title: Hematopoietic Loss of Y Chromosome Leads to Cardiac Fibrosis and Dysfunction and is Associated with Death due to Heart Failure [bulkRNAseq_HeartMacrophages]


title: Well-demarcated, unclassifiable intracranial tumor

status: Public on Jun 02 2022

city: Kyoto

first: Yasuhide

last: Takeuchi

state: Kyoto

address: 54 Shogoin Kawahara-cho, Sakyo-ku, Department of Diagnostic Pathology, Kyoto University Hospital

department: Department of Diagnostic Pathology

country: Japan

institute: Kyoto University Hospital

type: Methylation profiling by genome tiling array

summary: Here, we report a case with cerebral tumor with unclassifiable morphological/methylation-based features, well-defined border with the surrounding cerebral tissue, and a novel gene fusion detected by mRNA sequencing

overall_design: Single tumor sample was analyzed by Illumina Infinium Human Methylation EPIC BeadChip

first: Yoshiki

last: Arakawa


title: Melanoma GEMM Tumors, untreated or vemurafenib treated

status: Public on Jun 01 2022

city: South San Francisco

first: Dorothee

last: Nickles

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Fibrin is a critical regulator of neutrophil effector function at mucosal barrier sites

city: Bethesda

first: Niki

last: Moutsopoulos

address: 30 convent Dr

institute: NIDCR

summary: Plasminogen (Plg), the zymogen precursor of the serine protease plasmin, is synthesized by the liver and is present in high concentration in the circulation and in interstitial fluids to provide focal proteolysis, after being converted to plasmin by urokinase or tissue plasminogen activator. Homozygous or compound heterozygous mutations in the human Plg gene (PLG) typically lead to severe mucosal disease involvement suggesting, a critical role for this gene/pathway in mucosal immunity. Indeed, such patients present with deposition of fibrin at various mucosal sites leading to ocular disease (conjunctivitis), oral mucosal disease (ligneous periodontitis), lung, vaginal and gastrointestinal tract involvement.  In the oral mucosa, local deposition of fibrin is hypothesized to lead to severe soft tissue and bone destruction around teeth and often loss of the entire dentition in adolescence. Mucosal inflammation in areas surrounding the dentition and destruction of underlying bone are also the hallmarks of the common human oral mucosal disease, periodontitis. Plg-deficient mice phenocopy the human disease and we aim to use this animal model to understand the mechanism underlying fibrin-mediated periodontal immunopathology in vivo. Herein, we analyse the transcriptome of gingival tissues extracted from Plg-deficient mice in comparison to their wild-type littermates at 12 weeks of age.

overall_design: Examine the changes in the transcriptome in oral mucosal tissues of Plg-deficient mice compared with wild-type littermates.

first: Lakmali

last: Munasinghage Silva

first: Andrew

middle: D

last: Doyle

first: Teresa

last: Greenwell-wild

first: Nicolas

last: Dutzan

first: Collin

middle: L

last: Tran

first: Loreto

last: Abusleme

first: Lih

last: Jiin

first: Elizabeth

middle: M

last: Chun

middle: G

last: Lum

first: Cary

middle: S

last: Agler

first: Carlos

last: Zuazo

first: Megan

last: Sibree

first: Priyam

last: Jani

first: Vardit

last: Kram

first: Daniel

last: Martin

first: Kevin

last: Moss

first: Mihalis

last: Lionakis

first: Francis

middle: J

last: Castellino

first: Christian

last: Kastrup

first: Matthew

last: Flick

first: Kimon

last: Divaris

first: Thomas

middle: H

last: Bugge


title: SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues

city: New York

first: Siqian

last: Feng

address: 612 West 130th St, floor 9 Room L9-005

institute: Columbia University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We have developed SpyChIP, a method that depends on covalent isopeptide bond formation, to identify sites of cell type-specific transcription factor (TF) occupancy in native physiological contexts without tissue dissociation or nuclei sorting. Using SpyChIP, we characterized the genome-wide binding profiles of the Hox protein Ultrabithorax (Ubx) in two non-overlapping domains of the Drosophila haltere imaginal disc, revealing extensive region-specific Ubx-DNA binding events. The application of cell type-specific covalent bond formation to ChIP sets the stage for carrying out many other cell type-specific analyses and genetic manipulations in vivo that were previously unachievable.

overall_design: The 3xFLAG tag was inserted into the endogenous Hox genes Scr and Ubx. A 3xFLAG-Scr(YPWM*) allele, which encodes a mutant 3xFLAG-Scr protein unable to interact with the Hox cofactor Exd, was also generated. ChIP-seq (2 biological replicates) against various 3xFLAG-tagged Hox proteins was performed, and the wild type animals, which lacks the 3xFLAG tag, was used as negative control. ChIP-seq was also performed against the homeodomain TF Dll.

first: Richard

last: Mann


title: Hepatic gene expression and functional changes associated with nonalcoholic steatohepatitis

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

institute: Hirosaki University

summary: Non‑alcoholic steatohepatitis (NASH) is a pathological condition of the liver in which hepatocyte steatosis, invasion of inflammatory cells and hepatic injury occur without alcohol abuse. Despite the known risk of liver cancer and liver fibrosis that may progress to liver cirrhosis that exists with NASH, an understanding of related gene expression and associated functional changes remains insufficient. The present study used a mouse model of NASH induced by a high‑fat diet to examine gene expression in the liver and to search for transcripts that could predict early liver fibrosis in the future. Mice fed a high‑fat diet for 2 weeks showed typical NASH liver histology by hematoxylin and eosin staining, and increased fibrosis was confirmed by Sirius red staining after 6 weeks. Functional changes associated with liver damage, liver inflammation, liver steatosis and liver fibrosis were predicted by toxicological ontology analysis using Ingenuity Pathways Analysis. Downregulated microRNA (miR)‑21 and upregulated collagen type III α1 mRNA in the liver and upregulated exosomal miR‑21 in serum of mice fed a high‑fat diet for 1 and/or 2 weeks were confirmed by reverse transcription‑quantitative PCR, suggesting that these changes occur prior to histological confirmation of fibrosis. Therefore, it may be possible to predict future liver fibrosis by analyzing fibrosis‑related genes that shift prior to pathological findings.

overall_design: Gene expression in the livers of mice fed a control diet or a NASH-induced high-fat diet was examined by microarray analysis. Livers were harvested 1, 2, and 6 weeks after diet ingestion.

first: Kana

last: Matsumoto


title: Myh9 plays essential role in hematopoietic stem/progenitor cells survival and maintenance

city: Chengdu

first: Quanming

last: An

address: 26 Huacai road,Chenghua District

country: China

institute: Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC)

summary: Myosin heavy chain 9 (MYH9) gene encodes a protein named non-muscle heavy chain IIA (NMHC IIA), interacting with actin and participating in various biological processes. Mutations in MYH9 cause an array of autosomal dominant disorders, known as MYH9-related diseases (MYH9-RD). However, the role of MYH9 in normal hematopoiesis remains largely unexplored. By using Mx1-cre Myh9 conditional knockout mice, we established an inducible system to precisely inactivate Myh9 function in hematopoietic cells in vivo. The results showed that deletion of Myh9 led to severe defects in hematopoiesis, characterized by pancytopenia, drastic decreases of hematopoietic stem/progenitor cells (HSPC), and bone marrow failure, causing early lethality in mice. The defect in hematopoiesis caused by Myh9 ablation is cell autonomous. In addition, Myh9 deletion impairs HSPC repopulation capacity and increases apoptosis. RNA sequencing results revealed significant alterations in the expression of genes related to HSC self-renewal and maintenance, while multiple signal pathways were also involved, including genes for HSC and myeloid cell development, intrinsic apoptosis, targets of mTOR signaling, and maturity of hematopoietic cells. Collectively, our findings suggest an essential role for Myh9 in the survival and maintenance of HSPC in normal hematopoiesis.

overall_design: To explore the molecular mechanism of hematopoietic defects observed in Myh9-deficient mice. We sorted Lin-Sca1+c-Kit+ (LSK) cells from Myh9-deficient (cKO) and littermate control (CTRL) mice to performed RNA-seq as we described before(PMID:29434353, 31443434).

first: Feng

last: Ma


title: Targeted inducible delivery of immunoactivating cytokines reprograms glioblastoma microenvironment and inhibits growth in mouse models [Bulk RNA-seq]

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary:
We exploited a lentiviral vector-based platform to engineer hematopoietic stem cells ex vivo with the aim of releasing, via their tumor-infiltrating monocyte/macrophage progeny, IFN-a or IL-12 at the tumor site in a spatial and temporal regulated manner.
Taking advantage of a syngeneic GBM mouse model, we showed that inducible release of IFN-a within the TME achieved robust tumor inhibition up to eradication and outperformed systemic treatment with the recombinant protein in terms of efficacy, tolerability and specificity.
Single-cell RNAseq of the tumor immune infiltrate revealed reprogramming of the immune microenvironment towards a pro-inflammatory and anti-tumoral state associated with loss of a macrophage subpopulation predicting poor prognosis in human GBM.

overall_design: Bulk RNA-seq of sorted glioblastoma cells (GFP+) and unaffected brain hemisphere samples of IFN-a-DHFR gene therapy treated, recombinant IFN-a1 treated, and control mice.

first: Filippo

last: Birocchi

first: Melania

last: Cusimano

first: Federico

last: Rossari

first: Ivan

last: Merelli

first: Nadia

last: Coltella

first: Luigi

last: Naldini


title: Single-Cell Transcriptomic Analysis Reveals Neutrophil as Orchestrator during β-Glucan-Induced Trained Immunity in a Teleost Fish

city: Shanghai

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

summary: We establish a trained immunity activation model in turbot (Scophthalmus maximus) by training with β-glucan in vivo. Through single cell RNA-sequencing analysis, we annotate 16 clusters of immune cells and blood cells from head kidney and spleen, and successfully characterize that neutrophils exhibit distinguished feature of trained immunity.

overall_design: Single cell transcriptome analysis was performed to study the feature of β-Glucan induced trained immunity in a teleost fish

first: Di

last: Mu

first: Jin

first: Yu

last: Jiang

first: Zhuang

last: Wang

first: Weijie

last: Cheng

first: Jianchang

last: Huang

first: Yuanxing

last: Zhang

first: Qin

last: Liu

first: Dahai


title: A natural mutation of the NST1 gene arrests secondary cell wall biosynthesis in the seed coat of hull-less pumpkins

city: HangZhou

first: Xiaolong

last: Lyu

address: No. 866, yuhangtang Road, Xihu Distric

institute: ZheJiang University

summary:
Purpose: The goals of this study are to compare The difference of RNA expression between Pumpkins seed coat and hulled-less Pumpkins seed coat.
Methods:Using Trizol kit, total RNA was extracted from seed coats of squash with and without shells under the conditions of 5 DAP, 10 DAP and 20 DAP. Then, 1 µ g RNA was extracted from each sample using the Illumina Hiseq 2000 platform for sequencing.

overall_design: Total RNA was extracted from seed coats of hulled and hull-less pumpkins at 5 DAP, 10 DAP, and 20 DAP using a Trizol kit (Invitrogen, USA). Then, 1 µg RNA from each sample was taken for sequencing using an Illumina HiSeq 2000 platform. Three biological replicates were performed for each stage. Transcriptome analysis was performed as described by Trapnell et al.


title: Targeted inducible delivery of immunoactivating cytokines reprograms glioblastoma microenvironment and inhibits growth in mouse models

first: Stefano


title: RNA-seq of  CD4 T cells from the lungs of M. tuberculosis infected WT and vhl fl/fl cd4 cre mice

city: Solna

first: Martin

last: Rottenberg

address: Solna vägen 9

country: Sweden

institute: Karolinska Institutet

summary:
Purpose: We compared the transcriptomes of mouse CD4 T cells  lacking the vhl gene ( vhlfl/fl cd4 cre= vhl cKO)  with WT controls from the lungs of mice 8 weeks after aerosol infection with Mycobacterium tuberculosis.
Results: Using an optimized data analysis workflow, between 40-55 million sequence reads per sample to the mouse genome (build mm10) and identified  14700  transcripts in the CD4 T cells  of WT and mutant mice after performing HISAT2 alignements to the mm10 reference.
Conclusion: The  transcriptome of WT anf vhl cKO was compared. Groups did cluster differentially with regards to their transcript abundance. The WT group has enriched DNA synthesis/ proliferation pathways whereas the Vhl cKO was enriched in hypoxia pathways. Transcripts assocaited with T cell differentiation were increased in WT group while T cell inhibitory molecules was elevated in the transcriptome of vhl cKO CD4 T cells.

overall_design: Biological Replicates: 5 WT and 6 vhl cKO CD4 T cells samples.

first: Ruining


title: RNA seq of vhlfl/fl cd4 cre, hif1afl/fl vhlfl/fl cd4 cre and WT CD4 T cells before and after anti-CD3/CD28 stimulation

summary:
Purpose: We compared the transcriptomes of murine CD4 T cells lacking either the vhl gene ( vhlfl/fl cd4 cre (vhl cKO) ) or both vhl and hif1a (hif1afl/fl vhlfl/fl cd4 cre (dcKO)) with WT controls before and 24 h after T cell receptor stimulation using anti-CD3/CD28.
Results: Using an optimized data analysis workflow, about 45-60 million sequence reads per sample to the mouse genome (build mm10) and identified  ca 12500 transcripts in the CD4 T cells  of WT and mutant mice after performing HISAT2 alignements to the mm10 reference.
Conclusion: the segregation of the transcriptome of unstimulated WT CD4 T cells as compared to the other groups. Within the TCR-stimulated groups the gene expression of vhl cKO CD4 T cells differed to that of WT and vhl hif1a dcKO CD4 T cells which showed in comparison important similarity between them

overall_design: Biological Replicates: 4 WT, 4 dcKO and 3 vhl cKO anti-CD3/CD28 stimulated  and 3 unstimulated WT CD4 T cells.


title: Hematopoietic Loss of Y Chromosome Leads to Cardiac Fibrosis and Dysfunction and is Associated with Death due to Heart Failure [bulkRNAseq_WholeBloodNeutrophils]

city: Nagoya

first: Hayato

last: Ogawa

state: Aichi

address: Tsurumai-cho 65

department: Department of Cardiology

institute: Nagoya University Graduate School of Medicine

summary: Hematopoietic mosaic loss of Y chromosome (mLOY) is associated with increased risk of mortality and a variety of age-related diseases in men, but causal and mechanistic relationships have yet to be established. Here it is shown that mice reconstituted with bone marrow cells lacking the Y chromosome display increased mortality and age-related profibrotic pathologies including a progressive decline in cardiac function. Accelerated cardiac dysfunction and fibrosis were also observed in younger mice subjected to a pressure-overload model of heart failure. Bone marrow-derived, cardiac macrophages lacking the Y chromosome exhibited polarization toward a more fibrotic and less inflammatory phenotype. Treatment with a TGFb1  neutralizing antibody led to greater amelioration of heart failure in mice reconstituted with mLOY compared to wild-type bone marrow. Consistent with these data, a prospective study in men revealed that mLOY in blood is associated with an increased risk for cardiovascular disease and heart failure-associated mortality. Together, these results indicate that hematopoietic mLOY contributes to heart failure in men.

overall_design: NOT PROVIDED; REQUESTED

first: Nicholas

last: Chavkin

first: Anupreet

last: Kour

first: Keita

last: Horitani

first: Soichi

last: Sano

first: Kenneth

last: Walsh


title: Expression data from corpora lutea from cows supplemented with different forms of selenium (Se)

city: Lexington

first: Phillip

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

summary: The goal of this study was to test the hypothesis that sodium selenite (ISe) vs. a 1:1 blend (MIX) of ISe and SEL-PLEX in a basal vitamin-mineral (VM) mix would differentially alter corpora lutea transcriptome profiles in non-lactating beef cows. Predominately-Angus cows were randomly selected from herds of fall-calving cows consuming VM mixes that contained 35 ppm Se as ISe and MIX forms. Cows were depleted of Se for 45 d followed by a 45 d repletion period with ISe to bring all cows to Se adequate status. Cows were then randomly assigned to treatment (ISe, n=5; or MIX, n=5) with treatments administered for at least 90 days using in-pasture Calan gates. Corpora lutea samples were then collected on Day 7 post-estrus and examined for changes in global expression patterns by microarray analysis.

overall_design: 10 total samples were analyzed (n=5 for both ISe and MIX)

first: Benjamin

middle: R

last: Crites

first: Sarah

middle: N

last: Carr

first: James

middle: C

last: Matthews


title: Change in gene expression of SLIT2 KO cells

city: Toronto

first: Fan

last: Xia

state: ON

address: 144 College Street, Room 970

country: Canada

institute: University of Toronto

summary: RNAseq was performed to compared gene expressions of non-targeted control and SLIT2 KO cells

overall_design: CRISPR technology was used to generate non-targeted control and SLIT2 KO cells before RNA extraction, cDNA library generation, and NGS.

first: Yuan

last: Ma


title: Targeted inducible delivery of immunoactivating cytokines reprograms glioblastoma microenvironment and inhibits growth in mouse models [scRNA-seq]

last: Beretta

overall_design: Single-cell RNA-seq of CD45+ tumor-infiltrating (glioblastoma) mice cells belonging to control and gene therapy treated (IFN-a and IFN-a-DHFR) groups.

first: Filippo

last: Birocchi

first: Melania

last: Cusimano

first: Federico

last: Rossari

first: Ivan

last: Merelli

first: Nadia

last: Coltella

first: Luigi

last: Naldini


title: MicroRNAs changed in response to HDGF treatment

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: We determined the RNAs which were suggested to commonly increase or decrease in HepG2 and SK-Hep1 cells in response to exogenously supplied hepatoma-derived growth factor (HDGF).

overall_design: Two hepatoma-dereived cell lines (HepG2 and SK-Hep1) were stimulated by exogenous administration of HDGF, and microRNAs whose expression altered in response to HDGF stimulation were determined.

first: Hirayuki

last: Enomoto


title: Transcriptome profiling of vascular fragments in mice intracerebroventricular (ICV) injected with platelet derived dermal growth factor CC (PDGF-CC)

first: Manuel

last: Zeitelhofer

address: Biomedicum

department: MBB

institute: Karolinska Institute

summary: We isolated vascular fragments, representing the BBB, from left brain hemisphere of PDGF-CC and PBS ICV injected mice

overall_design: We analysed the transcriptome of vascular fragments 4h post PDGF-CC-ICV (n=4) compared to 4h post PBS-ICV (n=3) in  12 weeks old female C57BL/6N mice.


title: Oncogenic ZMYND11-MBTD1 fusion protein anchors the NuA4/TIP60 histone acetyltransferase complex to the coding region of active genes

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

institute: CHU de Québec - Université Laval

summary: In this study, we characterize the fusion protein produced by the ZMYND11-MBTD1 translocation in acute myeloid leukemia. We express the fusion protein and necessary controls in K562 Cells. The fusion protein assembles ZMYND11 factor with the full acetyltransferase NuA4/TIP60 complex. The fusion protein leads to mislocalization NuA4/TIP60 complex in gene bodies, thereby increasing H4ac in specific gene targets. Finally, chromatin aberration is linked to aberrant gene expression and spliced isoforms.

overall_design: Flag-ChIP sequencing of MBTD1, full length ZMYND11, truncated ZMYND11 [aa1-409], and ZMYND11-MBTD1 fusion-3xFlag-2xstrep in K562 cells, and Oxford Nanopore Technologies long-read RNA sequencing of ZMYND11 KO K562 cells expressing either MBTD13xFlag-2xstrep, truncated ZMYND11 3xFlag-2xstrep or ZMYND11-MBTD1 fusion 3xFlag-2xstrep in K562 cells. K562 cells expressing endogenous ZMYND11 and MBTD1 3xFlag-2xstrep are used as control.

first: Maeva

last: Devoucoux

first: Gabriel

last: Khelifi

first: Jacques

last: Côté


title: Mechanisms regulating transitory suppressive activity of neutrophils in newborns

status: Public on May 31 2022

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Transitory appearance of immune suppressive polymorphonuclear neutrophils (PMN) defined as myeloid-derived suppressor cells (PMN-MDSC) in newborns is important for their protection from inflammation associated with newly established gut microbiota. Here, we report that inhibition of the type I interferon (IFN1) pathway played a major role in regulation of PMN-MDSC suppressive activity during first weeks of life. Expression of the IFN1 receptor IFNAR1 was markedly lower in PMN-MDSC. However, in newborn mice, down-regulation of IFNAR1 was not sufficient to render PMN immune suppressive. That also required the presence of a positive signal from lactoferrin via its receptor LRP2. The latter effect was mediated via NF-kB activation, which was tempered  by IFN1 in a manner that involved SOCS3. Thus, we discovered a mechanism of tight regulation of immune suppressive PMN-MDSC in newborns, which may be used in the development of therapies of neonatal pathologies

overall_design: RNA-seq of PMN-MDSCs during mice development

first: Dmitry

last: Gabrilovich

first: Michela

last: Perego


title: Integrative analysis of gene expression and DNA methylation reveals epigenetic regulation of tumor suppressor genes and oncogenes involved in uterine leiomyoma pathogenesis

city: Valencia

first: Hortensia

last: Ferrero

state: Valencia

address: Avenida Fernando Abril Martorell 106, Torre A

department: Reproductive Medicine

country: Spain

institute: Instituto de Investigación Sanitaria La Fe / Fundación IVI

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

overall_design: Refer to individual Series


title: Aspergillus fumigatus-induced transcriptional changes on murine eosinophils

city: Erlangen

first: David

last: Voehringer

address: Wasserturmstrasse 3-5

department: Department of Infection Biology

country: Germany

institute: University Clinic Erlangen

summary: Eosinophilia is associated with various persisting inflammatory diseases and often coincides with chronic fungal infections or fungal allergy as in case of allergic bronchopulmonary aspergillosis (ABPA). However, the interactions between eosinophils and fungal pathogen leading to release of inflammatory mediators from eosinophils are poorly understood. Therefore, we established a co-culture system of mouse bone marrow derived eosinophils (BMDE) with Aspergillus fumigatus (Af) that we used in part to analyse transcriptional regulation induced by Af.

overall_design: Transcriptional profile of mouse bone marrow derived eosinophils either cultured alone or co-cultured with Aspergillus fumigatus.

first: Sebastian

last: Schruefer

first: Axel

last: Dietschmann

first: Philipp

last: Kirchner

first: Arif

last: Ekici

first: Daniel

last: Radtke

first: Sven

last: Krappmann


title: Gene expression profile at single cell level of two TDT patients' PBMCs after gene editing treatment.

status: Public on May 29 2022

city: SHANGHAI

first: Jiaoyang

last: Liao

address: Dongchuan Rd. 500

institute: East China Normal University

summary: BCL11A encodes for a zinc-finger transcription factor that plays an important role in B-cell and pDC development. Although the +58 BCL11A enhancer we disrupted was reported as a erythroid specific enhancer, we needed to further evaluate the potential down regulation of BCL11A in other subpopulations of edited PBMCs. To study the transcriptional impact of BCL11A enhancer gene editing, we performed single-cell RNA sequencing (scRNA-seq) on PBMCs.

overall_design:
Using microfluidics-based single-cell RNA sequencing (scRNAseq), we obtained in total 6 peripheral blood single-cell transcriptomes from 2 heathy donors (10X indicated data downloaded from 10 Genomics shared dataset), 1 patient sample before treatment and 2 patient samples after treatment.

**RAW data not provided. Human data needs strict approval.**

first: Bin

last: Fu

first: Yuxuan

last: Wu

first: Shuanghong

last: Chen


title: Transcriptomics and functional analysis of copper stress response in the sulfate-reducing bacteria Desulfovibrio alaskensis G20

city: Rapid City

first: Rajesh

middle: Kumar

last: Sani

state: SD

address: 501 E St. JOSEPH STREET

department: Chemical and Biological Engineering

institute: South Dakota School of Mines and Technology

summary: Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes in bacteria. However, excess Cu is hazardous and can generate pleiotropic effects. Cu has been the metal of choice for piping used in household water distribution systems. Due to its leaching from pipelines, Cu is present at an elevated concentration in groundwater and in soil which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to remove toxic levels of Cu. However, reports on the toxicity of Cu towards SRB have primarily focused on the degree of toxicity and subsequent elimination. In this study, we show in detail the Cu(II) stress-related effects on a model sulfate reducing bacteria, Desulfovibrio alaskensis G20. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5µM and 15µM). In the pairwise comparison of control vs 5µM, 61.43% of genes were downregulated and 38.57% genes were upregulated. In 15µM vs control, 49.51% genes were downregulated, and 50.5% genes were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in important biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentration. In addition, metabolomics analysis indicated the effect of certain organic acids and amino acids in cellular metal buffering system and reducing oxidative damage to cells. These results will help us better understand the mechanism of Cu(II) stress response and provide avenues for future research.

overall_design: Comparative examination of mRNA expression profile in Desulfovibrio alaskensis G20 at grown at 5µM and 15µM Cu(II) ions. The sample with no Cu(II) ions (0µM) was used as control. All the samples were (0µM, 5µM, 15µM Cu(II)) used as biological triplicates.

first: Abhilash

middle: K

last: Tripathi

first: Priya

last: Saxena


title: Vitamin D treatment induces in vitro and ex vivo transcriptomic changes indicating anti-tumour effects

city: Edinburgh

first: Peter

last: Vaughan-Shaw

address: Crewe Road

department: IGMM

country: United Kingdom

institute: University of Edinburgh

summary:
AIM  Vitamin D deficiency is associated with risk of several common cancers, including colorectal cancer (CRC). We investigated the effects of vitamin D on in vitro and ex vivo epithelial cell gene expression and assessed dysregulation of pathways involved in anti-tumour effects.    METHODS  We performed in vitro and ex vivo intervention studies using established CRC cell lines and patient-derived epithelial organoids developed from normal human colonic (resectional colorectal surgery) and rectal mucosa (rectal biopsy). RNA and protein were harvested after 16-24 hours’ calcitriol treatment. Gene expression was assessed by qRT-PCR, microarray and RNA-sequencing, and protein expression by immunoblotting and mass-spectrometry. Gene Ontology enrichment analysis was performed using GOrilla and Gene Set Enrichment Analysis.     RESULTS  Calcitriol increased the expression of the tumour suppressor gene CDH1 in CRC cell lines (SW480; FC=3.60, 95%CI 2.17-5.03) and patient-derived epithelial cell organoids (n=6, FC=1.64, 95%CI 1.49-1.80), with associated in vitro E-cadherin protein induction. Significant differential expression of a further 6 common genes was observed on microarray analysis of in vitro and ex vivo experiments, including genes with established links to carcinogenesis GADD45, EFTUD1 and KIAA1199. Numerous ontologies relevant to carcinogenesis were enriched (e.g. ‘regulation of Wnt signaling pathway’, ‘regulation of cell death’), with common enriched processes across in vitro and ex vivo cultures including ‘negative regulation of cell proliferation’, ‘regulation of cell migration’ and ‘regulation of cell differentiation’.    CONCLUSIONS  We report for the first time, common genes and pathways modulated by calcitriol treatment in both in vitro and ex vivo models, with several differentially expressed genes strongly linked to CRC tumourigenesis. Enrichment of biological pathways after calcitriol treatment provides further evidence of anti-tumour effects. These findings support epidemiological data and provide strong rationale for well-designed trials of vitamin D supplementation as a novel CRC chemopreventive and chemotherapeutic agent.
see above

overall_design: qRTPCR of 10 colorectal cell lines assessing CDH1 induction with calcitriol treatment when compared to ethanol control. Microarray analysis of RNA from 3 treated/ untreated cell lines. Treatment conditions was with 50nM calcitriol for 16 hours.

first: P

first: J

middle: P

last: Blackmur


title: Interleukin-27 signaling serves as an immunological checkpoint for innate cytotoxic cells to promote hepatocellular carcinoma

status: Public on May 27 2022

first: Priyankara

last: Wickramasinghe

summary: While some of the inflammatory mechanisms driving hepatocellular carcinoma (HCC) had been proposed, the regulators of anti-cancer immunity in HCC remain poorly understood. We found that IL-27 receptor (IL-27R) signaling promotes HCC development in vivo. High IL-27EBI3 or IL-27RA expression correlated with poor prognosis for patients with HCC. Loss of IL-27R suppressed HCC in vivo in two different models of hepatocarcinogenesis. Mechanistically, IL-27R signaling within the tumor microenvironment restrains the cytotoxicity of innate cytotoxic lymphocytes. IL-27R ablation enhanced the accumulation and activation, while depletion or functional impairment of innate cytotoxic cells abrogated the effect of IL-27R disruption. Pharmacological neutralization of IL-27 signaling increased infiltration of innate cytotoxic lymphocytes with upregulated cytotoxic molecules and  reduced HCC development. Our data reveal an unexpected role of IL-27R signaling as an  immunological checkpoint regulating innate cytotoxic lymphocytes and promoting HCC of different etiologies, thus indicating a therapeutic potential for IL-27 pathway blockade in HCC

overall_design: Single cell RNA-seq of hepatocellular carcinoma and normal liver CD45+NK1.1- and CD45+NK1.1+ cells

first: Turan

last: Aghayev

first: Ekaterina

last: Koltsova


title: RASA2 checkpoint ablation in T cells boosts antigen sensitivity and long-term function

city: San Francisco

first: Eric

last: Shifrut

address: 513 Parnassus Ave, HSW 1033

institute: University of California, San Franscisco

summary: Adoptive T cell therapies have been transformative in the treatment of a subset of hematological malignancies. However, many patients either fail to respond or relapse, and these therapies still have had much more limited success in solid tumors. A critical challenge for increasing patient response rates and achieving durable efficacy of adoptive T cell therapies is overcoming suppressive signals from both extrinsic factors and intrinsic inhibitory checkpoints. Targeted gene editing has the potential to enhance T cell therapeutic function and improve clinical responses. Here we perform multiple genome-wide CRISPR knock-out screens under different immunosuppressive conditions to nominate genes that could be targeted to prevent T cell dysfunction. These CRISPR screens converged on RASA2 as a target to confer resistance to suppressive conditions found in tumor microenvironments. We identify RASA2 as a signaling checkpoint in human T cells that is downregulated upon acute TCR stimulation but increases gradually with chronic antigen exposure. Antigen titration showed that genetic ablation of RASA2 enhances mitogen activated protein kinase (MAPK) signaling and CAR-T cell cytolytic activity in response to low antigen levels. Repeated tumor antigen stimulation in vitro revealed that RASA2-deficient TCR-T and CAR-T cells have increased activation, cytokine production, and metabolic activity compared to control cells, and show a striking advantage in persistent cancer cell killing. RASA2 KO CAR-T cells showed a competitive fitness advantage over CAR-T control cells in the bone marrow of an in vivo leukemia model. Deletion of RASA2 in multiple preclinical models of TCR- and CAR-T cell therapies prolonged survival in animals xenografted with either liquid or solid tumors. Altogether, our findings from multiple genome-wide screens and preclinical studies highlight RASA2 as a promising new target to enhance both persistence and effector function in TCR-T and CAR-T cell therapies for cancer treatment.

overall_design: Gene expression analysis of primary human T cells in a repeated antigen stimulation assay, comparing RASA2 KO to control edited T cells

first: Julia

last: Carnevale

first: Alan

last: Ashworth

first: Alexander

last: Marson


title: Recapitulating early human development with 8C-like cells [ChIP-seq]

city: Guangzhou

first: Manqi

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

summary: In human embryos, major zygotic genome activation (ZGA) initiates at the eight-cell (8C) stage. Abnormal ZGA leads to developmental defects and even contributes to the failure of human blastocyst formation or implantation. However, little is known about the mechanisms regulating human ZGA, because of many challenges and constraints on research on human embryos. Here we report one type of rare 8C-like cells (8CLCs) that are discovered specifically from human preimplantation epiblast-like stem cells (prEpiSCs) and naïve embryonic stem cells. 8CLCs express a list of human ZGA genes and their transcriptome closely resemble that of the human 8C embryo. An 8C-specific reporter is further developed to isolate 8CLCs from prEpiSCs and optimize the chemical-based culture condition that increases and maintains the 8CLC population. Functionally, 8CLCs can spontaneously form blastocyst-like structures. The discovery and maintenance of 8CLCs provides an opportunity to model human ZGA and recapitulate early human development.

overall_design: We investigated H3K4me3 landscape on the genome of  prEpiSCs using ChIP-seq. ChIP-seq was performed in prEpiSCs with the indicated antibody and IgG as control.

first: Xiu

last: Yu

first: Shiqi

last: Liang

first: Jichang

last: Wang


title: RNA-seq of single myofibers isolated from skeletal muscle of young and old mice

status: Public on May 20 2022

city: Rochester

first: Xu

last: Zhang

state: MN

address: 200 First St SW

department: Physical Medicine and Rehabilitation

institute: Mayo Clinic

summary: We report RNA-seq of single myofibers with different p21 expression level isolated from EDL muscle of  young and old mice.

overall_design: We isolated single myofibers from EDL muscle of  young (6 months) and old (24 months) mice. These myofibers were seperated to three groups based on their p21 expression value (RT-PCR). Three or four myofibers from each group were used for RNA-seq (Young-p21-Low (n=3), Old-p21-Low (n=3), and Old-p21-High (n=4). )

first: Nathan

last: LeBrasseur


title: Recapitulating early human development with 8C-like cells [ATAC-seq]

last: Chen

overall_design: We investigated chromatin state on the genome of  prEpiSCs using ATAC-seq.


title: CD40 stimulation of chronic lymphocytic leukemia (CLL) cells

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC (AMC)

summary: In this experiment we in vitro activated CLL cells on a layer of fibroblasts expressing CD40L (3T40) or nothing (3T3) for 48 hours. After the 48 hours, cells were taken off the fibroblasts and sorted for viable CD19+ cells. Then we performed RNA sequencing.

overall_design: Comparison between 3T40 and 3T3 conditions

first: F

first: E

last: Eldering

first: Z


title: NADPH oxidase 5 has a crucial role in cellular motility of colon cancer cells

first: Satoshi

last: Kondo

summary: NADPH oxidases (NOXs) are a family of transmembrane proteins that generates reactive oxygen species. We previously reported that patients with colon cancer who had high NOX5 expression had poor prognosis. However, no studies have studied the cellular functions of NOX5 in colon cancer. This study aimed to clarify the relationship between NOX5 and cancer development using an in vitro model. Real-time quantitative PCR was performed to determine the NOX5 expressions levels of colon cancer cell lines. NOX5 knockdown experiments were conducted, and the impact on cell proliferation, migration, and invasion were analyzed. In addition, mRNA microarray was conducted to assess changes in gene profile. NOX5 mRNA expression was high in HCT116 cells and moderate in SW48 cells. NOX5 knockdown significantly inhibited cell migration and invasion in both HCT116 and SW48 cells; however, NOX5 knockdown reduced cell proliferation in only HCT116 cells. mRNA microarrays showed a strong relationship between NOX5 expression levels and integrin-linked kinase signaling pathways. The NOX5 expression in colon cancer cells affects cancer progression, especially cell motility. NOX5 may be a novel therapeutic target for the future development of treatments for colon cancer.

overall_design: For the purpose of examining changes in the gene expression profiles of NOX5 siRNA-transfected HCT116 cells and control siRNA-transfected HCT116 cells, HCT116 cells were transfected with control siRNA (n = 1) and NOX5 siRNA (n = 1).  Total RNA was extracted from the cells using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol at 48 h after transfection.

first: Hiroki

last: Shimizu

first: Naoki

last: Ashizawa


title: Recapitulating early human development with 8C-like cells


title: Integrative analysis of gene expression and DNA methylation reveals epigenetic regulation of tumor suppressor genes and oncogenes involved in uterine leiomyoma pathogenesis [RNA-seq]

first: Hortensia

last: Ferrero

summary: Uterine leiomyomas (UL) are the most common benign tumors in women of reproductive age. Despite the high prevalence, its pathology remains unclear, which hampers the development of safe and effective treatments. Several works have pointed the involvement of epigenetic mechanisms in UL development. Specifically, DNA methylation plays an important role in gene expression regulation. We aim to determine the relationship between DNA methylation and gene expression in UL compared to adjacent myometrium (MM) to describe molecular mechanisms involved in UL formation that are under epigenetic control. Our results showed a different DNA methylation profile between UL and MM, leading to hypermethylation of UL, as well as a different global transcriptome profile. Integration of DNA methylation and transcriptome data resulted in 93 genes regulated by methylation, 22 hypomethylated/upregulated and 71 hypermethylated/downregulated. Functional enrichment analysis showed dysregulated biological processes involved in metabolism and cell physiology, response to extracellular signals, invasion, and proliferation in UL. Cellular components as cell membranes, vesicles, extracellular matrix, and cell junctions were dysregulated in UL. In addition, we found hypomethylation/upregulation of oncogenes (PRL, ATP8B4, CEMIP, ZPMS2-AS1) and hypermethylation/downregulation of tumor suppressor genes (EFEMP1, FBLN2, ARHGAP10, HTATIP2) in UL, which were related to proliferation, invasion, altered metabolism, deposit of extracellular matrix and Wnt/β-catenin pathway dysregulation. This confirms that key processes of UL development are under DNA methylation control. Finally, 5-aza-CdR treatment increased expression of hypermethylated/downregulated genes in UL cells. In conclusion, DNA methylation gene regulation is implicated in UL pathogenesis, and its reversion could be a potential therapeutic option.

overall_design: Prospective study of DNA methylation by methyl-seq and gene expression by RNAseq of uterine leiomyoma (UL) versus adjacent myometrium (MM) tissue. Samples were collected from women aged 27-49 years (n=31). RNAseq and GW-DNAmet results were statistically analyzed (FDR < 0.05) and validated by quantitative real-time PCR and pyrosequencing, respectively.  Participants were recruited between September 2018–September 2020 at Hospital Universitario y Politécnico La Fe.

first: María

last: Carbajo-García

first: Ana

last: Corachán

first: Elena

last: Juárez-Barber

first: Javier

last: Monleón

first: Vicente

last: Payá

first: Alexandra

last: Trelis

first: Alicia

last: Quiñonero

first: Greta

last: Carmona-Antoñanzas

first: Antonio

last: Pellicer


title: Tunable three-dimensional engineered prostate cancer tissues for in vitro recapitulation of heterogeneous in vivo prostate tumor stiffness

status: Public on May 24 2022

city: Auburn University

first: Elizabeth

middle: A

last: Lipke

state: AL

address: 212 Ross Hall

institute: Auburn University

summary: In this study we report the establishment and characterization of a three-dimensional in vitro, coculture engineered prostate cancer tissue (EPCaT) disease model based upon and informed by our characterization of in vivo prostate cancer (PCa) xenograft tumor stiffness. In prostate cancer, tissue stiffness is known to impact changes in gene and protein expression, alter therapeutic response, and be positively correlated with an aggressive clinical presentation. To inform an appropriate stiffness range for our in vitro model, PC-3 prostate tumor xenografts were established. Tissue stiffness ranged from 95 to 6,750 Pa. Notably, xenograft cell seeding density significantly impacted tumor stiffness; a two-fold increase in the number of seeded cells not only widened the tissue stiffness range throughout the tumor, but also resulted in significant spatial heterogeneity. To fabricate our in vitro EPCaT model, PC-3 castration-resistant prostate cancer cells were co-encapsulated with BJ-5ta fibroblasts within a poly(ethylene glycol)-fibrinogen matrix augmented with excess poly(ethylene glycol)-diacrylate to modulate the matrix mechanical properties. Encapsulated cells temporally remodeled their in vitro microenvironment and enrichment of gene sets associated with tumorigenic progression was observed in response to increased matrix stiffness. Through variation of matrix composition and culture duration, EPCaTs were tuned to mimic the wide range of biomechanical cues provided to PCa cells in vivo; collectively, a range of 50 to 10,000 Pa was achievable. Markedly, this also encompasses published clinical PCa stiffness data. Overall, this study serves to introduce our bioinspired, tunable EPCaT model and provide the foundation for future PCa progression and drug development studies.

overall_design: Bulk RNAseq analysis of our PF, PF+2%PEGDA, and PF+3%PEGDA EPCaTs on Day 15 of in vitro coculture, as well as bulk RNAseq analysis of a 2D coculture of PC-3 and BJ-5ta cells (RNA isolated from n > 2 EPCaTs or 1 million 2D cells).

first: Nicole

last: Habbit

first: Yuan

last: Tian

first: Balabhaskar

last: Prabhakarpandian

first: Peter

last: Panizzi

first: Robert

last: Arnold


title: Transcriptomes of OSCC cells treated with CGRP under different culture conditions

status: Public on May 14 2022

city: Shanghai

first: Yu

last: Zhang

address: No.150  Rd. Fenglin

institute: Zhongshan Hospital, Fudan University

summary: We compared the transcriptomes of OSCC cells (Cal27 cell line) with or without treatment of  CGRP under different culture conditions.

overall_design: H represents normal high-glucose DMEM culture media;0 represents glucose-deprived culture media and 2-DG represents addition of 5 mM 2-DG in high-glucose DMEM culture media. TG represents addtion of 10 nM rhCGRP, and capTG  represents control media. Rep 1,2,3 represents biological independent repetitions.

first: Tong

last: Ji


title: METTL3 preferentially enhances non-m6A translation of epigenetic factors and promotes tumorigenesis (eCLIP-seq)

status: Public on May 16 2022

city: Beijing

first: Yue

last: Huo

state: Beijing

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

summary: Methyltransferase-like 3 (METTL3) is the predominant catalytic enzyme which forms a stable complex with METTL14 and WTAP to promote m6A methylation in the nucleus. Recently, accumulating evidence has shown that METTL3 can express in the cytoplasm but the function of cytoplasmic METTL3 is not fully understood. Here, we demonstrated that METTL3 inhibition significantly delayed tumorigenesis in gastric cancer both in and ex vivo. Surprisingly, our data revealed that METTL3 could not only facilitate cancer progression via mRNA m6A modification, but also bind to numerous non-m6A-modified mRNAs, suggesting an unexpected role of METTL3 that was independent of m6A modification. Mechanistically, cytoplasm-anchored METTL3 interacted with poly(A) binding protein cytoplasmic 1 (PABPC1) to stabilize its association with cap-binding complex eIF4F, which preferentially promoted the translation of epigenetic factors without m6A modification. Clinical investigation using both xenograft models and patient samples showed that cytoplasmic distributed METTL3 was highly correlated with gastric cancer progression, and this finding could be expanded in prostate cancer patients. We therefore propose that cytoplasmic METTL3 enhances the translation of both m6A and non-m6A-modified epigenetic mRNAs thus serves as an oncogenic driver in cancer progression, and METTL3 subcellular distribution can assist diagnose and predict prognosis for cancer patients.

overall_design: eCLIP sequencing of wild type and the cytoplasmic METTL3 in MGC-803 cell line

first: Xueju

last: Wei

first: Jingnan

last: Pi

first: Yufeng

last: Gao

first: Shuan

last: Rao

first: Fang

last: Wang

first: Jia

last: Yu


title: Single cell RNA-seq of skeletal muscle from young and old mice

first: Xu

summary: We report the scRNA-seq of mononuclear cells isolated from skeletal muscle of young and old mice.

overall_design: We isolated single cells from skeletal muscle of young (6 months, n=3) and old (24 months, n=3) mice and performed the scRNA-seq using 10X Genomics system.

first: Nathan

last: LeBrasseur


title: RNA-seq analysis of SIRT6 and STAT6 regulated genes in intestinal epithelial cells (IECs)

status: Public on May 15 2022

city: Minneapolis

first: Hai-Bin

last: Ruan

department: Integrative Biology and Physiology

institute: University of Minnesota

summary: To investigate the roles of SIRT6 and IL4/IL13-STAT6 pathway in intestinal epithelium homeostasis, we generated IEC-specifc Sirt6 knockout mice and transgenic mice with IEC-specific overexpression of constitutively activated STAT6 (STAT6vt). IECs from these mice were isolated and RNA were extracted and performed RNAseq analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for IECs from Sirt6 knockout/LoxP mice and IECs from STAT6vt transgenic/WT mice

first: Xiwen

last: Xiong


title: Integrative analysis of gene expression and DNA methylation reveals epigenetic regulation of tumor suppressor genes and oncogenes involved in uterine leiomyoma pathogenesis [Methyl-Seq]

first: Hortensia

last: Ferrero

first: María

last: Carbajo-García

first: Ana

last: Corachán

first: Elena

last: Juárez-Barber

first: Javier

last: Monleón

first: Vicente

last: Payá

first: Alexandra

last: Trelis

first: Alicia

last: Quiñonero

first: Greta

last: Carmona-Antoñanzas

first: Antonio

last: Pellicer


status: Public on May 05 2022

city: New York

first: Aram

last: Modrek

state: NY

address: 460 E 26th Street

department: Radiation Oncology

institute: New York University School of Medicine

summary: Expression data of Glioma Stem Cells sorted for CD133 and PDPN expression.

overall_design: Glioma Stem Cells were sorted for CD133 and PDPN status, and subject to microarray transcriptome expresssion analysis.

first: Erik

last: Sulman


title: Human monocyte-derived macrophage response to Aspergillus fumigatus

status: Public on May 08 2022

city: Bethesda

first: Adam

middle: Christian

last: Knapp

state: Maryland

address: 7005 Clarendon Rd Apt 2

institute: University of Florida

summary: To investigate the influence of Aspergillus fumigatus on iron regulation in macrophages, we obtained macrophages in culture from human derived monocytes and co-cultured the monocyte-derived macrophages with Aspergillus conidia at a 1:1 ratio. We collected samples at 0, 2, 4, 6 and 8 hours and extracted RNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of control macrophages and macrophage co-cultured with Aspergillus fumigatus at five time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control human monocyte-derived macrophage and  human monocyte-derived macrophage co-cultured with Aspergillus fumigatus.

first: Bandita

last: Adhikari

first: Yogesh

last: Scindia

first: Luis

last: Sordo Vieira

first: Henrique

last: de Assis Lopes Ribeiro

first: Joseph

last: Masison

first: Ning

last: Yang

last: Fonseca

first: Matthew

last: Wheeler

first: Yu

last: Mei

first: Brian

last: Helba

first: Carl

last: Atkinson

first: Will

last: Schroeder

first: Borna

last: Mehrad

first: Reinhard

last: Laubenbacher


title: In Vivo Genome-wide PGR Binding in Pregnant Human Myometrium Identifies Potential Regulators of Labor [ChIP-seq]

city: Chicago

first: Ariel

last: Dotts

state: IL

address: 303 E Superior Street

institute: Northwestern University

summary: The alterations in myometrial biology during labor are not well understood. The myometrium is the contractile portion of the uterus and contributes to labor, a process that may be regulated by the steroid hormone progesterone. Thus, human myometrial tissues from term pregnant in-active-labor (TIL) and term pregnant not-in-labor (TNIL) subjects were used for genome-wide analyses to elucidate potential future preventive or therapeutic targets involved in the regulation of labor. Using myometrial tissues directly subjected to RNA sequencing (RNA-seq), progesterone receptor (PGR) chromatin immunoprecipitation sequencing (ChIP-seq), and histone modification ChIP-seq, we profiled genome-wide changes associated with gene expression in myometrial smooth muscle tissue in vivo. In TIL myometrium, PGR occupied predominatly promoter regions including the classical progesterone response element, whereas it bound predominantly to intergenic regions in TNIL myometrial tissue. Differential binding analysis uncovered over 1700 differential PGR-bound sites between TIL and TNIL with 1361 sites gained and 428 lost in labor. Functional analysis identified multiple pathways involved in cAMP-mediated signaling enriched in labor. A three-way integration of the data for ChIP-seq, RNA-seq and active histone marks uncovered the following genes associated with PGR binding, transcriptional activation and altered mRNA levels: ATP11A, CBX7, and TNS1. In vitro studies showed that ATP11A, CBX7, and TNS1 are progesterone responsive. We speculate that these genes may contribute to the contractile phenotype of the myometrium during various stages of labor. In conclusion, we provide novel labor associated genome-wide events and PGR-target genes that can serve as targets for future mechanistic studies.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for progesterone receptor and histone modifications H3K4me3 and H3K27ac in myometrial tissue


title: Recapitulating early human development with 8C-like cells [RNA-seq]

first: Manqi

last: Chen

overall_design: RNA-seq was applied on prEpiSCs and ci8CLCs to profile their transcriptomes.

first: Xiu

last: Yu

first: Shiqi

last: Liang

first: Jichang

last: Wang


title: Space-time Mapping Identifies Concerted Multicellular Patterns and Gene Programs in Healing Wounds and their Conservation in Cancers.

status: Public on May 28 2022

city: Houston

first: Kenneth

last: Hu

state: Texas

address: 7455 Fannin Street

department: Immunology

institute: MD Anderson

summary: Tissue repair responses in metazoans are highly coordinated by different cell types over space and time. However, comprehensive single-cell based characterization covering this coordination is lacking. Here, we captured transcriptional states of single cells over space and time during skin wound closure, revealing choreographed gene expression profiles. We identified shared and prominent space-time patterns of cellular and gene expression enrichment: which we call multicellular ‘movements’ and which spanned multiple cell types.  We validated some of the discovered space-time movements using large volume imaging of cleared wounds and demonstrated the value of this analysis to predict gene products made by macrophages or fibroblasts, which activated gene programs in the opposite cell type. Finally, using two different tumor models, we tested the hypothesis that tumors are like ‘wounds that never heal’ finding conserved wound healing movements in the tumor space, wherein some movements were preferentially used in one tumor versus another.

overall_design: Single cell RNA-Seq data of sorted immune and non-immune cells from unwounded mouse skin, and wounds d1,3,7,14 post wounding from 4 pooled wounds. Samples multiplexed based on time and radial position in wound

last: Krummel

first: Nicholas

last: Kuhn


title: Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

status: Public on May 06 2022

city: La Jolla

first: Cameron

last: Lamoureux

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

summary: We generated four strains of Escherichia coli K12 MG1655 with distinct proton motive force generation potential and performed the adaptive laboratory evolution of these strains to study how the system adapts to the loss of alternate electron transfer pathways of the Electron Transport System. RNA-Seq was performed to examine the underlying transcriptional rewiring.

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

overall_design: Growth of E. coli was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation.

first: Amitesh

last: Anand


title: Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (Spatial RNA-Seq)

status: Public on May 04 2022

city: Pittsburgh

first: Chandan

last: Sen

state: Pennsylvania

address: 450 Technology Drive

department: Surgery

institute: University of Pittsburgh

summary: Unbiased whole-genome methylome was studied in the wound-edge (WE) tissue of chronic wound patients. Methylation status of proximal promoter (1Kb) was calculated using MethylCap-Seq and PrEMeR-CG data analyses. A total of 4689 differentially methylated regions (DMRs) were identified in chronic WE compared to unwounded (UW) human skin. Hypermethylation was more frequently observed (3661 DMRs) in the chronic WE compared to hypomethylation (1028 DMRs). Twenty-six hypermethylated DMRs were involved in epithelial to mesenchymal transition (EMT). Bisulfite sequencing validated hypermethylation of a predicted specific upstream regulator TP53. Whole genome RNA sequencing analysis was performed to qualify findings from methylome analysis. Hierarchical clustering analyses identified a large set of genes, the expression of which were significantly downregulated in chronic WE compared to UW skin. Analysis of the downregulated genes identified the TP53 signaling pathway, including P63, P73, FOXO3, SIRT1 and HDAC1, as being significantly silenced. Direct comparison of hypermethylation and downregulated gene expression identified four genes, ADAM17, NOTCH, TWIST1 and SMURF1, that were common to both data sets and functionally represented the EMT pathway. Single cell RNA sequencing studies identified that these effects on gene expression were limited to the keratinocyte cell compartment.

overall_design: spatial transcriptomics analysis of human unwounded skin.

first: Kanhaiya

last: Singh

first: Yashika

last: Rustagi

first: Rajneesh

last: Srivastava


title: RNA-seq of skeletal muscle of young, old, and senolytics treated mice

first: Xu

last: Zhang

summary: We report RNA-seq of skeletal muscle (quadriceps) of young (6-month), old (24-month), and senolytic (Dasatinib + quercetin) treated mice

overall_design: C57BL/6 mice were separated into three groups: Young (6 months), Old-Vehicle (24 months, treated with vehicle), and Old-DQ (24 months, treated with senolytic). For senolytic treatment, mice were gavage with vehicle (10% ethanol, 30% polyethylene glycol, and 60% Phosal 50) or dasatinib (5 mg/kg) plus quercetin (50 mg/kg) for 3 continuous day treatment per 2 weeks for from 20-month to 24-month. After treatment, mice were euthanized and quadriceps muscle was collected for RNAseq.

first: Nathan

last: LeBrasseur


title: Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (RNA-Seq)

overall_design: Total RNAseq was performed from the RNA isolated from human chronic wound-edge and unwounded skin

first: Sashwati

last: Roy

first: Pearlly

last: Yan


title: Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (single cell RNA-Seq)

overall_design: In this work, scRNA-seq analyses of human chronic WE characterized its heterogenous cellular composition as compared to unwounded skin.

first: Ahmed

last: Abouhashem


title: Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition (MethylCap-seq)

type: Methylation profiling by high throughput sequencing

overall_design: MethylCap-seq was performed from the DNA isolated from human chronic wound-edge and unwounded skin


title: Effect of depletion of KMT2C on gene expression in psoriasiform keratinocytes

status: Public on Apr 30 2022

city: Jinan

first: Shan

last: Huang

address: 107 Wenhuaxi Road, Jinan, Shandong, China

institute: Shandong University Qilu Hospital

summary:
To investigate the function KMT2C in the psoriasis, we established M5(IL-17A, IL-22, oncostatin M, IL-1α, and TNF-α)-induced Ker-CT cell line in which has been knocked down by siKMT2C or contol.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ker-CT cells treated with siNC or siKMT2C.


title: Molecular Characteristics and Biological Functions of Hypoxic Microenvironment in Hepatocellular Carcinoma

status: Public on May 02 2022

city: Wuhan

first: Kuang-Chen

last: Tsai

state: State...

address: No.1095 Jie Fang Avenue, Hankou, Wuhan 430030, P.R. China.

institute: Huazhong university of science and technology

summary: Hypoxia is an important feature of the tumor microenvironment (TME) and is closely associated with cancer metastasis, immune evasion, and drug resistance. However, the precise role of hypoxia in hepatocellular carcinoma (HCC), as well as its influence on the TME, and drug sensitivity remains unclear. In this study, we first utilized unsupervised clustering to distinguish different hypoxic phenotypes in HCC, and signature genes were identified and used to construct a hypoxia-related prognostic score model, Hypoxia_DEGs_Score. We then found the excellent survival prediction value of this prognostic model. In hypoxic HCC, somatic mutation, copy number variation (CNV), and DNA methylation were closely related to hypoxic changes and affected tumorigenesis, progression, metastasis, and drug resistance. In HCC, aggravated hypoxic stress was found to be accompanied by an immune exclusion phenotype and increased infiltration of immunosuppressive cells. In the validation cohort, patients with high Hypoxia_DEGs_Score were found to have worse immunotherapeutic outcomes and prognoses, and may benefit from drugs against cell cycle signaling pathways rather than those inhibiting the PI3K/mTOR pathway. Hypoxia_DEGs_Score can predict the prognosis of HCC patients and has an excellent predictive capability of changes in the TME, the efficacy of immunotherapy, and the response of drugs. Therefore, Hypoxia_DEGs_Score can help develop personalized immunotherapy regimens and improve the prognosis of HCC patients.

overall_design: Tumor samples were obtained from 30 HCC patients. All patients underwent one-stage radical resection in Tongji Hospital from May 2015 to November 2015, without prior anticancer treatment.

first: Zeyang

last: Ding

first: Guangzhen

last: Cai

first: Ganxun

last: Li

first: Xiaoping

last: Chen


title: RNA-seq analysis regarding antiandrogen (enzalutamide) effect on gene expression in castration-resistant prostate cancer (CRPC) xenograft model

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: VCaP prostate cancer xenografts grown in castrated mice were treated with antiandrogen (enzalutamide), and samples were obtained during treatment response (Enza I: 5 days after initiation of the treatment) and after the treatment resistance had occurred (Enza II: 47 days after initiation of the treatment).

overall_design: Rna-seq analysis of Enza I (n = 10) and Enza II (n=10) tumor samples

first: Riikka

last: Huhtaniemi


title: Tumor-Induced Erythroid Precursor-Differentiated Myeloid Cells Mediate Immunosuppression and Curtail Anti-PD-1/PD-L1 Treatment Efficacy

city: Chongqing

first: Qingzhu

last: Jia

address: Xinqiao

department: Department of Onoclogy

institute: XinQiao Hospital

summary: Despite the unprecedented success of immune checkpoint inhibitors (ICIs) as anti-cancer therapy, it remains a prevailing clinical need to identify additional mechanisms underlying ICI therapeutic efficacy and potential drug resistance. Here, using lineage tracking in cancer patients and tumor-bearing mice, we demonstrate that erythroid progenitor cells lose their developmental potential and switch to the myeloid lineage. Single-cell transcriptome analyses reveal that, notwithstanding quantitative differences in erythroid gene expression, erythroid differentiated myeloid cells (EDMCs) are transcriptionally indistinguishable from their myeloid-originated counterparts. EDMCs possess multifaceted machinery to curtail T cell-mediated anti-tumor responses. Consequently, EDMC content within tumor tissues is negatively associated with T cell inflammation for the majority of solid cancers; moreover, EDMC enrichment, in accordance with anemia manifestation, is predictive of poor prognosis in various cohorts of patients undergoing ICI therapy. Together, our findings reveal a feed-forward mechanism by which tumors exploit anemia-triggered erythropoiesis for myeloid transdifferentiation and immunosuppression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To explore the differentiation of erythro-lineage cells, splenic CD11b-C-kit-CD45+Ter119+CD71+ cells (T-EPCs), and intratumoral CD45+Ter119+CD71+CD11b+Gr1+ (EDMCs) were isolated from LLC-bearing mice (day 21) and were subjected to scRNA-seq analysis. As references, splenic Ter119+CD71+ cells from acutely anemic mice (without specifying CD45 expression, A-EPCs), and overall intratumoral CD45+CD11b+Gr-1+ MDSCs (without specifying Ter119 or CD71 expression) were included in the analyses. For patient samples, CD235a+ bone marrow cells from bone-metastasis-free patients with advanced tumors, or CD45+CD235a+CD71+ cells from MPE were sorted, as indicated.
***Please note that raw data are not provided for the human samples*****

first: Haixia

last: Long

first: Liuyang

last: Wang

first: Zheng

last: Jin

first: Qi-Jing

first: Bo

last: Zhu


title: miRNA expression induced by Sorafenib in HepG2 cells and primary human hepatocytes

status: Public on Apr 28 2022

city: Sevilla

first: Patricia

last: de la Cruz-Ojeda

address: Avda. Manuel Siurot s/n

institute: Institute of Biomedicine of Seville

summary: miRNAs were profiled by qRT-PCR using the TaqMan® OpenArray® Human miRNA Panel (Ref. 4470187, Life Technologies, Carlsbad, USA)

overall_design: miRNA expression was assessed in HepG2 cells treated with Sorafenib at 6 and 24 hours, and in primary human hepatocytes at 24 hours. Three biological replicates are provided for Sorafenib and control treated cells.

first: Jordi

last: Muntané


title: Genome-Wide DNA Hypermethylation in the Wound-Edge of Chronic Wound Patients Opposes Closure by Impairing Epithelial to Mesenchymal Transition

first: Chandan

last: Sen

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

overall_design: Refer to individual Series


title: Role of maternal Wnt11b in cortical rotation and axis formation

city: Iowa City

first: Douglas

middle: William

last: Houston

state: IA

department: Dept. of Biology

institute: The University of Iowa

summary: Asymmetric signalling centres in the early embryo are essential for axis formation in vertebrates. These regions, namely the dorsal morula, yolk syncytial layer, and distal hypoblast/anterior visceral endoderm (in amphibians, teleosts and mammals, respectively), require the localised stabilisation of nuclear Beta-catenin (Ctnnb1), implying that localised Wnt/Beta-catenin signalling activity is critical in their establishment. However, it is becoming increasingly apparent that the stabilisation of Beta-catenin in this context may be initiated independently of secreted Wnt growth factor activity. In Xenopus, dorsal Beta-catenin stabilisation is initiated by a requisite microtubule-mediated symmetry-breaking event in the fertilised egg: “cortical rotation”. Vegetally-localised wnt11b mRNA has been implicated upstream of Beta-catenin in this context, as has the dorsal enrichment of Wnt ligand-independent activators of Beta-catenin, but the extent that each of these processes contribute to axis formation in this paradigm remains unclear. Here we describe a maternal effect mutation in Xenopus laevis wnt11b.L, generated by CRISPR mutagenesis. We demonstrate a maternal requirement for timely and complete gastrulation morphogenesis and a zygotic requirement for proper left-right asymmetry. We also show that a subset of maternal wnt11b mutants have axis and dorsal gene expression defects, and we find that microtubule assembly and cortical rotation are reduced in wnt11b mutant eggs, leading to less organised and directed vegetal microtubule arrays. mRNA sequencing was used to determine the extent of dorsal and other gene dysregulation during gastrulation.

overall_design: Bulk mRNA sequencing of gastrula gene expression in maternal-zygotic wnt11b mutants.

middle: W

first: Karen

last: Elliott

first: Kelsey

last: Coppenrath

first: Marcin

last: Wliza

first: Marko

middle: E

last: Horb


title: Impaired efferocytosis enables apoptotic osteoblasts to escape osteoimmune surveillance during aging

city: Nanjing

first: Rongyao

last: Xu

address: 140 Hanzhong Road, Nanjing, Jiangsu Province 210029, China.

institute: Nanjing medical university

type: Non-coding RNA profiling by high throughput sequencing


title: Combining Stem Cell Rejuvenation and Senescence Targeting to Synergistically Extend Lifespan

status: Public on Apr 24 2022

city: Singapore

first: Nicholas

last: Tolwinski

address: 16 #01-220, College Ave West

country: Singapore

institute: Yale-NUS College

summary: We combine transient stem cell rejuvenation with targeted removal of senescent cells to test the hypothesis that simultaneously targeting both cell-fate based aging mechanisms will maximize life and health span benefits.

overall_design:
Drosophila midgut RNA profiles of tubGal80ts > UAS-TdTomato (WT), armGal4; tubGal80ts > UAS-OKSM (OKSM), armGal4; tubGal80ts > UAS-Sen (Sen) and armGal4; tubGal80ts > UAS-Sen; UAS-OKSM (Sen_OKSM); tubGal80ts > UAS-TdTomato (WT), esgGal4; tubGal80ts > UAS-OKSM (OKSM), esgGal4; tubGal80ts > UAS-Sen (Sen) and esgGal4; tubGal80ts > UAS-Sen; UAS-OKSM (Sen_OKSM)

Updates: [Sept. 20, 2022] The GSM6058923 and GSM6058926 metadata were swapped in accordance with the sample identities. The associated data files did not change but were renamed accordingly.

first: Prameet

last: Kaur

first: Agimaa

last: Otgonbaatar

first: Anupriya

last: Ramamoorthy

first: Ellora

last: Chua

first: Nathan

last: Harmston

first: Jan

last: Gruber


summary: Hepatocellular carcinoma (HCC) is one of the most common causes of death worldwide and the fourth most prevalent type of cancer. Whereas curative treatments such as liver transplantation, ablation or surgery are optimal for early stages, only paliative treatments are given to intermediate and advanced stages of the disease. Despite the introduction of immune regulators as first-line treatments for advanced stages, Sorafenib is still the standard of care in the clinical practice. In cell lysates, anti-tumoral properties of Sorafenib were related to upregulation of miR-200c-3p (anti-tumoral miRNA) at 6 hours of treatment and downregulation of miR-222-5p and miR-512-3p (pro-tumoral miRNAs) at 24 hours. We have identified these miRNA biomarkers of Sorafenib treatment response in plasma of patients with advanced HCC treated with Sorafenib. In particular, miR-200c-3p has been related to increased survival benefit whereas miR-222-5p and miR-512-3p have been related to worse prognosis. Our study has sequenced HepG2 cells treated with Sorafenib and miR-200c-3p inhibitor, and transfected with miR-222-5p and miR-512-3p mimics to unravel the molecular pathways governing Sorafenib response

overall_design: Transcriptomic analysis of  hepatocellular carcinoma cell lines HepG2 treated with Sorafenib and transfected with miR-200c-3p inhibitor, and miR-222-5p and miR-512-3p mimics. Three biological replicates are provided for miRNA and control transfected cells, as well as Sorafenib and control treated cells.

first: Tobias

last: Schmid

first: Bernhard

last: Brüne


title: Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears [miRNA-seq]

status: Public on Apr 21 2022

city: Harbin

first: He

last: Shengyuan

state: Heilongjiang

address: Baojian Road 157

institute: Harbin Medical University

summary: The purpose of this study is to identify dysregulated ncRNAs and understand how they influence  Rotator cuff tears (RCT). We performed RNA sequencing and miRNA sequencing on 5 pairs of torn supraspinatus muscles and matched unharmed subscapularis muscles to identify RNAs dysregulated in RCT patients. Based on the results of differential expression analysis and miRNA targeting information, we constructed lncRNA/circRNA-associated dysregulated ceRNA networks in RCT. We found the largest module in the ceRNA network and identified several important ncRNAs in this module, which may have critical roles in RCT.

overall_design:
5 female patients with unilateral shoulder pain were enrolled in this study. The torn supraspinatus and intact subscapularis were confirmed by irrigation and debridement in intraarticular and subacromial space, then a small piece of muscle belly from each muscle was carefully collected by a grasper. After that, the supraspinatus tear was repaired using suture anchors. A total of 10 samples from 5 patients were stored in liquid nitrogen for further analysis.
***Raw data not available due to patient privacy concerns***

first: Yichong

last: Zhang

first: Jianhai

last: Chen

first: Shengyuan

last: He

first: Yun

last: Xiao

first: Aiyu

last: Liu

first: Dianying

first: Xia

last: Li


title: Binaprofen induced zebrafish liver injury by mitochondria pathway

status: Public on Apr 02 2022

city: hangzhou

first: zhaolun

last: wang

address: cangqian street

institute: inheregene

summary: The aim was to study the mechanism of liver injury of Binaprofen at genetic level

overall_design: zebrafish were treated with Binaprofen, serum biomarkers detection, MDA and GSH content detection , liver cell pathological morphous, DAPI analysis, electron microscopic detection, microarray analysis, quantitatite realtime PCR were done in 12h-48h to analyze the liver injury mechanism of Binaprofen.

first: QiuPing

last: Guo

first: Qingchun

last: Ni


title: miR-200c-3p, miR-222-5p and miR-512-3p are outcome circulating biomarkers in patients with hepatocarcinoma under Sorafenib treatment

first: Patricia

last: de la Cruz-Ojeda


title: RNA-sequencing of Group 1, Group 2 and Group 3 ILCs used for Hi-C

status: Public on Apr 01 2022

city: Philadelphia

first: John James

last: Tello-Cajiao

address: Curie Blvd 421

department: Genetics

institute: university of Pennsylvanya

summary:
We performed a multi-omic analysis of each group of ILCs to decipher ILC ontogenesis
Gene expression of ILCs was assessed by performing RNA-sequencing on splenic NK cells, ex vivo expended ILC2s and MNK3 cell line

overall_design: RNA-profiling of Group 1, Group 2 and Group 3 ILCs

first: Michaël

middle: F

last: Michieletto

first: John

first: Walter

last: Mowel

first: Aditi

last: Chandra

first: Sora

last: Yoon

first: Leonel

last: Joannas

first: Megan

middle: L

last: Clark

first: Monica

middle: T

last: Jimenez

first: Jasmine

last: Wright

first: Patrick

last: Lundgren

first: Adam

last: Williams

first: Christoph

last: Thaiss

first: Golnaz

last: Vahedi

first: Jorge

last: Henao-Mejia


title: Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears

first: He

last: Shengyuan


title: multi-omic analysis


title: Bone Marrow - scRNA-sequencing

summary: The goal of this experiment was to address when during development, deletion of the locus control region 1 (LCR1), impact the development of ILC2 in the bone marrow.

overall_design: In order to determine consequences of LCR1 deletion on ILC2 development, 8-12 weeks old WT and LCR1-/- C57BL/6J mice were sacrified and BM cells were extracted by crushing bones. Following BM cell extraction, ACK lysis for performed to remove red blood cell. Cells were filtered through a 70uM   strainer and sequentially with viability dye and flow cytometry antibodies (in FACS buffer). Cells were then filtered again and sorted using a FACS ARIA II (BD). Viable, CD45+, Lineage-, CD127+ cells were sorted with a purity >90% then prepared for 10X Genomics scRNAsequencing experiment. scRNAseq experiment was performed following manufacturer's recommendations.

middle: M


title: ATAC-sequencing MNK3 sample in parallel of HiC and RNA-seq

summary:
We performed a multi-omic analysis of each group of ILCs to decipher ILC ontogenesis
Chromatin accessibility of the ILC3-like cell line was assessed by ATAC-Seq

overall_design: ATAC-Seq profiling of the ILC3-like MNK3 cell line

middle: J


title: Pigment epithelium–derived factor promotes peritoneal dissemination of ovarian cancer through induction of immunosuppressive macrophages

status: Public on Apr 25 2022

city: Toyoake

first: Eiji

last: Sugihara

state: Aichi

address: 1-98, Dengakugakubo, Kutsukake-cho,

institute: Fujita Health University

summary: Peritoneal dissemination of ovarian cancer (OC) correlates with poor prognosis, but the mechanisms underlying the escape of OC cells from the intraperitoneal immune system have remained unknown. We here identify pigment epithelium–derived factor (PEDF) as a regulator of OC cell dissemination, which functions through induction of CD206+ IL-10–producing macrophages. High PEDF gene expression was associated with poor prognosis in OC patients. Concentrations of PEDF in ascites and serum were significantly higher in OC patients than those with more benign tumors and correlated with early recurrence of OC patients, suggesting that PEDF might serve as a prognostic biomarker. Bromodomain and extraterminal (BET) inhibitors were found to reduce PEDF expression and limit both OC cell survival and CD206+ macrophage induction in the peritoneal cavity. Our results thus implicate PEDF as a driver of OC dissemination and identify a BET protein–PEDF–IL-10 axis as a promising therapeutic target for OC.

overall_design: To characterize the mechanisms by which OC cells disseminate into the peritoneal cavity, we established a new cell line through in vivo selection of ID8 mouse OC cells that express GFP (ID8G cells). 3 to 4 months after i.p. injection of ID8G cells, GFP-positive cells were isolated from omental tumors by the cell sorter and were termed GO cells. GO cells  were subsequently recycled with i.p. injection. GFP-positive cells isolated from the resulting omental tumors were designated GO2 cells. To identify the genes involved in peritoneal dissemination of ovarian cancer,we compared global gene expression profiles in ID8G and GO2 cells using Agilent mouse genome microarray.

first: Sayaka

last: Ueno

first: Tamotsu

last: Sudo

first: Hideyuki

last: Saya


title: Dapl1 is a critical regulator of CD8 T cell function and exhaustion in cancer immunity

status: Public on Apr 13 2022

city: Houstion

first: Xiaofei

last: Zhou

institute: UT MD Anderson Cancer Center

summary: We report the application of 10x Genomics single-cell sequencing technology for high-throughput profiling of gene regulation difference between wildtype and Dapl1 deficient T cell in tumor microenvironments (TILs). Unsupervised clustering identified 6 clusters of CD8 TILs. We find that Dapl1 was predominantly expressed in a TCF1hi CD8 T cell cluster. The Dapl1 deficiency results in expansion of an effector memory-like CD8 TIL subpopulation and concomitant reduction in a subpopulation of exhausted CD8 TILs highlighting a role for Dapl1 in regulating the intratumoral dynamics of CD8 T cells.

overall_design: Examine the different gene expression profile between wildtype and Dapl1 deficient T cells in tumor microenvironments.

first: Lele

last: Zhu

first: Shao

last: Sun


title: Zona pellucida removal affects pre- and post-implantation development and gene expression in mouse embryos

status: Public on Mar 31 2022

city: Sapporo

first: FAN

last: WEIHONG

state: Hokkaido

address: Kita 8, Nishi 5, Kita-ku

department: Graduate School of Agriculture

institute: Hokkaido University

summary: The zona pellucida plays a crucial role in the process of fertilization to early embryonic development, including cellular arrangement and communication between blastomeres. However, little is known regarding the role of the zona pellucida in pre- and post-implantation embryonic development associated with gene expression. We investigated the effects of the zona pellucida on the development and gene expression of pre- and post-implantation embryos. After the zona pellucida was removed at the 2-cell stage, compaction occurred earlier. In addition, the expression of differentiation-related genes in the inner cell mass (ICM) (Oct4, Sox21) and trophectoderm (TE) (Cdx2, Eomes, and Tfap2c) was significantly altered in both zona free (ZF) morula and blastocyst compared to zona intact embryos. After embryo transfer, the implantation rate and number of live fetuses were lower in ZF embryos than in control embryos, whereas the fetal weight at birth was not different. However, placental weight was significantly increased in ZF embryos. RNA-seq analysis of the placenta showed that a total of 473 differentially expressed genes that significantly influenced the biological process. The present study suggests that zona pellucida removal at the 2-cell stage not only disturbs the expression pattern of ICM/TE-related genes, but affects the post-implantation development of mouse embryos. Overall, this study provides a deeper insight into the role of the zona pellucida during early mouse embryonic development and the viability of post-implantation development. It also provides a valuable basis for future research related to the production of ZF embryos in mammals and the developmental properties of blastomeres.

overall_design: ICR female mice at 8 weeks of age were used for IVF, after 2-cell stage for the zona removal and cultured until blastocyst. Zona intact (ZI) embryos and zona free (ZF) embryos were cultured in the cWOW system until blastocyst for gene expression examination and immunostaining, then E3.5 early blastocysts were performed the embryo transfer (ET), after ET, the E17.5 placenta of ZI and ZF groups were obtained for RNA seq.

first: Weihong

last: Fan

first: Tengda

last: Huang

first: Tian

last: Wu

first: Hanako

last: Bai

first: Manabu

last: Kawahara

first: Masashi

last: Takahashi


title: Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears [mRNA-lncRNA/circRNA]

first: Yichong

last: Zhang

first: Jianhai

last: Chen

first: Shengyuan

last: He

first: Yun

last: Xiao

first: Aiyu

last: Liu

first: Dianying

first: Xia

last: Li


title: 3D-Atlas of Group 1, Group 2 and Group 3 ILCs

first: John James

last: Tello-Cajiao

summary:
We performed a multi-omic analysis of each group of ILCs to decipher ILC ontogenesis
We performed Hi-C on representative cell of Group 1, Group 2 and Group 3 ILCs

overall_design: Hi-C profiling of NK, ILC2 and ILC3-like MNK3

first: Michaël

last: Michieletto

first: John

first: Walter

last: Mowel

first: Aditi

last: Chandra

first: Sora

last: Yoon

first: Leonel

last: Joannas

first: Megan

last: Clark

first: Monica

last: Jimenez

first: Jasmine

last: Wright

first: Patrick

last: Lundgren

first: Adam

last: Williams

first: Christoph

last: Thaiss

first: Golnaz

last: Vahedi

first: Jorge

last: Henao-Mejia


title: Visium spatial gene expression analysis for human ureters

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Tissue engineering offers a promising treatment strategy for ureteral strictures. Successful ureter engineering is necessitated by detailed understanding of the tissue architecture, cellular heterogeneity, and signaling pathways underlying regeneration. We define and spatially map cell populations within the human ureter by using a combinatorial approach: single-cell RNA sequencing, 10X Visium spatial transciptomics, and immunofluorescence. The stromal and urothelial cell populations are analyzed in detail, and we infer potential cell-cell communication networks underpinning the bi-directional crosstalk between these compartments. Specifically, we analyze and experimentally validate the importance of Sonic Hedgehog (SHH) signaling pathway in adult stem cell maintenance. The SHH-expressing basal cells support organoid generation in vitro, and accurately predict the differentiation trajectory of basal stem cells, to terminally differentiated umbrella cells, in vivo. Our results highlight essential processes involved in adult ureter tissue homeostasis, and provide a toolkit for guiding ureter tissue engineering.

overall_design: Two normal human ureters each were subjected to spatial transcriptomics using 10X Genomics Spatial Gene Expression. Data was processed using Spaceranger 1.3.0 and anayzed using Seurat v4.0.4 to better understand the architecture and cellular heterogeneity of the ureter. These samples have matching single cell RNAseq data, which were used to enhance and validate the Spatial Gene Expression data.

first: Byron

last: Lee

first: Matthew

last: Bradley

first: Pierre-Emmanuel

last: Desprez


title: Genome-Scale CRISPR Knockout Screening Identifies BACH1 as a Key Regulator of Aflatoxin B1-Induced Oxidative Damage

status: Public on Mar 25 2022

first: Shengsong

last: Xie

state: Hubei

address: 1st Shizishan Street, Hongshan

institute: Huazhong Agricultural University

summary: Overall data for CRISPR screening + RNA-Seq

overall_design: CRISPR screening + RNA-Seq


title: Transcriptome analysis and weighted gene co-expression network reveal candidate genes and pathways responses to lactate dehydrogenase inhibition (oxamate) in hyperglycemic human renal proximal epithelial tubular cells

city: Kongens Lyngby

first: Xiao

last: Wang

address: Bagsværdvej 103, ST

country: Denmark

institute: Konge Larsen Aps

summary: Diabetic kidney disease (DKD) is the leading cause of both chronic kidney disease (CKD) and end-stage renal disease (ESRD). In this study, we performed transcriptome gene expression profiling of kidney tissues in human renal proximal epithelial tubular cell line (HK-2) treated with high D-glucose (HG) for 7 days before the addition of 40 mM oxamate for a further 24 hours in the presence of HG. Afterwards, we analyzed the differentially expressed (DE) genes and investigated gene relationships based on weighted gene co-expression network analysis (WGCNA). Accordingly, enrichment analyses of GO terms and KEGG pathways showed that several pathways (e.g., lysosome (hsa04142) and p53 signaling pathway (hsa04115)) may be involved in a response of HK-2 cells to oxamate. Moreover, via WGCNA, we identified two modules: both the turquoise and blue modules were enriched in pathways associated with lysosome. However, the P53 signaling pathway was only found using all 3,884 DE genes. Furthermore, the key hub genes IGFBP3 interacted with 6 up-regulated and 12 down-regulated DE genes in the network that were enriched in the P53 signaling pathway. This is the first study reporting co-expression patterns of a gene network after lactate dehydrogenase inhibition in HK-2 cells. Our results may contribute to our understanding of the underlying molecular mechanism of in vitro reprogramming under hyperglycemic stress that orchestrates the survival and functions of HK-2 cells.

overall_design: Six replicates of HK-2 cells were firstly exposed to HG treatments for seven days, then three replicates of them were exposed 40 mM oxamate (case group), while the other three replicates were still under the same HG condition but 40 mM oxamate expose (control group). Unfortunately, one replicate of case group failed in RNA sample preparation, so five replicates of cells were finally chosen for RNA sequencing in this study.

first: Zhimin

first: Dan

last: Hao

first: Dong

last: Fang

first: Jiating

last: Yu

first: Guijun

last: Qin


title: Genome-Scale CRISPR Knockout Screening Identifies BACH1 as a Key Regulator of Aflatoxin B1-Induced Oxidative Damage [RNA-seq]

summary: Explore the potential downstream signaling pathways that resist AFB1 toxicity after knocking out BACH1 by RNA-seq analysis.

overall_design: For RNA high-throughput sequencing (RNA-seq), RNA libraries were created from each group, for example, BACH1_KO cells (BACH1_KO, BACH1_KO_AFB1) and WT cells (WT, WT_AFB1). Three replicates were conducted for each sample.

first: Shuhong

last: Zhao

first: Jinfu

last: Zhang

first: Changzhi


title: Host inflammatory response is the major factor in the progression of Chlamydia psittaci pneumonia

status: Public on May 16 2022

city: Tai'an

first: Zhenjie

state: Shandong

address: 2 Yingsheng East

institute: Shandong First Medical University

summary: To clarify the host inflammatory response in psittacosis,we compared transcriptome data and concentrations of serum cytokines and chemokines in pneumonia and bronchitis cases.

overall_design: Compared transcriptomic profiles in pneumonia and bronchitis cases.

first: Weifeng

last: Shi


title: The confused cell identity is associated with aggressiveness in esophageal squamous cell carcinoma

status: Public on Mar 16 2022

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

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

institute: Sichuan University

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

overall_design: Refer to individual Series


title: A 102 kb RepABC plasmid of xenologous origin modulates chromosomal gene expression in Dinoroseobacter shibae

status: Public on Mar 13 2022

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: The model organism Dinoroseobacter shibae and many other marine Rhodobacterales (Roseobacteraceae, Alphaproteobacteria) are characterized by a multipartite genome organization. Here we show that the original isolate (Dshi-6) contained six extrachromosomal replicons (ECRs), whereas the strain deposited at the DSMZ (Dshi-5) lacked a 102 kb plasmid. To determine the role of the sixth plasmid, we investigated the genomic and physiological differences between the two strains. Therefore, both genomes were (re-)sequenced and gene expression, growth and substrate utilization were examined. For comparison, we included additional plasmid-cured strains in the genome analysis. In the Dshi-6 population, the conjugative 102 kb RepABC-9 plasmid was only present in about 50 % of the cells, irrespective of its experimentally validated stability. In the presence of the sixth plasmid, copy number changes of other ECRs, in particular a decrease of the 86 kb plasmid, were observed. The most conspicuous finding was the strong influence of plasmids on the chromosomal gene expression, especially the repression of the CtrA regulon and the activation of the denitrification gene cluster. The expression is inversely controlled either by the presence of the 102 kb or the absence of the 86 kb plasmid. We identified global regulatory genes on both plasmids, i.e. a sigma 70 factor, and a quorum sensing synthase, that might be responsible for these major changes. The tremendous effects challenge the current understanding of the relevance of volatile plasmids not only for the original host, but also for new recipients after conjugation.

overall_design: Five different strains of Dinoroseobacter shibae, each in three replicates

first: Sonja

last: Koppenhöfer

first: Victoria

last: Ringel

first: Lukas

last: Birmes

first: Henner

last: Brinkmann

first: Cathrin

last: Spröer

first: Michael

last: Jarek

first: Hui

first: Silke

last: Pradella

first: Irene

last: Wagner-Döbler

first: Jörn

last: Petersen


title: The confused cell identity is associated with aggressiveness in esophageal squamous cell carcinoma [scRNA-Seq]

summary: Seven tumor samples and one distal normal sample from five pathologically confirmed ESCC patients were analyzed with 10X Genomics scRNA-seq. To better represent the squamous epithelial cells, we optimized the dissociation protocol. Total 44,206 cells were obtained, including 16,657 normal and malignant squamous epithelial cells. The squamous epithelial cells, glandular epithelial cells, immune cells, endothelial cells and other tumor microenvironmental cells were clearly separated and identified with classic markers.Seven tumor samples and one distal normal sample from five pathologically confirmed ESCC patients were analyzed with 10X Genomics scRNA-seq. To better represent the squamous epithelial cells, we optimized the dissociation protocol. Total 44,206 cells were obtained, including 16,657 normal and malignant squamous epithelial cells. The squamous epithelial cells, glandular epithelial cells, immune cells, endothelial cells and other tumor microenvironmental cells were clearly separated and identified with classic markers.

overall_design: The cell identity of malignant cells and how they acquire it are fundamental for our understanding of cancer. Here, we report that esophageal squamous cell carcinoma (ESCC) cells display molecular features similar but distinct to all three types of normal esophageal epithelial cells, which we term as confused cell identity (CCI). CCI is an independent prognostic marker associated with poor prognosis in ESCC. Further, we identify tripomyosin 4 (TPM4) as a critical CCI gene that promotes the aggressiveness of ESCC in vitro and in vivo. And TPM4 creates CCI through activating the JAK/STAT-SOX2 pathway. Thus, our study suggests a precedent unrecognized feature of ESCC cells, which might be of value for clinic prognosis and potential interference.

first: Xiangyu

first: Jian

last: Wang

first: Linjie

last: Guo

first: Jiajia

last: Du

first: Chong

last: Chen

first: Yu

last: Liu


title: Transcriptomics and phenotyping define signatures associated with echinocandin resistance in Candida auris

city: Vienna

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

country: Austria

institute: Max Perutz Labs

summary: Transcriptomic analysis of different Candida auris clinical isolates

overall_design: RNA Sequencing was performed of 5 Candida auris clinical isolates. Cells were grown to the exponential phase in YPD at 30oC. Cultures were harvested and three biological replicates were subjected for RNA isolation and sequencing library preparation.

first: Raju

last: Shivarathri

first: Karl

last: Kuchler

first: Neeraj

last: Chauhan


title: MicroRNA-sequencing of plasma from patients in the Osteoarthritis Initiative Cohort

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

institute: Schroeder Arthritis Institute

summary:
Objective: we aimed to identify circulating microRNAs associated with fast-progressing knee osteoarthritis (OA) as compared to slow-progressing knee OA and non-progressing knee OA using sujects from the Osteoarthritis Initiative (OAI) cohort.
MicroRNA libraries were prepared from plasma using the QIAseq miRNA Library Kit (QIAGEN) and sequenced on the Illumina NextSeq550 using a single-end 75-base read protocol to an average depth of 11.6 ± 2.6 SD million reads per sample.

overall_design: MicroRNA-sequencing was performed on plasma collected at baseline and 4-year follow-up from N=20 fast-progressors (Kellgren-Lawrence [KL] grade 0/1 at baseline to KL 3/4 by 4-year follow-up), N=35 slow-progressors (KL 0/1 at baseline and 4-year follow-up to KL 2/3/4 by 8-year follow-up), and N=51 non-progressors (KL 0/1 at baseline through to 8-year follow-up).

first: Shabana

last: Ali

first: Osvaldo

last: Espin-Garcia

first: Andy

last: Wong

first: Pratibha

last: Potla

first: Chiara

last: Pastrello

first: Madison

last: McIntyre

first: Starlee

last: Lively

first: Rajiv

last: Gandhi


title: Identification of RAC1 in Promoting Brain Metastasis of Lung Adenocarcinoma using Single-cell Transcriptome Sequencing

city: Shanghai

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

summary: Brain metastases are common in lung adenocarcinoma (LUAD) patients, and by far, the metastasis mechanisms are not fully understood. We performed a comprehensive single-cell level transcriptomic analysis on one LUAD patient with CTC, primary tumor tissue and metastatic tumor tissue using scRNA-seq approach to identify metastasis related biomarkers. Further scRNA-seq were performed on 7 patients to validate the cancer metastatic hallmark. with single cells collected from either metastatic or primary LUAD tissues. we obtained a more comprehensive picture over lung cancer metastasis in the single-cell level, giving a new perspective to the role of RAC1 in the LUAD brain metastasis, and related pathways to participate in the metastasis process.

overall_design: ScRNA-seq data analysis of 8 patients who either donated primary tumor biopsy, metastasis tumor tissue, para-metastasis tissue, CTCs from blood, or all of the tissues

first: Mingyu

first: Hanyue

last: Li

first: Xiaolin

last: Xu

first: Xunxia

last: Bao

first: Lei

last: Xue

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