title: Activation of NLRP3 Inflammasome by Virus-like Particles of Human Polyomaviruses in Macrophages

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: Viral antigens can activate phagocytes inducing inflammation but the mechanisms are barely explored. This study aimed to investigate the capability of viral oligomeric proteins of different structure to induce inflammatory response in macrophages. Human THP-1 cell line was used to prepare macrophages which were treated with filamentous nucleocapsid-like particles (NLPs) of paramyxoviruses and spherical virus-like particles (VLPs) of human polyomaviruses. The effects of viral proteins on cell viability, pro-inflammatory cytokines’ production and formation of NLRP3 inflammasome components, ASC specks, were investigated. Filamentous NLPs did not induce inflammation markers while spherical VLPs mediated inflammatory response followed by NLRP3 inflammasome activation. Inhibitors of cathepsins and K+ efflux decreased IL-1β levels and cell death indicating a complex inflammasome activation process. Similar activation pattern was observed in primary human macrophages treated with VLPs. Single cell RNAseq analysis of THP-1 cells revealed several cell activation states characterized by high expression of inflammation-related genes. This study provides new insights into interaction of viral proteins with innate immune cells and suggests that structural properties of oligomeric proteins may define cell activation pathways.

overall_design: Single-cell RNA sequencing of in vitro differentiated macrophages treated with PBS (control, n=1), KI polyomavirus recombinant major capsid protein viral particles (KIPyV VLPs, n=1), or MC polyomavirus recombinant major capsid protein viral particles (MCPyV VLPs, n=1).

first: Asta

last: Lučiūnaitė

first: Indrė

last: Dalgėdienė

last: Žilionis

first: Kristina

last: Mašalaitė

first: Milda

last: Norkienė

first: Andrius

last: Šinkūnas

first: Alma

last: Gedvilaitė

last: Kučinskaitė-Kodzė

first: Aurelija

last: Žvirblienė


title: Transcriptome Analysis of the different expressed genes affected by ClpP in B. abortus 2308

status: Public on Feb 22 2022

city: Beijing

first: Hao

last: Dong

address: Huatuo road NO.31

country: China

institute: National Institutes for Food and Drug Control

type: Expression profiling by high throughput sequencing

summary: Purpose:To gain insight into the spectrum of Brucella gene affected by the ClpP protease, as well as the genetic basis for the distinctive phenotypic properties exhibited by the clpP mutant strain. Methods: Three B. abortus 2308 and the three clpP mutant were grown in TSB at 37℃ until the log phase was reached, total RNA was isolated using the TRIzol according to the manufacturer’s instructions.The sequencing library of each RNA sample was prepared by using NEB Next Ultra Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer.The HiSeq 4000 platform was used to perform the transcriptome sequencing. Results: In total, 772 genes that exhibited different expression (Fold change>4, and FDR<0.05) were identified in the clpP mutant. In the clpP mutant strain, 376 genes were up-regulated and 396 genes were down-regulated. Conclusions: According to the result of COG analysis, the different expressed genes were mainly involved in Energy production and conversion, Cell wall/membrane/envelope biogenesis, and Carbohydrate transport and metabolism. KEGG pathway analysis demonstrated that the genes exhibited significant difference were primarily enriched in ABC transporters, beta-Lactam resistance, Oxidative phosphorylation, Cationic antimicrobial peptide (CAMP) resistance, Limonene and pinene degradation, Lysine degradation, Valine, leucine and isoleucine degradation, Chloroalkane and chloroalkene degradation, Ascorbate and aldarate metabolism, Tryptophan metabolism, Citrate cycle (TCA cycle), and Histidine metabolism.

overall_design: mRNA profiles of Three B. abortus 2308 and three clpP mutant were generated by deep sequencing using HiSeq 4000 platform


title: Role of H3K36 methylation in regulating transcription coupled-nucleotide excision repair

status: Public on Feb 21 2022

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

country: USA

institute: Washington State University

summary: We characterized the role of H3K36 methylation in regulating repair of UV damage from the transcribed strand (TS) of yeast genes by the transcription coupled nucleotide excision repair (TC-NER) pathway. TC-NER is triggered when RNA polymerase stalls at UV damage, such as a UV-induced cyclobutane pyrimidine dimer (CPD). During transcription, the histone methyltransferase Set2 methylates histone H3K36, but it is not known if H3K36 methylation regulates TC-NER. Here, we report genome-wide repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast cells containing mutants in histone H3K36 (or set2).

overall_design: UV-induced CPD lesions were mapped in yeast cells both immediately after UV damage formation (0hr time point) and following two hours of repair (2hr time point) using the CPD-seq method. Repair of CPD lesions was measured in yeast cells mutated in the histone H3 gene (H3K36A) or a WT control. Repair was also analyzed in rad16∆H3K36A or rad16set2∆ double mutants, which is deficient in the global genomic NER (GG-NER) pathway.

first: Kathiresan

last: Selvam


title: Single-cell Transcriptome of Human Choroidal Endothelial Cells and Macrophages in Health and Atrophic Macular Degeneration

city: Iowa City

first: Andrew

middle: P

last: Voigt

state: IA

address: 375 Newton Road

institute: University of Iowa

summary:
Purpose: The goals of this study were to identify expression patterns in a large population of human donor choroids, including donors with early atrophic AMD
Methods: Independent libraries were prepared for choroidal cells from twenty human donors. Macular samples from donors 1,2,3,5, 11, and 12 were acquired, analyzed, and uploaded in previous experiments (GSE135922 - donors 1,2, 11, and 12; GSE149100- donors 3 and 5). Choroidal punches were gently dissociated in collagenase II for 1 hour before cryopreservation. Thawed cells underwent endothelial cell enrichment by incubating with anti-CD31-microbeads. Final libraries were sequenced on an Illumina NovaSeq system. Sequenced reads were mapped to the human genome build hg38 with CellRanger(v6.0.0) and filtered to remove cells likely to be doublets or cells with a high proportion of mitochondrial reads. Feature selection was performed with the variance stabilizing transformation before integration was performed with Seurat (v4).
Results: A total of 30416 cells were recovered after filtering with 5,607,479,828 corresponding reads. A total of 17097 cells were recovered from AMD donor libraries while 13319 cells were recovered from control donors. Clusters were assigned to known choroidal cell types based on expression of distinguishing marker genes. Differential expression analysis identified genes enriched in each population of cells originating from AMD versus control libraries. Particular emphasis was given to choriocapillaris endothelial cells.
Conclusions: This study characterizes new gene expression signatures for several choroidal cells, including tissue resident macrophages, inflammatory macrophages, arterioles, and venules.

overall_design: mRNA profiles for thousands of cells from the central choroid were generated from four human donor eyes using 10X Genomics Chromium single-cell system followed by sequencing on an Illumina NovaSeq.

first: Robert

middle: F

last: Mullins

first: Todd

middle: E

last: Scheetz


title: Notch-mediated Ephrin signaling disrupts islet architecture and β cell function

city: Madrid

first: Alberto

last: Bartolomé

state: Madrid

address: Arturo Duperier 4

country: Spain

institute: Instituto de Investigaciones Biomédicas Alberto Sols (CSIC/UAM)

summary: Altered islet architecture is associated with β cell dysfunction and Type 2 Diabetes (T2D) progression, but molecular effectors of islet spatial organization remain mostly unknown. Although Notch signaling is known to regulate pancreatic development, we observed “re-activated” β cell Notch activity in obese mouse models. To test the repercussions and reversibility of Notch effects, we generated doxycycline-dependent, β cell-specific Notch gain-of-function mice. As predicted, we found that Notch activation in post-natal β cells impaired glucose stimulated insulin secretion (GSIS) and glucose intolerance, but we observed a surprising remnant glucose intolerance after doxycycline withdrawal and cessation of Notch activity, associated with a marked disruption of normal islet architecture. Transcriptomic screening of Notch-active islets revealed increased Ephrin signaling. Commensurately, exposure to Ephrin ligands increased β cell repulsion, and impaired murine and human pseudo-islet formation. Consistent with our mouse data, Notch and Ephrin signaling are increased in metabolically-inflexible β cells in patients with T2D. These studies suggest than islet architecture can be permanently altered by β cell Notch/Ephrin signaling during a morphogenetic window in early life.

overall_design: RNA-seq of pancreatic islets from beta cell NICD-gain of function model

first: Utpal

middle: B

last: Pajvani


title: Inositol pyrophosphate InsP8 acts as intracellular phosphate signal in Arabidopsis

city: Shanghai

first: Mingguang

last: Lei

address: No. 3888, Chenhua Road

institute: Shanghai Center for Plant Stress Biology

summary: The maintenance of cellular phosphate (Pi) homeostasis is of paramount importance in living organisms. Little is known about how cells sense intracellular Pi status in multi-cellular eukaryotes. Here, we report the identification of inositol pyrophosphate InsP8, a ligand that binds to the Pi sensor protein SPX1 to inhibit PHR1, the central regulator of Pi starvation responses in Arabidopsis. The concentration of InsP8, synthesized by diphosphoinositol pentakisphosphate kinases VIH1 and VIH2, depends on cellular Pi level and the double mutants accumulated higher amounts of Pi. The paradox of Pi toxicity and induction of Pi starvation inducible genes indicated that the cells could not sense cellular Pi without InsP8. Our study reveals that InsP8 acts as a Pi signaling molecule and binds to the receptor SPX1 to regulate Pi homeostasis.

overall_design: mRNA profiles of 12-day-old wild-type (Col-0) and double mutant (vih1vih2) Arabidopsis seedlings were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Jinsong

first: Viswanathan

last: Satheesh


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. [Jurkat_ATACseq]

city: Philadelphia

first: YEQIAO

last: ZHOU

state: PA

address: 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Purpose: To investigate the mechanisms of 3D genome organization in drug-resistant T-ALL
Methods: We used multiple epigenomics, chromatin conformation, and transcriptomic assays to study the mechanisms of chromatin adaptation in GSI-sensitive and GSI-resistant T-ALL
Results: We report here that T/B cell lineage determining transcription factors are differentially expressed in GSI-resistant T-ALL cells, driving enhancer switching and genome folding reorganization events to promote GSI-resistance.
Conclusions: These observations suggest a general mechanism that diffenrential activity of pioneering factors can be exploited to evade addiction to oncogenic signals.

overall_design: ATAC-seq was performed in triplicates in Jurkat-E-6-1-Cas9 with LRG2.1-LEF1-g3 and/or LRmCherry2.1-TCF7-g5 and control cells sorted 6 days post sgRNA transduction.

first: Yeqiao

last: Zhou

last: Faryabi


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells.[DND41_4C]

overall_design: UMI 4C-seq was performed in DMSO-treated parental, 24-hour GSI-treated parental, GSI-resistant, DMSO-treated reversed, and 24-hour GSI-treated reversed DND41 cells in triplicates.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. [DND41_panel_seq]

overall_design: Ultra-deep genomic sequencing of parental and GSI-resistant DND41 cells was performed using CLIA-approved clinical assay.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells.[DND41_HiChIP]

overall_design: SMC1a HiChIP was performed in parental and GSI-resistant DND41 cells in duplicates.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. [DND41_RNA-seq]

overall_design: Strand-specific RNA-seq was performed in triplicates in parental and GSI-resistant-reversed DND41 treated with DMSO or 125 nM GSI for 24 hours and GSI-resistant DND41 refreshed with media containing 125 nM GSI for 24 hours. DND41-Res-Cas9 cells with control or LRmCherry2.1-EBF1-g7 were sorted 6 days post sgRNA transduction


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. [DND41_Cut&Run]

overall_design: Cut&Run was performed in DMSO-treated parental, 24-hour GSI-treated parental and GSI-resistant DND41 cells in duplicates.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells.[DND41_HiC]

overall_design: In situ HiC was performed in parental and GSI-resistant DND41 cells, and DND41-Res-Cas9 control and LRmCherry2.1-EBF1-g7 cells sorted 6 days post transduction.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. [DND41_ATACseq]

overall_design: For comparison of chromatin accessibility in parental and GSI-resistant DND41 cells, parental DND41 was treated with DMSO or 125 nM GSI for 24 hours and GSI-resistant cells were refreshed with media containing 125 nM GSI for 24 hours. For assessing the impact of LEF1 or TCF1 loss on parental DND41 genome, DND41-Cas9 cells carrying LRG2.1-LEF1-g3 or LRmCherry2.1-TCF7-g5 were sorted 6 days post transduction. To assess the impact of LEF1 and TCF1 loss on parental DND41 genome, DND41-Cas9 carrying LRG2.1-LEF1-g3 and LRmCherry2.1-TCF7-g5 were sorted 3, 6 and 9 days post transduction. DND41-Cas9 carrying LRG2.1 and LRmCherry2.1 were sorted 3 days post transduction as control.To assess the impact of EBF1 loss on GSI-resistant DND41 genome, DND41-Res-Cas9 with LRmCherry2.1-EBF1-g7 were sorted 3, 6 and 9 days post transduction and control cells were sorted 3 days post transduction. ATAC-seq experiment was performed in triplicates.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells.[Granta_ATACseq]

overall_design: ATAC-seq was performed in triplicates in Granta519-Cas9 with LRmCherry2.1-EBF1-g7 and control cells sorted 3 days post sgRNA transduction.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells.[DND41_ChIP-seq]

overall_design: ChIP-seq was performed in DMSO-treated parental, 24-hour GSI-treated parental, GSI-resistant, DMSO-treated reversed, and 24-hour GSI-treated reversed DND41 cells in duplicates.


title: miRNA expression profiling of locally advancer cervical cancer

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

summary: MiRNA expression in totally 200 locally advanced cervical tumor biopsies were analysed by sequencing of small RNAs with Illumina HiSeq 2500. Based on the RNA isolation protocols, 90 samples were assigned to an experimental cohort, and 110 samples were assigned to a validation cohort (validation cohort1). The miRNA expression data was used to investigate miRNAs associated with prognosis and clinocopathological features in cervical cancer patients. Further we used the miRNA expression data to discover target genes by mathed sample miRNA-mRNA expression analysis with mRNA expression data.

overall_design:
miRNA expression profiling by small RNA sequencing of totally 200 tumor biopsies of locally advanced cervical cancer. ***Raw data are not publicly available due to patient privacy concerns.
----------------------------------------------
Authors state the following:
Does not  contains raw data files due to patient privacy concerns (seq. data).
Raw data files will be submitted to the EGA-database for controlled access.

first: Anja

last: Nilsen


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells.[MB157_HiChIP]

overall_design: SMC1a HiChIP was performed in doxycycline-induced MB157 transduced with pInducer20-TCF1 and -EBF1.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells.[MB157_ATACseq]

overall_design: ATAC-seq was performed in MB157 and doxycycline-induced MB157 transduced with pInducer20-LEF1, -TCF1 and -EBF1 in triplicates.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. [MB157_ChIP-seq]

overall_design: ChIP-seq was performed in MB157 and doxycycline-induced MB157 transduced with pInducer20-TCF1 and -EBF1 in duplicates.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. [MB157_RNA-seq]

summary:
Purpose: To investigate the mechanisms of 3D genome organization in drug-resistant T-ALL
Methods: We used multiple epigenomics, chromatin conformation, and transcriptomic assays to study the mechanisms of chromatin adaptation in GSI-sensitive and GSI-resistant T-ALL
Results: We report here that T/B cell lineage determining transcription factors are differentially expressed in GSI-resistant T-ALL cells, driving enhancer switching and genome folding reorganization events to promote GSI-resistance.
Conclusions: These observations suggest a general mechanism that diffenrential activity of pioneering factors can be exploited to bypass addiction to oncogenic signals.

overall_design: Strand-specific RNA-seq was performed in MB157 and doxycycline-induced MB157 transduced with pInducer20-TCF1 and -EBF1 in triplicates.


title: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells.

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

overall_design: Refer to individual Series


title: Contribution of the hedgehog-signaling pathway to Wolffian Duct development.

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary:
Introduction and objectives: Proper In utero Wolffian duct (WD) development requires androgens and is essential to epididymis formation and male fertility. However, non-hormonal factors that control WD homeostasis and development remain largely unknown. In this study, we investigated the contribution of Hedgehog signaling pathway to Wolffian duct development by combining pharmacological approaches on organotypic cultures of WD with microarray profiling.
Methods: WD were collected from embryos isolated from 16.5 days post-coitum pregnant mice and cultured in air-liquid condition at 37oC during 72 hours in the presence of either: 1) Cyclopamine (25 µM): Hh inhibitor; 2) Smoothened agonist (0.5 µM ; SAG): Hh activator; 3) Culture media (control). WD pictures were taken and analyzed on ImageJ. At the end of the culture, WD were snap-frozen to perform transcriptomic microarray analyses. Three to four biological replicates per condition, i.e. control (n=3), SAG (n=4) and cyclopamine (n=3), were used for microarray analyses. The quality of the RNA was determined using an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and displayed a RIN ranging from 9.10 to 9.60 out of 10 for the different samples. Microarray analyses were carried out on Affymetrix Mouse Clariom S arrays (Thermofisher) according to the Affymetrix standard protocol. In brief, 100 ng total RNA samples were labeled using the GeneChip® WT Plus Reagent Kit protocol and hybridized to the arrays as described by the manufacturer (Affymetrix, Thermofisher). The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After a 16-h hybridization period, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol. The arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Command Console Software (AGCC) (Affymetrix, Thermofisher) to produce the probe cell intensity data (CEL). The imaged data were then analyzed using the Affymetrix Expression Console Software to perform the quality control, background subtraction and normalization of probe set intensities using Robust Multiarray Analysis (RMA). Microarray processing was performed by the Gene Expression Core facility of the Genomic platform of the Centre Hospitalier Universitaire de Quebec Research Center. The microarray CEL files were imported and analyzed with Transcriptome Analysis Console (TAC) Software 4.0.2 (Applied Biosystems), and submitted to RMA normalization. Samples were included within three different treatment groups (control, SAG and cyclopamine) and compared by Analysis of Variance. Principal Component Analysis and heat maps were performed with Partek Pathway (Partek Incorporated). Biological pathways analyses were performed by using 5 distinct algorithms (i.e. DAVID, STRING, GOrilla, Metascape, GSEA and BLAST2GO).
Conclusion: The data made available on GEO repository provide new insights regarding the mechanisms that control epididymis morphogenesis and male fertility. Financially supported by a CIHR grant to CB.

overall_design: Three conditions, 3-4 Biological replicates each

first: Clémence

last: Belleanée

first: Laura

last: Girardet

first: Agathe

last: Bernet

first: Denis

last: Soule

first: Maíra

last: Alves


title: WNT11/ROR2 signaling is associated with tumor invasion and poor survival in breast cancer [patients]

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

country: Germany

institute: Institute of Bioinformatics

summary: Breast cancer is the most common cancer in women with more than two million new cases diagnosed in 2018. Patients frequently develop metastases in the course of their disease which limit survival due to the lack of a curative treatment. One signaling pathway that is frequently involved in cancer initiation and progression is the WNT pathway. Breast cancer has been associated with activation of the WNT signaling pathway, although the underlying molecular mechanisms are still unclear. Here, we found the WNT receptor ROR2 to be highly expressed in aggressive breast tumors and associated with worse metastasis-free survival. In this study we addressed this question and demonstrated for the first time that WNT11 is a novel ligand for ROR2 in humans. WNT11 binds to the CRD of ROR2 and mediates WNT/PCP signaling via the RHO/ROCK pathway that confers an aggressive phenotype to breast cancer cells. ROR2 and WNT11 are both highly expressed in human brain metastases and linked with short patient survival.

overall_design: We collected samples from 31 patients with brain metastases and characterized them by RNA-Seq. With the obtained data, we performed a gene enrichment analysis looking at three different gene sets, either associated with canonical, non-canonical, or regulation of WNT signaling. Next, we isolated RNA from seven metastases as well as normal brain tissue and analysed the expression of ROR2 and its ligand WNT11 by quantitative real-time PCR. To confirm the role of ROR2/WNT11 in metastasis, we correlated the expression levels of ROR2 and WNT11 in the metastatic tissue with patient outcome using the gene expression data obtained by RNA-Seq.

first: Kerstin

last: Menck

first: Saskia

last: Heinrichs

first: Maren

last: Sitte

first: Helen

last: Noeding

first: Andreas

last: Janshoff

first: Hannes

last: Treiber

first: Torben

last: Ruhwedel

first: Bawarjan

last: Schatlo

first: Christian

last: von der Brelie

first: Stefan

last: Wiemann

first: Tobias

last: Pukrop

first: Tim

last: Beißbarth

first: Claudia

last: Binder

first: Annalen

last: Bleckmann


title: Histone H3 dopaminylation in ventral tegmental area underlies heroin-induced maladaptive plasticity

status: Public on Feb 20 2022

city: New York

first: Sasha

middle: Leilani

last: Fulton

state: NY

address: 3227 Broadway

institute: Columbia University

summary: Persistent transcriptional events in ventral tegmental area (VTA) and other reward relevant brain regions contribute to enduring behavioral adaptations that characterize substance use disorder (SUD). Recent data from our laboratory indicate that aberrant accumulation of the newly discovered histone post-translational modification (PTM), H3 dopaminylation at glutamine 5 (H3Q5dop), contributes significantly to cocaine-seeking behavior following prolonged periods of abstinence. It remained unclear, however, whether this modification is important for relapse vulnerability in the context of other drugs of abuse, such as opioids. Here, we showed that H3Q5dop plays a critical role in heroin-mediated transcriptional plasticity in midbrain. In rats undergoing abstinence from heroin self-administration (SA), we found acute and persistent accumulation of H3Q5dop in VTA. By attenuating H3Q5dop during abstinence, we both altered gene expression programs associated with heroin withdrawal and reduced heroin-primed reinstatement behavior. These findings thus establish an essential role for H3Q5dop, and its downstream transcriptional consequences, in opioid-induced plasticity in VTA.

overall_design: To explore the functional consequences of H3Q5dop accumulation during heroin abstinence, we used a lentiviral vector that expresses the H3 variant, H3.3, with a glutamine-to-alanine substitution at position 5 (H3.3Q5A), which cannot be dopaminylated. This H3.3Q5A vector has previously been shown to strongly express the mutant H3.3Q5A protein in a nuclear-specific manner in adult neurons, resulting in downregulation of H3Q5dop. We delivered this H3.3QA vector into rodent VTA vs. H3.3 wildtype (WT) vs. empty vector controls in order to evaluate the impact of reducing H3Q5dop accumulation on gene expression programs during prolonged abstinence. After 10 d of heroin SA, rats were infected intra-VTA with one of the three viruses (on day 11), followed by a 30 d period of enforced abstinence to ensure maximal expression of viral transgenes. Following 30 d of forced abstinence, infected VTA tissues were microdissected and processed for RNA-seq.

first: Ian

last: Maze


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes

city: changsha

first: dan

last: zhu

address: hunan

institute: Hunan University

summary: Neural precursor cells (NPCs) tend to aggregate and develop into three-dimensional (3D) spheres, which in return help maintain the stemness of the cells. This close relationship between spherical environment and cell stemness direct us to assume that 3D spheres of astrocytes may facilitate the acquiring of stem cell-like features and generate sufficient seed cells for regeneration of neurons. Primary astrocytes (ASTs) were isolated from the cerebra of postnatal day 1 to day 2 C57BL/6 mouse. ASTs were loaded onto the agarose-coated dishes and cultured to induce the formation of AST spheres. The status of the ASTs over time in cell spheres was characterized by immunochemistry, flow-cytometry, western blotting, and RNA-sequencing. The potency of AST-derived stem cells (A-iSCs) in repairing neural injuries was evaluated in mouse models of middle cerebral artery occlusion (MCAO), spinal cord injury (SCI), and peripheral nerve injury (PNI). In vitro results confirmed that mouse astrocytes cultured on agarose surfaces spontaneously formed cell spheres and exhibited molecular features similar to stem cells, capable of further differentiating into neurons particularly and forming functional synaptic networks with synchronous burst activities. RNA-sequencing results revealed the similarity of A-iSCs to NPCs in global gene expression profiles. It was observed that the transplanted A-iSCs expressed a series of markers for neural differentiation, such as NeuN, Tuj1, and Map2, indicating the conversion of the transplanted A-iSCs into neurons in these scenarios. We also found that the injured mice injected with A-iSCs exhibited significant improvements in sensorimotor functions over 8 weeks compared with the sham and control mice. Taken together, mouse astrocytes form cell spheres on agarose surfaces and acquire stem cell-associated features, and the derived A-iSCs possess the capacity to differentiate into neurons and facilitate the regeneration of damaged nerves across the nervous system.

overall_design:
To elucidate the mechanism involved in the induction of ASTs in 3D cell spheres, global gene expression profile of ASTs (0 day incubation, negative control) and A-iSCs (5 days incubation) were characterized by RNA-sequencing, with the profiles of brain-derived P56-NPCs and P0-NPCs as positive controls. Three replicates per sample.

***Submitters declare that the raw data has been deleted and can not be recovered***

first: Dan

last: Zhu

first: Zheming

last: Cao

first: Xiaoyang

last: Pang

first: Wei

last: Jiang


title: A Population of Radio-Resistant Macrophages in the Deep Myenteric Plexus Contributes to Postoperative Ileus Via Toll-Like Receptor 3 Signaling

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Postoperative ileus (POI) is triggered by an innate immune response in the muscularis externa (ME) and is accompanied by bacterial translocation. Bacteria can trigger an innate immune response via toll-like receptor (TLR) activation, but the latter’s contribution to POI has been disproved for several TLRs, including TLR2 and TLR4. Herein we investigated the role of double-stranded RNA detection via TLR3 and TIR-domain-containing adapter inducing interferon-b (TRIF) signaling pathway in POI. POI was induced by small bowel intestinal manipulation in wt, TRIF-/-, TLR3-/-, type I interferon receptor-/- and interferon-b reporter mice, all on C57BL/6 background, and POI severity was quantified by gene expression analysis, gastrointestinal transit, and leukocyte extravasation into the ME. TRIF/ TLR3 deficiency reduced postoperative ME inflammation and prevented POI. With bone marrow transplantation, RNA-sequencing, flow cytometry, and immunohistochemistry we revealed a distinct TLR3-expressing radio-resistant MHCIIhiCX3CR1- IBA-1+ resident macrophage population within the deep myenteric plexus. TLR3 deficiency in these cells, but not in MHCIIhiCX3CR1+ macrophages, reduced cytokine expression in POI. While this might not be an exclusive macrophage-privileged pathway, the TLR3/TRIF axis contributes to proinflammatory cytokine production in MHCIIhiCX3CR1- IBA-1+ macrophages during POI. Deficiency in TLR3/TRIF protects mice from POI. These data suggest that TLR3 antagonism may prevent POI in humans.

overall_design: Examination of MHCII+ CX3CR1- and MHCII+ CX3CR1+ cells  isolated from the muscularis externa of the small bowel

first: Jana

last: Enderes

first: Kristof

middle: J

last: Hupa

first: Patrick

last: Günther

first: Sven

last: Wehner


title: An Orobanche cernua x Orobanche cumana segregating population provides insight into the regulation of germination specificity in a parasitic plant

city: Blacksburg

first: James

middle: H

last: Westwood

state: VA

address: 401 Latham Hall

department: School of Plant and Environmental Sciences

institute: Virginia Tech

summary: Germination of seeds of Orobanche species requires specific chemicals exuded by host roots. A family of “divergent” KARRIKIN INSENSITIVE2 (KAI2d) genes encode proteins that recognize strigolactone (SL) class germination simulants. We explored specificity of germination stimulant detection by analyzing interspecific segregants of a cross between Orobanche cernua and O. cumana, closely related species that differ in stimulant response. O. cernua parasitizes tomato and germinates in response to the SL orobanchol, while O. cumana parasitizes sunflower and responds to dehydrocostus lactone (DCL). KAI2d genes were catalogued in parents and in segregants that showed stimulant specificity. KAI2d genes were also functionally assayed in the Arabidopsis kai2 mutant background. We identified five full-length KAI2d genes in O. cernua and eight in O. cumana. The O. cernua KAI2d2, as well as its ortholog in O. cumana, are associated with SL perception. A cluster of O. cumana KAI2d genes was genetically linked to DCL perception, although no specific receptor gene was identified by heterologous complementation. These findings support the KAI2d-mediated perception of SLs, but fall short of explaining how O. cumana perceives DCL. The ability of some O. cumana KAI2d genes to detect SLs points to the involvement of additional factors in regulating stimulant specificity.

sample_organism:
Orobanche cernua
Orobanche cernua var. cumana

overall_design: Seeds of 2 Orobanche species were sequenced at 3 different times and with 2 different germination stimulants applied for the final time point. All samples were replicated 2 times, resulting in a total of 16 datasets.

first: Hailey

last: Larose

first: Dina

last: Plakhine

first: Hanan

last: Eizenberg

first: Yaakov

last: Tadmor


title: Tissue Specific Methylation and Expression Patterns of ADCA-DN Patients

city: Thousand Oaks

first: Xianglong

last: Zhang

state: CA

address: One Amgen Center Dr.

department: Department of Cardiometabolic Disorders

institute: Amgen Inc.

type: Methylation profiling by high throughput sequencing

summary: Autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCA-DN) is a late onset disorder, due to mutations in DNA methyltransferase type 1 (DNMT1). Yet our understanding of how these mutations in DNMT1 lead to the clinical phenotypes of ADCA-DN is still unclear. To address this, we used fibroblasts, induced pluripotent stem cells (iPSCs) and induced neurons (iNs) generated from patients with ADCA-DN and controls, to determine the underlining epigenomic changes. Here we show that the differential expression pattern and differential methylation spectrum between patients and controls were tissue-specific. Furthermore, methylation and gene expression changes were negatively correlated in iPSCs and iNs. In addition, we identified a group of genes associated with clinical phenotypes of ADCA-DN, including PDGFB and PRDM8 for cerebellar ataxia, psychosis and dementia, and NR2F1 for deafness and optic atrophy. We further showed that ZFP57, which is required to maintain gene imprinting through DNA methylation during early development, was hypomethylated in promoters and exhibited upregulated expression in patients with ADCA-DN in both iPSC and iNs. Our results provide insight into the molecular changes associated with ADCA-DN, with potential implications for genes associated with related phenotypes.

overall_design: Investigated tissue specific DNA methylation and gene expression patterns in induced neurons derived from induced pluripotent stem cells (iPSCs) from patients with ADCA-DN.

first: Kasey

last: Davis

first: Melanie

last: Plastini

first: Ling

last: Lin

first: Shining

last: Ma

first: Ruth

last: O’Hara

first: Wing

last: Wong

first: Niklas

last: Dahl

last: Hallmayer

first: Emmanuel

last: Mignot

first: Alexander

last: Urban


title: Expression data from OsUBA-overexpressed, RNA interferenced, and wild-type  rice seedlings

city: Shijiazhuang

first: Caili

last: Bi

state: Hebei

address: No.20 Road East. 2nd Ring South, Yuhua District

department: College of life sciences

institute: Hebei Normal University

summary: OsUBA encodes a NBR1 protein in rice, which may function as autophagy receptor.This study aims to explore the possible biologial process OsUBA may involve in.

overall_design: Four- leave seedlings of OsUBA-overexpressed(OX),RNA interferenced(R), and wild-type(WT) rice plants were  collected for chip assay.Two biological replictes were included.

first: Liwei

last: Wang


title: Cytokine drivers and contributing immune cells of dexamethasone-treatable vaccine-associated enhanced respiratory pathology in COVID-19 hamsters

city: Berlin

first: Dylan

last: Postmus

state: Berlin

address: Charitépl. 1

department: Institute of Virology

institute: Charité – Universitätsmedizin Berlin

summary: A range of vaccines against COVID-19 have been developed, which reduce transmission rates and confer protection. We have analysed two model vaccines, a TH1-biased measles vaccine-derived candidate and TH2-biased Alum-adjuvanted, non-stabilized Spike protein, utilizing a hamster model of severe COVID-19.

overall_design: RT-qPCR, western blotting, histopathology, immunohistochemistry, total RNAseq and single cell RNAseq were performed on samples taken from Syrian hamsters infected with SARS-CoV-2 following mock immunisation or immunisation with one of two model vaccines: a TH1-biased measles vaccine-derived candidate and TH2-biased Alum-adjuvanted, non-stabilized Spike protein.

first: Aileen

last: Ebenig

first: Samada

last: Muraleedharan

first: Julia

last: Kazmierski

first: Daniel

last: Todt

first: Arne

last: Auste

first: Martina

last: Anzaghe

first: André

last: Gömer

first: Patricia

last: Gogesch

first: Marc

last: Niles

first: Roland

last: Plesker

first: Csaba

last: Miskey

first: Michelle

middle: G

last: Serra

first: Angele

last: Breithaupt

first: Cindy

last: Hörner

first: Carina

last: Kruip

first: Rosina

last: Ehmann

first: Zoltan

last: Ivics

first: Zoe

last: Waibler

first: Stephanie

last: Pfaender

first: Emanuel

last: Wyler

first: Markus

last: Landthaler

first: Alexandra

last: Kupke

first: Geraldine

last: Nouailles

first: Christine

last: Goffinet

first: Richard

last: Brown

first: Michael

middle: D

last: Mühlebach


title: Transcription factor-mediated intestinal metaplasia and the role of a shadow enhancer

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Epigenetic analysis on mouse gastric organoids overexpressing either CDX2, HNF4A or control GFP. Epigenetic analyses include ATAC-seq, Cut&Run. Mouse gastric and intestinal stem cell ATAC-seq and mouse gastric antrum and intestinal villus ChIP-seq.

overall_design: We used lentiviral transduction to generate isogenic mouse gastric organoid lines expressing intestinal TFs CDX2 or HNF4A. For comparison we expressed a neutral product (GFP) in gastric organoids and CDX2 in squamous esophageal organoids. In these perturbed organoids we assessed chromatin accessibility using the assay for transposase-accessible chromatin (ATAC-seq), specific TF occupancy using CUT&RUN, and transcriptional changes using RNA-seq. We used CRISPR-Cas9 cutting to delete a novel Cdx2 enhancer in the mouse germline and dCas9-conjugated transcriptional repressor KRAB to further assess this cis-element in gastric organoids.

first: Harshabad

last: Singh

first: Davide

last: Seruggia

first: Shariq

last: Madha

first: Madhurima

last: Saxena

first: Ankur

middle: K

last: Nagaraja

first: Zhong

last: Wu

first: Jin

last: Zhou

first: Aaron

last: Huebner

first: Adrianna

last: Maglieri

first: Juliette

last: Wezenbeek

first: Konrad

last: Hochedlinger

first: Stuart

last: Orkin

first: Adam

last: Bass

first: Jason

last: Hornick

middle: A


title: Bariatric surgery mediated weight loss reduces breast cancer risk by reducing estrogen receptor alpha activity

city: Chicago

first: Swati

last: Kulkarni

state: Illinois

address: 600 N. Lake Shore Drive, Apt 3602

department: Surgery

institute: Northwestern University

summary: Bariatric surgery mediated weight loss has been shown to significantly reduce breast cancer incidence in women. We hypothesize that loss of excessive adiposity, reduces net Estrogen Receptor Alpha activation which in turn lowers breast cancer risk. A differential gene expression analysis and subsequent pathway enrichment analysis would reveal the relevant molecular mechanism behind the preventive effect of weight loss. We will correlate our RNASeq data findings with serum and breast tissue concentration of hormones as well as expression of proteins regulating hormone synthesis in breast. For this study, we recruited 30 patients who were prescribed baritaric surgery and met our selection criteria (no familial or personal history of breast cancer and free of other confounding conditions). Breast tissue and blood was collected at the day of surgery and at follow up after the patient lost 25% excess body weight. The breast core biopsy was preserved in RNALater till rna isolation and library preparation.

overall_design:
Differential gene expression in breast tissue before and after Bariatric surgery
---------------------------
Artificial Intelligene (AI, www.artificialintelligene.com)

first: Manish

last: Ranjan


title: Structural and Genome-wide Analysis Support a Role for SETMAR in Transcriptional Regulation

city: Indianapolis

first: Millie

middle: M

last: Georgiadis

state: IN

address: 635 Barnhill Dr. MS4032

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: Approximately 50 million years ago, the Hsmar1 transposon entered the primate lineage giving rise to a new protein, a chimeric fusion of a SET domain and the Hsmar1 transposase. This protein, SETMAR or Metnase, is broadly expressed in human tissues and has been shown to retain its ancestral sequence-specific binding to Hsmar1 terminal inverted repeat (TIR) sequences found at the ends of the transposons. Despite the fact that there were estimated to be anywhere from 1500-7000 TIR sites within the human genome, the relevance of SETMAR-TIR interactions was unknown. Here, we report the crystal structure of the SETMAR DNA-binding domain (DBD) complexed with TIR DNA at 2.37 Å. The DBD structure includes two helix-turn-helix motifs (HTH1 and HTH2), which dimerize through HTH1, and confer sequence-specific recognition of the TIR through nucleobase-specific interactions with R371 in HTH1 and R417, H427, S428, and R432 in HTH2. The extent of genome-wide binding was determined by chromatin immunoprecipitation sequencing (ChIP-seq) analysis yielding a total of 7457 SETMAR bound sites. The effect of SETMAR on the transcriptome was assessed by RNA-seq analysis; among the 177 differentially regulated transcripts, a cluster of histones on chromosome 6 were found to be repressed. The dimeric SETMAR structure with each DBD bound to TIR DNA, the presence of eleven TIR sites within the histone gene cluster, and previously reported DNA looping activity are consistent with a direct regulatory mechanism in which SETMAR represses mRNA expression for specific genes through chromatin looping.

overall_design: Two independent ChIP DNA samples were immunoprecipitated using anti-FLAG resin from HEK293T cells transfected with FLAG-tagged SETMAR(wt) or SETMAR(R371A). Since R371 is a key amino acid residue for DNA-binding activity, SETMAR(R371A) ChIP DNA sample serves as a control to increase the accuracy of binding sites identification.

first: Qiujia

last: Chen

first: Rondal

middle: C

last: Wek


title: Coordinated changes of gut microbiome and lipidome differentiates nonalcoholic steatohepatitis (NASH) from isolated steatosis

city: Nanjing

first: MINYI

last: QIAN

address: Longmiandadao

institute: CPU

summary: Following 21-week of high fat diet (HFD)-feeding, obese mice were classified into two groups termed as isolated steatosis and NASH based on H&E staining of liver

overall_design: Three hepatic samples of  mice in steatosis and NAH groups were selected randomly. RNA were isolated and sequenced by deep sequencing using Illumina HiSeq 4000

first: Minyi

last: Qian

first: Haiyang

last: HU

first: Lirui

last: Wang


title: RNA sequencing identifies gene expression profile changes associated with CREB3L1 gene silencing by transcriptional interference in HuCCT1 cells

first: Guohe

last: Song

state: Shanghai

address: 180, fenglin road

institute: Fudan university

summary: The goals of this study are to examine changes in the expression profiles of genes in HuCCT1 cells following  CREB3L1 gene silencing. In this study, three groups of  Si-Ctrl HuCCT1 cells and three groups of Si-CREB3L1 HuCCT1 cells  were used to study the change in expression of the different genes after CREB3L1 gene silencing by RNA-seq.

overall_design: Examination of 2 mRNA profiles of Si-Ctrl and Si-CREB3L1 in HuCCT1 cells.

first: Yang

last: Shi

first: Lu

last: Meng


title: Serine Metabolism Orchestrates Macrophage Polarization by Regulating the IGF1–p38 Axis

status: Public on Feb 19 2022

city: tianjin

first: xiao

last: shan

address: No. 22, Meteorological Station Road, Heping District

institute: tian jin medical university

summary: Here we show that suppressing the serine biosynthesis pathway, either by inhibiting the activity of the key enzyme phosphoglycerate dehydrogenase or by exogenous serine and glycine restriction, robustly enhances polarization of interferon-g-activated macrophages (M(IFN-g)) but suppresses that of interleukin-4-activated macrophages (M(IL-4)) both in vitro and in vivo.To further explore its mechanism, we used high-throughput sequencing technology (RNA-seq) to assess gene expression in serine-deficiency or not BMDMs

overall_design: Examination of differential expressive genes between control group and Serine deficiency group in bone marrow derived macrophages.

first: Xiao

last: Shan

first: Qiujing

last: Yu


title: Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment

city: Nagoya

first: Aya

last: Naiki-Ito

address: 1-Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Experimental Pathology and Tumor Biology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

summary: The gene expression profiling between Control and Luteolin in 22Rv1

overall_design: Two-condition experiment, Control vs. Luteolin. 22Rv1 cells were treated  25 μM luteolin for 48 hours.


title: Genome-wide maps of gene transcription levels in HEK293T transfected with Mycobacterium tuberculosis protein CdhM.

city: Wuhan

first: Peng

last: Xu

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary: We report the application of RNA-seq technology for high-throughput profiling of gene transcription in HEK293T. By obtaining over six billion bases of sequence from mRNA, we generated genome-wide gene transcription maps of HEK293T transfected with Mycobacterium tuberculosis protein CdhM. We find that numerous genes involved in ER stress are significantly affected by CdhM. This finding indicates that CdhM may induce ER stress during Mtb infection of host cells.

overall_design: Examination of gene expression levels in HEK293T transfected with Mycobacterium tuberculosis protein CdhM.

first: Zhengguo

last: He


title: RNA-seq analysis of resting and inflamed human neutrophils

city: Heidelberg

first: Ricardo

last: Grieshaber-Bouyer

address: Im Neuenheimer Feld 410

department: Division of Rheumatology

institute: Heidelberg University Hospital

summary: This study includes RNA-seq profiles of neutrophils from healthy donors and patients with inflammatory arthritis.

overall_design:
RNA-seq of FACS-sorted live, CD15+ CD66b+ neutrophils from healthy donors, patients with inflammatory arthritis and LPS-stimulated cells (typically 30,000 per sample). Separate libraries were created for CD177neg and CD177pos neutrophils and averages were created for each donor as well.  Raw data not available due to patient privacy concerns

**RAW DATA not provided due to patient privacy concerns**

first: Peter

last: Nigrovic


title: BTA1 controls tiller angle and shoot gravitropism by regulating auxin transport and signaling in rice

city: Shenyang

first: Xiaoxue

state: Liaoning

address: 120 Dongling Road, Shenhe District

department: Rice Research Institute

institute: Shenyang Agricultural University

summary: Tiller angle is a key factor determining rice plant architecture, planting density, light interception, photosynthetic efficiency, disease resistance, and grain yield. The distribution of auxin and shoot gravitropism play important roles in regulating tiller angles of rice. Several tiller angle-associated genes have been cloned. However, the mechanisms underlying tiller angle control are far from clear. In this study, we isolate bta1-1, a mutant with an enlarged tiller angle throughout its life cycle. A detailed analysis reveals that BTA1 has multiple functions because several major agronomic traits, including tiller and panicle number, biomass production, secondary branch number per panicle, panicle weight, grain size, and grain weight, are increased in bta1-1 plants. Moreover, BTA1 is a positive regulator of shoot gravitropism in rice. Shoot responses to gravistimulation are disrupted in bta1-1 under both light and dark conditions. Gene cloning reveals that bta1-1 is a novel mutant allele of LA1. LA1 is able to rescue the tiller angle and shoot gravitropism defects observed in bta1-1. BTA1/LA1 is required to regulate the expression of auxin transporters and signaling factors that control shoot gravitropism and tiller angle. High-throughput mRNA sequencing is performed to elucidate the molecular and cellular functions of BTA1/LA1. The results show that BTA1/LA1 may have multiple functions in regulating nucleosome and chromatin assembly, and protein and DNA interactions. Our results provide new insight into the mechanisms whereby BTA1/LA1 controls shoot gravitropism and tiller angle in rice.

overall_design: 7-day-old seedlings of WT (termed WTZ) and mutant (termed MuZ)  grown under 14 h light and 10 h dark are sequenced with two bioligical replicates.

first: Mo

last: Zhu

first: Yanjuan

last: Hu

first: Aizi

last: Tong

first: Bowen

last: Yan

first: Yanpeng

last: Lv

first: Shiyu

first: Zhibo

last: Cui


title: The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation

city: St. Louis

first: Jeannine

last: Basta

state: MO

department: Internal Medicine/Nephrology

institute: Washington University in St. Louis

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

overall_design: Refer to individual Series


title: The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation [ChIP-seq]

summary: Binding of Brg1, Sall1, H3K4me1, H3K27ac, and RNA Pol2 Ser2 to chromatin was measured by performing ChIP-seq in E16.5 wild type kidney.

overall_design: Binding of Brg1, Sall1, H3K4me1, H3K27ac, and RNA Pol2 Ser2 to chromatin was measured by comparing specific chromatin binding to Input chromatin.

first: Michael

last: Rauchman


title: The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation [RNA-seq]

summary: RNA expression was measured by RNA-seq in E17.5 in Brg1flx/flx and Six2Cre-Brg1flx/flx mutant kidney.

overall_design: RNA expression in mutant kidney was compared to wild type stage matched kidney.


title: The microbial taxonomic and functional compositions at the Jasper Ridge Global Change Experiment

city: Beijing

first: yang

last: sihang

address: Haidian district Shuangqing road #30

institute: Tsinghua University

summary: Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies focused on how fire affects both the taxonomic and functional diversity of soil microbial communities, along with plant diversity and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects for a grassland ecosystem 9-months after an experimental fire at the Jasper Ridge Global Change Experiment (JRGCE) site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis indicating that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa were able to withstand the disturbance. In addition, fire decreased the relative abundances of most genes associated with C degradation and N cycling, implicating a slow-down of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated plant growth, likely enhancing plant-microbe competition for soil inorganic N.  To synthesize our findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for the significantly higher soil respiration rates in burned sites. In conclusion, fire is well-documented to considerable alter the taxonomic and functional composition of soil microorganisms, along with the ecosystem functioning, thus arousing feedback of ecosystem responses to affect global climate.

overall_design: 64 samples were collected from burned plots at JRGCE, with 4 replicates for each treatment

first: Sihang

last: Yang

first: Yunfeng


title: TrmB-like family transcription factor OxsR regulates the oxidative stress response in Haloferax volcanii

status: Public on Feb 18 2022

city: Durham

first: Amy

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

summary: Haloarchaea tolerate high levels of reactive species that are naturally present in hypersaline environments. Hundreds of sRNAs, transcripts, and proteins are found altered in abundance when haloarchaea are exposed to reactive species, yet the regulators that control these responses are not well characterized. Here we report the function of Haloferax volcanii OxsR (redox stress responsive regulator, HVO_2970), a standalone  winged-helix DNA binding domain protein of the TrmB-like family. Here we demonstrate that OxsR is important for growth in the presence of hypochlorite and binds specific regions of genomic DNA during hypochlorite stress by ChIP-seq analysis. The OxsR-bound intergenic regions were located nearby operons  encoding oxidative stress functions, including the biosynthesis of low molecular weight thiols and thiol relay systems. Further analysis by qRT-PCR revealed that OxsR functions during oxidative stress largely as a transcriptional activator, and occasionally as a repressor. The conserved cysteine residue (C24) of OxsR and a CG-rich binding motif upstream of BRE/TATA box promoter elements were found important in the transcriptional activation of select operons during hypochlorite stress. 3D-modeling of OxsR revealed C24 to be located at a homodimer interface formed by antiparallel α1 helices, suggesting that C24 forms an intersubunit disulfide bond in the presence of oxidant that stabilizes the homodimer. The phylogenetic distribution of OxsR homologs with the conserved cysteine suggests this type of redox signaling mechanism is widespread in Archaea.

overall_design: ChIP-seq determination of OxsR genome-wide binding sites in hypochlorite stress vs non-stress conditions

first: Julie

last: Maupin-Furlow

first: Paula

last: Mondragon

first: Sungmin

last: Hwang


title: Transcriptomic analysis in Caenorhabditis elegans exposed to organic and inorganic forms of arsenic or mercury

city: Mions

first: Aline

last: de Conti

address: 16 Route de Corbas

country: France

institute: iarc

summary: Arsenic and mercury are known chemical hazards. The differences in effects from organic and inorganic forms of these toxic elements is less well understood, however. The nematode Caenorhabditis elegans (C. elegans) is a suitable model to investigate the toxicity of environmental hazards. In this study, the transcriptomic profiles of C. elegans exposed to inorganic mercury chloride (HgCl2) and sodium (meta)arsenite (NaAsO2) were assessed alongside organic methylmercury chloride (meHgCl) and dimethylarsinic acid (DMA). For this purpose, adult C. elegans were exposed for 24 h to NaAsO2 (10 µg/ml), DMA (200 µg/ml), HgCl2 (2 µg/ml), and meHgCl (0.5 µg/ml), concentrations that were equitoxic in juveniles for developmental delay. Whole genome gene expression profiles were determined by using Cellegans_UnrestrictedGE_G2519F_020186 Microarray (Agilent Technologies, Santa Clara, CA). The results showed significant changes in the transcriptome of adult C. elegans exposed to NaAsO2, DMA, HgCl2, or meHgCl relative to the control group (C. elegans treated with water). A total of 927 and 1221 differentially expressed genes (DEGs) were found in C. elegans treated with 10 µg/ml NaAsO2 or 200 µg/ml DMA, respectively. Interestingly, only 161 DEGs were in common for these two chemicals. Exposure to 2 µg/ml HgCl2 or 0.5 µg/ml meHgCl altered the expression of 670 and 485 genes, respectively, and out of these genes, 154 were commonly altered by the two treatments. Analysis of DEGs revealed that organic and inorganic forms of arsenic and mercury have different effects on the transcriptome of adult C. elegans.

overall_design: 16 samples, C. elegans treated with water (4 samples), 10 µg/ml NaAsO2 (3 samples), 200 µg/ml DMA (3 samples), 2 µg/ml HgCl2 (3 samples), or 0.5 µg/ml meHgCl (3 samples) for 24 hours.

first: Igor

last: Pogribny

first: Jessica

last: Camacho

first: Robert

last: Sprando

first: Piper

middle: R

last: Hunt


title: Global identification of Hfq-bound RNA and transcriptional start site mapping in Serratia marcescens.

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: In order to identify mRNA and sRNAs associated with the RNA-binding protein Hfq in Serratia marcescens strain Db10, Hfq-bound RNA was immunoprecipitated from a strain encoding an Hfq-3FLAG fusion protein at the normal location and sequenced, in parallel with the wild type strain (no fusion) as negative control. Additionally global transcriptional start site mapping was performed on total RNA, with or without TEX treatment, isolated from wild type Serratia marcescens. The data was used to identify regions of mRNA and sRNAs associated with Hfq in this organism. Associated work in Serratia marcescens Db10, an opportunistic bacterial pathogen, has shown that Hfq is essential for virulence in several models and exerts a wide-ranging impact on the transcriptome and, particularly, genes encoding virulence factors.

overall_design: RIP-seq analysis of Hfq-FLAG and control samples and RNA-seq analysis of wild type RNA +/-TEX treatment in Serratia marcescens

first: Sarah

last: Murdoch

middle: U

first: Cynthia

last: Sharma

last: Coulthurst


title: Transcriptome of LG-ESS Patient

city: Quebec City

first: Deepthi

last: Sudarshan

address: 9 Rue Mc Mahon

institute: Université Laval

summary: In this study, we characterize translocations that are frequent in Low Grade Endometrial Stromal Sarcoma (LG-ESS) and Ossifying FibroMyxoid Tumors (OFMT). We find that the fusion protein assembles a mega-complex harboring both NuA4/TIP60 and PRC2 subunits and enzymatic activities and leads to mislocalization of chromatin marks in the genome, linked to aberrant gene expression.

overall_design: mRNA sequencing from  frozen LG-ESS Patient samples, Sample 1 (Endometrial Tumor with JAZF1-SUZ12 fusion) and Sample 5 (Endometrial Normal) are paired samples. Sample 3 is another LG-ESS patient sample with the JAZF1-SUZ12 fusion. DE comparisons were done by pair-wise comparisons (1_Vs_5 and 3_Vs_5)

first: Jacques

last: Côté


title: Transcriptome of JAZF1-SUZ12 translocation

overall_design: mRNA sequencing from K562 cells expressing JAZF1-SUZ12


title: Molecular mechanism of EPC1-PHF1 fusion protein  (CUT and RUN-seq Homo Sapiens)

summary: In this study, we characterize the fusion protein produced by the EPC1-PHF1 translocation in Low Grade Endometrial Stromal Sarcoma (LG-ESS) and Ossifying FibroMyxoid Tumors (OFMT). We express the fusion protein and necessary controls in K562 Cells. The fusion protein assembles a mega-complex harboring both NuA4/TIP60 and PRC2 subunits and enzymatic activities and leads to mislocalization of chromatin marks in the genome, linked to aberrant gene expression.

overall_design: CUT and RUN-sequencing (anti-HA) in K562 cells expressing HA tagged EPC1-PHF1 fusion protein or tag only.


title: PD-L1+CD8+ T cells enrichment in lung cancer exerted regulatory function and tumor-promoting tolerance

city: Shanghai

first: zheyi

last: chen

address: 1665 Kong Jiang Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Targeting checkpoint blockade to rescue exhausted regulatory T cells (Tregs) has become an essential immunotherapy strategy in treating cancer. Until now, the CD4+ Tregs and PD-1+CD8+ T cells were demonstrated to reduce immunogenic responses. In contrast, little is known about the PD-L1 graphic pattern and characteristics in CD8+ T cells. We performed two high-throughput analysis approaches on tumor-infiltrating CD8+ T cells in lung cancers. We discovered PD-L1+CD8+ T cells enriched in tumor lesions, localized with PD-1+CD8+ affected T cells, and owned regulatory functions. Moreover, tumor-derived IL-27 promoted the development of PD-L1+CD8+ T cells through STAT1/STAT3 signaling. Single-cell RNA sequencing data analysis further clarified the enrichment of PD-L1+CD8+ T cells related to the downregulation of adaptive immune response. Additionally, enrichment of this subset was correlated with poor survival of lung cancer patients. Our data collectively demonstrated that PD-L1+CD8+ T cells potentially become a prognostic biomarker in lung cancer.

overall_design: CD8 T cells were stimulated with IL-27 for 48 hours, CD8+PD-L1+ and CD8+PD-L1- T cells were sorted into tubes containing lysis buffer, and transcriptome amplifications were performed following the Smart-Seq2 protocol.

first: Yingxia

last: Zheng

first: Li

last: Han

first: Zheyi

last: Chen


title: Transcriptomic characterisation of haematopoietic stem and progenitor cells from adult human spleen

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

summary: Haematopoietic stem and progenitor cells (HSPCs), the precursors of all blood cells, reside predominantly in the bone marrow. Yet, a  small proportion (<1%) of phenotypic HSPCs is also found in extramedullary tissues, such as spleen, where they contribute to blood production under stress conditions. However, the detailed characterization of extramedullary HSPCs remains poor. Here, we analyse the single-cell composition of the adult human HSPC pool within the spleen from two patients with hereditary spherocytosis (HS), a disorders causing abnormal red blood cells. 10x scRNA-seq of CD19- CD34+ HSPCs was paired with single-cell functional analysis using most immature haematopoietic stem cells and multipotent progenitors (HSC/MPPs). We find that HSC/MPPs from HS spleens have a stronger transcriptional and functional bia towards the erythroid lineage than control sample.

overall_design: Spleen cells from two patients (1 female, 1 male) were stained with a customised catalogue of TotalSeqA (biolegend), CD19- CD34+ cells were sorted by flow cytometry and pooled in a 1:1 ratio before library preparation with the 10x sequencing v3.1 protocol

first: Elisa

last: Laurenti

middle: P

first: Nicole

last: Mende

first: Emily

last: Mitchell


title: RNA Sequencing of livers from ApoE-/- mice treated with HIF1a inhibitor PX-478 or Saline

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive NE

department: Biomedical Engineering

institute: Georgia Tech & Emory University

summary:
Purpose: HIF1a inhibitor PX-478 prevents hypercholesterolemia in ApoE-/- mice fed Western diet for 3 months. The goal of this study was to determine the mechanisms in the liver through which PX-478 regulates cholesterol.
Methods: 4-week old ApoE-/- mice were fed a Western diet and injected intraperitoneally, bi-weekly with either PX-478 (40 mg/kg) or Saline for 3 months. The livers of 3 PX-478-treated mice and 4 Saline-treated mice were used for this RNA-seq study.
Results: We identified 800+ differentially expressed genes in the PX-478-treated ApoE-/- mice livers relative to the saline-treated control livers. A subset of these genes were found to play important roles in cholesterol regulation and were further validated by qPCR analysis.
Conclusions: Our study details potential hepatic cholesterol regulating mechanisms for HIF1a inhibitor PX-478. These results, coupled with our findings on the effect of PX-478 on two different mouse models of atherosclerosis, demonstrate that PX-478 is a potential anti-atherogenic and anti-hypercholesterolemic drug.

overall_design: Liver mRNA profiles of ApoE-/- mice fed Western diet for 3 months and treated bi-weekly via IP injection with either Saline (n=4) or PX-478 (40 mg/kg, n=3)

first: Nicolas

last: Villa-Roel


title: Transcriptomic analysis of Col  responding to aluminum

city: Qingdao

first: Liu

middle: jia

last: jia

address: NO. 72, Bin Hai Road

institute: shandong university

summary: Our objective is to study root development under aluminum stress. We isolated total RNA from the roots of 7-day-old Col-0 seedlings. New genes after responding to aluminum treatment, during the root development, are discovered.

overall_design: We isolated total RNA from the roots of 7-day-old Col-0 seedlings with or without aluminum treatment.

first: Jiajia

last: Liu

first: ZhaoJun

last: Ding


title: Natural Flavonoid Pectolinarigenin Alleviated Hyperuricemic Nephropathy via Suppressing TGFβ/SMAD3 and JAK2/STAT3 Signaling Pathways

city: chengdu

first: Qian

last: Ren

state: China

address: 三住7楼

institute: 四川大学华西临床医学院肾内科

summary: Natural flavonoid pectolinarigenin (PEC) was reported to alleviate tubulointerstitial fibrosis of unilateral ureteral obstruction (UUO) mice in our previous study. To further investigate nephroprotective effects of PEC in hyperuricemic nephropathy (HN), adenine and potassium oxonate induced HN mice and uric acid-treated mouse kidney epithelial (TCMK-1) cells were employed in the study. As a result, PEC significantly lowered serum uric acid level and restored hyperuricemia-related kidney injury in HN mice. Meanwhile, PEC alleviated inflammation, fibrosis and reduced adipokine FABP4 content in the kidneys of HN mice and uric acid-treated TCMK-1 cells. Mechanistically, PEC inhibited the TGF-β1 expression as well as the phosphorylation of transcription factor SMAD3 and STAT3 to regulate the corresponding inflammatory and fibrotic gene expression in kidney tissues. In conclusion, our results suggested that PEC could inhibit the activation of SMAD3 and STAT3 signaling to suppress inflammation and fibrosis, thereby alleviate HN in mice.

overall_design: Renal mRNA profiles of pectolinarigenin-treated hyperuricemic mice

first: Bo

last: Wang

first: Liang

last: Ma

first: Zhouke

last: Tan


title: m6A-modified transcripts in the context of MI

city: Nanjing

first: yingjie

last: Zhang

address: No.300 Guangzhou Road

institute: Department of Rehabilitation Medicine, the First Affiliated Hospital of Nanjing Medical University

summary: Roles of m6A-modified mRNA transcripts in the context of MI were preliminarily verified. In the context of m6A methylation, three hub mRNAs were validated to impact the process of apoptosis/angiogenesis. Our study provided theoretical basis and innovative targets for treatment of MI and paved the way for future investigations aiming at exploring upstream epigenetic mechanisms of pathogenesis after MI.

overall_design: N6-methyladenosine methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were examined (interacted) to select m6A-modified mRNAs with samples collected from sham operation and MI rat models. m6A methylation regulated mRNAs were interacted with apoptosis/angiogenesis related genes in GeneCards. Afterwards, MeRIP-quantitative real-time PCR (MeRIP-qRT-PCR) was performed to measure m6A methylation level of hub mRNAs. m6A methylation variation was tested under different oxygen concentration or hypoxic duration in H9c2 cells and HUVECs. In addition, western blot and qRT-PCR were employed to detect expression of hub mRNAs and relevant protein level. Flow cytometry and Tunel assay were conducted to assess apoptotic level. CCK-8, EdU, and tube formation assay were performed to measure cell proliferation and tube formation ability.

first: Yu

first: Xiao

last: Lu

first: Yingjie


title: Transcriptome analysis after GPX4 knockdown in primary mouse chondrocyte（mcc）

last: Miao

address: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

summary: Osteoarthritis (OA) is the most common joint disease and is the leading cause of chronic disability among older people. Chondrocyte death was involved in OA pathogenesis. Ferroptosis is an iron-dependent cell death associated with peroxidation of lipids. Expression of GPX4 in the OA cartilage from OA patients were significantly lower than normal cartilage.In order to analyze the mechanism of GPX4, we conducted RNA-sequencing in mouse chondrocytes with or without GPX4 knockdown.Our results showed that Gpx4 downregulation could increase the sensitivity of chondrocytes to oxidative stress and aggravate ECM degradation in chondrocytes.


title: Targeting KDM4C upregulates the transcriptional activity of Cxcl10 to enhance the efficacy of combining radiotherapy and immunotherapy in lung cancer

first: hua

middle: xiao

last: jie

address: Xinhua Road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: The use of checkpoint blockade immunotherapy has revolutionized the field of cancer therapy. Although Immune checkpoint blockade (ICB) can achieve persistent response in several cancers, only 20-40% of patients can benefit from this therapeutic method. Preclinical and clinical evidence show that Radiotherapy (RT) can enhance tumor immunogenicity and improve the effects of immune checkpoint inhibitors. However, the actual outcomes are not satisfactory. Our previous studies revealed that the oncogene, Lysine-specific demethylase 4C (KDM4C) could regulate the radiosensitivity of lung cancer cells in vitro and in vivo. However, the role of KDM4C in antitumor immunity remains inconclusive. To that end, we analyzed the composition of infiltrating immune cells in our mouse tumor model using flow cytometry and found that KDM4C silencing could promote the intratumoral infiltration of CD8+ T cells. Further functional analysis showed that KDM4C silencing could promote proliferation, migration and activation of CD8+ T cells in vivo and in vitro and delay CD8+ T cells exhaustion. Mechanistically, using RNA-seq and Chip-PCR analysis, we determined that KDM4C silencing promotes the binding of H3K36me3 to the Cxcl10 promoter region to increase its transcriptional activity and thus induce CD8+ T cell-mediated antitumor response. Our results suggest that KDM4C-specific inhibitor, SD70 can reprogram the epigenetic state and improve the tumor microenvironment. More importantly, we found that the combined use of SD70, RT, and PD-L1 monoclonal antibodies exhibited the strongest antitumor effects and prolonged the survival time of tumor-bearing mice. Together, our findings suggest that a combination of KDM4C-targeted treatment, radiotherapy, and immune checkpoint blockade is safe and efficient for treating lung cancer.

overall_design: Lewis cells treated with DMSO or SD70 for 24 hours were analyzed by RNA-seq.

first: Gang

last: Wu

first: Shuangbing

last: Xu

first: Xiaohua

last: Jie

first: Yunshang

last: Chen

first: Ye

last: Zhao


title: comparison of primary epicardium explant derived CDCs and primary Epicardial cells

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

summary: The analysis showed differences of transcriptomes between primary epicardium explant derived CDCs and primary Epicardial cells directly isolated from the heart epicardium.SB-431542 was an effective TGF-b pathway inhibitor that could obviously inhibit the epicardial cells Epithelial-mesenchymal transition. SB-432542 treatment could produce some epithelial clones in the CDCs,which showed epicardiac specific expression  profile, compared with the CDCs.

overall_design: primary CDCs, primary Epicardial cells and SB-431542 induced epithelial clone-1 mRNA profiles were generated by deep sequencing, in triplicate, using BGIseq500 platform.

first: Zhenglong

last: Guo


title: Highly selective HSP90 inhibitor, pimitespib, demonstrates its potent growth suppressive activity to adult T-cell leukemia in preclinical models (Su9T01).

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

institute: Oita university, Faculty of Medicine

summary: Adult T-cell leukaemia-lymphoma (ATL) is a highly chemoresistant malignancy of peripheral T lymphocytes caused by human T-lymphotropic virus type I (HTLV-1). ATL cells constitutively activate anti-apoptotic signals through nuclear factor kappaB (NF-κB)-mediated gene expression. The molecular chaperon heat shock protein 90 (HSP90) plays a crucial role on NF-κB-mediated anti-apoptotic activity in ATL cells and HSP90 inhibitors, such as 17-DMAG and NVP-AUY922, have demonstrated their anti-ATL activities. A novel class of orally active inhibitors of cytosolic HSP90α and β, pimitespib, demonstrated its highly selective anti-ATL cell effects both ex-vivo and in vivo preclinical models. Ten ATL-related cell lines achieved their IC50 below 0.5µM dose of TAS-116 while CD4 lymphocytes derived from healthy donors were less harmed than ATL cells. TAS-116 efficiently induces Tax-degradation and IκB-α accumulation to Tax-positive cell-lines. DNA microarray profiling followed by a variety of pathway analysis revealed that TAS-116 down-regulated NF-κB activating pathways in Tax-positive cells and cell cycle promoting pathways in Tax-negative cells and induces anti-ATL effect. Oral administration of TAS-116 to ATL-cell xenograft model mice also demonstrated the growth inhibitory effects against tumor cells. Consequently, TAS-116, one of the most evolved HSP90 inhibitor, may become a promising option against ATL therapy.

overall_design: To identify differentially expressed genes after the treatment with TAS-116, ATL cell lines were treated with DMSO or TAS-116 for 16h. Then, total RNAs were collected from these cell lines and subsequently subjected to gene expression microarray analysis.

first: Emi

last: Ikebe

first: Shunsuke

last: Shimosaki

first: Hiroo

last: Hasegawa

first: Hidekatsu

last: Iha

first: Yoshitaka

last: Imaizumi

first: Yasushi

last: Miyazaki

first: Katsunori

last: Yanagihara

first: Jun-ichi

last: Fujisawa

first: Kazuhiro

last: Morishita


title: Highly selective HSP90 inhibitor, pimitespib, demonstrates its potent growth suppressive activity to adult T-cell leukemia in preclinical models (Pt1-3).

overall_design: To identify differentially expressed genes after the treatment with TAS-116, ATL cells from patients were treated with DMSO or TAS-116 for 16h. Then, total RNAs were collected from these cells and subsequently subjected to gene expression microarray analysis.


title: Highly selective HSP90 inhibitor, pimitespib, demonstrates its potent growth suppressive activity to adult T-cell leukemia in preclinical models (LYM1, KK1).


title: Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns

first: Rasim

last: Barutcu

address: 6 Davis Drive

institute: ScitoVation

summary: The nucleus is highly compartmentalized through the formation of distinct classes of membraneless domains, yet the composition and function of many of these structures is not well understood. Using APEX2-mediated proximity labelling and RNA sequencing, we surveyed transcripts associated with nuclear speckles, several additional domains, and the lamina. Remarkably, speckles and lamina are associated with distinct classes of retained introns enriched in genes that function in RNA processing, translation, and the cell cycle. In contrast to the lamina-proximal introns, retained introns associated with speckles are relatively short, GC-rich, and enriched for functional sites of RNA binding proteins that are concentrated in these domains. They are also highly differentially regulated across diverse cellular contexts, including the cell cycle. Our study thus provides a resource of nuclear domain-associated transcripts and further reveals speckles and lamina as hubs of distinct populations of retained introns linked to gene regulation and cell cycle progression.

overall_design: Profiling of transcripts and alternative splicing events associated with nuclear compartments using APEX2-seq

first: A

first: Mingkun

last: Wu

first: Ulrich

last: Braunschweig

first: Boris

last: Dyakov

first: Zheng

last: Luo

first: Kyle

last: Turner

first: Tanj

last: Durbic

first: Zhen-Yuan

last: Lin

first: Robert

last: Weatheritt

first: Philipp

last: Maass

first: Anne-Claude

last: Gingras

first: Benjamin

last: Blencowe


title: RNA-seq analysis of macrophages co-cultured with hepatocytes with and without HBV

city: LA

first: Yumei

last: Li

state: CALIFORNIA

address: HMR404, 2011 Zonal avenue

department: MMI

institute: USC

summary:
Purpose: The goal of this study is to identify genes and pathways in macrophages that may be altered by hepatocytes with replicating HBV
Methods: THP-1 monocytic cells were treated with PMA for differentiation into macrophages (M0). These macrophages were co-cultured for 4 days with HepAD38 cells with (HBV-) or without (HBV+) the treatmetn of tetracycline and then lysed for the isolation of RNA using NEBNext Ultra II RNA Library Prep Kit for Illumina. The polyA+ RNA-seq was conducted in triplicate, and about 30 million sequence reads per sample that passed quality filters were analyzed by Partek Flow. The qRT–PCR validation of the results was performed using SYBR Green assays. M0 macrophages without co-culturing with HepAD38 cells were also analyzed to serve as the control (M0).
Results: To understand how HBV might affect THP-1 macrophages and how macrophages suppressed HBV replication, we conducted the RNA-seq analysis to determine the gene expression profiles in THP-1 macrophages (Mϕ) without co-culturing with HepAD38 cells (M0), THP-1 macrophages co-cultured with HepAD38 cells in the presence of tetracycline (HBV-), and THP-1 macrophages co-cultured with HepAD38 cells in the absence of tetracycline (HBV+). The analysis of RNA-seq results revealed 3946 differentially expressed genes (DEGs) between Mϕ(HBV+) and Mϕ(M0) cells, 3333 DEGs between Mϕ(HBV-) and Mϕ(M0) cells, and 783 DEGs between Mϕ(HBV+) and Mϕ(HBV-) cells (Figure 2A). The heatmap analysis revealed that Mϕ(HBV+) cells expressed significant higher levels of M1 markers including IL-1β and lower levels of M2 markers than in Mϕ(HBV-) cells (Figure 2B). The induction of IL-1β in Mϕ(HBV+) cells was also highly prominent when the cytokine expression profiles were analyzed by the volcano plot (Figure 2C). This induction of IL-1β was confirmed by RT-qPCR analysis (Figure S2E). These results indicated that THP-1 macrophages co-cultured with cells containing replicating HBV would undergo the M1 polarization. Interestingly, the heat map analysis of top 20 DEGs, based on low false discovery rate and high Log2 fold changes, between Mϕ(HBV+) and Mϕ(HBV-) cells revealed that seven of them were mitochondria-encoded genes that regulate the OXPHOS (Figure 2D). The pathway analysis indicated that the OXPHOS pathway was indeed upregulated in MΦ(HBV+) cells, although some pathways in these cells were also downregulated (e.g., Sirtuin signaling) and some were not affected (e.g., insulin receptor signaling) (Figure 2E).
Conclusions: Our study provided the detailed analysis of the response of macrophages to hepatocytes containing replicating HBV. Our results indicated that HBV-could induce the M1 polarization of THP-1-derived macrophage. The induction of CXCL1 expression in macrophages by HBV likely plays an important role in the hepatic infiltration of neutrophils, whih express a high level of CXCR1 , the receptor of CXCL1. Our finding of an increased expression of mitochondria-encoded genes that regulate OXPHOS also suggested that HBV might promote OXPHOS in macrophages.

overall_design: mRNA expression profiles of THP-1-derived macrophages co-cultured with hepatocytes with or without activate HBV replication

first: Jing-Hsiung

last: Ou


title: Weakened sarcomeric contractility distinguishes Facio Scapulo Humeral Dystrophy muscle fibers

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

institute: Aix-Marseille Université - Marseille Medical Genetics

summary: To gain further insights into the specificity of the muscle alteration in this disease, we derived induced pluripotent stem cells from patients affected with type 1 and 2 FSHD, differentiated these cells into contractile innervated muscle fibers and analyzed their transcriptome by RNA Seq.

overall_design: In order to identify pathways involved in FSHD which are specific to the muscle, we took advantage of our collection of induced pluripotent stem cells and our recently developed procedure for production of innervated and contractile skeletal Muscle Fibers (MFs) to analyze gene expression in cells from FSHD1 or FSHD2 patients compared to healthy donors at day 30 post-differentiation. Given the implication of SMCHD1 in both FSHD2 and bosma arhinia microphthalmia syndrome (BAMS), but the absence of muscle symptoms in BAMS, RNA Seq was also carried in BAMS MFs to identify pathways that are specific to FSHD. For FSHD1, RNA seq was performed on cells from one patient affected with FSHD carrying a short D4Z4 allele (FQMR19, FQMR20; 7 RU) and cells from a mosaic patient (FQMR17, 18, 27, 28; 25% of mosaicism, clinically affected). For this patient, we compared two isogenic clones, one with a short allele (2 RU, 4qA haplotype, diseased clone: FQMR17, 18) and one with a long healthy allele (15 RU; 4qA haplotype: healthy clone: FQMR27, 28). For patients with SMCHD1 variants, we compared FSHD2 cells with a missense mutation in the ATPase domain, never reported in BAMS that abrogates SMCHD1 enzymatic activity (FQMR21, 22; Q194P) to BAMS cells with a variant in the ATPase domain (FQMR23, 24; E136G) that causes a gain of the enzymatic activity.

first: Frédérique

first: Camille

last: Laberthonnière

first: Raphael

last: Chevalier


title: Highly selective HSP90 inhibitor, pimitespib, demonstrates its potent growth suppressive activity to adult T-cell leukemia in preclinical models (OATL4).

first: Yoshiyuki

last: Tsukamoto

first: Emi

last: Ikebe

first: Shunsuke

last: Shimosaki

first: Hiroo

last: Hasegawa

first: Hidekatsu

last: Iha

first: Yoshitaka

last: Imaizumi

first: Yasushi

last: Miyazaki

first: Katsunori

last: Yanagihara

first: Jun-ichi

last: Fujisawa

first: Kazuhiro

last: Morishita


city: ZhenJiang

first: Jiabin

last: Huang

state: JiangSu

address: 8 Dianli Road, Runzhou District

institute: Affiliated People's Hospital of Jiangsu University

summary: Here we systematically analyze the modification pattern of m6A mRNA in adenocarcinoma at the esophagogastric junction.In adenocarcinoma of esophagogastric junction samples, a total of 4775 new m6A peaks appeared, and 3054 peaks disappeared. The unique m6A-related genes in adenocarcinoma of esophagogastric junction are related to cancer-related pathways. There are hypermethylated or hypomethylated m6A peaks in AEG in differentially expressed mRNA transcripts. This study preliminarily constructed the first m6A full transcriptome map of human adenocarcinoma of esophagogastric junction. This has a guiding role in revealing the mechanism of m6A-mediated gene expression regulation.

overall_design: Examination of m6A-mediated gene expression regulation site

first: Yu

last: Fan


title: CDH18 is an epicardial biomarker regulating epicardial specification and differentiation towards vascular smooth muscle cells

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

summary: The epicardium is a mesothelial layer covering the myocardium and contributes to different cardiac lineage descendants during cardiogenesis. Fine-tuned balanced signaling defines epicardial specification and regulates cell plasticity and cell-fate decisions of epicardial-derived cells (EPCDs) by epicardial-to-mesenchymal transition (EMT). However, powerful tools to investigate epicardial cell function, including markers with pivotal roles in developmental signaling, are still lacking. Here, we recapitulated embryonic epicardiogenesis using human induced pluripotent stem cells (hiPSCs) and identified type II classical cadherin CDH18 as a novel biomarker defining lineage specification in human developing epicardium. The loss of CDH18 led to the onset of EMT and specific differentiation towards cardiac smooth muscle cells. Furthermore, GATA4 regulated epicardial CDH18 expression. These results demonstrate the production and enrichment of hiPSC-derived epicardial cells via the tracing of CDH18 expression, providing a model for investigating epicardial function in human development and disease and enabling new possibilities for regenerative medicine.

overall_design: human induced pluripotent stem cells (hiPSCs) were differentiated into EPI cells (hiPSC-EPI). On day 12 and 24, cells were treated to undergo EMT towards smooth muscle cells (iSMC) and cardiac fibroblast (iCF). hiPSC-EPI were also transfected with a siRNA against CDH18 to evaluate the causal role in the loss of function

first: Julia

last: Junghof

first: Antonio

last: Lucena-Cacace

first: Megumi

last: Narita


title: Therapeutic modulation of NKG7 in CD8+ T cells increases anti-tumor cytotoxicity and improves response to immune checkpoint inhibitors

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: Monoclonal antibodies that block PD-1/PD-L1 inhibitory signaling have been successfully used to treat a variety of solid tumor malignancies, but only a subset of patients benefit from this treatment.  It remains unclear why the majority of patients fail to respond and what other limiting factors are at play.  Here we show that natural killer cell granule protein-7 (NKG7) is critical for the anti-tumor activity of CD8+ T cells and response to anti-PD-1 therapy.  We performed single-cell RNA sequencing analysis of peripheral CD8+ T cells from patients treated with anti-PD-1 and found that NKG7 gene expression was decreased in the non-responding patients.

overall_design: This study included a total of 8 individual patients; n=4 responders to anti-PD-1 therapy; n=4 non-responders to anti-PD-1 therapy.  There are two representative samples from each patient, matching "BL" (baseline) and "PT" (12 weeks post initiation of treatment) timepoints.  8 samples also included VDJ library sequencing, as detailed in sample description below.

first: Ti

last: Wen

first: Whitney

last: Barham

first: Ying

last: Li

first: Henan

last: Zhang

first: Joanina

last: Gicobi

first: Jacob

middle: B

last: Hirdler

first: Xin

last: Liu

first: Hyoungjun

last: Ham

first: Fabrice

last: Lucien

first: Hu

first: Cristina

last: Correia

first: Dileep

last: Monie

first: Zesheng

last: An

first: Susan

last: Harrington

first: Xiaosheng

last: Wu

first: Ruifeng

last: Guo

first: Roxana

middle: S

last: Dronca

first: Aaron

last: Mansfield

first: Yiyi

last: Yan

first: Svetomir

middle: N

last: Markovic

first: Sean

last: Park

first: Hong

last: Qin

first: Minetta

first: George

last: Vasmatzis

first: Daniel

last: Billadeau

first: Haidong

last: Dong


title: Expression data from bladder cancer cells T24 treated with ox-LDL or vehicle

first: Jingya

last: Sun

address: 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary:
Target genes regulated by ox-LDL treatment in bladder cancer cells T24 were identified by microarrays.
In this dataset, we include the expression data obtained from bladder cancer cells T24 starved with serum-free medium and then treated with 20 μg/mL ox-LDL or vehicle for 24 h. These data are used to obtain genes that are differentially expressed in response to ox-LDL treatment.

overall_design: 6 Total samples were analyzed. We generated the following pairwise comparisons: CON and OXLDL. Genes with P≤0.001 and a fold-change ≥1.5 were selected.

first: Jun


title: Transcriptome sequencing and expression analysis of green sulcus and yellow culm in Phyllostachys violascens cv. Viridisulcata

city: china

first: wei

last: hanhantian

state: china

address: wusu street

institute: zhejiang A&F university

summary: In this study, we performed transcriptomics across P. violascens to identify the main pigments contributing to colorful culm and try to reveal a plausible transcriptional regulatory mechanism. The green sulci and yellow culms were collected from the middle of three bamboo’s longest internodes and the chosen bamboos were approximately in the same size which were both 3 meters high, in April 24, 2019. A total of 1,163,327,390 clean reads representing a total of 174.49 Gb nucleotides were generated, with an average GC content of 48.03%. A total 421 differentially expressed genes were identified in the pool.

overall_design: RNAs were collected from green sulcus and yellow culm, each have three replications.

first: Hantian

last: Wei

first: Xinchun

last: Lin

first: Dan

last: Hou


title: Highly selective HSP90 inhibitor, pimitespib, demonstrates its potent growth suppressive activity to adult T-cell leukemia in preclinical models (ED).

first: Yoshiyuki

last: Tsukamoto

first: Emi

last: Ikebe

first: Shunsuke

last: Shimosaki

first: Hiroo

last: Hasegawa

first: Hidekatsu

last: Iha

first: Yoshitaka

last: Imaizumi

first: Yasushi

last: Miyazaki

first: Katsunori

last: Yanagihara

first: Jun-ichi

last: Fujisawa

first: Kazuhiro

last: Morishita


title: Gene expression profile of sma-3 mutant Caenorhabditis elegans

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

summary: N2 (wildtype) control animals vs. sma-3 mutants vs. sma-6 mutants; 5 replicates each.


title: Transcriptional modifications driven by STING activation in polarizing TH1 and Th9 cells

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

institute: CGFL

summary: We assessed the global transcriptional changes driven by STING activation with the cyclic dinucleotide 2'3'-cGAMP TH1 and TH9 cells polarized in vitro for 16h and 48h. Our data indicated that STING activation led to an upregulation of Type I Interferon, Interferon Stimulated Genes and pro-inflammatory molecule production that was maintained over time. Furthermore, not only STING activation enhanced the transcription of TH1 and TH9 main effector cytokines (respectively Ifng and Il9) but they also also globally enhanced their differentiation programs.

overall_design: Naive CD4+ T cells isolated from C57BL/6J mice were transfected with 2'3'-cGAMP or Control dinucleotide before in vitro polarization into TH1 or TH9 cells for 16h and 48h. Triplicates obtained from three independent experiments were subjected to RNAseq.

first: Elise

last: Jacquin

first: Isis

last: Benoit-Lizon

first: Lionel

last: Apetoh

first: Corentin

last: Richard


title: RNA immunoprecipitation sequencing (RIP-seq) in four types of cancer cell lines

first: Zhiyong

last: Liu

address: changhai road 168

institute: Changhai Hospital

summary: The ribosomal protein S6 (RPS6) antibody used for RIP to measure the landscape associated RNA by sequencing

overall_design: RNA immunoprecipitation (RIP) was performed using the Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore, USA) according to the manufacturer’s instructions. An aliquot of lysate was removed as an input control.RNA sequencing was performed with Illummina HiSeq X Ten Sequencer

first: Shanrong

first: Yanan

last: Pang


title: Highly selective HSP90 inhibitor, pimitespib, demonstrates its potent growth suppressive activity to adult T-cell leukemia in preclinical models (HuT102).

first: Yoshiyuki

last: Tsukamoto

first: Emi

last: Ikebe

first: Shunsuke


title: Gene expression of central amygdala of mice

status: Public on Feb 17 2022

city: Chongqing

first: Ma

last: Huan

address: Daping Street

institute: Daping Hospital,Army Medical University

summary:
Purpose: The goals of this study are to screen out the changes of gene expression profile in response to high fat diet, an mRNA-seq was performed in central amygdala
Methods: 6-week-old male wild-type mice were fed with high fat diet (HFD, containing 45% fat) or normal chow diet (ND) for 5 months. And then their central amygdala tissues were removed and total RNA was extracted to perform RNA sequencing.
Results:The KEGG pathway analysis showed that genes related to neuroactive ligand-receptor interaction and calcium signaling pathway were dramatically upregulated after HFD
Conclusions: Our study represents the first detailed analysis of central amygdalar transcriptomes of mice subjected to high fat diet, with biologic replicates, generated by RNA-seq technology. Our results show genes related to neuroactive ligand-receptor interaction and calcium signaling pathway were dramatically upregulated after high fat diet feeding,which hint at the importance of ion channel in central amygdala after high fat feeding.

overall_design: Cental amygdalar mRNA profiles of mice challenged with 20-week normal chow diet or high fat diet

first: Huan

last: Ma

first: Zhiming

last: Zhu


title: Medicago truncatula seedling treatment with Pythium oligandrum oospores within in-vitro system.

city: Castanet Tolosan

first: Bernard

last: Dumas

address: Chemin de Borde Rouge

institute: LRSV

summary: The objective of this study was to evaluate the effect of mycoparasite and roo tendophyte P. oligandrum on the A17 M. truncatula transcriptome.

overall_design: A total of 48 samples were analyzed comprising 6 biological replicates of the kinetic (3, 5, 7, 14 days) for both treated (P.oligandrum) and control A17 M. truncatula treatments.

first: Maryam

last: Hashemi

first: Thomas

last: Rey

first: Marine

last: Veyssière

first: Helene

last: Clemente

first: Marielle

last: Aguilar


title: Leptin secreted from testicular microenvironment modulates hedgehog signaling to augment the endogenous function of Leydig cells

city: Miami

first: Derek

last: Van Booven

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

summary: Although testosterone deficiency (TD) may be present in 1 out of 5 men 40 years or older, the factors responsible for TD remain largely unknown. Leydig stem cells (LSCs) differentiate into adult Leydig cells (ALC) and produce testosterone in the testes under the pulsatile control of luteinizing hormone (LH) from the pituitary gland. However, recent studies have suggested that the testicular microenvironment (TME), which is comprised of Sertoli and peritubular myoid cells (PMC), plays an instrumental role in LSC differentiation and testosterone production under the regulation of the desert hedgehog signaling pathway (DHH). It was hypothesized that TME releases paracrine factors to modulate LSC differentiation. For this purpose, cells (Sertoli, PMCs, LSCs and ALCs) were extracted from men undergoing testis biopsies for sperm retrieval and were evaluated for the paracrine factors in the presence or absence of TME (Sertoli and PMC). The results demonstrated that TME secretes leptin which induces LSC differentiation and increases T production. Leptin’s effects on LSC differentiation and T production, however, are inversely concentration-dependent: positive at low doses and negative at higher doses. Mechanistically, leptin acts on LSCs upstream of DHH; leptin-DHH regulation functions unidirectionally insofar as DHH gain or loss of function has no effects on leptin levels. Taken together, these findings identify leptin as a key paracrine factor released by cells within the TME that modulates LSC differentiation and testosterone release from mature Leydig cells, a finding with important clinical implications for TD.

overall_design: RNA-seq profiling of Leydig cells+Sertoli cells+PMC exposed to increasing concentrations of leptin ranging from 0, 0.25, 1, and 10ng/ml.

first: Himanshu

last: Arora

middle: J