title: Comparative functional genomics identifies unique molecular features of EPSCs

summary:
Extended pluripotent or expanded potential stem cells (EPSCs) possess the superior developmental potential to embryonic stem cells (ESCs). However, the molecular underpinning of their in vitro maintenance is not well defined. We comparatively studied transcriptome, chromatin accessibility, active histone modification chromatin marks and relative proteomes of ESCs and the two well-established EPSCs to probe the molecular foundation of their unique developmental potential. We found a great overlap in the transcriptomic and chromatin accessibility profiles and reliance on pluripotency factors Oct4, Sox2, and Nanog for self-renewal between ESCs and EPSCs. Importantly, we identified a subset of genomic, transcriptomic, and proteomic signatures that distinguish EPSCs from ESCs in transcriptional and translational regulation as well as epigenetic and metabolic control. We also identified molecular differences between the two well-established EPSCs. Our study provides a rich resource for dissecting the regulatory network underlying the developmental potency of EPSCs and exploring alternative states of totipotency.

This SuperSeries is composed of the SubSeries listed below.

overall_design: ChIP-seq, ATAC-seq, and RNA-seq analysis of mouse extended pluripotent or expanded potential stem cells (EPSCs) and embryonic stem cells (ESCs).


title: RNA sequencing profiling of mRNAs, lncRNAs and circRNAs in Trigeminal Ganglion following Temporomandibular Joint inflammation

status: Public on Jul 23 2022

city: ZHENGZHOU

first: Qian

last: Bai

address: NO2 JINGBA ROAD

country: China

institute: Second Affiliated Hospital of Zhengzhou Uni

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary:
The collected TGs from experimental (Complete Freund’s Adjuvant, CFA) and control (Saline) groups were processed for deep RNA sequencing.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different groups(Saline/CFA3D/CFA6D).

overall_design: Comparative gene expression profiling analysis of RNA-seq data in trigeminal ganglia for 3 different groups(Saline/CFA3D/CFA6D).


title: Transcriptional regulation by the Velvet complex during asexual development in Neurospora crassa

status: Public on Jul 20 2022

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

country: Spain

institute: University of Seville

summary: Comparative transcriptomic analysis of genes regulated by light and conidiation in the wild type and the ∆ve-1 mutant.Identification of light regulated genes during vegetative growth.Identification of DEGs during asexual development

overall_design: In this study, we perform an RNAseq analysis to examine the regulatory role of VE-1 in gene expression during different stages of growth and light conditions

first: Sara

last: Cea-Sánchez

first: María

last: Corrochano-Luque

last: Gutiérrez

first: N

middle: L

last: Glass

first: David

last: Cánovas

first: Luis

middle: M

last: Corrochano


title: N-terminus of Drosophila MSL1 interacts with DNA-binding proteins and is critical for the recruitment of the dosage compensation complex to the X chromosome

status: Public on Aug 30 2022

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The male-specific lethal dosage compensation complex (MSL complex or DCC), which consists of five proteins and two non-coding roX RNAs, is necessary for the transcriptional enhancement of X-linked genes to compensate for the sex chromosome monosomy in Drosophila XY males, compared with XX females. MSL2 is a single protein component of the DCC that is expressed only in males and is essential for the specific recruitment of the DCC to the high-affinity “entry” sites (HASs) on the X chromosome. MSL2, together with MSL1, forms the heterotetrameric DCC core. Here, we demonstrated that the N-terminal unstructured region of MSL1 interacts with many different DNA-binding proteins that contain clusters of the C2H2 zinc-finger domains. Amino acid deletions in the N-terminal region of MSL1 strongly affect the binding of the DCC to the HASs on the male X chromosome. However, the binding of MSL2 to autosomal promoters was unaffected by amino acid deletions in MSL1. Males expressing mutant variants of MSL1 died during the larvae stage, demonstrating the critical role played by the N-terminal region in DCC activity. Our results suggest that MSL1 interacts with a variety of DNA-binding proteins to increase the specificity of DCC recruitment to the male X chromosome.

overall_design: ChIP-seq signal of the MSL1, MSL2 and MSL3 proteins occupancy in adult males and females represented as wt, M1[wt], M1[wt]_M2, M1[Δ41-85]_M2 and M1[Δ1-15]_M2 lines.

first: O

last: Maksimenko


title: Gene expression in mice oviductal organoids before and after E2 and DBZ induced multiciliated cell differentiation

status: Public on Jul 16 2022

city: Nanjing

first: Ruiwei

last: Jiang

address: No.321 Zhongshan Road

department: Drum Tower Hospital Affiliated to Medical School

institute: Nanjing University

summary: To further explore the mechanisms through which CDC42 regulates multiciliated cell differentiation, RNA-seq was performed to compare the transcriptomes of Cdc42f/f (F/F), PgrcreCdc42f/f (PgrKO) and adenovirus expressing the Cre recombinase gene (Ad-Cre) mediated Cdc42 knockout (AdKO) mice oviductal organoids before and after induced multiciliated cell differentiation.

overall_design: mRNA profiles of  Cdc42f/f mice oviduct organoids, PgrCre/+Cdc42f/f mice oviduct organoids and Ad-cre mediated Cdc42 knockout oviduct organoids


title: Lewis Lung Carcinoma (LLC) cells in the lung model express lung-specific genes compared to subcutaneous engraftment cells.

status: Public on Jul 19 2022

city: Kyoto

first: Ryo

last: Miyata

state: Kyoto

address: 54 Kawaharacho, Shogoin, Sakyoku

department: Thoracic Surgety

country: Japan

institute: Kyoto University Graduate School of Medicine

summary: We revealed that tumor cells in the bleomycin-injured lungs (BLM lungs) are differently influenced by their unique lung fibrogenic microenvironment compared to those in subcutaneous tumor models in vivo or in 2-dimensional monolayer culture in vitro.

overall_design: The gene expression profiles of LLC cells grown in 2-dimensional monolayer culture, in subcutaneous tumors, and in BLM lungs were analyzed (n=3/group).


title: Transcriptome effects of media and methotrexate on T-ALL cell lines

status: Public on Jul 15 2022

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

country: USA

institute: Emory University

summary: Human T-ALL cells become chemoresistant to multiple chemotherapies if exposed to adipocyte-secreted factors.   To identifiy gene alterations underlying adipocyte-mediated chemoresistance, we performed RNA-sequencing analysis on untreated human T-ALL cells and those treated with the chemotherapy metotrexate.

overall_design: Human T-ALL cell lines (n=3; Jurkat, Loucy and Peer) were cultured in unconditoned, bone marrow stromal cell, or adipocyte-conditioned medium (CM) for 48 hours and then processed for RNA-sequencing.

first: C

middle: D

middle: J

last: Henry

first: M

last: Lee


title: Ergot alkaloid induced changes during late gestation in ewes

status: Public on Jul 18 2022

city: Clemson

first: Susan

middle: K

last: Duckett

state: SC

address: 112 Biosystems Research Complex

department: Animal and Veterinary Sciences

institute: Clemson University

summary: Pregnant Suffolk ewes (n = 19; 81.2kg ± 7.7) estimated to be carrying twins were assigned to endophyte-infected tall fescue seed (E+; 4.14 µg ergovaline + ergovalinine/g seed) or a control diet (CON; 0 µg ergovaline + ergovalinine) and evaluated at different stages of gestation (gd85 [pre-treatment, n = 3], gd110 [n = 4/treatment] or gd133 [n = 4/treatment). Ewes were individually fed a basal diet with (E+) or without (CON) endophyte-infected tall fescue seed from gd86 to gd110 or gd133. A terminal necropsy was performed, and uterine components were evaluated for size, weight, and type. Data were analyzed using a priori contrasts to test effects of stage of gestation (gd85 vs. gd110 or gd110 vs. gd133) and adaptive responses to feeding E+ fescue seed versus CON at gd110 and gd133. Serum prolactin concentrations were greater (P < 0.05) at gd110 than gd85, and then remained constant to gd133. Feeding E+ tall fescue seed reduced (P < 0.05) serum prolactin concentrations compared to CON at both gd110 and gd133. From gd85 to gd110, placentome type and number changed from type A to type B (P < 0.05) but did not change (P > 0.05) after gd110. Total fetal weight per ewe increased 2977 g from gd85 to gd110 (P = 0.011) and then 3151 g from gd110 to 133 (P = 0.012). Brain weight as a percentage of fetal body weight was higher (P = 0.029) for E+ fetuses on gd110 compared to CON, which demonstrates asymmetrical growth and intrauterine growth restriction (IUGR). In total, 15,961 genes were identified in the cotyledon through mapping to the ovine genome across all samples. There were 136 genes differentially expressed (FDR < 0.05; log2foldchange < -1 and > 1) from gd85 to gd110 with ovarian steroidogenesis and steroid biosynthesis pathways enriched and 469 genes differentially expressed from gd110 to gd133 with ribosome and oxidative phosphorylation pathways enriched. Exposure to E+ fescue resulted in differential expression of 22 genes at gd110 but only one gene at gd133 compared to CON. These results show that there are major changes in fetal growth and placental remodeling during the late gestation period that are influenced by exposure to ergot alkaloids from endophyte-infected tall fescue seed; however, major changes in the transcriptome of the cotyledon tissue in response to E+ fescue were not observed and other factors must be involved in the reduction of placental efficiency and fetal growth observed with E+ fescue exposure.

overall_design: For this study, the 15 samples are divided into five groups of 3 replicates each. Three of the groups are control groups at gestation date 85, 110, and 133. Two groups are experimental at gestation date 110 and 133.

first: Jessica

last: Britt

first: Maslyn

middle: A

last: Greene

first: J

last: Klotz

first: S

last: Justice

first: Rhonda

middle: R

last: Powell

first: Rooksana

middle: E

last: Noorai

first: Christopher

last: McMahan

first: Terri

middle: F

last: Bruce


title: SUMOylation restrains the degradation of ACE2 through TOLLIP-mediated selective autophagy to facilitate the host susceptibility to SARS-CoV-2 infection

city: guangzhou

first: shi

middle: jun

last: jie

institute: sysu

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Alongside investigations into the virology of SARS-CoV-2, understanding the host–virus dependencies are vital for the identification and rational design of effective antiviral therapy. Here, we report the dominant SARS-CoV-2 entry receptor, ACE2, conjugates with small ubiquitin-like modifier 3 (SUMO3) through a proteome-wide protein interaction analysis. We further demonstrate that E3 SUMO ligase PIAS4 prompts the SUMOylation and stabilization of ACE2, whereas deSUMOylation enzyme SENP3 reverses this process. Conjugation of SUMO3 with ACE2 at lysine (K) 187 hampers the K48-linked ubiquitination of ACE2, thus suppressing its subsequent cargo receptor TOLLIP-dependent autophagic degradation. Pharmacological intervention of ACE2 SUMOylation blocks the entry of SARS-CoV-2 and viral infection-triggered immune responses. Collectively, our findings suggest selective autophagic degradation of ACE2 orchestrated by SUMOylation and ubiquitination can be targeted to future antiviral therapy of SARS-CoV-2.

overall_design:
We analyzed the transcriptome expression of SARS-CoV-2-infected Calu-3 cells with or without 2-D08 treatment, non-treated infection group as control.
We analyzed the transcriptome expression of SARS-CoV-2-infected Calu-3 cells transfected with siNC or siTollip, non-treated infection group as control.

first: Shouheng

last: Jin

first: Xing

last: He

first: Ling

last: Ma

first: Jun

last: Cui


title: Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [OGAP-seq]

city: Sheffield

first: Sherif

last: El-Khamisy

state: South Yorkshire

address: Firth Court, University of Sheffield, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

summary:
Purpose: To assess the role of NuMA (TDIF) in DNA repair, NuMA (TDIF) ChIP-seq, 4sU-seq in hydrogen peroxide treated and untreated WT and NuMA (TDIF) KD cells, and OGAP-seq in hydrogen peroxide treated and untreated WT and NuMA (TDIF) KD cells
Methods: 4sU-seq was carried out in WT and NuMA (TDIF) KD (using  a doxycyclin inducible system) untreated and peroxide treated duplicate RPE cells. The data was mapped using STAR, the bams coverted into bigwigs and differential expression between the conditions carried out using DE-seq2. NuMA (TDIF) ChIP-seq and OGAP-seq data was mapped using BWA. Both sets of mapped data were subsequently used to generate bigwigs showing fold-change relative to inputs using MACS2 and to generate metagene profiles using the CGAT suite of bioinformatics tools. Both sets of data were also run through FeatureCounts to count reads overlapping promoter regions.
Results: Through our 4sU-seq data we identified a set of genes whose expression upon exposure to oxidative stress is dependent upon the presence of NuMA (TDIF). NuMA (TDIF) ChIP revealed increased occupancy of NuMA (TDIF) at promoters, which was increased for NuMA (TDIF)-regulated genes, paused genes and early response genes. OGAP-seq in the presence and absence of NuMA (TDIF) demonstrated that in the absence of NuMA (TDIF) there is increased damage across gene bodies and particularly promoters.
Conclusions: Our study indicates that NuMA (TDIF) plays a role in the protection from and response to oxidative damage. This protective effect appears to be particularly strong at promoters regions, and may differ between distinct subsets of gene categories.

overall_design: Identification of NuMA (TDIF) regulated genes by comparing levels of newly transcribed RNA through 4sU-seq in duplicate WT and NuMA (TDIF) KD untreated and peroxide treated cells. Assessment of NuMA (TDIF) binding within the genome through NuMA (TDIF) ChIP-seq in duplicate MRC5 cell samples. Investigation into the effects of NuMA (TDIF) KD upon levels of oxidative damage across the genome through OGAP-seq in duplicate WT and NuMA (TDIF) KD samples derived from RPE1 cells.

first: Swagat

last: Ray

first: Arwa

last: Abugable

first: Jacob

last: Parker


title: Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [NuMA (TDIF) and TDP1 CUT&RUN RPE1]

summary: Purpose: To assess the role of NuMA (TDIF) in DNA repair  Methods: CUT&RUN was carried out in untreated/hydrogen peroxide treated RPE1 cells in duplicate. The data was mapped using bwa mem and subsequently used to generate bigwigs showing fold-change relative to inputs using MACS2 and various meta-feature profiles using the CGAT suite of bioinformatics tools  Results: The data revealed increased occupancy of NuMA (TDIF) at promoters and enhancers, which increases upon hydrogen peroxide treatment  Conclusions: Our study indicates that NuMA (TDIF) plays a role in the protection from and response to oxidative damage. This protective effect appears to be particularly strong at promoter and enhancer regions, and may differ between distinct subsets of gene categories.

overall_design:
Assessment of NuMA (TDIF) and TDP1 binding within the genome through CUT&RUN in RPE1 cells under untreated and hydrogen peroxide treated conditions in duplicate.
MH = Untreated/H2O2-, 90R = H2O2 treated 90 minute recovery, I = IgG, N = NuMA (TDIF), T = TDP1

first: A


title: Taz protects aged hematopoietic stem cells from exhaustion [scRNA-seq]

status: Public on Jul 14 2022

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

summary:
We report here the analysis of young and aged hematopoietic stem and progenitor cells (HSPCs) by transcriptional profiling (bulk RNA-Seq, CITE-Seq) and chromatin profiling (ATAC-Seq, scATAC-Seq). We use here a Clca3a1 as a surface marker to further fractionate HSPCs.
Young hematopoietic stem cells (HSCs) were isolated by flow cytometry, transduced ex vivo with different shRNA constructs (shRen, shPU1 No1, shPU1 No2) and transplanted into lethally irradiated mice. Two months after transplantation, transduced (GFP+)HSPCs were isolated by flow cytometry. The different samples were pooled and the shRNA per cell was identified by a specific dialout PCR (amplifying the mirE shRNA construct together with the 10x cell barcode)  to link the cell barcodes with the the different shRNA constructs. Here mirE_R1 contains the UMI and the cell barcode whereas mirE_R2 contains the shRNA sequence.

overall_design: Examination of transcriptional and chromatin changes during aging of HSPCs.


title: hiPSC-derived bone marrow milieu identifies a clinically actionable driver of niche-mediated treatment resistance in leukemia

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

summary: Pal,D. et al. develop a synthetic human bone marrow milieu and identify that CDH2 mediates niche-dependent leukemia proliferation and treatment resistance. They show that CDH2 is targetable in vivo via ADH-1, which shows high efficacy and low toxicity in a very aggressive leukemia PDX model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for leukaemia samples before and after co-culture on iMSC and iANG cells

first: Deepali

last: Pal

first: Helen

last: Blair

first: Sirintra

last: Nakjang


title: A lysosomal regulatory circuit essential for the development and function of microglia

city: Stanford

first: Harini

last: Iyer

state: California

address: 279 Campus Drive, B300 Beckman Center

department: Developmental Biology

institute: Stanford University

summary: We performed Illumina NovaSeq on macrophages isolated from zebrafish

overall_design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS, RNA was extracted, and sequencing was performed.

first: William

middle: S

last: Talbot


title: Effect of two compounds on HBV gene expression in HBV-infected primary human hepatocytes.

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

overall_design: Comparative time-series gene expression profiling analysis of HBV RNA-seq data derived from cultured primary human hepatocytes treated with two compounds, RO21 and RO22, and vehicle compounds.

first: Milad

last: Adibi

first: Erich

last: Küng


title: Comparative functional genomics identifies unique molecular features of EPSCs [RNA-seq]

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Extended pluripotent or expanded potential stem cells (EPSCs) possess the superior developmental potential to embryonic stem cells (ESCs). However, the molecular underpinning of their in vitro maintenance is not well defined. We comparatively studied transcriptome, chromatin accessibility, active histone modification chromatin marks and relative proteomes of ESCs and the two well-established EPSCs to probe the molecular foundation of their unique developmental potential. We found a great overlap in the transcriptomic and chromatin accessibility profiles and reliance on pluripotency factors Oct4, Sox2, and Nanog for self-renewal between ESCs and EPSCs. Importantly, we identified a subset of genomic, transcriptomic, and proteomic signatures that distinguish EPSCs from ESCs in transcriptional and translational regulation as well as epigenetic and metabolic control. We also identified molecular differences between the two well-established EPSCs. Our study provides a rich resource for dissecting the regulatory network underlying the developmental potency of EPSCs and exploring alternative states of totipotency.

overall_design: RNA-seq analysis of mouse extended pluripotent or expanded potential stem cells (EPSCs) and embryonic stem cells (ESCs).

first: Xin

last: Huang

first: Ruge

last: Zang


title: Taz protects aged hematopoietic stem cells from exhaustion

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

overall_design: Refer to individual Series


title: Taz protects aged hematopoietic stem cells from exhaustion [ATAC-seq]

summary:
We report here the analysis of young and aged hematopoietic stem and progenitor cells (HSPCs) by transcriptional profiling (bulk RNA-Seq, CITE-Seq) and chromatin profiling (ATAC-Seq, scATAC-Seq). We use here a Clca3a1 as a surface marker to further fractionate HSPCs.
HSPCs were sorted by flow cytometry. Where indicated, LT-HSCs were further fractionated into a Clca3a1 high or low population using a monoclonal antibody (10.1.1) purchased from the Developmental Studies Hybridoma Bank - DSHB.

overall_design: Examination of chromatin changes during aging of HSPCs.


title: Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [OGAP-seq SH-SY5Y]

first: Sherif

last: El-Khamisy

summary: Purpose: To assess the role of NuMA (TDIF) in DNA repair  Methods: OGAP-seq was carried out in in each pairwise combination of untreated/hydrogen peroxide treated and no doxycyclin (NuMA (TDIF) WT)/doxycyclin treated (NuMA (TDIF) KD) SH-SY5Y cells in duplicate. The data was mapped using bwa mem and subsequently used to generate bigwigs showing fold-change relative to inputs using MACS2 and various meta-feature profiles using the CGAT suite of bioinformatics tools  Results: The data revealed elevated OGAP-seq signal in promoter and enhancer regions upon NuMA (TDIF) KD  Conclusions: Our study indicates that NuMA (TDIF) plays a role in the protection from and response to oxidative damage. This protective effect appears to be particularly strong at promoter and enhancer regions.

overall_design:
Assessment of oxidative damage within the genome through OGAP-seq in SH-SY5Y cells under each pairwise combination of untreated/hydrogen peroxide treated and no doxycyclin (NuMA (TDIF) WT)/doxycyclin treated (NuMA (TDIF) KD) SH-SY5Y cells in duplicate
MH = Untreated/H2O2-, R90 = H2O2 treated 90 minute recovery, WT = Wild type with respect to NuMA (TDIF), KD = NuMA (TDIF) Knockdown, IN = Input, IP = OGAP-seq

first: S

first: J


title: Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [PolII ChIP-seq RPE1]

summary: Purpose: To assess NuMA (TDIF)’s role in facilitating PolII pausing  Methods:Pol2 ChIP-Seq was carried out in each pairwise combination of untreated/hydrogen peroxide treated and no doxycyclin (NuMA (TDIF) WT)/doxycyclin treated (NuMA (TDIF) KD) RPE1 cells in duplicate. The data was mapped using bwa mem and subsequently used to generate bigwigs showing fold-change relative to inputs using MACS2 and various meta-feature profiles using the CGAT suite of bioinformatics tools  Results: The data revealed increased occupancy of PolII at promoter regions and increased pausing ratios for genes in H2O2- cells after NuMA (TDIF) KD relative to controls, but decreased occupancy in NuMA (TDIF) KD in H2O2+ cells compared to controls.  Conclusions: Our study indicates that NuMA (TDIF) plays a role in PolII pause-release.

overall_design:
Assessment of PolII binding within the genome through ChIP-seq in RPE1 cells under untreated/hydrogen peroxide treated conditions and no doxycyclin (NuMA (TDIF) WT)/doxycyclin treated (NuMA (TDIF) KD) conditions in duplicate
MH = Untreated/H2O2-, PH = H2O2 treated, ND = No doxycyclin/WT with respect to NuMA (TDIF), PD = post-doxycyclin/NuMA (TDIF) KD, IN = Input, IG = IgG, Pol2 = RNA polymerase II

last: Ray

first: A


title: PARP14 is a Novel Target in STAT6 Mutant Follicular Lymphoma

status: Public on Jul 17 2022

city: Munich

first: Michael

last: Mentz

state: Bavaria

address: Marchioninistrasse 15

department: 1Department of Internal Medicine III

institute: Ludwig-Maximilians University of Munich

summary: The variable clinical course of follicular lymphoma (FL) is determined by the molecular heterogeneity of tumor cells and complex interactions within the tumor microenvironment (TME). IL-4 producing follicular helper T cells (TFH) are critical components of the FL TME. Binding of IL-4 to IL-4R on FL cells activates JAK/STAT signaling. We identified STAT6 mutations (STAT6MUT) in 13% of FL (N = 33/258), all clustered within the DNA binding domain. Gene expression data and immunohistochemistry showed upregulation of IL-4/STAT6 target genes in STAT6MUT FL, including CCL17, CCL22, and FCER2 (CD23). Functionally, STAT6MUT was gain-of-function by serial replating phenotype in pre-B CFU assays. Expression of STAT6MUT enhanced IL-4 induced FCER2/CD23, CCL17 and CCL22 expression and was associated with nuclear accumulation of pSTAT6. RNA sequencing identified PARP14 -a transcriptional switch and co-activator of STAT6- among the top differentially upregulated genes in IL-4 stimulated STAT6MUT lymphoma cells and in STAT6MUT primary FL cells. Quantitative chromatin immunoprecipitation (qChIP) demonstrated binding of STAT6MUT but not STAT6WT to the PARP14 promotor. Reporter assays showed increased IL-4 induced transactivation activity of STAT6MUT at the PARP14 promotor, suggesting a self-reinforcing regulatory circuit. Knock-down of PARP14 or PARP-inhibition abrogated the STAT6MUT gain-of-function phenotype. Thus, our results identify PARP14 as a novel therapeutic target in STAT6MUT FL.

overall_design: Gene expression profiling analysis of RNA-seq data from OCI-Ly1 cell lines stably expressing either wild-type or mutant STAT6 after IL-4 stimulation

last: Keay

first: Carolin

last: Strobl

first: Martina

last: Antoniolli

first: Louisa

last: Adolph

last: Heide

first: Axel

last: Lechner

first: Sarah

last: Häbe

first: Elisa

last: Osterode

first: Robert

last: Kridel

first: Christoph

last: Ziegenhain

first: Lucas

last: Wange

first: Johannes

last: Hildebrand

first: Tanaya

last: Shree

first: Elisabeth

last: Silkenstedt

first: Annette

last: Staiger

first: German

last: Ott

first: Heike

last: Horn

first: Monika

last: Szczepanowski

first: Julia

last: Richter

first: Ronald

last: Levy

first: Andreas

last: Rosenwald

first: Wolfgang

last: Enard

first: Ursula

last: Zimber-Strobl

last: von Bergwelt-Baildon

last: Hiddemann

first: Wolfram

last: Klapper

first: Marc

last: Schmidt-Supprian

first: Deepak

last: Bararia

last: Rudelius

first: Verena

last: Passerini

first: Oliver

last: Weigert


title: Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [NuMA (TDIF) CUT&RUN SH-SY5Y]

first: Sherif

last: El-Khamisy

summary: Purpose: To assess the role of NuMA (TDIF) in DNA repair  Methods: CUT&RUN was carried out in untreated and hydrogen peroxide treated SH-SY5Y cells in triplicate. The data was mapped using bwa mem and subsequently used to generate bigwigs showing fold-change relative to inputs using MACS2 and various meta-feature profiles using the CGAT suite of bioinformatics tools  Results: The data revealed increased occupancy of NuMA (TDIF) at promoters and enhancers, which increases upon hydrogen peroxide treatment  Conclusions: Our study indicates that NuMA (TDIF) plays a role in the protection from and response to oxidative damage. This protective effect appears to be particularly strong at promoter and enhancer regions, and may differ between distinct subsets of gene categories.

overall_design:
Assessment of NuMA (TDIF) binding within the genome through NuMA (TDIF) CUT&RUN in SH-SY5Y cells under untreated and hydrogen peroxide treated conditions in triplicate.
MH = Untreated/H2O2-, PH = H2O2 treated, IG = IgG T = NuMA (TDIF)

first: S

last: Ray

first: A

last: Abugable

first: J

last: Parker


title: The oxidoreductase CLIC4 is required to maintain mitochondrial function and resistance to exogenous oxidants in breast cancer cells.

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

summary: We report the different transcriptom of 6DT1 (murine mammary cancer cell line) wildtype cells or CLIC4-KO (by CRISPR cas9) untreated or treated 1uM H2O2 for 24 hours.

overall_design: 6DT1 transduced with lentivirus to express CLIC4 (lenti) or with lentivirus to express an empty vector (empty) cells were untreated or treated with 1uM H2O2 for 24 hours.

first: Heba

last: Al Khamici

first: Vanesa

middle: C

last: Sanchez

first: Hualong

last: Yan

first: Christophe

last: Cataisson

first: Aleksandra

last: Michalowski

middle: H

first: Luowei

last: Li

first: Maxwell

middle: P

last: Lee

first: Jing

last: Huang

first: Stuart

last: Yuspa


title: Differential dynamics of response at single cell resolution following CAR-T therapy in refractory B-cell lymphoma

status: Public on Jul 13 2022

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

state: MA

address: 75 Ames St

institute: Broad Institute

overall_design:
Single-cell RNA sequencing of PBMCs and infusion products from 32 patients treated with CD19 CAR-T therapy
NOTE FROM SUBMITTER: Raw sequencing data will be available at controlled access,  dbGAP.

first: Mark

middle: B

last: Leick

first: Katie

last: Maurer

first: Satyen

last: Gohil

first: Catherine

last: Wu

first: Gad

last: Getz

first: Marcela

middle: V

last: Maus


first: Harini

last: Iyer


title: Taz protects aged hematopoietic stem cells from exhaustion [scATAC-seq]

first: Bjoern

last: von Eyss

summary:
We report here the analysis of young and aged hematopoietic stem and progenitor cells (HSPCs) by transcriptional profiling (bulk RNA-Seq, CITE-Seq) and chromatin profiling (ATAC-Seq, scATAC-Seq). We use here a Clca3a1 as a surface marker to further fractionate HSPCs.
HSPCs were sorted by flow cytometry. LT-HSCs were fractionated into a Clca3a1 high or low population using a monoclonal antibody (10.1.1) purchased from the Developmental Studies Hybridoma Bank - DSHB.


title: Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [ChIP-Seq]

first: Sherif

last: El-Khamisy

first: Swagat

last: Ray

first: Arwa

last: Abugable

first: Jacob

last: Parker


title: Taz protects aged hematopoietic stem cells from exhaustion [bulk RNA-seq II]

summary:
We report here the analysis of young and aged hematopoietic stem and progenitor cells (HSPCs) by transcriptional profiling (bulk RNA-Seq, CITE-Seq) and chromatin profiling (ATAC-Seq, scATAC-Seq). We use here a Clca3a1 as a surface marker to further fractionate HSPCs.
Old (Clca3a1_high) hematopoietic stem cells (HSCs) were isolated by flow cytometry, transduced ex vivo with different shRNA constructs (shRen, shTaz_Seq1, shTaz_Seq2) and transplanted into lethally irradiated mice. Four months after transplantation, transduced (GFP+)HSPCs were isolated by flow cytometry and subsequently analyzed by low input RNA-Seq. Per sample two mice were pooled in order to obtain sufficient RNA for library prep.


title: RORγt expression in mature Th17 cells safeguard the lineage stability by inhibiting conversion to Th2 cells [ATAC-seq]

status: Public on Jul 12 2022

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: RORγt is the lineage-specific transcription factor for T helper 17 (Th17) cells and an attractive drug target for treating Th17-associated diseases. Though the critical role of RORγt in early Th17 cell differentiation has been well recognized, whether it maintains mature Th17 cell phenotypes remains largely unexplored. Here, we show that genetic deletion of Rorc in mature Th17 cells inhibited their pathogenic functions. Mechanistically, loss of RORγt led to a closed chromatin structure at key Th17-specific gene loci, particularly at those so called “super enhancer” regions. Furthermore, RORc deletion in effector Th17 cells resulted in a strongly Th2-biased cell phenotype at both epigenetic and transcriptional levels, in an IL-4-dependent manner. Our results thus reveal a crucial function of RORγt in effector Th17 cells in maintaining Th17 cell program and constraining Th2 cell conversion, offering new considerations in therapeutic targeting of RORγt.

overall_design: ATAC-seq of WT and 4-OHT induced Rorc KO in vitro cultured Th17 cells.

first: Xinxin

last: Chi

first: Xiaohong

last: Zhao

first: Xiaohu

last: Wang


title: RORγt expression in mature Th17 cells safeguard the lineage stability by inhibiting conversion to Th2 cells


title: Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques [RNA-Seq]


title: Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types

status: Public on Jul 11 2022

city: Cambridge

first: Wenjun

last: Yan

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

summary: The anterior segment of the eye consists of the cornea, iris, ciliary body, crystalline lens and aqueous humor outflow pathways. Together, these tissues are essential for the proper functioning of the eye. Disorders of vision have been ascribed to defects in all of them; some, including glaucoma and cataract, are among the most prevalent causes of blindness. To characterize the cell types that comprise these tissues, we generated an anterior segment cell atlas of the human eye using high throughput single-nucleus RNA sequencing (snRNAseq). We profiled 191,992 single nuclei from non-diseased anterior segment tissues from 6 human donors, identifying >60 cell types. Many are discrete, whereas others in lens and cornea form continua, corresponding to known developmental transitions that persist in adulthood. Having profiled each tissue separately, we performed an integrated analysis of the entire anterior segment revealing that some cell types are unique to single structure whereas others are shared across tissues. This integrated cell atlas was then used to investigate cell type-specific expression patterns of more than >900 human ocular disease genes identified either through Mendelian inheritance patterns or genome-wide association studies (GWAS).

overall_design: To build a better understanding of the complex tissues comprising the human anterior segment, we generated a cell atlas using high throughput single-nucleus RNA sequencing (snRNAseq). We profiled 191,992 single nuclei from non-diseased anterior segment tissues, applied computational methods to cluster them based on transcriptomic similarity, and used histological techniques to assign cell type identities to the clusters. After investigating each dataset independently, we pooled nuclei from multiple tissues and performed an integrated analysis. In this way, we were able to show that some cell types are confined to specific tissues whereas others are shared across two or more tissues. Finally, we used this cell atlas to investigate cell type-specific expression patterns of human ocular disease genes identified either through Mendelian inheritance patterns or genome-wide association studies (GWAS).

first: Tavé

last: van Zyl

first: Alexi

last: McAdams

first: Aboozar

last: Monavarfeshani

first: Gregory

last: Hageman

first: Joshua

last: Sanes


title: Analysis of the Role of NuMA (TDIF) in DNA repair Through Next Generation Sequencing Techniques


title: The role of somatosensory innervation of adipose tissues

status: Public on Jul 10 2022

city: La Jolla

first: Yu

state: CA

address: 10550 N. Torrey Pines Rd.

institute: Scripps Research

summary: To investigate the role of somatosensory innervation of adipose tissues, we unilaterally ablate sensory innervation of adipose tissues, and profiled the gene expression in the inguinal adipose tissues 4 weeks after sensory ablation surgery.

overall_design: Mice receive unilateral sensory ablation via AAV labeling. 3-4 weeks after surgery, mice are exposed to room temperature or cold (4C) for 5h. Inguinal adipose tissues are extracted for transcriptional profiling comparing ablated side versus control side within the same animal. N=5 mice for RT and N=4 mice for Cold.

first: Verina

last: Leung

first: Yunxiao

last: Zhang

first: Victoria

last: Nudell

first: Meaghan

last: Loud

first: M

last: Servin-Vences

first: Dong

last: Yang

first: Kristina

first: Ardem

last: Patapoutian

first: Li

last: Ye


title: Real-time quantitative PCR analysis of apple seeds

status: Public on Jul 07 2022

city: Warsaw

first: Katarzyna

last: Ciacka

address: Nowoursynowska 166

country: Poland

institute: Warsaw University of Life Sciences

summary:
Apple seeds were subjected to accelerated aging. After 7, 14, and 21 days of aging, embryos were isolated. Part of the embryos were shortly fumigated with nitric oxide (NO). After 48 h of embryos culture (aged embryos or aged embryos treated with NO), embryonic axes were used to extract the total RNA. RT-qPCR were done to analyze the changes in the expression of genes related to seed aging.
Short-term (3 h) treatment of embryos isolated from accelerated aged apple seeds (Malus domestica Borkh.) with NO partially reduced the effects of aging. The aim of the study was to investigate the impact of the short-term NO treatment of embryos isolated from apple seeds subjected to accelerated aging on the expression of genes potentially linked to the regulation of seed aging. Apple seeds were artificially aged for 7, 14, or 21 days. Then the embryos were isolated from the seeds, treated with NO, and cultured for 48 h. Progression of seeds aging was associated with the decreased transcript levels of most of the analyzed genes (Lea1, Lea2a, Lea4, Hsp70b, Hsp20a, Hsp20b, ClpB1, ClpB4, Cpn60a, Cpn60b, Raptor, and Saur). The role of NO in the mitigation of seed aging depended on the duration of the aging. After 7 and 14 days of seed aging, a decreased expression of genes potentially associated with the promotion of aging (Tor, Raptor, Saur) was noted. NO-dependent regulation of seed aging was associated with the stimulation of the expression of genes encoding chaperones and proteins involved in the repair of damaged proteins. After NO application, the greatest upregulation of ClpB, Pimt was noted in the embryos isolated from seeds subjected to 7-day long accelerated aging, Hsp70b, Hsp70c, Cpn in the embryos of seeds aged for 14 days, and Lea2a in the embryos of seeds after 21 days of aging.

overall_design: The expression of genes (Lea1, Lea2a, Lea2b, Lea4, Hsp90, Hsp70a, Hsp70b, Hsp70c, Hsp20a, Hsp20b, ClpB1, ClpB4, Cpn60a, Cpn60b, Tor, Raptor, Pimt, and Saur)  were analyzed in the axes of apple embryos after 7, 14, and 21 days of aging and  in the axes of apple embryos after 7, 14, and 21 days of aging,  treated with NO. The expression levels were normalized using two reference genes and calculated using the method described by Vandesompele et al. (2002) and Hellemans et al. (2007). The experiments were done in three biological replicates, in three technical repetitions.


title: CDK11 phosphorylates SF3B1 and is essential for constitutive splicing.

status: Public on Jul 09 2022

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München


title: Inhibition of the m6A Reader IGF2BP2 as a Strategy against T-cell Acute Lymphoblastic Leukemia

status: Public on Jul 04 2022

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

institute: Qilu Hospital

type: Methylation profiling by high throughput sequencing

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignant leukemia with extreme limited treatment for relapsed patients. N6‐methyladenosine (m6A) reader Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) participates in the initiation and growth of cancers by communicating with various targets. Here, we found IGF2BP2 is highly expressed in T-ALL. Gain and loss of IGF2BP2 demonstrated IGF2BP2 was essential for T-ALL cell proliferation in vitro and loss of IGF2BP2 prolonged animal survival in a human T-ALL xenograft model. Mechanistically, IGF2BP2 directly bound to T-ALL oncogene NOTCH1 via an m6A dependent manner. Furthermore, we identified a small-molecule IGF2BP2 inhibitor JX5 and treatment of T-ALL with JX5 showed similar functions as knockdown of IGF2BP2. These findings not only shed light on the role of IGF2BP2 in T-ALL, but also provide an alternative γ‑Secretase inhibitors (GSI) therapy to treat T-ALL.

overall_design: Investigating m6A-modified mRNA transcriptome in Jurkat cells

first: Panpan

last: Feng

first: Dawie

last: Chen

first: Xia

last: Wang

first: Yanxia

last: Li

first: Zhenyu

first: Boya

first: Yupeng

first: Wei

first: Jingru

first: Jingjing

first: Baobing

last: Zhao

first: Jingxin


title: Wnt5a–Vangl1/2 signaling regulates the position and direction of lung branching through the cytoskeleton and focal adhesions

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

institute: University of California, San Francisco

summary: Lung branching morphogenesis requires reciprocal interactions between the epithelium and mesenchyme. How the lung branches are generated at a defined location and projected toward a specific direction remains a major unresolved issue. In this study, we investigated the function of Wnt signaling in lung branching in mice. We discovered that Wnt5a in both the epithelium and mesenchyme plays an essential role in controlling the position and direction of lung branching. The Wnt5a signal is mediated by Vangl1/2 to trigger a cascade of non-canonical or planar cell polarity (PCP) signaling. In response to non-canonical Wnt signaling, lung cells undergo cytoskeletal reorganization and change focal adhesions. Perturbed focal adhesions in lung explants are associated with defective branching. Moreover, we observed changes in the shape and orientation of the epithelial sheet and the underlying mesenchymal layer in regions of defective branching in the mutant lungs. Thus, PCP signaling helps define the position and orientation of the lung branches. We propose that mechanical force induced by non-canonical Wnt signaling mediates a coordinated alteration in the shape and orientation of a group of epithelial and mesenchymal cells. These results provide a new framework for understanding the molecular mechanisms by which a stereotypic branching pattern is generated.

overall_design: Examination the gene expression difference between Control and Wnt5a or Vangl1-2 deficient lungs

first: Kuan

first: Erica

last: Yao

first: Ethan

first: Biao

first: Evelyn

middle: Y

first: Regan

last: Volk

first: Katherine

last: Hofmann

first: Balyn

last: Zaro


title: A lysosomal regulatory circuit essential for the development and function of microglia

first: Harini

last: Iyer

summary: We performed Illumina NovaSeq on zebrafish larvae with or without Zymosan A injection

overall_design: Zymosan A was injected into wildtype animals and tfeb; tfe3a; tfe3b triple mutants to examine the extent to which Tfeb and Tfe3 activate lysosomal pathways in response to inflammatory challenge. rraga mutant larvae were included in the experiment for comparison.

first: William

last: Talbot


title: Pd1 regulates proliferation and differentiation of neural progenitors during brain development

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To gain a total insight into how Pd1 regulates embryonic neurogenesis, RNA-seq was performed to compare the different expressed genes ar E13. Approximately approximately one thousand transcripts showed differential expression between the Pd1fl/fl and Pd1CKO mice brain cortex, with a fold change ≥1.5 and p value <0.05. These results indicated the importance of Pd1 in cortical development. RNA-seq based transcriptome characterization would provide a global understanding how Pd1 gene contribute to brain cortical development.

overall_design: Total RNA were extracted from E13 telencephalic tissue of 2 Pd1fl/fl and 2 Pd1CKO mice. Then the total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Ptc 225 Peltier Thermal Cycler.

first: Fen


title: Crossfeeding relationship between Ruminococcus gauvreauii IPLA60001 and Ruminocoides biliarensis IPLA60002

status: Public on Jul 05 2022

city: Villaviciosa

first: Natalia

last: Molinero Garcia

state: Asturias

address: IPLA-CSIC, Paseo Rio Linares S/N

department: DEPARTMENT OF MICROBIOLOGY AND BIOCHEMISTRY OF DAIRY PRODUCTS

institute: Dairy Products Institute of Asturias (IPLA-CSIC)

summary: Little is known about the bacteria that reside in human gallbladder and the mechanisms that allow them to survive within this harsh environmental niche. Furthermore, certain bacterial species are considered to exhibit antagonistic activities whilst others may form mutualistic interactions through, for example, cross-feeding. We isolated two new strains from healthy human bile samples, one belonging to Ruminococcus gauvreauii, of Lachnospiraceae family, and other constituting a new specie in Ruminococcaceae family, named Ruminocoides biliarensis. The two strains differed markedly in their carbohydrate metabolism as R. gauvreauii mainly metabolised sugar alcohols, including inositol, to form acetate as unique fermentation product, and Rc. biliarensis mainly metabolised resistant starches to mainly form formate and acetate as fermentation end products. Both strains exhibited resistance to different bile salts, and the ability to sporulate. Amino acid and vitamin biosynthesis profiles also markedly differed between the two bile isolates. Finally,RNAseq was used to analyse the co-cultures of both isolates, to analyze the activities involved in the possible cross-feeding relationship.

sample_organism:
Ruminococcus gauvreauii
Ruminococcoides bili

overall_design: The analysis contains 4 different samples, that belongs to: the pure culture of R.gauvreauii in M2 medium supplemented to D-glucose in 8hours, the pure culture of R.biliarensis in M2 medium supplemented to Starch from Rice in 8hours, the coculture of R.gauvreauii and R. biliarensis in M2 medium supplemented to Starch from Rice in 6hours and the coculture of R.gauvreauii and R. biliarensis in M2 medium supplemented to Starch from Rice in 8hours. Each sample was studied by triplicate

last: Molinero

first: Elena

last: Conti

first: Alan

middle: W

last: Walker

first: Abelardo

last: Margolles

first: Sylvia

last: Duncan

first: Susana

last: Delgado


title: Integrative Analyses of mRNA and MicroRNA Expression Profiles Reveals the Innate Immune Mechanism for the Resistance to Vibrio parahaemolyticus Infection in Epinephelus coioides [RNA-seq]

status: Public on Jul 03 2022

city: Guangzhou

first: yuyou

last: lu

address: Xiaoguwei street

institute: Sun Yat-sen university

summary:
V. parahaemolyticus and E. coioides were served as research objects to explore the interaction mechanism between pathogen and host. infection.
The mRNA-miRNA integrated analysis of the spleen of E. coioides infected with V. parahaemolyticus was performed, and several crucial pathways were screened, which may contribute to treatment of V. parahaemolyticus infection.

overall_design: Comparative gene expression profiling analysis of mRNA-seq data for V. parahaemolyticus infected group and control group.

first: Xifeng

last: Qiao

first: Yuyou

last: Lu

first: Jiachang

last: Xu

first: Niuniu

last: Deng

first: Wenjie

last: Lai

first: Ziyi

last: Wu

first: Haoran

last: Lin

first: Yong

last: Zhang

first: Danqi


title: Integrative Analyses of mRNA and MicroRNA Expression Profiles Reveals the Innate Immune Mechanism for the Resistance to Vibrio parahaemolyticus Infection in Epinephelus coioides [miRNA-seq]

overall_design: Comparative microRNA expression profiling analysis of miRNA-seq data for V. parahaemolyticus infected group and control group.


title: β-hydroxybutyrate restores T cell metabolism and function in severe COVID-19

status: Public on Jul 01 2022

city: Bonn

first: Katarzyna

last: Placek

address: Carl-Troll-Str. 79

institute: Univeristy of Bonn

summary: Anorexia and fasting are host adaptations to acute infection, inducing a metabolic switch towards ketogenesis and the production of ketone bodies, including β-hydroxybutyrate (BHB). However, whether ketogenesis metabolically influences the immune response in pulmonary infections remains unclear. Here we report impaired production of BHB in humans with SARS-CoV-2-induced but not influenza-induced acute respiratory distress syndrome (ARDS). BHB promotes the survival and the production of Interferon-g from CD4+ T cells. Using metabolic tracing analysis, we uncovered that BHB provides an alternative carbon source to fuel oxidative phosphorylation (OXPHOS) and the production of bioenergetic amino acids and glutathione, which is important for maintaining the redox balance. T cells from patients with SARS-CoV-2-induced ARDS were exhausted and skewed towards glycolysis, but can be metabolically reprogrammed by BHB to perform OXPHOS, thereby increasing their functionality. Finally, we find that ketogenic diet (KD) reduced pulmonary fibrosis, a feature particular pronounced in COVID-19 ARDS and delivery of BHB as ketone ester drink reduces the mortality of SARS-CoV-2 infected mice. Altogether, our data suggest that impaired ketogenesis in patients with SARS-CoV-2 infection accounts, at least partially for disease progression and that supplementation ketone ester might represent an easy-to-implement treatment to improve the clinical outcome of COVID-19 patients.

overall_design: comprehensive gene expression analysis of RNA-seq data of cells isolated from bronchoalveolar lavage (BALF) of patients with acute respiratory distress syndrome (ARDS) caused either by COVID19, Influenza infection, bacterial infections or others

first: Fotios

last: Karagiannis

first: Konrad

last: Peukert

first: Laura

last: Surace

first: Marcel

last: Michla

first: Fabian

last: Nikolka

first: Mario

last: Fox

first: Patricia

last: Weiss

first: Caroline

last: Feuerborn

first: Paul

last: Maier

first: Susanne

last: Schulz

first: Burcu

last: Al

first: Benjamin

last: Seeliger

first: Tobias

last: Welte

first: Sascha

last: David

first: Inge

last: Grondman

first: Aline

last: de Nooijer

first: Peter

last: Pickkers

first: Jan

last: Lukas Kleiner

first: Marc

last: Moritz Berger

first: Thorsten

last: Brenner

first: Christian

last: Putensen

first: Hiroki

last: Kato

first: Natalio

last: Garbi

first: Mihai

middle: G

last: Netea

first: Karsten

last: Hiller

last: Bode

first: Christoph

last: Wilhelm


title: Transcription factor Sp9 is a negative regulator of D1-type MSN development [scRNA-Seq]

status: Public on Jul 06 2022

city: Shanghai

first: Zhenmeiyu

last: Li

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary: The striatum is the main input structure of the basal ganglia, receiving information from the cortex and the thalamus and consisting of D1- and D2- medium spiny neurons (MSNs). D1-MSNs and D2-MSNs are essential for motor control and cognitive behaviors and have implications in Parkinson’s Disease. In the present study, we demonstrated that Sp9 positive progenitors produced both D1-MSNs and D2-MSNs and that Sp9 expression was rapidly downregulated in postmitotic D1-MSNs. Furthermore, we found that sustained Sp9 expression in lateral ganglionic eminence (LGE) progenitor cells and their descendants led to promoting D2-MSNs identity and repressing D1-MSNs identity during striatal development. As a result, sustained Sp9 expression resulted in an imbalance between D1-MSNs and D2-MSNs in the mouse striatum. In addition, the fate-changed D2 like-MSNs survived normally in adulthood. Taken together, our finding supported that Sp9 was sufficient to promote D2-MSNs identity and repress D1-MSNs identity, and Sp9 was a negative regulator of D1-MSNs fate.

overall_design: Single-cell RNA sequencing was performed using 10X Genomics Chromium technology V3 on E14.5 LGE (8 total samples)

first: Zhengang

last: Yang


title: Taz protects aged hematopoietic stem cells from exhaustion [CITE-seq]

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

institute: Leibniz Institute on Aging

summary:
We report here the analysis of young and aged hematopoietic stem and progenitor cells (HSPCs) by transcriptional profiling (bulk RNA-Seq, CITE-Seq) and chromatin profiling (ATAC-Seq, scATAC-Seq). We use here a Clca3a1 as a surface marker to further fractionate HSPCs.
HSPCs were sorted by flow cytometry. During the staining procedure for flow cytometry, the antibody cocktail also included antibodies labelled with oligos (antibody-derived tags =ADTs) which can later be analyzed by the 10x Chromium controller.

overall_design: Examination of transcriptional changes during aging of HSPCs.


title: A role for the Saccharomyces cerevisiae Rtt109 histone acetyltransferase in R-loop homeostasis and associated genome instability

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

summary: The stability of the genome is occasionally challenged by the formation of DNA-RNA hybrids and R-loops, which can be influenced by the chromatin context. This is mainly due to the fact that DNA-RNA hybrids hamper the progression of replication forks, leading to fork stalling and, ultimately, DNA breaks. Through a specific screening of chromatin modifiers performed in the yeast Saccharomyces cerevisiae, we have found that the Rtt109 histone acetyltransferase is involved in several steps of R-loop-metabolism and their associated genetic instability. On one hand, Rtt109 prevents DNA-RNA hybridization by the acetylation of histone H3 lysines 14 and 23, and on the other hand, it is involved in the repair of replication-born DNA breaks, such as those that can be caused by R-loops, by acetylating lysines 14 and 56. In addition, Rtt109 loss renders cells highly sensitive to replication stress in combination with R-loop-accumulating THO-complex mutants. Our data evidence that the chromatin context simultaneously influences the occurrence of DNA-RNA hybrid-associated DNA damage and its repair, adding complexity to the source of R-loop-associated genetic instability.

overall_design: Mononucleosomal DNA was isolated after MNase treatment and was then prepared for sequencing.

first: Juan

last: Cañas

first: María

middle: L

last: García-Rubio

first: Alicia

last: García

first: Francisco

last: Antequera

first: Belén

last: Gómez-González


title: Transcription factor Sp9 is a negative regulator of D1-type MSN development

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

overall_design: Refer to individual Series


title: Functional Portrait of Irf1 (Orf19.217), a Regulator of Morphogenesis and Iron Homeostasis in Candida albicans [ChIP-Seq]

city: Paris

first: Lasse

middle: van

last: Wijlick

address: 25-28 Rue du Dr Roux

department: Mycology

country: France

institute: Institut Pasteur

summary: The fungus Candida albicans is part of the human microbiome and mainly colonises the GI tract of healthy individuals. However, when the balance in the GI tract is disturbed, the fungus can switch from a commensal to a virulent lifestyle and can turn into a life-threatening pathogen. Life in the host is characterised by a constant struggle for nutrients, essential trace elements such as iron, copper and zinc are particularly important. To protect itself from pathogens, the human host has developed a strategy to limit the availability of trace elements, this strategy is also described as nutritional immunity. C. albicans has developed a whole range of counter-strategies to obtain sufficient trace elements. In this manuscript, we have characterised the transcription factor Orf19.217, which acts at the interface between trace element scavenging and acquisition and is therefore particularly important in adaptation to life in the host. According to its identified function, we named the transcription factor Irf1, Iron-dependent Regulator of Filamentation. The transcription factor was previously identified in a systematic screen of genes whose overexpression contributes to morphological changes in C. albicans. We have comprehensively investigated the function of Irf1 using state-of-the-art functional genomics approaches, including ChIP-seq, transcriptomics and bioinformatics analyses. Analysis of the Irf1 gene-regulatory network indicates that the transcription factor is involved in the regulation of genes important for iron uptake. Using phenotypic analysis, we confirmed that Irf1 acts in a pathway parallel to known iron uptake regulators and is also required for hyphal formation induced by iron deficiency, a process that allows the fungus to access more viable body niches. Through epistasis experiments, we were also able to identify downstream effectors of Irf1 that are involved in this process. Our study provides new insights into how C. albicans adapts to iron deficiency and establish a direct functional link between hyphal formation and iron uptake.

overall_design: ChIP-Seq of Irf1-HA, in triplicate including samples from no-tag control strain

last: van Wijlick

first: Sadri

last: Znaidi

first: Sophie

last: Bachellier-Bassi

first: Christophe

last: d'Enfert


title: Integrative Analyses of mRNA and MicroRNA Expression Profiles Reveals the Innate Immune Mechanism for the Resistance to Vibrio parahaemolyticus Infection in Epinephelus coioides

first: yuyou

last: lu


title: A novel in vivo model of Glioblastoma radiation resistance identifies long non-coding RNAs and targetable kinases

city: Birmingham

first: Christopher

middle: Douglas.

last: Willey

state: Alabama

address: 619 19th St S, HSROC 2232C

department: Radiation Oncology

institute: The University of Alabama at Birmingham

summary: Glioblastomas (GBM) are the most common primary CNS tumor. GBMs often recur as highly aggressive, intractable, therapy resistant tumors.  Key molecular regulators of acquired radiation resistance in recurrent GBM are largely unknown with a dearth of accurate pre-clinical models. To address this, we generated eight GBM patient-derived xenograft (PDX) models of acquired radiation-therapy selected (RTS) resistance compared with same-patient, treatment naïve (RTU) PDX. A novel bioinformatics pipeline analyzed phenotypic, transcriptomic and kinomic alterations, identifying long non-coding RNAs (lncRNAs) and targetable, PDX-specific kinases. We observed differential transcriptional enrichment of DNA damage repair (DDR) pathways in our RTS models. Multiple molecular routes to acquired radiation-resistance were revealed in our models including PDX-specific kinases that we validated with targeted small molecule inhibitors (SMIs). We identified 184, mostly novel, lncRNAs differentially regulated between RTU and RTS PDX. Several of these lncRNAs were associated with transcriptional changes in DDR, cell cycle progression, stemness, and chromatin remodeling pathways. This study identifies lncRNAs as potential key regulators in recurrent GBM and therapy resistance. We also demonstrate that SMIs aimed at lncRNA-related signaling pathways may represent a novel therapeutic approach for recurrent GBM tumors.

overall_design: Examination of baseline differences between patient matched primary and recurrent tumors following serial radiation selection

first: Christian

middle: T

last: Stackhouse

first: G

last: Gillespie

middle: D


title: Taz protects aged hematopoietic stem cells from exhaustion [bulk RNA-seq]

summary:
We report here the analysis of young and aged hematopoietic stem and progenitor cells (HSPCs) by transcriptional profiling (bulk RNA-Seq, CITE-Seq) and chromatin profiling (ATAC-Seq, scATAC-Seq). We use here a Clca3a1 as a surface marker to further fractionate HSPCs.
HSPCs were sorted by flow cytometry. Where indicated, LT-HSCs were further fractionated into a Clca3a1 high or low population using a monoclonal antibody (10.1.1) purchased from the Developmental Studies Hybridoma Bank - DSHB.

We report here the analysis of old LSK cells after Taz S89A overexpression.
LSK cells were sorted by flow cytometry. The cells were infected in vitro with the indicated constructs and subjected to RNA-Seq analysis.

We report here the analysis of BM-HPC#5 cells after PU1 knockdown.
BM-HPC#5 cells with the indicated constructs were subjected to RNA-Seq analysis.


title: The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination (probing_3_igg)

city: Rockville

first: Johannes

last: Goll

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

summary: Current seasonal and pre-pandemic influenza vaccines induce short-lived predominantly strain-specific and limited heterosubtypic responses. To better understand how vaccine adjuvants AS03 and MF59 may provide improved antibody responses to vaccination, we interrogated serum from subjects who received 2 doses of inactivated monovalent influenza A/Indonesia/05/2005 vaccine with or without AS03 or MF59 using hemagglutinin (HA) microarrays (NCT01317758 and NCT01317745). The arrays were designed to reflect both full length and globular head HA derived from 17 influenza A subtypes (H1 to H16 and H18) and influenza B strains. We observed significantly increased strain-specific and broad homo- and hetero-subtypic antibody responses with both AS03 and MF59 adjuvanted vaccination with AS03 achieving a higher titer and breadth of IgG responses relative to MF59.  Adjuvanted vaccine was also associated with the elicitation of stalk directed antibody. We established good correlation of the array antibody responses to H5 antigens with standard HA inhibition and microneutralization titers.

platform_organism:
Influenza A virus
Influenza B virus

overall_design: We constructed two sets of influenza-specific high-density protein microarrays which comprised purified HA proteins derived from 17 influenza A virus subtypes and influenza B virus strains,  including conformationally correct stabilize trimers.  Our present study was designed to measure the landscape of the antibody responses in response to vaccination with an inactivated, monovalent, subvirion influenza A/Indonesia/05/2005 (H5N1) strain vaccine when administered alone (unadjuvanted) or with AS03 or MF59 adjuvant. Importantly, using stabilized trimeric headless stalk protein (HA2) in competitive inhibition assays, we indirectly assessed the elicitation of stalk-directed antibodies. Finally, the concordance between microarray subtype specific antibody levels and HAI and MN titers were evaluated.

first: Aarti

last: Jain

first: Travis

last: Jensen

first: Rafael

last: Assis

first: Rie

last: Nakajima

first: Algis

last: Jasinskas

first: Lynda

last: Coughlan

first: Sami

middle: R

last: Cherikh

first: Casey

middle: E

last: Gelber

first: S

last: Khan

first: D

last: Davies

first: Philip

last: Meade

first: Daniel

last: Stadlbauer

first: Shirin

last: Strohmeier

first: Florian

last: Krammer

first: Wilbur

last: Chen

last: Felgner


title: The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination (probing_4_iga)

last: Goll


title: The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination (probing_4_igg)

last: Jain


title: The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination (probing_3_iga)

last: Jensen


title: RORγt expression in mature Th17 cells safeguard the lineage stability by inhibiting conversion to Th2 cells [RNA-Seq]

first: Chen

last: Dong

address: Haidian District

institute: Tsinghua University

summary: RORγt is the lineage-specific transcription factor for T helper 17 (Th17) cells and an attractive drug target for treating Th17-associated diseases. Though the critical role of RORγt in early Th17 cell differentiation has been well recognized, whether it maintains mature Th17 cell phenotypes remains largely unexplored. Here, we show that genetic deletion of Rorc in mature Th17 cells inhibited their pathogenic functions. Mechanistically, loss of RORγt led to a closed chromatin structure at key Th17-specific gene loci, particularly at those so called “super enhancer” regions. Furthermore, RORc deletion in effector Th17 cells resulted in a strongly Th2-biased cell phenotype at both epigenetic and transcriptional levels, in an IL-4-dependent manner. Our results thus reveal a crucial function of RORγt in effector Th17 cells in maintaining Th17 cell program and constraining Th2 cell conversion, offering new considerations in therapeutic targeting of RORγt.

overall_design: RNA-seq of WT and 4-OHT induced Rorc KO in vitro cultured Th17 cells, and CD4+ T cells isolated from colon tissues of  WT and Rorc-Cd4cre naïve T cell transfer induced colitis model.

first: Xinxin

last: Chi

first: Xiaohong

last: Zhao

first: Xiaohu

last: Wang


title: The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination (probing_1_igg)

first: Johannes

first: Aarti

first: Travis

first: Rafael

last: Assis

last: Nakajima

last: Jasinskas

last: Coughlan

last: Cherikh


title: Prenatal immune stress blunts microglia reactivity which impairs neurocircuitry [Adult_ATAC-seq]

city: Baltimore

first: Lindsay

middle: N

last: Hayes

state: Maryland

address: 600 North Wolfe Street, Meyer 4-136

department: Neuroscience

institute: Johns Hopkins University

summary: Recent studies suggested that microglia, the primary brain immune cells, can affect circuit connectivity and neuronal function. Microglia infiltrate the neuroepithelium early in embryonic development and are maintained in the brain throughout adulthood. Several maternal environmental factors, such as aberrant microbiome, immune activation, and poor nutrition, can influence prenatal brain development. Nevertheless, it is unknown how changes in the prenatal environment instruct the developmental trajectory of infiltrating microglia, which in turn affect brain development and function. Here we show that after maternal immune activation (MIA) microglia from the offspring have a long-lived decrease in immune reactivity (blunting) across the developmental trajectory. The blunted immune response was concomitant with changes in the chromatin accessibility and reduced transcription factor occupancy of the open chromatin. Single-cell RNA sequencing revealed that MIA does not induce a distinct subpopulation but rather decreases the contribution to inflammatory microglia states. Prenatal replacement of MIA microglia with physiological infiltration of naïve microglia ameliorated the immune blunting and restored a decrease in presynaptic vesicle release probability onto dopamine receptor type-two medium spiny neurons, indicating that aberrantly formed microglia due to an adverse prenatal environment impacts the long-term microglia reactivity and proper striatal circuit development.

overall_design: ATAC-seq of FACS-sorted microglia (Cd11b+, Cd45-low, P2ry12+) from the striatum of control and maternal immune activation mice of 8- to 10-week-old mice after saline or LPS treatment.

first: Akira

last: Sawa


title: Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis

city: St. Louis

first: Ting

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

summary: Non-small cell lung cancer (NSCLC) is one of the most commonly diagnosed and deadliest cancers worldwide, owing in large part to roughly half of all patients initially presenting with both primary and metastatic disease. While the major events in the metastatic cascade have been identified, a mechanistic understanding of how NSCLC routinely, successfully colonizes the brain is largely unknown. Recent studies have begun demonstrating the role of epigenetic mis-regulation within tumorigenesis as well as in the metastatic process, including widespread changes in DNA methylation and histone modifications.  To better understand the role of DNA methylation alterations in NSCLC metastasis to brain, we measured DNA methylation during disease progression for 12 patients, globally profiling the methylation of their normal lung, primary lung tumor, and brain metastasis. We found that the variation in methylation is just as great; albeit less coordinated across genomic features, during metastatic spread as compared to primary tumorigenesis. The greatest recurrent methylation changes during metastatic progression occurred over DNA methylation valleys (DMVs) harboring H3K9me3 as well as bivalent marks H3K27me3 and H3K4me1 enrichment in normal lung. Mapping EZH2, the catalytic subunit of polycomb repressive complex 2 (PCR2), binding locations in H1299, a lymph node-derived lung cancer cell line, revealed a loss of EZH2 binding within DMVs accompanied by an increase in DNA methylation, exemplifying epigenetic switching. The vast majority of these differentially methylated region-associated DMVs harbor developmental genes, suggesting that altered epigenetic regulation of developmentally important genes may confer a selective advantage during metastatic progression.

overall_design: Samples: 2 separate ChIP-seq replicates were completed for the identification of EZH2 in the cell line H1299. Both replicates consist of paired-end reads. Data are included from both the EZH2 IP and input.

first: Jennifer

middle: A

last: Karlow

first: Siddhartha

last: Devarakonda

first: Xiaoyun

last: Xing

first: Hyo

middle: S

last: Jang

first: Ramaswamy

last: Govindan

first: Mark

last: Watson


title: Prenatal immune stress blunts microglia reactivity which impairs neurocircuitry [Adult_FACS]

overall_design: RNA-seq of FACS-sorted microglia (Cd11b+, Cd45-low, P2ry12+) from the striatum of control and maternal immune activation mice of 8- to 10-week-old mice after saline or LPS treatment.


title: Prenatal immune stress blunts microglia reactivity which impairs neurocircuitry [Neonatal_MACS]

overall_design: RNA-seq of MACS-sorted microglia from the whole brain of control and maternal immune activation (MIA) mice at neonatal age (P3-5).


title: Prenatal immune stress blunts microglia reactivity which impairs neurocircuitry


title: Metabolic reprogramming of skeletal muscle by resident macrophages points to CSF1R inhibitors as muscular dystrophy therapeutics (RNA-Seq).

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

summary: The role of tissue resident macrophages during tissue regeneration or fibrosis is not well-understood, mainly due to the lack of a specific marker for their identification. Here, we identified two populations of skeletal muscle resident macrophages: TIM4- macrophages which are replenished from the blood and LYVE1+TIM4+ macrophages that locally self-renew (self-renewing resident macrophages, SRRMs). Using a CSF1R inhibition/withdrawal approach to specifically deplete SRRMs, we found that they provide a non-redundant function in clearing damage-induced apoptotic cells early after extensive acute injury. In contrast, in chronic mild injury as seen in a mouse model of Duchenne muscular dystrophy, we showed that depletion of both resident populations through long term CSF1R inhibition changes muscle fiber composition from damage-sensitive glycolytic fibers towards damage-resistant glycolytic-oxidative fibers protecting muscle against contraction induced injury. This later finding reveals a new role for resident macrophages in modulating tissue metabolism and has therapeutic potential in light of the ongoing clinical testing of CSF1R inhibitors.

overall_design: Characterization of skeletal muscle resident macroophages; identification of their role in muscle regeneration and fibrosis;

first: Farshad

last: Babaeijandaghi

first: Lin

last: Tung

first: Tara

last: Stach


title: The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination (probing_2_iga)

first: Johannes

last: Goll

last: Jain

last: Jensen

last: Assis

first: Rie

first: Algis

first: Lynda

first: Sami

first: Casey

last: Gelber

first: S

last: Khan

first: D

middle: H

last: Davies

first: Philip

last: Meade

first: Daniel

last: Stadlbauer

first: Shirin

last: Strohmeier

first: Florian

last: Krammer

first: Wilbur

last: Chen

last: Felgner


title: Prenatal immune stress blunts microglia reactivity which impairs neurocircuitry [Adult_scRNA-seq]

first: Lindsay

last: Hayes

summary: Recent studies suggested that microglia, the primary brain immune cells, can affect circuit connectivity and neuronal function. Microglia infiltrate the neuroepithelium early in embryonic development and are maintained in the brain throughout adulthood. Several maternal environmental factors, such as aberrant microbiome, immune activation, and poor nutrition, can influence prenatal brain development. Nevertheless, it is unknown how changes in the prenatal environment instruct the developmental trajectory of infiltrating microglia, which in turn affect brain development and function. Here we show that after maternal immune activation (MIA) microglia from the offspring have a long-lived decrease in immune reactivity (blunting) across the developmental trajectory. The blunted immune response was concomitant with changes in the chromatin accessibility and reduced transcription factor occupancy of the open chromatin. Single cell RNA sequencing revealed that MIA does not induce a distinct subpopulation but rather decreases the contribution to inflammatory microglia states. Prenatal replacement of MIA microglia with physiological infiltration of naïve microglia ameliorated the immune blunting and restored a decrease in presynaptic vesicle release probability onto dopamine receptor type-two medium spiny neurons, indicating that aberrantly formed microglia due to an adverse prenatal environment impacts the long-term microglia reactivity and proper striatal circuit development.

overall_design: 10X genomics scRNA-seq of FACS-sorted microglia (Cd11b+, Cd45-low, P2ry12+) from the striatum of control and maternal immune activation mice of 8-10 week old mice 18 hours after LPS treatment.

first: Akira

last: Sawa


title: Metformin prevents age-associated ovarian fibrosis by modulating the immune landscape in female mice

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

institute: Ottawa Hospital Research Institute

summary: Ovarian fibrosis is a pathological condition associated with aging and is responsible for a variety of ovarian dysfunctions. Given the known contributions of tissue fibrosis to tumorigenesis, it is anticipated that ovarian fibrosis may contribute to ovarian cancer risk. We recently reported that diabetic postmenopausal women using metformin had ovarian collagen abundance and organization that were similar to premenopausal ovaries from non-diabetic women. In this study, we investigated the effects of aging and metformin on mouse ovarian fibrosis at a single-cell level. We discovered that metformin treatment prevents age-associated ovarian fibrosis by modulating the proportion of fibroblasts, myofibroblasts and immune cells. We identified the emergence of a metformin responsive subpopulation of macrophages, unique to the aged mice treated with metformin. Our results demonstrate that metformin can modulate specific populations of immune cells and fibroblasts to prevent age-associated ovarian fibrosis and offers a new strategy to prevent ovarian fibrosis

overall_design: In this study, we sought to determine if metformin can prevent and/or reverse the formation of ovarian fibrosis. Since ovarian fibrosis is substantially increased between 15 and 18 months of age in mice, we designed our prevention study by treating adult female mice C57BL/6 beginning at the age 14 months (pre-fibrosis development; 5/group) with 350mg/kg/day of metformin (Sigma) in their drinking water for 6 months (no drug as control). We also determined if existing fibrosis can be reversed by using naturally aged mice at 18 months of age, when collagen deposition is high. We treated the aged mice with the same metformin treatments in the drinking water for 6 months as a fibrosis reversal study. We selected this drug concentration in the drinking water as it achieves plasma concentrations similar to the doses taken by T2D patients (i.e. 5-10μM metformin) (76). At the end of the 6-month period, experimental mice were euthanized in static microisolators by CO2 asphyxiation delivered at a flow of 20-30% chamber volume per minute followed by cervical dislocation. We also euthanized two more experimental conditions based on age with no treatments, defined as young (n=5; 3 months old) and middle-aged (n=5; 14 months old). All mice were dissected to collect the ovaries. The left ovary of the first three mice of each group was used for single cell RNA sequencing while the right ovary of the same mice was collected for histologic analysis.

last: Landry

middle: P


title: 3' sequencing of placenta form Mbnl2 and Mbnl3 KOs

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

summary: To investigate the impact of Mbnl2 and Mbnl3 in placenta development and function through the regulation of alternative poly-adenylation, we have generated 3'-seq data from placenta from single and double KO mice at different developmental stages.

overall_design: We dissected foetal placenta from E13.5 and labyrinth from E18.5 and perform Lexogen Quantseq Reverse.

first: T

last: Spruce

first: M


title: The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination (probing_1_iga)

first: Johannes

last: Goll

middle: B

first: Aarti

last: Jain

first: Travis

last: Jensen

first: Rafael

first: Rie

last: Nakajima

first: Algis

last: Jasinskas

last: Coughlan

last: Cherikh


title: Prenatal immune stress blunts microglia reactivity which impairs neurocircuitry [Adult_Rescue]


title: The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination (probing_2_igg)

last: Assis

first: Lynda

first: Sami

first: Casey

last: Gelber

first: S

last: Khan

first: D

last: Davies

first: Philip

last: Meade

last: Stadlbauer

last: Strohmeier


title: Functional and evolutionary impact of Mbnl2 and Mbnl3 genes in eutherian placenta


title: Prenatal immune stress blunts microglia reactivity which impairs neurocircuitry [Adult_MACS]

first: Lindsay

last: Hayes

overall_design: RNA-seq of MACS-sorted microglia from the frontal cortex and striatum of control and maternal immune activation mice of 8- to 10-week-old mice after saline or LPS treatment.

first: Akira

last: Sawa


title: Monocyte-derived alveolar macrophages autonomously determine severe outcome of respiratory viral infection [bulk RNA-seq]

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

institute: ETH Zürich

summary: Various lung insults can result in replacement of resident alveolar macrophages (AM) by blood monocyte-derived (BMo)-AM. However, the dynamics of this process and its long-term consequences for respiratory viral infections remain unclear. Using several mouse models and a marker to unambiguously track fetal monocyte-derived (FeMo)-AM and BMo-AM, we established the kinetics and extent of replenishment and their function to recurrent influenza virus (IAV) infection. Massive loss of FeMo-AM resulted in rapid replenishment by self-renewal of survivors followed by generation of BMo-AM, which progressively outcompeted FeMo-AM over several months due to increased glycolytic and proliferative capacity. The presence of both naïve and experienced BMo-AM conferred severe pathology to IAV infection, which was associated with a pro-inflammatory phenotype. Furthermore, upon aging of naïve mice, FeMo-AM are gradually replaced by BMo-AM, which contribute to IAV disease severity in a cell autonomous manner. Taken together, our results suggest that origin rather than training of AM determines long-term function to respiratory viral infection and provide an explanation for increased severity in elderly.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from alveolar macrophages differentiated from different precursor cells or after infection.

first: Fenqqi

last: Li

first: Federica

last: Piattini

first: Lea

last: Pohlmeier

first: Qian

last: Feng

first: Hubert

last: Rehrauer


title: Effects of Nfat1 knockout on the expression of pain-related genes in spinal cord

city: nantong

first: Bao-Chun

last: Jiang

state: Jiangsu Province

address: 9 seyuan Road

institute: Nanytong University

summary: To investigate the impact of the Nfat1 knockout on pain processing-associated genes in the spinal cord, we performed microarray analysis.

overall_design: Mice were divided into a Sham WT control group (WT-Sham), spinal nerve ligation (SNL) WT group (WT-SNL), and SNL Nfat1 knockout group (Nfat1-/--SNL).  Total RNA was isolated from the L5 spinal cord segment 5 days after surgery and submitted for microarray hybridization.

first: Yong-Jing

last: Gao


title: The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination

first: Johannes

last: Goll


title: Functional Validation of Common Idiopathic Pulmonary Fibrosis Genetic Risk Variants [mRNA sequencing]

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado Anschutz Medical Campus

summary:
Rationale: To identify functionally relevant common genetic risk variants associated with idiopathic pulmonary fibrosis (IPF), we performed expression quantitative trait loci (eQTL) and methylation quantitative trait loci (mQTL) mapping, followed by co-localization of eQTL and mQTL with genetic association signals as well as mediation analysis.
Methods: Illumina MEGA genotyping arrays, mRNA sequencing, and Illumina 850k methylation arrays were performed on lung tissue of participants with IPF (234 RNA and 345 DNA samples) and non-diseased control (188 RNA and 202 DNA samples). Transcriptome and methylome datasets were normalized for unknown batch effects using Probabilistic Estimation of Expression Residuals (PEER). eQTL, cell type-interaction eQTL, and mQTL analyses were performed in FastQTL and co-localization analysis in eCAVIAR separately for cases and controls.  Benjamini-Hochberg false discovery rate was used for adjustment for multiple comparisons.
Results: After appropriate adjustment, we identified 4,745 genes with significant eQTLs in controls and 6,047 in cases (FDR-adjusted p<0.05). Focusing on genetic variants within 10 primary IPF-associated genetic loci, we identified 27 eQTLs in controls and 24 eQTLs in cases (FDR-adjusted p<0.05). Among these signals, we identified association of rs35705950 with expression of MUC5B (Chr11 locus) and rs2076295 with expression of DSP (Chr6 locus) in both cases and controls. To address cell specificity, we performed cell type-interaction eQTL analysis and identified an association of rs2076295 with expression of DSP in smooth muscle cells. mQTL analysis identified CpGs in gene bodies of MUC5B (cg17589883) and DSP (cg08964675) associated with the lead variants in these two loci. eCAVIAR demonstrated strong co-localization of eQTL/mQTL and genetic signal in MUC5B (rs35705950) and DSP (rs2076295) in both cases and controls. Mediation analysis demonstrated partial mediation of the effect of common variants in MUC5B and DSP loci on disease risk though MUC5B and DSP gene expression. Functional validation of the mQTL in MUC5B demonstrates that the CpG is within a putative internal repressor element that interacts through a 3D loop with the enhancer containing the rs35705950 genetic variant.
Conclusions: Using lung eQTL/mQTL, co-localization, and mediation analyses, we have established the functional validation of the common IPF genetic risk variants for MUC5B (rs35705950) and DSP (rs2076295). These results provide additional evidence that both MUC5B and DSP are involved in the etiology of IPF.

overall_design:
Illumina MEGA genotyping arrays, mRNA sequencing, and Illumina 850k methylation arrays were performed on lung tissue of participants with IPF (234 RNA and 345 DNA samples) and non-diseased control (188 RNA and 202 DNA samples).
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

first: Raphael

last: Borie

first: Jonathan

last: Cardwell

first: Iain

last: Konigsberg

first: Camille

last: Moore

first: Weiming

last: Zhang

first: Avram

last: Walts

first: Julie

last: Powers

first: Janna

last: Brancato

first: Evgenia

last: Dobrinskikh

first: Mauricio

last: Rojas

first: Paul

last: Wolters

first: Kevin

middle: K

last: Brown

first: Timothy

last: Blackwell

first: Tomoko

last: Nakanishi

first: J

last: Richards

first: Tasha

last: Fingerlin

first: Norman

last: Sachs

first: Sara

last: Pulit

first: Zach

last: Zappala

first: David

last: Schwartz

middle: V


title: Metabolic reprogramming of skeletal muscle by resident macrophages points to CSF1R inhibitors as muscular dystrophy therapeutics (scRNA-Seq).

first: Fabio

last: Rossi

first: Farshad

last: Babaeijandaghi

first: Lin

middle: W

last: Tung

first: Tara

last: Stach


title: The impact of Prdm16 deletion on the transcriptome of the developing cochlear duct cells

city: Downers Grove

first: Michael

last: Ebeid

state: IL

address: 555 31st St, Anatomy

department: Anatomy

institute: Midwestern University

summary: The PR domain containing 16 (PRDM16) is a key transcription regulator in the development of craniofacial, adipose, neural, and hematopoietic tissues. Our lab identified PRDM16 expression in the epithelial cells of the Kölliker’s organ (KO) starting around E13.5 and maintained until the disappearance of the KO around P10. Bulk RNA sequencing of cochlear duct cells at E14.5 followed by quantitative real time PCR and mRNA Fluorescence in-situ hybridization identified differentially expressed genes in Prdm16-null versus littermate control cochleae.

overall_design: Cochlear duct mRNA profiles of embryonic day 14.5 (E14.5) wild type (WT), Prdm16-het and Prdm16-null mice


title: PHARMACOLOGICAL INHIBITION AND REVERSAL OF PANCREATIC ACINAR DUCTAL METAPLASIA

city: Gainesville

first: Thomas

last: Schmittgen

state: FL - FLORIDA

address: 2033 Mowry Road

department: Pharmacy

institute: Univ of Florida

summary: Acinar ductal metaplasia (ADM), is believed to be one of the earliest precursor lesions towards the development of pancreatic ductal adenocarcinoma, and maintaining the pancreatic acinar cell phenotype suppresses tumor formation. We report that pStat3 and HDAC inhibition can attenuate ADM in vitro and TSA treatment reverses the dedifferentiated phenotype to one that is more acinar. Our findings suggest that pharmacological inhibition or reversal of pancreatic ADM represents a potential therapeutic strategy for blocking ductal reprogramming of acinar cells.

overall_design: Following KC mouse acini undergoing ADM for 2 days, 500 nM of TSA or LLL12B was added to the cultures for an additional 2 days. Cells from the LLL12B, TSA, or day 4 untreated controls cells in triplicate were subjected to whole transcriptome sequencing.

first: Lais

last: da Silva

first: Jinmai

last: Jiang

first: Hesamedin

last: Hakimjavadi

first: Srikar

last: Chamala


title: Functional Validation of Common Idiopathic Pulmonary Fibrosis Genetic Risk Variants

first: Ivana

last: Yang

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Transcriptomics of trophoblast stem cells and extraembryonic endoderm stem cells

first: Manuel

last: Irimia

summary: To identify splicing regulators with unique regulation in placenta and the trophectoderm lineage, we sequenced trophoblast stem (TS) and Extraembryonic endoderm stem (XEN) cells.

overall_design: Different lines of TS and XEN cells were grown in their corresponding media and RNA was extracted using standard protocols.

first: T

last: Spruce

first: B

last: Pernaute

first: M


title: RNF213-associated urticarial lesions with hypercytokinemia

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Urticarial lesions are observed in both cutaneous and systemic disorders. Familial forms of urticarial syndromes are rare and can be encountered in systemic auto-inflammatory diseases. We investigated a large family with dominantly inherited chronic urticarial lesions associated with hypercytokinemia. We performed a genetic linkage analysis in 14 patients from a 5-generation family, as well as whole-exome sequencing, cytokine profiling and transcriptomic analyses on samples from two patients. The identified candidate protein was studied after in vitro expression of the corresponding normal and mutated recombinant proteins. An unsupervised proteomic approach was followed to unveil the associated protein network. The disease phenotype of the most affected family members is characterized by chronic urticarial flares associated with extremely high plasma levels of pro- (IL-1b, IL-6, TNF-a) and anti-inflammatory (IL-10, IL1-RA) cytokines, with no secondary organ dysfunction, no susceptibility to infections, no fever and normal C-reactive protein levels. Monocyte transcriptomic analyses identified an immunotolerant profile in the most affected patient. Affected family members carried a loss-of-function mutation in RNF213 that encodes mysterin, a protein of poorly known physiological role. We identified the deubiquitinase CYLD, a major regulator of inflammation, as an RNF213 partner and showed that CYLD expression is inhibited by wild-type but not mutant RNF213. We identified a new entity characterized by chronic urticarial lesions associated with a clinically-blunted hypercytokinemia. This disease, due to a loss of function of RNF213, reveals mysterin’s key role in the complex molecular network of innate immunity.

overall_design: We performed RNA-seq analysis on monocytes from two patients presenting a RNF213 loss-of-function mutation and compared them to two healthy individuals. In an attempt to identify a possible dysregulation of gene networks associated with the observed hypercytokinemia, we analyzed the lists of differentially expressed genes in the patients' monocytes.

first: Irina

last: Giurgea

first: Serge

last: Amselem

first: Camille

last: Louvrier


title: Functional Validation of Common Idiopathic Pulmonary Fibrosis Genetic Risk Variants [850k methylation arrays]

overall_design: Illumina MEGA genotyping arrays, mRNA sequencing, and Illumina 850k methylation arrays were performed on lung tissue of participants with IPF (234 RNA and 345 DNA samples) and non-diseased control (188 RNA and 202 DNA samples).

first: Raphael

last: Borie

first: Jonathan

last: Cardwell

first: Iain

last: Konigsberg

last: Moore

first: Weiming

last: Zhang

first: Avram

last: Walts

first: Julie

last: Powers

first: Janna

last: Brancato

first: Evgenia

last: Dobrinskikh

first: Mauricio

last: Rojas

first: Paul

last: Wolters

first: Kevin

last: Brown

first: Timothy

last: Blackwell

first: Tomoko

last: Nakanishi

first: J

last: Richards

first: Tasha

last: Fingerlin

first: Norman

last: Sachs

first: Sara

last: Pulit

first: Zach

last: Zappala

first: David

last: Schwartz


title: Gene expression in Cdc42f/f and PgrCreCdc42f/f mice oviduct

status: Public on Jul 16 2022

city: Nanjing

first: Ruiwei

last: Jiang

address: No.321 Zhongshan Road

department: Drum Tower Hospital Affiliated to Medical School

institute: Nanjing University

summary: Our results indicated that conditional knockout of Cdc42 in the epithelial cells of the oviduct isthmus led to defective embryo transport, resulting in blastocytes retention in oviduct, and contributing to the pregnancy failure in PgrCreCdc42f/f mice. To further determine the role of CDC42 in oviduct, RNA-seq analysis was applied in the Cdc42f/f and PgrCreCdc42f/f mice oviduct on day 2 of pregnancy.

overall_design: mRNA profiles of Cdc42f/f and PgrCre/+Cdc42f/f mice oviduct on D2 of pregnancy.


title: Effects of Pim1 inhibition with TP-3654 on hematopoietic progenitors of Jak2V617F mice

city: Charlottesville

first: Golam

last: Mohi

state: Virginia

address: 1340 Jefferson Park Ave

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: Myelofibrosis (MF) is the deadliest form of myeloproliferative neoplasm (MPN). Pim1 expression is significantly elevated in MPN/MF hematopoietic progenitors. So, we investigated the role of Pim1 in myelofibrosis. We show that genetic ablation of Pim1 blocked the development of myelofibrosis induced by Jak2V617F and MPLW515L. Pharmacologic inhibition of Pim1 with a second-generation Pim kinase inhibitor TP-3654 significantly reduced leukocytosis, splenomegaly and attenuated bone marrow fibrosis in Jak2V617F and MPLW515L mouse models of MF. Combined treatment of TP-3654 and Ruxolitinib resulted in greater reduction of spleen size, normalization of blood leukocyte counts and abrogation of bone marrow fibrosis in murine models of MF. TP-3654 treatment also preferentially inhibited Jak2V617F mutant hematopoietic progenitors in mice. Our results suggest that Pim1 plays an important role in the pathogenesis of MF, and inhibition of Pim1 with TP-3654 might be useful for treatment of MF.

overall_design: RNA sequencing analysis was performed on sorted LSK cells from Mx1Cre; Jak2VF/VF mice treated with vehicle or TP-3654 (150 mg/kg/day) for 6 weeks. There are three biological replicates for each treatment group and six samples in total.

first: Avik

last: Dutta

first: Dipmoy

last: Nath

first: Bao

last: Le


title: Transcriptomic analysis of wild-type microglia isolated from fluorescent reporter mice

status: Public on Jun 30 2022

first: Tajie

last: Harris

state: VA

address: 200 Jeanette Lancaster Way

summary: Microglia isolated from tamoxifen-inducible Cx3cr1 cre mice harboring expression of a ZsGreen transgene in the ROSA26 locus were analyzed by RNA-sequencing. The purpose of this dataset is to serve as experimental controls as part of broader analyses of microglial-mediated neuroprotection during CNS infection with Toxoplasma gondii.

overall_design: mRNA profiles of wildtype microglia were generated using an Illumina MiSeq

first: Maureen

last: Cowan


title: Microglial STAT1-sufficiency is required for resistance to toxoplasmic encephalitis

summary: RNA-seq experiment examining the transcriptional profiles of FACS-sorted wild-type and STAT1-deficient microglia isolated from mice infected with the Me49 strain of T. gondii.

overall_design: Differential gene expression analysis of FACS-sorted brain-resident wild-type or STAT1-deficient microglia from mice challenged with T. gondii and analyzed at 12 days post-infection.


title: Identifying Novel Molecules Implicated in Early Mesendoderm Specification by a Broad Transcriptomic Approach

city: Ioannina

first: Carol

last: Murphy

address: University Campus of Ioannina, Building E5

country: Greece

institute: Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology Hellas

summary: H1 embryonic Stem Cells maintained in pluripotency by Activin A and  induced with BMP4

overall_design: H1 cells were adapted to Activin A based mTeSR for at least 10 passages. The cells were subsequently split in 3 full 6-well plates and incubated in the same medium until they reached approximately 50% confluency. At that point, the cells were induced with 50ng/mL BMP4 for 1hr or 4hrs. A full 6-well plate served as a non-induced control. RNA was extracted from all the conditions with the experiment being repeated 3 times using cells from three consecutive passages for statistical significance.

first: Angelos

last: Papadopoulos


title: Placenta transcriptomics of Mbnl2 and Mbnl3 KOs (RNA-seq)

first: Manuel

last: Irimia

summary: To investigate the impact of Mbnl2 and Mbnl3 in placenta development and function, we have generated RNA-seq data from placenta from single and double KO mice at different developmental stages.

overall_design: We dissected foetal placenta from E11.5 and E13.5 and labyrinth from E18.5 and perform RNA-seq

first: T

last: Spruce

first: E

last: Bechara

first: M