middle: M

last: Lim

first: Ssang-Goo

last: Cho

first: Jae-Yol


title: Impact of LCL161 on gene expression in human TAC T cells stimulated with antigen-coated microbeads

city: Hamilton

first: Jonathan

middle: L

last: Bramson

address: 1280 Main St W

institute: McMaster University

summary:
SMAC mimetics such as LCL161 are a novel class of anti-cancer drug that have been shown to induce costimulation in human T cells and augment anti-tumor capabilities.
We investigated what impacts LCL161 has on gene expression in engineered anti-BCMA TAC T cells. TAC T cells were stimulated with BCMA-coated microbeads to deliver controlled antigenic signal alone.

overall_design: 12 samples were analyzed, containing 3 biological (donor) replicates and 2 time points. Samples stimulated containing DMSO were control and used for pairwise comparison against stimulations containing LCL161 drug.

first: A

last: Afsahi

first: J


title: PRC2.1 and PRC2.2 Specific Accessory Proteins Drive Recruitment of Different Forms of Canonical PRC1 [RNA-seq]

city: Dublin

first: Cheng

last: Wang

address: College Green

department: Genetics

country: Ireland

institute: Smurfit Institute of Genetics, Trinity College Dublin

summary: Polycomb repressive complex 2 (PRC2) mediates H3K27me3 deposition, which is thought to recruit canonical PRC1 (cPRC1) via chromodomain-containing CBX proteins to promote stable repression of developmental genes. PRC2 forms two major subcomplexes, PRC2.1 and PRC2.2, but their specific roles remain unclear. Through genetic knockout and replacement of PRC2 subcomplex-specific subunits in naïve and primed pluripotent cells, we uncover distinct roles for PRC2.1 and PRC2.2 in mediating the recruitment of different forms of cPRC1. PRC2.1 catalyses the majority of H3K27me3 at Polycomb target genes and is sufficient to promote recruitment of CBX2/4-cPRC1, but not CBX7-cPRC1. Conversely, while PRC2.2 is poor at catalysing H3K27me3, we find that its accessory protein JARID2 is essential for recruitment of CBX7-cPRC1 and the consequent 3D chromatin interactions at Polycomb target genes. We therefore define distinct contributions of PRC2.1 and PRC2.2 specific accessory proteins to Polycomb mediated repression and uncover a new mechanism for cPRC1 recruitment.

overall_design: ESCs and EpiLCs RNA was extracted by Qiagen RNeasy mini kit. Three replcates of each condition were collected and prepared for RNA-seq.

first: Eleanor

last: Glancy

first: Adrian

last: Bracken


title: Anti-NR2F1 scCUT&Tag on FAC-sorted Isl1MN-GFP rhombomere 4 neurons from wildtype and HCFP1 Fam5snv/snv E10.5 mouse embryos

city: Boston

first: Elizabeth

middle: C

last: Engle

address: 3 Blackfan Circle

country: USA

institute: Boston Childrens Hospital

summary: We found hereditary congenital facial paralysis type 1 (HCFP1) is caused by variants that duplicate or change cis regulatory elements (cREs) controlling the neuronal expression of the GATA2 transcription factor. The single nucleotide variants (SNVs) alter a previously uncharacterized cis regulatory element (we named cRE2). A subset of these variants disrupted a consensus sequence for the COUP transcription factor family (NR2F1 and NR2F2). We performed low-input scCUT&Tag with antibodies against NR2F1 and found it bound to the predicted cRE2 sequence in embryonic mouse rhombomere 4 motor neurons in vivo. We generated an HCFP1 SNV mouse model that harbored Mm10:Chr6:88,224,892 A>G in the NR2F1 binding site (Fam5snv/snv)  and found it disrupted NR2F1 binding in vivo.

overall_design: scCUT&Tag  (see “Single Cell CUT and Tag on 10X genomics platform” protocol from www.protocol.io) (https://www.protocols.io/view/single-cell-cut-and-tag-on-10x-genomics-platform-bqbnmsme) was performed on FAC-sorted WT and Fam5snv/snv mouse embryonic rhombomere 4 motor neurons marked by the motor neuron-specific Isl1MN-GFP transgenic reporter. Cells were collected at E10.5 (replicate 1: n=26 WT and 8 Fam5snv/snv embryos; replicate 2: n=26 WT and 16 Fam5snv/snv embryos), and processed for scCUT&Tag using an antibody against the COUP-TFI/NR2F1 transcription factor (Millipore-Sigma cat#ABE1425). Libraries were sequenced on an Illumina NextSeq 500 using a NextSeq 500/550 High Output v2.5 (75 cycles) kit (Illumina). Raw sequence data was demultiplexed, filtered and aligned using CellRanger-ATAC software (10x Genomics) to generate fastqs and peak files for deposit.

first: Alan

middle: P

last: Tenney

first: Wai-Man

last: Chan


title: Non-coding variants alter Gata2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis

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

overall_design: Refer to individual Series


title: The landscape of circular RNAs in neuroblastoma III

city: Berlin

first: Steffen

last: Fuchs

address: Augustenburger Platz 1

department: Pediatric Oncology

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: Circular RNAs (circRNAs), a noncoding RNA class originating from alternative splicing, are highly abundant in neural tissues and were shown to regulate gene expression e.g. by interacting with microRNAs and RNA-binding proteins. Neuroblastoma is an embryonal neoplasia, which arises from undifferentiated neural crest cells. Here, we aimed to explore, whether circRNAs influence the pathogenesis of high-risk neuroblastoma. We performed whole-transcriptome sequencing of 104 primary neuroblastoma samples of all risk-groups and identified 5,203 unique circRNAs involving 2,302 genes. Candidate circRNA expression did not correlate with host gene expression, indicating independent regulatory mechanisms. circRNAs were significantly downregulated in the MYCN-amplified high-risk tumors. These findings were independently reproduced in a tetracycline-inducible MYCN-overexpression system based on a non MYCN-amplified neuroblastoma cell line, suggesting that MYCN drives this global circRNA repression. We identified the RNA helicase DHX9 as a mediator of this global suppressive effect of MYCN on circRNAs. Comparing our RNA sequencing data with other cancers and controls revealed a circRNA subset specifically upregulated in neuroblastoma that included a circRNA derived from the ARID1A tumor suppressor gene. Specific circARID1A knockdown resulted in reduced proliferation, cell numbers and viability, prompted apoptosis and induced a differentiated phenotype. Neither knockdown, nor overexpression of circARID1A influenced ARID1A mRNA and protein levels significantly. To dissect the potential mode of function, we performed a pulldown assay with subsequent mass spectrometry. We identified the RNA-binding protein KHSRP as an interaction partner that participates in the mechanism of action of circARID1A. In summary, this study highlights an important role of circRNAs in neuroblastoma biology and may establish this RNA class as a future therapeutic target and biomarker.

overall_design: Knockdown of KHSRP with 2 different siRNAs in the neuroblastoma cell line IMR-5

first: Louisa-Marie

last: Kruetzfeldt

first: Johannes

last: Schulte


title: Sepsis related ACLF mouse model

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

summary: Background and aims: Acute-on-chronic liver failure (ACLF) is an acute liver and multisystem failure in patients with previously stable cirrhosis.  A common cause of ACLF is sepsis secondary to bacterial infection.  Sepsis-associated ACLF involves a loss of differentiated liver function in the absence of direct liver injury, and its mechanism is unknown. We aimed to study the mechanism of sepsis associated ACLF using a novel mouse model.  Approach and Results: Sepsis-associated ACLF was induced by cecal ligation and puncture procedure (CLP) in mice treated with thioacetamide (TAA). The combination of TAA and CLP resulted in a significant decrease in liver synthetic function and high mortality. These changes were associated with reduced metabolic gene expression and increased C/EBPβ transcriptional activity.  We found that C/EBPβ binding to its target gene promoters was increased. In humans C/EBPβ chromatin binding was similarly increased in ACLF group compared to control cirrhosis. Hepatocyte specific Cebpb knockout mice had reduced mortality and increased gene expression of hepatocyte differentiation markers in TAA/CLP mice, suggesting that C/EBPβ promotes liver failure in these mice. C/EBPβ activation was associated with endothelial dysfunction, characterized by reduced Angiopoietin-1/Angiopoietin-2 ratio and increased endothelial production of HGF. Angiopoietin-1 supplementation or Hgf knockdown reduced hepatocyte C/EBPβ accumulation, restored liver function, and reduced mortality, suggesting that endothelial dysfunction induced by sepsis drives acute-on-chronic liver failure via HGF-C/EBPβ pathway.  Conclusion: The transcription factor C/EBPβ is activated in both mouse and human ACLF and is a potential therapeutic target to prevent liver failure in patients with sepsis and cirrhosis.

overall_design: Whole liver mRNA analysis in mice treated with TAA or water as a control and subjected to CLP or sham surgeries

first: Michal

last: Schonfeld


title: Dynamics and stage-specificity of between-population gene expression divergence in the Drosophila melanogaster larval fat body (pooled RNA-seq in a derived and an ancestral population)

city: Planegg-Martinsried

first: Amanda

last: Glaser-Schmitt

address: Grosshaderner Str. 2

department: Biology

institute: LMU München

summary: We used RNA-seq to examine coding and non-coding gene expression variation in the larval fat body of an ancestral African and a derived European Drosophila melanogaster population across three developmental stages spanning ten hours of larval development.

overall_design: Gene expression profiles of a Zambian (ZI, 10 isofemal strains) and a Dutch (NL, 12 isofemale strains) population of D. melanogaster. RNA-seq data was generated  for pooled population samples of dissected female larval fat bodies in 3 larval/prepupal stages (early and late wandering third instar larvae and white prepupae) with 3 biological replicates per population and stage.

first: John

last: Parsch


title: Dynamics and stage-specificity of between-population gene expression divergence in the Drosophila melanogaster larval fat body (RNA-seq in a derived population)

summary: We  used RNA-seq in a derived European Drosophila melanogaster population from Germany (MU) to examine coding gene expression variation in the larval fat body during the late wandering third instar stage.

overall_design: Gene expression profiles of  five isofemale strains from a German (MU) population of D. melanogaster. This RNA-seq data was generated for dissected female larval fat bodies during the late wandering third instar stage with 2-3 biological replicates per isofemale strain.


title: Hepatocyte SREBP signaling mediates clock communication within the liver [ATAC-seq]

city: Houston

first: Dongyin

last: Guan

state: TX

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine

summary: Rhythmic intraorgan communication coordinates environmental signals and cell-intrinsic clock to maintain organ homeostasis. Hepatocyte-specific knockout of core components of the molecular clock, Rev-erba and b (ReverbhDKO), alters cholesterol and lipid metabolism in hepatocytes as well as rhythmic gene expression in non-parenchymal cells (NPC) of the liver. Here we report that in diet induced obesity (DIO)-caused fatty liver, hepatocyte SREBP cleavage-activating protein (SCAP) is required for ReverbhDKO-induced diurnal rhythmic remodeling and epigenomic reprogramming in Kupffer cells (KC). Integrative analyses of isolated hepatocytes and Kupffer cells uncovered potential signals, including secreted polypeptides and metabolites, that gain rhythmicity in the absence of REV-ERBs in a SCAP-dependent manner. These results shed light on the signaling mechanisms by which hepatocytes regulate diurnal rhythms in NPCs in DIO and fatty liver disease.

overall_design: ATAC-seqencing in isolated Kupffer cells from control, ReverbhDKO, and Reverb/ScaphDKO liver

first: Mitchell

last: Lazar


title: Ptip is essential for tooth development via regulating Wnt pathway

city: wuhan

first: Jianfei

last: Liang

address: No. 237, Luoyu Road, Hongshan District,

country: China

institute: wuhan university

summary:
Purpose: the goals of this study are to explore the effect of loss of Ptip in Sp7 positive dental progenitor cells  on CD45- Ter119- Tie2- dental progenitor cells
Methods:  CD45- Ter119- Tie2- dental progenitor cells  were sorted by FACs in lower incisors from Ptipf/f and Ptipf/f;Sp7-cre  mice and performed RNAseq
Our finding reveals that Ptip as crucial regulator in tooth homeostasis, functioning to safeguard the Sp7+ progenitor cells epigenome from a breach in lineage confinement that triggers irreversible tooth defects.
Conclusions: loss of Ptip unregulate dental development and active Wnt signal pathway

overall_design: RNA was extracted from freshly CD45-Ter119-Tie2- progenitor cells sorted by FACS from lower incisors from  Ptipf/f and Ptipf/f;Sp7-cre  mice

first: Yufeng

last: Zhang


title: Uncovering small non-coding RNAs involved in carcinogenesis of Glioma

city: Rourkela

first: Dr. Bibekanand

last: Mallick

state: Odisha

address: NIT Rourkela

department: Department of Life Science

country: India

institute: National Institute of Technology

summary: To determine which signalling pathways are affected by small RNAs (piRNAs, miRNAs) through target regulation in Glioblastoma Multiforme (GBM), we performed high-throughput next-generation sequencing in U87-MG GBM cell line. The RNA sequencing (RNA-Seq) of small RNAs and transcriptomes discovered both known and novel piRNAs and miRNAs as well other transcriptomes of protein-coding genes, lncRNAs and pseudogenes expressed in this GBM cell line. These small RNAs and target transcriptomes can be further investigated to decode novel molecular mechanisms underlying oncogenesis of this malignancy.

overall_design: Small RNA and transcriptome profiles of glioblastoma cell line were generated by Illumina HiSeq 2500 platform. After single-end sequencing of small RNAs and pair-end sequencing of transcriptomes, the adapter was trimmed, and filtered reads analyzed to discover the known and novel small RNAs and mRNAs, which might be involved in tumorigenesis of glioblastoma.

first: Rojalin

last: Nayak

first: Bibekanand


title: Hepatocyte SREBP signaling mediates clock communication within the liver [scRNA-seq]

overall_design: Single-cell RNA sequenceing in enriched non-parenchymal cells (NPC)  from control, ReverbhDKO, and Reverb/ScaphDKO liver


title: Hepatocyte SREBP signaling mediates clock communication within the liver [RNA-seq]

overall_design: RNA-sequencing in isolated hepatocytes and Liver macrophages from control, ReverbhDKO, and Reverb/ScaphDKO liver


title: Translational Reprogramming as a Driver of Antimony-drug Resistance in Leishmania

city: Medellin

first: Sneider

middle: Alexander

last: Gutierrez Guarnizo

state: Antioquia

country: Colombia

institute: Universidad de Antioquia

summary:
Purpose: In this study, we have used a translatomic approach by coupling polysome profiling and deep RNA-sequencing to estimate changes in the translatome of antimony-resistant Leishmania parasites

Methods: Leishmania tropica promastigotes were stepwise selected for resistance to trivalent antimony. Two different strains were studied, the L. tropica SbIII-sensitive or wildtype strain (WT) and the derived highly resistant strain (HR).  After polysome profiling four types of samples were evaluated by deep RNAseq: total mRNA used as input, monosomes (MS), light polysomes (LP), and heavy polysomes (HP). The DESeq2 algorithm was used for differential expression analysis to identify translational changes at the basal level (HR Vs. WT), translational changes to combat the drug (HR+SbIII Vs. HR), and to compare translatomic Vs. transcriptomic changes (HP Vs. Total input) [see overall design section below].

Results: Differential translational analysis (cutoff of fold change ≥ 1.5 and p-value corrected by Benjamini-Hochberg FDR ≤ 0.05) showed that transcripts composition per polysome fraction was different in the resistant strain. It included several upregulated (Up) and downregulated (Down) transcripts. At the basal level, 2431 different transcripts were differentially translated:  monosome (Down: 4, Up: 0), light polysomes (Down: 906, Up: 951), and heavy polysomes (Down: 1096, Up: 1064). Under the antimony challenge, 189 different transcripts were differentially translated:  monosome (Down: 0, Up: 2), light polysomes (Down: 9, Up: 57), and heavy polysomes (Down: 30, Up: 134). Overall, most of the changes were identified in polysome fraction when compared with monosomes or total transcriptome.

Conclusions: Our study shows evidence that translational control has a main role in coordinating the resistance to antimony in Leishmania parasites. We propose a novel model that establishes translational control as a major driver of antimony-resistant phenotypes in Leishmania parasites.

overall_design:
Three experimental conditions were considered to estimate changes at the translational level: WT strain growing without drug challenge (WT w/o SbIII), HR strain growing without drug challenge (HR w/o SbIII), and HR strain growing under drug challenge (HR + SbIII).

Four types of samples were evaluated: total mRNA used as input for polysome profiling. After polysome profiling and automatic fractionation the mRNAs under translation were grouped into three additional categories representing increasing levels of translational efficiency: monosomes (MS), light polysomes (LP), and heavy polysomes (HP). Each experimental condition was evaluated in three biologically independent experiments. As a result, 36 samples  (3 conditions X 4 types of samples X 3 biological replicates) were submitted to sequencing in Illumina Hiseq 2000 platform, with read length of 150 nt, and an estimated of 40M PE reads per sample (20M in each direction).

After sequencing, three different comparisons were evaluated by differential gene expression analysis. Comparison 1: changes at the translational level in drug-resistant strain occurring in the absence of the drug (general basal changes. HR Vs. WT). Comparison 2: Changes occurring when the resistant parasites are growing under SbIII exposure (changes to combat the drug, HR+SbIII Vs. HR). Comparison 3: Changes occurring at the transcriptional or at the translational level (HP Vs. total mRNA).

first: Elena

middle: B

last: Tkhonova

first: Andrey

last: Karamyshev

first: Carlos

middle: E

last: Muskus

first: Zemfira

middle: N

last: Karamysheva


title: Transcriptional analysis for off-target effects by sgRNA variants in E.coli BL21(DE3)

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: Five different sgRNAs targeting mCherry gene (wild-type, without a spacer, and three truncated variants) were used to investigate the off-target effects of CRISPR interference.

overall_design: Total RNA sequencing data from E. coli expressing CRISPRi system targeting mCherry gene with synthetic sgRNAs

first: Gibyuck

last: Byun

first: Jina

last: Yang

first: Sang

middle: W


title: Next-generation RNA sequencing of Acetate treated primary cultured mouse astrocytes in the presence or absence of Aβ

status: Public on Apr 03 2023

city: Daejeon

first: C Justin

last: Lee

address: 55, Expo-ro, Doryong-dong, Yuseong-gu

department: Center for Cognition and Sociality

institute: Institute for Basic Science

summary: Reactive astrogliosis is a well-known and recognised marker of Alzheimer's Disease (AD). The aim of this study is to functionally visualise reactive astrocyte-mediated neuronal hypometabolism in the brains that is associated with AD and neuroinflammation. To investigate alterations of acetate and glucose metabolism and the effect thereof in AD-like astrocytes, primary astrocyte cultures were treated with acetate in the presence or absence of amyloid beta (Aβ) oligomers. On comparison, we found that acetate treatment upregulated the expression of acetate transporter MCT1 (Slc16a1) as well as that of enzymes involved in the urea cycle and subsequent GABA synthesis. We could, therefore, conclude that MCT1-mediated uptake of acetate into astrocytes triggered GABA synthesis by upregulating enzymes involved in putrescine production and degradation.

overall_design: Primary cultured astrocytes (P0-P1) were treated with Aβ oligomers (1μM) for 5 days (DIV8-12). On the 4th day (DIV11), culture media was replaced with glucose-free medium and supplemented with sodium acetate (10mM). The next day, RNA was isolated from the cultured cells and processed to prepare cDNA libraries compatible with Illumina HiSeq NEXT Generation high-throughput sequencer. After the 2 x 100bp Illumina HiSeq paired-end sequencing run was complete, data in the form of BCL files was procured and processed to obtain relevant findings.

first: MinHo

last: Nam

first: Mridula

last: Bhalla

first: C


title: Changes in the expression pattern of OsWUS negatively regulate plant stature and panicle development in rice

city: Guangzhou

first: Limin

last: Wang

address: zhongkai road 501

institute: Zhongkai University of Agriculture and Engineering

summary: WUSCHEL (WUS) and WUSCHEL-RELATED HOMEOBOX (WOX) encode transcription factors and play important roles in regulating the formation and maintenance of shoot and floral meristems. OsWUS have distinct functions in meristem development with slightly tuned expression. However, the mechanisms regulating the specific expression of OsWUS need to be further explored. In this study, an abnormal expression mutant of OsWUS, called Dwarf and aberrant panicle 1 (Dap1) were used. In order to identify the causal gene in Dap1, high-efficiency Thermal Asymmetric Interlaced (hiTAIL)-PCR and co-segregation analysis were performed. We surveyed the growth and yield traits in Dap1 and wild-type. Changes in gene expression between Dap1 and wild-type were determined by RNA-seq. The Dap1 mutant is due to the T-DNA inserted at 3,628-bp upstream of the translation start codon of OsWUS. Plant height, tiller numbers, panicle length, the number of grains per main panicle and the number of secondary branches was significantly reduced in the Dap1 mutant. The expression of OsWUS was markedly increased in Dap1 mutant plants compared to the wild-type, which might be due to a disruption in the genomic sequence integrity. Simultaneously, the expression levels of gibberellic acid (GA)-related genes and genes involved in panicle development were significantly changed in the Dap1 mutant. Our results suggest that OsWUS is a precise regulatory element, its specific spatio-temporal expression pattern is critical for its function, and both loss-of-function and gain-of-function mutations lead to abnormal plant growth.

first: Huiwu

last: Tang

first: Jinlan

last: Fan

first: Ru

first: Jiahui

last: Zhu

first: Xinzhu

last: Xiang

first: Jingfang

last: Dong

first: Lingyan

last: Zhou


title: Transcriptional Profiling of liver fibrosis induced by CCl4 injections

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: The human liver has a remarkable capacity to regenerate and thus compensate over decades for fibrosis caused by toxic chemicals, drugs, alcohol, or malnutrition. To date, no protective mechanisms have been identified that help the liver tolerate these repeated injuries. In this study, we revealed dysregulation of lipid metabolism and mild inflammation as protective mechanisms by studying longitudinal multi-omic measurements of liver fibrosis-induced by repeated CCl4 injections in mice (n = 45). Based on comprehensive proteomics, transcriptomics, blood- and tissue-level profiling, we uncovered three phases of early disease development - Initiation, Progression, and Tolerance. Using novel multi-omic network analysis, we identified multi-level mechanisms that are significantly dysregulated in the injury-tolerant response. A public data analysis and shows that these profiles are altered in human liver diseases, including fibrosis and early cirrhosis stages. Our findings mark the beginning of the Tolerance phase as the critical switching point in liver response to repetitive toxic doses. After fostering extracellular matrix accumulation as an acute response, we observe a deposition of tiny lipid droplets in hepatocytes only in the Tolerant phase. Our comprehensive study shows that lipid metabolism and mild inflammation may serve as biomarkers and are putative functional requirements to resist further disease progression.

overall_design: In the present study, by using whole genome Affymetrix microarrays (MoGene-2_0-st; Agilent Technologies, Santa Clara, CA), we examined the transcriptomic profiles in the fibrosed livers after 2, 4, 6, 8 and 10 weeks of CCl4 injections compared with control.

first: Seddik

last: Hammad

first: Steven

last: Dooley


title: Single cell RNA sequencing (scRNAseq) on mouse embryonic cranial motor neurons and surrounding tissue from wildtype and HCFP1 cRE1dup/+ mice.

first: Elizabeth

last: Engle

summary: We found hereditary congenital facial paralysis type 1 (HCFP1) is caused by variants that duplicate or change cis regulatory elements (cREs) controlling the neuronal expression of the GATA2 transcription factor. We generated an HCFP1 mouse model in which tandem copies of the human version of a GATA2 regulatory element we term cRE1 were inserted proximal to the mouse cRE1 (cRE1dup/+; hg19: chr3:128,175,708-128,176,563). We report the use of single cell RNA sequencing (scRNAseq) for transcriptomic analysis of developing rhombomere 4(r4)-derived wild type (WT) and cRE1dup/+ facial branchial motor neurons (FBMNs) and inner ear efferent neurons (IEEs), as well as surrounding tissue, from embryos aged 9.5-12.5 post coitus (E9.5-12.5).

overall_design: scRNAseq (10x Genomics) libraries were generated from  FAC-sorted WT and cRE1dup mouse embryonic cranial motor neurons spanning r3 (trigeminal motor neurons) to r7 (hypoglossal and glossopharyngeal motor neurons) marked by the motor neuron-specific Isl1MN-GFP transgenic reporter. GFP negative cells from the surrounding tissue were included for transcriptional and anatomic context. Cells were collected at E9.5 (n= 17 WT, 18 cRE1dup/+ embryos from 2 litters), E10.5 (n=12 WT, 7 cRE1dup/+ embryos from 2 litters), E11.5 (n=5 WT, 2 cRE1dup/+ embryos from 1 litter), and E12.5 (n=3 WT,  5 cRE1dup/+ embryos from 1 litter). Single cell cDNA libraries were generated using a Chromium Next GEM Single Cell 3? Library Kit v3.1. Libraries from littermate WT and cRE1dup/+ preparations were sequenced on common flow cells on a NextSeq 500 DNA sequencer using a NextSeq 500/550 High Output v2.5 kit (75 cycles) (Illumina). Raw sequence data was processed, filtered and aligned on the Cell Ranger analytic pipeline (10x Genomics) to generate FASTQ and filtered feature bc matrix files for deposit.

first: Alan

last: Tenney

first: Wai-Man

last: Chan


title: Functional and comparative analysis of SWAT cells

city: Copenhagen

first: Søren

last: Nielsen

address: Blegdamsvej 9

department: 1The Centre for Physical Activity Research

country: Denmark

institute: Rigshospitalet

summary:
Human adipose stem and progenitor cells (ASPCs) develop into heterogenous cultures of adipogenic and Structural Wnt-regulated Adipose Tissue resident (SWAT) cells upon induction of adipogenic differentiation.
To investiagte the function of SWAT cells and compare them with proliferating ASPCs, we enriched the SWAT cells from the adipogenic cells using density gradient centriguation.
The enriched SWAT cells were cultured for 24 hours in proliferation media or differentiation media for 24 hours. 4 density gradient centrifugations were performed, resulting in 4 technical replicates per media type. We included proliferating ASPCS (undifferentiated) as control.
We then performed gene expression profiling analysis using data from RNA-Seq of 4 samples per condition (proliferating ASPCs, SWAT cells in proliferation media, SWAT cells in differentiation media)

overall_design: Comparative gene expression profiling analysis of RNA-seq data from proliferating human ASPCs and SWAT cells cultured in proliferation media or differentiation media for 24 hours.

first: Nagendra

last: Palani

first: Carla

last: Horvath

first: Soren

first: Camilla

last: Scheele


title: A-to-I edited miR-411-5p targets MET and promotes TKI response in NSCLC-resistant cells

city: Richmond

first: Mario

last: Acunzo

state: Virginia

address: 1220 East Broad Street

department: Internal Medicine

institute: VCU

summary: Non-small cell lung cancer (NSCLC) patients carrying an epidermal growth factor receptor (EGFR) mutation have an initial favorable clinical response to the tyrosine kinase inhibitors (TKIs). Unfortunately, rapid resistance occurs mainly because of genetic alterations, including amplification of the hepatocyte growth factor receptor (MET) and its abnormal activity. The RNA post-transcriptional modifications that contribute to aberrant expression of MET in cancer are largely under-investigated and among them is the adenosine-to-inosine (A-to-I) RNA editing of microRNAs. A reduction of A-to-I editing in position 5 of miR-411-5p has been identified in several cancers, including NSCLC. In this study, thanks to cancer-associated gene expression analysis, we assessed the effect of the edited miR-411-5p on NSCLC cell lines. We found that edited miR-411-5p directly targets MET and negatively affects the itogen-activated protein kinases (MAPKs) pathway. Considering the predominant role of the MAPKs pathway on TKI resistance, we generated NSCLC EGFR mutated cell lines resistant to TKI inhibitors and evaluated the effect of edited miR-411-5p overexpression. We found that the edited miR-411-5p reduces proliferation and induces apoptosis, promoting EGFR TKI response in NSCLC-resistant cells\

overall_design: H1299 and H520 were transfected with ed.miR-411-5p and Scr as control, and, after 48h hours, cells were collected and RNA isolated.


title: Human adipose stem and progenitor cells across brown and white depots split into Adipogenic and SWAT cells during early differentiation

summary:
Human adipose stem and progenitor cells (ASPCs) develop into heterogenous cultures of adipogenic and Structural Wnt-regulated Adipose Tissue resident (SWAT) cells upon induction of adipogenic differentiation.
In vitro proliferating ASPC and differentiating adipocytes were collected from multiple timepoints to identify the trajectory of cells.
Cells from two white depots (subcutaneous abdominal & visceral abdominal) and two brown depots (supraclavicular & perirenal) were used for the study.
Progenitors from all 4 depots show similar differentiation trajectories during early differentiation.

overall_design: Single-cell RNA-seq from white and brown adipose progenitors, and from differentiating cells until day 6.


title: Integrative Single Cell Multiomic Profiling Analysis Reveals HOX-PBX Gene Regulatory Network Regulating the Survival of mTOR Hyperactive Cells [snRNA-Seq]

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Lymphangioleiomyomatosis (LAM) is a rare, debilitating lung disease that predominantly affects women of reproductive age. LAM cells carry deleterious mutations of tuberous sclerosis complex (TSC1/TSC2) genes, resulting in hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1) and ultimately dysregulated cell growth. The integrative single cell omics data identified the activation of uterine specific HOX-PBX transcriptional programming in pulmonary LAMCORE cells. Network analysis predicted homeobox transcription factors including PBX1 and HOXD11 as key regulators controlling LAMCORE cell fate. Targeting the HOX-PBX network may have therapeutic value in LAM and TSC-related diseases, and possibly in other mTORC1-hyperactive neoplasms.

overall_design:
In this study, we employed single cell/ single nuclei RNAseq and ATACseq data integration and gene regulatory network approach in conjunction with biochemical and functional assays using in vivo and in vitro LAM models to gain better understanding on molecular mechanisms responsible for the survival of LAM cells and inform the development of novel therapeutic targets for LAM.
Submitter states that raw data will be submitted to dbGap.

first: Tasnim

middle: F

last: Olatoke

first: Andrew

last: Wagner

first: Aristotelis

last: Astrinidis

first: Minzhe

last: Guo

first: Erik

middle: Y

last: Zhang

middle: G

first: Ushodaya

last: Mattam

last: Kopras

first: Nishant

last: Gupta

first: Eric

last: Smith

first: Magdalena

last: Karbowniczek

first: Maciej

last: Markiewkski

first: Kathryn

last: Wikenheiser-Brokamp

first: Jeffrey

last: Whitsett

first: Francis

middle: X

last: McCormack

first: Jane

last: Yu


title: Dynamics and stage-specificity of between-population gene expression divergence in the Drosophila melanogaster larval fat body

first: Amanda

last: Glaser-Schmitt

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

overall_design: Refer to individual Series


title: Integrative Single Cell Multiomic Profiling Analysis Reveals HOX-PBX Gene Regulatory Network Regulating the Survival of mTOR Hyperactive Cells

last: Xu


title: Identification of the unique gene expression profile in MyoD-tdTomato Low- and MyoD-tdTomato High-expressing muscle stem cells (MuSCs) populations

city: Tsukuba

first: Ryo

last: Fujita

state: Ibaraki

department: Transborder Medical Research Center

country: Japan

institute: University of Tsukuba

summary: We generated MyoD-KI mice to distinguish the heterogenous MuSCs populations based on MYOD expression. Using the mice, we performed RNA-seq to identify the unique gene expression profile in the heterogenous MuSCs population.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MyoD-tdTomato low- , MyoD-tdTomato High-expressing MuSCs, and freshly isolated quiescent MuSCs from Pax7-YFP mice.

first: Takehito

last: Sugasawa


title: Development of an improved in vitro model of bovine trophectoderm differentiation

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

summary: The mechanisms regulating early stages of placentation and trophectoderm differentiation in the ruminant conceptus remain poorly understood. Here we present a model of trophectoderm (TE) differentiation in vitro from outgrowths of individual in vitro derived embryos. Cell outgrowths expressed markers of mononucleate (MNC) and binucleate (BNC) TE cells. The percentage of BNC ranged from 14-39% in individual outgrowths as determined by flow cytometry. Pregnancy-associated glycoproteins (PAGs), produced by BNC, were measured in culture media on days 35 to 54. Continuous secretion of PAGs was observed and indicative of BNC functionality. Gene expression was evaluated in 20 embryo cell outgrowths derived from two different sires. Expression of HAND1, which is involved in TE differentiation, and CSH2, a BNC-specific gene, was altered in cell outgrowths between the two sires tested. Single-cell RNA-seq analysis of day 40 TE cell outgrowths revealed 11 distinct cell populations, with specific clusters genes involved in TE lineage specification, proliferation, and differentiation. In addition, whole -RNAseq analysis was performed in day 35 and 40 TE cell outgrowths and confirmed sustained expression of genes expressed by BNC, such as CSH2 and some PAGs. The developed in vitro bovine embryo outgrowth culture found evidence for MNC and BNC differentiation and continuous production of PAGs, recapitulating key features of early bovine placenta development. This model can be used to understand the developmental biology of TE cells, provide insights into paternal influences on TE differentiation, and impact our understanding of early pregnancy loss in cattle.

overall_design: Samples of trophectoderm cell outgrowths from in vitro produced embryos.

first: MSofia

first: Jason

last: Rizo

first: Jessica

last: Drum

first: Eleanore

middle: V

last: O’Neil

first: Ky

last: Pohler

first: Karl

last: Kerns

last: Schmelze

first: Jonathan

last: Green

first: Thomas

last: Spencer


title: Hepatocyte SREBP signaling mediates clock communication within the liver

first: Dongyin

last: Guan


title: PAR-CLIP of Slf1 and Sro9 during optimal growth and oxidative stress

city: Manchester

first: Graham

middle: D

last: Pavitt

address: Dover Street

department: MCF/SBS/FBMH

country: United Kingdom

institute: University of Manchester

summary: We quantified the binding sites of the La related RNA-binding proteins Slf1 and Sro9 within RNAs using PAR-CLIP. Datasets were obtained for yeast cells during optimal growth and during the cellular response to peroxide stress.

overall_design: Untagged transcriptomic changes in WT and slf1/sro9 deleted cells with and without stress (in duplicate). PAR-CLIP study of Slf1-TAP and Sro9-TAP binding sites with and without stress (in duplicate) along with matched totals.

first: Martin

last: Jennings

first: Priya

last: Srivastava

first: Christopher

last: Kershaw

first: David

last: Talavera

last: Grant


title: Temporal transcriptomic profiles of brain regions following acute and chronic demyelinating injury

city: College Station

first: Jianrong

last: Li

address: VBEC Receiving, VICI Bldg Rm127, 4458 TAMUS

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

summary: Purpose: The central nervous system (CNS) possesses intrinsic remyelination capabilities in response to demyelinating injury. However, this remyelination potential is diminished as demyelinating disease such as multiple sclerosis progresses overtime. To better understand myelin repair processes, the goal of this study was to determine temporal transcriptomic changes in cerebral white matter (corpus callosum) and gray matter (cortex and hippocampus) after acute and chronic demyelinating injury. The cuprizone mouse model of de- and remyelination was used for this investigation.      Methods: Adult C57BL/6 mice were exposed to cuprizone diet (0.2%) for 3, 5 or 12 weeks followed by returning to normal diet for up to 12 weeks for recovery. Brain regions were dissected for bulk RNA-seq.     Conclusion: RNA-seq analyses suggest common and distinct spatiotemporal transcriptional alterations during CNS demyelination and remyelination. Dataset for this study represents the first that covers gene expression landscapes of three brain regions over extended regenerative periods after chronic CNS demyelination.

overall_design: Performed bulk RNA sequencing using isolated corpus callosum, hippocampus, cortex at different time points after acute (3-5 wks) and chronic (12 wks) cuprizone exposure.

first: Grace

last: Samtani

first: Sunja

last: Kim

first: Kranti

last: Konganti

first: Andrew

last: Hillhouse


title: Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits in adipocytes using LipocyteProfiler

city: Cambridge

first: Melina

last: Claussnitzer

state: MA

address: 75 Ames Street

institute: Broad Institute of MIT and Harvard

summary: We report LipocyteProfiler, which is an unbiased high-throughput profiling assay, that uses a combination of dyes that make it amenable to large-scale and high-capacity profiling of lipid accumulating cell types. As exemplified by its application in adipocytes, we demonstrate that our customised morphometric approach is capable of surveying diverse cellular mechanisms by generating depot-specific, trait/process-specific and allele-specific morphological and cellular profiles. The approach demonstrated here paves the way to large-scale and high-capacity arrayed and pooled forward and reverse phenotypic genetic profiling in lipid storing cell types

overall_design: Examination of 208 samples; two adipocyte depots at four differentiation time points

first: Samantha

last: Laber

first: Sophie

last: Strobel

first: Josep-Maria

last: Mercader

first: Hesam

last: Dashti

first: Alina

last: Ainbinder

first: Julius

last: Honecker

first: Garrett

last: Garborcauskas

first: Aaron

last: Leong

first: Kat

last: Figueroa

first: Nasa

last: Sinnott-Armstrong

first: Maria

last: Alimova

first: Giacomo

last: Deodato

first: Elizabeth

last: McGonagle

first: Adam

last: Stefek

first: Alycen

last: Harney

last: Stirling

first: Gregory

last: Way

first: Alham

last: Saadat

first: Sierra

last: Harken

first: Saskia

last: Reibe-Pal

first: Virtu

last: Calabuig

first: Beth

last: Cimini

first: Hans

last: Hauner

first: Miriam

last: Udler

first: Anne

last: Carpenter

first: Jose

last: Florez

first: Cecilia

last: Lindgren

first: Suzanne

last: Jacobs


title: TBBPA, TBBPS and TCBPA disrupt hESCs hepatic differentiation and promote the proliferation of differentiated cells seemingly via up-regulating the FGF10 signaling pathway

city: 北京市

first: Renjun

last: Yang

state: 北京

address: 双清路18号林业大学北门

institute: RCEES

summary: Halogenated flame retardants (HFRs) Tetrabromobisphenol A (TBBPA), Tetrabromobisphenol S (TBBPS) and Tetrachlorobisphenol (TCBPA) are wildly applied in manufacturing industry to improve the fire safety of the products. Recent reports demonstrated that TBBPA, TBBPS and TCBPA can be detected in pregnant women serum at nanomolar-level. Considering TBBPA have also been detected in the cord serum and the structural similarity of the 3 HFRs, it is necessary to pay attention to their development toxicity. Liver is the important detoxic organ but also target of TBBPA since it has been demonstrated that TBBPA exposure lead to increased liver weight in mouse and rat. So the developmental hepatic toxicity of the 3 HFRs were studied in this current research with the transcriptomic and human embryonic stem cells hepatic differentiation based toxicity evaluation system. A hepatic differentiation specific lineage development map and cell lineage - gene expression annotations were made and used for easily assessing the lineage alternations caused by toxicant treatment. Together with GO and KEGG analysis, this study mainly demonstrated that, the 3 HFRs have many common disruptive effect on hepatic differentiation, while only TCBPA significantly inhibited hepatic differentiation. The up-regulation of genes related to cell cycle and FGF10 signaling pathway at relatively late stage of hepatic differentiation indicates the proliferation of hepatoblasts were promoted by the 3 HFRs, likely via up-regulating the FGF10 signaling pathway. The proliferating promoting effect may partly explain why liver gain weight in rodents exposed to TBBPA.

overall_design: A total of 24 samples analyzed, with 2 H9 samples here, 16 samples in our unpublished research (GSM3712591-GSM3712606 in GSE129412 and GSM4473072-GSM4473087 here), and 6 samples (GSM3518767-GSM3518772) from our previously published research.

first: Shaojun

last: Liang

first: Shuyu

last: Liu

first: Xiaoxing

first: Linshu

last: Jiang

first: Nuoya

last: Yin

first: Francesco

last: Faiola


title: Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity

city: San Francisco

first: Sujin

last: Lee

state: CA

institute: University of California San Francisco

summary: Little is understood about how the two major types of heterochromatin domains (HP1 and Polycomb) are kept separate.  In the yeast Cryptococcus neoformans, the Polycomb-like protein Ccc1 prevents deposition of H3K27me3 at HP1 domains.  Here we show that phase separation propensity underpins Ccc1 function.  Mutations of the two basic clusters in the intrinsically disordered region or deletion of the coiled-coil dimerization domain alter phase separation behavior of Ccc1 in vitro and have commensurate impacts on formation of Ccc1 condensates in vivo, which are enriched for PRC2.  Importantly, mutations that alter phase separation trigger ectopic H3K27me3 at HP1 domains.  Supporting a direct condensate-driven mechanism for fidelity, Ccc1 droplets efficiently concentrate recombinant C. neoformans PRC2 in vitro while HP1 droplets do so only weakly.  These studies establish a biochemical basis for chromatin regulation in which mesoscale biophysical properties play a key functional role.

overall_design: ChIP-seq to investigate H3K27 methylation in C. neoformans

first: Hiten

last: Madhani


title: ArgRS, MetRS, and SRRM2 dependent changes in mRNA splicing and exon usage

city: La Jolla

first: Paul

last: Schimmel

state: California

address: 10550 North Torrey Pines Road, BCC379

department: Molecular Medicine

institute: The Scripps Research Institute

summary: Arginine is involved in inflammation and amino acid signaling, in part through the mTORC1 pathway. In cell-based assays and in the mouse, we found that arginine regulates nuclear levels of arginyl-tRNA synthetase (ArgRS) and that nuclear ArgRS interacts and co-localizes with the Serine/Arginine Repetitive Matrix Protein 2 (SRRM2), a spliceosomal protein crucial for the formation of nuclear speckle condensates. Arginine depletion or ArgRS knock down, both of which decreased nuclear ArgRS levels, mobilized SRRM2 for trafficking from nuclear condensates and altered mRNA processing and splice junction usage while minimally affecting expression of other cellular RNAs. These splice junction changes included a subset that were inversely correlated with SRRM2 knock down induced changes and the affected genes encompassed components of the mTORC1 pathway. This inverse correlation suggests that the nuclear ArgRS-SRRM2 interaction regulates SRRM2 nuclear trafficking and alternative splicing in the physiological response to changed arginine levels resulting from inflammation.

overall_design: RNAseq of HepG2 cells expressing either a shSCR control or an shRNA against RARS1 or an shRNA against MARS1 or an shRNA against SRRM2

first: Haissi

last: Cui

first: Ryan

last: Nottingham

first: Alan

last: Lambowitz


title: Dasatinib Overcomes Glucocorticoid Resistance in B-cell Acute Lymphoblastic Leukemia

status: Public on Apr 02 2023

city: Stanford

first: Jolanda

last: Sarno

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

summary:
Bulk RNA-Seq of sorted B cell populations revealed glucocorticoid pathway being coordinated with B-cell development.
Bulk RNA-Seq of human BCP-ALL cell lines treated with dexamethasone identified pathways of resistance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for B-cell sorted populations in 3 heathy donors and cell lines (NALM6, REH wt and REH GCR) treated with vehicle or dexamethasone.

first: Pablo

last: Domizi

first: Felice-Alessio

last: Bava

first: Kara

last: Davis


title: Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with 20 uM Carnosic Acid

first: Farhana

last: Ferdousi

address: Tennodai 1-1-1

summary:
Gene expression profiling reveals multiple tissue-specific functionality of carnosic acid in a stem-based tool.
We evaluated the effects of carnosic acid on human amniotic epithelial stem cells. We performed an untargeted whole-genome transcriptome analysis to explore functionality of carnosic acid in a stem cell-based tool.

overall_design: According to the manufacturer's guide, the RNA was extracted using Isogen kit (Nip-pon Gene Co. Ltd., Japan). Then, RNA quantity and quality were determined using the NanoDrop 2000 spectrophotometer (ThermoScientific, USA). DNA microarray analysis was conducted on control and CA-treated hAESC samples using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer's instructions. In brief, complementary DNA (cDNA) was synthesized from 100 ng of RNA solutions. cRNA was synthesized from in vitro transcription of cDNA and then purified and reverse transcribed. Finally, single-stranded cDNA (ss-cDNA) was synthesized, purified, fragmented, and labeled following the manufacturer's instructions. Cartridge Array Hybridization was performed using the Clariom S array (Human; ThermoFisher Scientific) on the GeneChip™ Fluidics Station (ThermoFisher Scientific). Scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data obtained after scanning were analyzed using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific). The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space) were considered as differentially expressed genes (DEGs).


title: Kinase-independent activity of DYRK1A promotes viral entry of highly pathogenic human coronaviruses [RNAseq]

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

summary: We demonstrate that DYRK1A regulates ACE2 and DPP4 transcription independent of its catalytic kinase function to support SARS-CoV, SARS-CoV-2, and MERS-CoV entry. We show that DYRK1A promotes DNA accessibility at the ACE2 promoter and a putative distal enhancer, facilitating transcription and gene expression. Finally, we validate that the proviral activity of DYRK1A is conserved across species using cells of monkey and human origin and an in vivo mouse model.

overall_design: RNA-seq of Vero-E6 cell line

first: Wesley

last: Cai

first: Strine

last: Madison

first: Wilen

last: Craig


title: Reduced representation bisulfite sequencing (RRBS) profiles of  human induced pluripotent stem cells exposed to varied chemicals

status: Public on Apr 01 2023

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

type: Methylation profiling by high throughput sequencing

summary: We studied the effects of chemical exposure on global DNA methylation by using mCherry-MBD-nls human iPS cells. By using 135 chemical library, we could devide the effects of global DNA methylation into 3 categories; reduction (hypomethylation), increase (hypermethylation) and little/no effect. We further performed both genome-wide DNA methylation and stemness-related gene expression (100 genes) analyses, and results indicated that hypermethylation agents increased DNA methylation and downregulated the expression of genes involved in cell cycle or development.

overall_design: Exposure to DMSO, etoposide, propyl gallate, theophylline, or 5-aza-dc for 48 hrs.

first: Satoshi

last: Otsuka

first: Tomohiro

last: Ito

first: Hideko

last: Sone


title: Mitochondrial dynamics define muscle fiber type by modulating cellular metabolism pathways

city: Toyonaka

first: Naotada

last: Ishihara

state: Osaka

address: 1-1, Machikaneyamacho

institute: Osaka University

summary: Skeletal muscle is highly developed after birth, consisting of glycolytic fast- and oxidative slow-twitch fibers; however, the mechanisms of fiber type-specific differentiation are poorly understood. Here, we found an unexpected role for mitochondrial fission in the differentiation of fast-twitch oxidative fibers. Depletion of the mitochondrial fission factor dynamin-related protein 1 (Drp1) in mouse skeletal muscle and cultured myotubes resulted in the specific reduction of fast-twitch muscle fibers independently of respiratory function. Altered mitochondrial fission caused the activation of the Akt/mammalian target of rapamycin (mTOR) pathway via the mitochondrial accumulation of mTOR complex 2 (mTORC2), and rapamycin administration rescued the reduction of fast-twitch fibers in vivo and in vitro. Under Akt/mTOR activation, the mitochondria-related cytokine growth differentiation factor-15 was upregulated, which repressed fast-twitch fiber differentiation. Our findings reveal a novel role for mitochondrial dynamics in the activation of mTORC2 on mitochondria, resulting in the differentiation of muscle fibers.

overall_design: Gene expression in WT, Drp1-KO, and Drp1-KO exogenously expressing FLAG-Drp1 C2C12 cells at 4 days after differentiation.

first: Tatsuki

last: Yasuda


title: Knockdown Gene Expression Profile of potential key drivers for Alzheimer’s Disease in human iPSC-derived neurons.

city: Tucson

first: Syed Shujaat Ali

last: Zaidi

address: 1656 E Mabel St

department: Department of Immunobiology

institute: University of Arizona

summary: In this study, we construct network models by integrating multi-omics data in ROSMAP and MAYO cohort in AMP-AD consortium and infer 19 potential key drivers for Alzheimer’s Disease and related dementia (ADRD). To validate these 19 targets in modulating AD-related pathology (Amyloid-beta and phosphorylated-Tau) and investigating the biological functions and pathways they regulate, we performed RNAi-based knockdown of 19 targets inferred by computational systems biology model in human iPSC-derived neurons (iNs) and measured gene expression profile for each knockdown by RNAseq.

overall_design: Differential gene expression analysis of RNA-seq data for human iPSC-derived neurons samples. The differential expression analysis is perform to compare the gene expression profile between knockdown of each 19 target versus controls.

first: Julie

last: Merchant

first: Branden

last: Lau

first: Tracy

last: Young-Pearse

first: Rui

last: Chang


title: The Potent G-Quadruplex-Binding Compound QN-302 Downregulates S100P Gene Expression in Cells and in an In Vivo Model of Pancreatic Cancer

city: London

first: Stephen

last: Neidle

address: Brunswick Square

department: School of Pharmacy

institute: UCL

summary: The naphthalene diimide compound QN-302, designed to bind to G-quadruplex DNA sequences within the promoter regions of cancer-related genes, has high anti-proliferative activity in pancreatic cancer cell lines and anti-tumor activity in several experimental models for the disease. We show here that QN-302 also causes down-regulation of the expression of the S100P gene and the S100P protein in cells and in vivo. This protein is well-established as being involved in key proliferation and motility pathways in several human cancers and has been identified as a potential biomarker in pancreatic cancer. The S100P gene contains 60 putative quadruplex-forming sequences, one of which is in the promoter region, 48 nucleotides up-stream from the transcription start site. We report biophysical and molecular modeling studies showing that this sequence forms a highly stable G-quadruplex in vitro, which is further stabilized by QN-302. We also report transcriptome analyses showing that S100P expression is highly upregulated in tissues from human pancreatic cancer tumors, compared to normal pancreas material. The extent of up-regulation is dependent on the degree of differentiation of tumor cells, with the most poorly differentiated, from more advanced disease, having the highest level of S100P expression. The experimental drug QN-302 is currently in pre-IND development (as of Q1 2023) and its ability to down-regulate S100P protein expression supports a role for this protein as a marker of therapeutic response in pancreatic cancer. These results are also consistent with the hypothesis that the S100P promoter G-quadruplex is a potential therapeutic target in pancreatic cancer at the transcriptional level for QN-302.

overall_design: RNA-seq analyses were performed on a set of 2 poorly differentiated, 2 more highly differentiated human pancreatic tumor samples and 3 normal pancreas tissue. The 4 PDAC RNA samples were obtained from pancreatic tumor tissues with ethical approval from the NRES Committee North-west – Liverpool Central, MREC 07/H1005/87. The normal pancreas samples were obtained commercially from OriGene Technologies GmbH Germany (Cat #: CR560569, CR562915, CR561640). Differential expression analyses were performed: 2 pooly differentiated PDAC VS 3 normal pancreatic samples and  2 more highly differentiated PDAC VS 3 normal pancreatic samples.

first: Ahmed

middle: A

last: Ahmed


title: Integrative Single Cell Multiomic Profiling Analysis Reveals HOX-PBX Gene Regulatory Network Regulating the Survival of mTOR Hyperactive Cells [snATAC-Seq]

first: Yan

last: Xu

summary: Lymphangioleiomyomatosis (LAM) is a rare, debilitating lung disease that predominantly affects women of reproductive age. LAM cells carry deleterious mutations of tuberous sclerosis complex (TSC1/TSC2) genes, resulting in hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1) and ultimately dysregulated cell growth. The integrative single cell omics data identified the activation of uterine specific HOX-PBX transcriptional programming in pulmonary LAMCORE cells. Network analysis predicted homeobox transcription factors including PBX1 and HOXD11 as key regulators controlling LAMCORE cell fate. Targeting the HOX-PBX network may have therapeutic value in LAM and TSC-related diseases, and possibly in other mTORC1-hyperactive neoplasms.

overall_design:
In this study, we employed single cell/ single nuclei RNAseq and ATACseq data integration and gene regulatory network approach in conjunction with biochemical and functional assays using in vivo and in vitro LAM models to gain better understanding on molecular mechanisms responsible for the survival of LAM cells and inform the development of novel therapeutic targets for LAM.
Submitter states that raw data will be submitted to dbGap.

first: Tasnim

last: Olatoke

first: Andrew

last: Wagner

first: Aristotelis

last: Astrinidis

first: Minzhe

last: Guo

first: Erik

last: Zhang

first: Alan

first: Ushodaya

last: Mattam

first: Elizabeth

middle: J

last: Kopras

first: Nishant

last: Gupta

first: Eric

last: Smith

first: Magdalena

last: Karbowniczek

first: Maciej

last: Markiewkski

first: Kathryn

last: Wikenheiser-Brokamp

first: Jeffrey

last: Whitsett

first: Francis

last: McCormack

first: Jane

last: Yu


title: Hypothalamic astrocytes TRAP-seq in ORX/HFD mice

city: Oxford

first: Thomas

last: Monfeuga

address: Innovation Building, Old Road Campus, Roosevelt Drive

institute: Novo Nordisk Research Centre Oxford

summary: 3' mRNA-sequencing of the immunoprecipitated and supernatant fractions after Translating Ribosome Affinity Purification (TRAP) targeted to hypothalamic astrocytes RNA (from Aldh1l1eGFP-L10a mice) for 3 experimental conditions: chow diet; high-fat diet; high-fat diet + orchiectomy (Sham-chow n=7, Sham-HFD n=6, ORX-HFD n=7)

overall_design: 3' mRNA-sequencing; Sham-chow n=7, Sham-HFD n=6, ORX-HFD n=7

first: Mauricio

last: Dorfman

first: Susan

last: Melhorn

first: Jenny

last: Kanter

first: Jeremy

middle: M

last: Frey

first: Rachael

last: Fasnacht

first: Anandhakumar

last: Chandran

first: Emaad

last: Lala

first: Inmaculada

last: Velasco

first: Katya

last: Rubinow

middle: H

last: Meek

first: Ellen

last: Schur

first: Karin

last: Bornfeldt

first: Joshua

last: Thaler


title: Kinase-independent activity of DYRK1A promotes viral entry of highly pathogenic human coronaviruses [ATACseq]

first: Qin

last: Yan

overall_design: ATAC-seq of Vero-E6 cell line

first: Wesley

middle: L

last: Cai

first: Strine

last: Madison

first: Wilen

last: Craig


title: Gene expression profiling of in vitro activated mouse CD8+ T cells treated with or without spermidine

city: Meguro-ku, Tokyo

first: Sana

last: Hibino

address: T block (56th Bldg.), Komaba 4-6-1

institute: University of Tokyo

summary:
Recently, we have elucidated a novel role for the oncometabolite spermidine; intracellular spermidine is well-characterized as an essential metabolic fuel in growing cancer cells, but extracellular spermidine, released by dying cancer cells, also contributes to tumor progression by impairing effector activities of CD8+ T cells through the interference with proximal TCR signal transduction.
In order to decipher how spermidine modulates T cell signaling and effector programs, we conducted a comprehensive gene expression analysis by microarray for in vitro cultured mouse CD8+ T cells treated with or without spermidine.

overall_design: Mouse CD8+ T cells were cultured for 3 days with or without spermidine in the presence of anti-CD3/CD28 stimulation plus IL-2, then subjected to a transcriptome analysis by microarray (Clariom S Assay, Mouse, Thermo Fisher Scientific, Inc.).


title: Effect of 2 millimolar sodium acetate on unspecifically activated naive T cells

city: Erlangen

first: Michael

last: Frech

address: Ulmenweg 18

department: Department of Internal Medicine 3 - Rheumatology and Immunology

institute: University Hospital Erlangen

summary: Alcohol is among the most widely consumed dietary substances. While excessive alcohol consumption damages the liver, heart and brain, clinical observations also suggest that alcohol has strong immunoregulatory properties. However, little is known about the mechanistic effects of alcohol on the immune system. In this context, we investigated the effect of acetate, the metabolite of alcohol, on primary mouse T cells, unspecifically activated with dynabeads.

overall_design: Naive CD4+ T cells were treated with 2 mM sodium acetate or vehicle (R10 medium) containing R10 medium for 4 hours. RNA was isolated using the RNeasy micro kit (Qiagen) according to the manufacturer's instructions.

first: Vugar

last: Azizov

first: Mario

last: Zaiss


title: Understanding the molecular basis leading the virulence of vesicular stomatitis virus in pigs

city: Orient Point

first: James

middle: Jiangtao

last: Zhu

state: NY

department: Plum Island Animal Disease Center

institute: USDA-ARS

summary: Comparison of the transcriptiomic profile using microarray analysis betwween primary porcine macrophages infected with recombinant vesicular stomatitis viruses

overall_design: Infections of  recombinant vesicular stomatitis viruses (VSV) were carried out on primary swine porcine macrophages. Six well plates containing 1x10^7 cells per well were infected at MOI of 10 TCID50 with each virus and incubated for five hours at 37 °C under 5% of CO2. Infections were conducted on triplicates. As a mock-infected samples 3 wells were incubated in the same conditions with macrophage media.  After incubation, total RNA was extracted and used in microarray analysis using DNA microarrays (Array design #:Agilent-069270; 4 X 44k per slide) manufactured by Agilent Technologies. Low input RNA two color labeling kit (Agilent Technologies) was used to lable cRNA. Total RNA isolated from mock-infection was labeled with Cy5 as universal control. All samples including mock-infection were labeled with Cy3. One Cy3 labled sample was cohybrided with the Cy5 labled control in one hybridization chamber. After hybridization and washing, the arrays were scanned with a GenPix 4000B and the images were saved as tiff files. The expression data were extracted with Genpix 7.0 software for statisitcal analysis using R with librarys(limma, MASS, statmod, splines). LOESS method was applied to normalize interarray variation. The pig gene sequences were mapped to human genes with BLAST and manual annotation. Annotated probes were mapped to human genes, and human gene Entrezid were used in bioinformatic analysis with The Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool.

first: Lauro

last: Velazquez-Salinas


title: Reduction of Neutrophil Activation by Phosphodiesterase 4 Blockade in Behçet's Disease

city: Paris

first: Paul

last: Régnier

address: 83 boulevard de l'hôpital

country: France

institute: AP-HP

summary:
Objective: Behçet's disease (BD) is a systemic vasculitis with inflammatory lesions mediated by cytotoxic T cells and neutrophils. Apremilast, an orally available small-molecule that selectively inhibits phosphodiesterase 4 (PDE4), has been recently approved for the treatment of BD. We aimed to investigate the effect of PDE4 inhibition on neutrophil activation in BD.
Methods: We studied surface markers and reactive oxygen species (ROS) by flow cytometry, neutrophils extra cellular traps (NETs) and molecular signature of neutrophils by transcriptomic before and after PDE4 inhibition.
Results: Activation surface markers (CD64, CD66b, CD11b and CD11c), ROS production and NETosis were up-regulated in BD as compared to Healthy Donors (HD) neutrophils. Transcriptome analysis showed 1021 significantly dysregulated neutrophils genes between BD and HD. Among dysregulated genes, we highlighted a great enrichment for pathways linked to innate immunity, intracellular signaling and chemotaxis in BD. Skin lesions of BD showed increased infiltration of neutrophils that co-localized with PDE4. Inhibition of PDE4 by apremilast strongly inhibited neutrophil surface activation markers as well as ROS production, NETosis, and genes and pathways related to innate immunity, intracellular signaling and chemotaxis.
Conclusion: We pointed out key biological effects of apremilast on neutrophils in BD.

overall_design: We performed microarray assay on neutrophils extracted from 5 healthy donors (HD, P1 to P5) and 4 patients with Behçet's disease (BD, P1 to P4), either untreated or treated with Apremilast (a PDE4 inhibitor).

first: Alexandre

last: Le Joncour

first: Anna

last: Maciejewski-Duval

first: Erwan

last: Charles

first: Stéphane

last: Barete

first: Pierre

last: Fouret

first: Michelle

last: Rosenzwajg

first: David

last: Klatzmann

first: Patrice

last: Cacoub

last: Saadoun


title: Effect on gene expression of CDK12/13 inhibition by THZ531 in combination with lapatinib or nilotinib  in Hs578T TNBC cells

city: Leiden

first: Bob

last: van de Water

state: Leiden

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

summary: We performed whole transcriptome expression profiling in Hs578T cells after treatment with THZ531, nilotinib, lapatinib or a combination thereof to study the effect of these combination treatments on the transcriptome.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hs578T treated with DMSO (control), THZ531 (0.1 uM and 1 uM), nilotinib (1 uM), lapatinib (3.16 uM) or a combination thereof.

first: Vera

last: van der Noord


title: RNA sequencing analysis of OTUD6B-knockdown KYSE30 and KYSE450 cells

city: beijing

first: li

last: lei

address: 17 Panjiayuan Nanli

institute: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using RNA sequencing analysis to test the effects of OTUD6B-knockdown on the mRNA of KYSE30 and KYSE450 cells.  Methods: KYSE30 and KYSE450 cells were transfected with negative control or siOTUD6B for 48 hours in 1640 medium plus 10% serum. Three independent replicates were plated, transfected in parallel for each negative control and siOTUD6B. Results: Log-fold changes of mRNAs between negative control and siOTUD6B group were selected with a significance threshod of p<0.05. Conclusions: Our study determined the mRNA changes of OTUD6B-knockdown KYSE30  and KYSE450 cells.

overall_design: KYSE30 and KYSE450 cells mRNA profiles of NC (transfected with negative control siRNA) and siOTUD6B (transfected with OTUD6B siRNA) were generated by RNA sequencing.

first: Li

last: Lei


title: Octopamine metabolically reprograms astrocytes to confer neuroprotection against α-synuclein

city: Chicago

first: Marc

last: Mendillo

state: IL

address: 303 E Superior St

institute: Northwestern University

summary: Octopamine is a well-established invertebrate neurotransmitter involved in fight-or-flight responses. In mammals, its function was replaced by norepinephrine. Nevertheless, it is present at trace amounts and can modulate the release of monoamine neurotransmitters by a yet unidentified mechanism. Here, through a multidisciplinary approach utilizing in vitro and in vivo models of a-synucleinopathy, we uncovered an unprecedented role for octopamine in driving the conversion from toxic to neuroprotective astrocytes in the cerebral cortex by fostering aerobic glycolysis. Neuron-derived octopamine acts on astrocytes via a TAAR1-Orai1-Ca2+-calcineurinmediated signaling pathway to stimulate lactate secretion. Lactate uptake in neurons via the MCT2-calcineurin-dependent pathway increases ATP and prevents neurodegeneration. Pathological increases of octopamine caused by a-synuclein halts lactate production in astrocytes and short-circuits the metabolic communication to neurons. Our work provides a novel function of octopamine as a modulator of astrocyte metabolism and hence neuroprotection with implications to a-synucleinopathies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for rat primary neuronal cultures infected with either control or alpha synuclein-A53T variant and treated with either sub-saturating (0.2 µM) or saturating (2.0 µM) doses of FK506 or the vehicle control DMSO.

first: Andrew

last: Shum

first: Sofia

last: Zaichick

first: Gregory

middle: S

last: McElroy

first: Karis

last: D’Alessandro

first: Michaela

last: Novakovic

first: Wesley

last: Peng

first: Daayun

last: Chung

first: Margaret

last: Flanagan

first: Roger

last: Smith

first: Alejandro

last: Morales

first: Laetitia

last: Stumpf

first: Kaitlyn

last: McGrath

first: Dimitri

last: Krainc

first: Murali

last: Prakriya

first: Navdeep

last: Chandel

first: Gabriela

last: Caraveo


title: Transcriptome profiling of hESC-derived neural cultures after acute glucocorticoid induction

city: Farmington

first: Olusegun

middle: B

last: Babaniyi

state: CT

address: 400 Farmington avenue

department: Genetics and Developmental Biology

institute: UCONN Health

summary: We examined the transcriptome of 2 hESC derived neural cultures treated with dexamethasone for 6 hours to identify differentially expressed genes in response to acute glucocorticoid exposure. We identified 31 differentially expressed (DE) genes common to cultures derived from both hESC lines with similar magnitudes and direction of change.

overall_design: mRNA profiling of 10 week old hESC-derived neural cultures treated with Vehicle and Dexamethasone for 6 hours.

first: Marc

last: Lalande

first: Jonathan

last: Covault


title: A sporulation-independent way of life for Bacillus thuringiensis in the late stages of an infection

city: Jouy-en-Josas

first: Leyla

last: Slamti

state: État

address: Domaine de Vilvert

department: Micalis

institute: INRAE

summary: The formation of endospores has always been considered as the unique mode of survival and transmission of sporulating Firmicutes due to the exceptional resistance and persistence of this bacterial cell form. In this study, we investigated the behavior of a bacterial population in the late stages of an infection as well as the characteristics of the Spo- bacterial form in the B. thuringiensis/Galleria mellonella infection model. Using fluorescent reporters coupled to flow cytometry as well as molecular markers, we demonstrated that the Spo- cells compose the majority of the population two weeks post-infection (pi) and that these bacteria present vitality signs. However, a protein synthesis and a growth recovery assay indicated that they are in a metabolically slowed-down state. Interestingly, they were found to be extremely resistant to the cadaver environment which proved deadly for in-vitro grown vegetative cells and, more strikingly, did not support the germination of spores. A transcriptomic analysis of this subpopulation at 7 days pi revealed a signature profile of this state. Analysis of the expression profile of individual genes at the cell level suggests that iron homeostasis is important at all stages of the infection, whereas the oxidative stress response seems of particular importance as the survival time increases. Altogether, these data indicate that non-sporulated bacteria engage in a profound adaptation process that leads to their persistence in the host cadaver.

overall_design: RNA-seq data for 7 days post-infection (dpi) Bacillus thuringiensis cells extracted from Galleria mellonella cadavers (3 samples) versus 30°C LB in vitro-grown Bacillus thuringiensis cells in exponential (3 samples) and early stationnary growth-phase (3 samples)

first: Hasna

last: Toukabri

first: Didier

last: Lereclus


title: Transcriptional profiles of biliary epithelial cells from non-pregnant mice and pregnant mice at dpc8

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

institute: Institute of Science Tokyo

summary: We report transcriptional profiles of liver biliary epithelial cells (BECs) from non-pregnant mice and pregnant mice. By RNA-sequencing of FACS-isolated BECs, we revealed that genes related to tissue morphogenesis and actin cytoskeleton were upregulated on dpc8.

overall_design: The BECs were isolated from the liver of non-pregnant mice and pregnant mice at dpc8.  RNA was extracted from the BECs and subjected to RNA sequencing.

first: Satoshi

last: Kozuki

first: Satoko

last: Sakurai

first: Takuya

last: Yamamoto


title: Tumor cells modulate macrophage phenotype in a novel in vitro co-culture model of the non-small cell lung cancer tumor microenvironment

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

summary: Introduction: Macrophage phenotype in the tumor microenvironment correlates with prognosis in non-small cell lung cancer (NSCLC). Immunosuppressive macrophages promote tumor progression, while pro-inflammatory macrophages may drive an anti-tumor immune response. How individual NSCLCs impact macrophage phenotype is a major knowledge gap.  Methods: To systematically study the impact of lung cancer cells on macrophage phenotypes, we developed an in vitro co-culture model comprised of molecularly and clinically-annotated patient-derived NSCLC lines, human cancer-associated fibroblasts, and murine macrophages. Induced macrophage phenotype was studied through qRT-PCR and validated in vivo using NSCLC xenografts through quantitative immunohistochemistry and clinically with TCGA “matched” patient tumors.  Results: 72 NSCLC cell lines were studied. The most frequent highly induced macrophage-related gene was Arginase-1, reflecting an immunosuppressive M2-like phenotype. This was independent of multiple clinicopathologic factors, which also did not impact M2:M1 ratios in matched TCGA samples. In vivo, tumors established from high Arginase-1-inducing lines (Arghi) had a significantly elevated density of Arg1+ macrophages. Matched TCGA clinical samples to Arghi NSCLC lines had a significantly higher ratio of M2:M1 macrophages.   Conclusions: In our preclinical model, a large panel of patient-derived NSCLC lines most frequently induced high expression Arginase-1 in co-cultured mouse macrophages, independent of major clinicopathologic and oncogenotype-related factors. Arghi cluster-matched TCGA tumors contained a higher ratio of M2:M1 macrophages. Thus, this preclinical model reproducibly characterizes how individual NSCLCs modulate macrophage phenotype, correlates with macrophage polarization in clinical samples, and can serve as an accessible platform for further investigation of macrophage-specific therapeutic strategies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 15 unique co-cultures were submitted for RNA seq and human transcripts were filtered out.

first: Josiah

last: Voth Park

first: Raghav

last: Chandra

first: Rolf

last: Brekken

first: John

last: Minna


title: Ribosome profiling and RNA-seq of Rat whole brain

city: Montreal

first: Senthilkumar

last: Kailasam

state: Quebec

address: 740 Dr. Penfield Avenue, #4200

department: Human Genetics

institute: McGill University

summary: Local translation in neurons is mediated in part by the reactivation of stalled polysomes. However, the mechanism for stalling of the polysomes is not understood. Stalled polysomes may be enriched in neuronal RNA granules defined by dense collections of compacted ribosomes found in the pellet of sucrose gradients used to separate polysomes from monosomes. We find that this fraction, isolated from P5 rat brains of both sexes, is enriched in proteins implicated in stalled polysome function, such as the fragile X mental retardation protein (FMRP) and Up-frameshift mutation 1 homolog (UPF1). Ribosome profiling of this fraction showed an abundance of footprint reads derived from mRNAs of cytoskeletal proteins implicated in neuronal development, as well as an enrichment of footprint reads on RNA binding proteins. The footprint reads were extended than those usually found in ribosome profiling studies on the 3’end and were found in reproducible peaks in the mRNAs with a bias towards the first half of the message. These footprint reads were enriched in motifs previously associated with mRNAs cross-linked to FMRP in vivo, independently linking the ribosomes in the sedimented pellet to the ribosomes associated with FMRP in the cell. The data supports a model in which specific sequences in mRNAs act to stall translation elongation in neurons, attracting FMRP and beginning a process where stalled ribosomes are packaged and transported in RNA granules.

overall_design: Ribosome profiling and RNA-seq samples of Rat whole brain. Treatment condition: Cycloheximide vs Vehicle;  salt vs vehicle

first: Mina

last: Anadolu

first: Konstanze

last: Simbriger

first: Seyed

last: Mehdi Jafarnejad

first: Francois

last: Lefebvre

first: Christos

last: Gkogkas

first: Wayne

last: Sossin

first: Jingyu

last: Sun


title: Polysome Profiling in Isoleucine tRNA Isoswitch Cells

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

summary: Polysome Profiling was used to evaluated whether changes in abundance of tRNAIleUAU and tRNAIleGAU would affect codon dependent translation and quantify the abundance of these tRNAs in highly translated fractions.

overall_design: Examination of highly translated transcripts under Isoleucine tRNA modulation (increased tRNAIleUAU expression and decreased tRNAIleGAU expression via CRISPRi)

first: Lisa

last: Noble


title: Ribosome Profiling in Isoleucine tRNA Isoswitch Cells

summary: Ribosome Profiling was used to evaluated whether changes in abundance of tRNAIleUAU and tRNAIleGAU would affect codon dependent translation and quantify dwell times over isoleucyl codons

overall_design: Examination of ribosomal occupancy of isoleucyl codon enriched transcripts under Isoleucine tRNA modulation (increased tRNAIleUAU expression and decreased tRNAIleGAU expression via CRISPRi)

first: Sohail

last: Tavazoie


title: Expression Profiling Identifies Key Genes in GIST Patients with Liver Metastasis

status: Public on Mar 31 2023

city: GuangZhou

first: Jianrong

last: Guo

address: Dongfengdong Road NO.651

institute: SYSUCC

summary:
GIST (gastrointestinal stromal tumor) is the most prominent mesenchymal neoplasms of the gastrointestinal tract, and liver is the most common metastasis site for GIST. The molecular mechanism leading to liver metastasis of GIST is currently unclear. With the goal of revealing the underlying mechanism, we performed whole-genome gene expression profiling in 18 pairs of RNA samples comprised of liver metastasis tissues and corresponding non-tumor tissues.
To reveal the underlying mechanism leading to liver metastasis of GIST

overall_design: 20 paired GIST tissues of patients with liver metastasis and corresponding non-tumor tissue

first: Haibo

last: Qiu


title: Gene expression in MEC1 and TCL1-355 CLL cell lines treated with the flavagline FL3

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

summary: mRNA profiles of MEC-1 and TCL1-355 cells treated with DMSO or FL3 were generated by 3'-sequencing

overall_design: mRNA profiles from MEC-1 and TCL1-355 cells treated in vitro for 24h with DMSO or 50 nM FL3

first: Jerome

last: Paggetti


title: Type I inteferon signaling in airway neutrophils in an in vitro model of ARDS

city: Birmingham

first: Camilla

last: Margaroli

address: 901 19th St S

institute: University of Alabama at Birmingham

summary: To investigate the contribution of type I interferon to neutrophil adaptation to the lung during ARDS and COVID-induced ARDS.

overall_design: Blood neutrophils from healthy donors were isolated and transmigrated in vitro towards ARDS airway fluid derived from patients supplemented with control human IgG (IgG cells) or with Anifrolumab (IFNAR cells). Each donor was transmigrated towards both conditions.

first: Amit

last: Gaggar


title: Transcriptional analysis of airway neutrophils in an in vitro model of ARDS

summary: To investigate neutrophil adaptation to the lung during ARDS and COVID-induced ARDS.

overall_design: Blood neutrophils from healthy donors were isolated and transmigrated in vitro towards either a chemoattractant control (A1 cells) or towards ARDS airway fluid derived from patients (A2 cells). Each donor was transmigrated towards both conditions.


title: Interferon-dependent signaling is critical for viral clearance in airway neutrophils

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

overall_design: Refer to individual Series


title: Sorting nexin 10 sustains platelet-derived growth factor receptor signaling in glioblastoma stem cells via endosomal protein sorting

city: San Diego

first: Jeremy

last: Rich

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

summary: Glioblastoma is the most malignant primary brain tumor for which the prognosis is still dismal despite aggressive surgical, medical, and radiation therapies. Glioblastoma stem cells (GSCs) promote therapeutic resistance and cellular heterogeneity due to their self-renewal properties and capacity for plasticity. To understand the molecular processes essential for maintaining GSCs, we performed an integrative analysis comparing active enhancer landscapes, transcriptional profiles, and functional genomics profiles of GSCs and non-neoplastic neural stem cells (NSCs). We identified sorting nexin 10 (SNX10), an endosomal protein sorting factor, as selectively expressed in GSCs compared to NSCs and essential for GSC survival. Targeting SNX10 impaired GSC viability and proliferation, induced apoptosis, and reduced self-renewal capacity. Mechanistically, GSCs utilized endosomal protein sorting to promote platelet-derived growth factor receptor β (PDGFRβ) proliferative and stem cell signaling pathways via post-transcriptional regulation of the PDGF receptor tyrosine kinase. Targeting SNX10 expression extended survival of orthotopic xenograft-bearing mice, and high SNX10 expression correlated with poor glioblastoma patient prognosis, suggesting its potential clinical importance. Thus, our study reveals an essential connection between endosomal protein sorting and oncogenic receptor tyrosine kinase signaling and suggests that targeting endosomal sorting may represent a promising therapeutic approach for glioblastoma treatment.

overall_design: RNA Sequencing for human patient derived glioblastoma stem cells following treatment with 3 independent non-overlapping shRNAs targeting SNX10 or a non-targeting shRNA control

first: Gimple

last: Ryan C

first: Zhang

last: Guoxin

first: Wang

last: Shuai

first: Huang

last: Tengfei

first: Lee

last: Jina

first: Taori

last: Suchet

first: Lv

last: Deguan

first: Dixit

last: Deobrat

first: Halbert

last: Matthew E.

first: Morton

last: Andrew

first: Kidwell

last: Reilly L.

first: Dong

last: Zhen

first: Prager

last: Briana C

first: Kim

last: Leo

first: Qiu

last: Zhixin

first: Zhao

last: Linjie

first: Xie

last: Qi

first: Wu

last: Qiulian

first: Agnihotri

last: Sameer

first: Rich

last: Jeremy N.


title: Fate restricted stromal fibroblasts and adipocytes demonstrate multi-modal responses to tissue injury

city: Munich

first: Dongsheng

last: Jiang

address: Max-Lebsche-Platz 31

department: Institute of Regenerative Biology and Medicine

institute: Helmholtz Zentrum München

summary: Adult connective tissues rearrange themselves during injury, disease, and aging. This response is widely considered to involve cross-lineage conversion between two differentiated stromal cell types: fibroblasts and adipocytes. Here, using lineage tracing approach, we explore the transcriptome profiles of Adipoq-lineage positve mature adipocytes and En1-lineage postive fibroblasts in in vivo mouse skin wounds. The data presented here show that wound adipocytes and fibroblasts still possess distinct molecular signatures, and do not undergo cross-lineage conversion.

overall_design: Wound adipocytes and fibroblasts were FACS sorted as GFP+ cells from day 10 and day 21 wounds from AdipoqCre;R26mTmG and En1Cre;R26mTmG mice. Sorted cells were subjected to RNA-sequencing. Comparative gene expression profiling analysis of RNA-seq data of wound adipocytes and fibroblasts.

first: Jiakuan

last: Zhao

first: Ruoxuan

last: Dai

first: Yue

last: Lin

first: Yuval

last: Rinkevich


title: Epigenome analysis of liver samples from C57BL/6J, CD1, and Sv129Ev mice in lifelong chronic psychosocial stress (LCPS)

city: Minneapolis

first: Maria

last: Razzoli

state: Minnesota

department: Integrative Biology and Physiology

institute: University of Minnesota

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of liver tissues from 17 months old male mice belonging to either the C57BL/6J, the CD1 or the Sv129Ev strain and exposed to LCPS. The Illumina Infinium Mouse Methylation Beadchip  was used to obtain DNA methylation profiles across approximately 285,000 CpGs in liver samples. Samples included 19 C57Bl/6J mice, 12 CD1 mice, and 16 Sv129Ev mice.

overall_design: Bisulphite converted DNA from the 47 samples were hybridised to the Illumina Infinium Mouse Methylation Beadchip


title: Angiotensin II Increases Oxidative Stress and Inflammation in Female, But Not Male, Endothelial Cells

city: College Park

first: Alisa

last: Morss Clyne

state: MD

address: 8278 Paint Branch Dr.

institute: University of Maryland

summary: To investigate sex differences in endothelial cell response to AngII, male and female human umbilical vein endothelial cells (HUVEC) were treated with AngII for 24 hours. RNA seq was run, and demonstrated that female HUVEC had elevated genes associated with oxidative stress and inflammatory responses compared to male HUVEC following AngII treatment.

overall_design: Male and female HUVEC (pooled from 3 donors per sex) were treated with 1 uM AngII for 24 hours before isolating RNA and running RNA sequencing

first: Callie

last: Weber

first: Mikayla

last: Harris

first: Sophia

last: Zic

first: Gurneet

last: Sangha

first: Nicole

last: Arnold

first: Douglas

last: Dluzen

last: Clyne


title: Injury prevents Ras mutant cell expansion in mosaic skin

city: New Haven

first: Valentina

last: Greco

address: 333 Cedar Street NSB 388

department: Genetics

institute: Yale University

summary: Healthy skin is a tapestry of wild-type and mutant clones. Although injury can cooperate with Ras mutations to promote tumorigenesis, the consequences in genetically mosaic skin are unknown. Here, we show that wild-type cells suppress oncogenic Ras-induced aberrant growth after injury. While HrasG12V/+ and KrasG12D/+ cells outcompete wild-type cells in uninjured, mosaic tissue, their expansion is prevented after injury due to an increase in the fraction of proliferating wild-type cells. Mechanistically, we show that, unlike HrasG12V/+ cells, wild-type cells respond to autocrine and paracrine secretion of EGFR ligands, and this differential activation of the EGFR pathway explains the competitive switch during injury-repair. Inhibition of EGFR by both drug and genetic approaches diminished the proportion of dividing wild-type cells after injury, leading to the expansion of HrasG12V/+ cells. Increased wild-type cell proliferation through a global loss of the cell cycle inhibitor p21 counteracted the expansion of HrasG12V/+ cells even without injury. Thus, injury plays an unanticipated role in switching the competitive balance between oncogenic and wild-type cells in genetically mosaic skin.

overall_design: Interfollicular epidermis of mice ear punches, either injured or uninjured, in wild-type or HRASG12V/+ background.

first: Sara

last: Gallini

first: Karl

last: Annusver

first: Nur-Taz

last: Rahman

first: David

last: Gonzalez

first: Sangwon

last: Yun

first: Catherine

last: Matte-Martone

first: Tianchi

last: Xin

first: Elizabeth

last: Lathrop

first: Kathleen

middle: C

last: Suozzi

last: Kasper


title: The Role of Mechanoregulated YAP/TAZ in Erectile Dysfunction

city: Su Zhou

first: Shiyou

last: Wang

state: Jiang Su

address: Chong Wen street

department: Suzhou Institute of Systems Medicine

institute: Peking Union Medical College

summary: Phosphodiesterase type 5 inhibitors (PDE5is) are the primary therapeutic option for erectile dysfunction. However, 30% of patients do not respond to PDE5is treatment, making the quest for a new treatment modality a central endeavor. Here, we found a new pathway in erectile function control, mechano-regulated YAP/TAZ activate Adrenomedullin transcription, which sustains smooth muscle cells (SMCs) relaxation to maintain the erection. We first found that penile erection stretches the SMCs, dominating YAP/TAZ activity. Subsequently, we showed that YAP/TAZ plays a vital role in erectile function and penile rehabilitation using genetic lesions and several animal models. The mechanism relies on the regulation of Adrenomedullin on penile SMCs contraction, which we identify here as a direct YAP/TAZ transcript. Notably, conventional PDE5is targeting NO-cGMP signaling do not cure YAP/TAZ deficient ED. In contrast, by activating YAP/TAZ-Adrenomedullin cascade, mechano-stimulation improved erectile function, including PDE5is non-responders in both experimental models and clinical trials. Our studies lay the groundwork for exploring mechano-YAP/TAZ-Adrenomedullin as prospective targets in the treatment of ED

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Data from samples with erectile dysfunction

first: Mingtao

last: Ji